MacでHMMERを使う

2010-06-16 (水) 18:48:14 (2533d) | Topic path: Top / バイオ・データ・マイニング / MacでHMMERを使う

はじめに

HMMER」は,隠れマルコフモデル(HMM)を用いたたんぱく質一次構造の相同性検索ツールです.

Linux用とMac OS X用のバイナリー(実行形式)ファイルが配布されていますが,ここでは,コンパイルする方法を説明します.

次の環境で確認しました.

  • Mac OS X 10.6.3
  • HMMER 3.0
  • Pfam 24.0
  • TAIR 9

必要なもの

  • make
  • gcc

ダウンロード

DownloadのSourceのところにある「FTP」または「HTTP」をクリックして,hmmer-3.0.tar.gzをダウンロードします.

インストール

ダウンロードしたhmmer-3.0.tar.gzをダブル・クリックして展開します.

ターミナルを起動して展開されたディレクトリーに移動し,次を実行します.

./configure
make
make check
sudo make install

実行

ここでは,シロイヌナズナのたんぱく質データに対して,Bcl 2ファミリーを検索する例を示します.

プロファイルHMMのダウンロード

Pfamから検索クエリーとなるプロファイルHMMをダウンロードします. Pfamは,プロファイルHMMを集めて公開しているサイトです.

Bcl-2ファミリーのページへ移動し,左のガイドにある「Curation & models」をクリックしてBcl-2ファミリーについての説明とプロファイルHMMの情報を表示します.

ここで,一番下のdownloadを右クリックし,「リンク先のファイルを別名でダウンロード」します. ここでは,ファイル名を「PF00452」として説明します.

たんぱく質データのダウンロード

TAIRから検索対象となる配列データをダウンロードします. TAIRは,シロイヌナズナに関する情報を集めた研究用ポータル・サイトです.

具体的には,ターミナルを起動し,次のように実行します.

$ ftp ftp.arabidopsis.org

すると,FTPサーバーにつながり,ユーザー名とパスワードを求められます.

Connected to ftp.arabidopsis.org.
220 (vsFTPd 2.0.5)
Name (ftp.arabidopsis.org:username):

そこで,ユーザー名は「anonymous」,パスワードはナシでログインします.

ログインすると,こんなメッセージが表示されます.

230-Welcome to ftp.arabidopsis.org, the guest ftp server for the TAIR
230-project.
230-
230-If you have any trouble with this server, first try logging in again
230-with a minus sign (-) as the first character of your password.  This
230-will turn off a feature that may be confusing your ftp client program.
230-
230-Please send any questions, comments or problem reports to 
230-curator@arabidopsis.org.
230-
230-Anonymous access is now available, as well as the previous method
230-where a password was required.
230-
230-You may access this server using the URL
230-
230-	ftp://ftp.arabidopsis.org
230-or
230-	ftp://tairpub@ftp.arabidopsis.org/home/tair
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.

まず,たんぱく質の配列データが置かれているディレクトリーに移動します.

ftp> cd /Sequences/blast_datasets/other_datasets/CURRENT

ちなみに,lsコマンドを使うとExtended Passive Modeに突入して止まったように見えますが,しばらくするとファイルのリストが表示されます.

それから,たんぱく質データをダウンロードします.

ftp> get At_GB_all_prot.gz
ftp> get gp_GB_all_prot.gz

これらのファイルは,FASTA形式で記述されたテキスト・ファイルをgzip圧縮したものです. Atはシロイヌナズナだけのたんぱく質データ,gpはシロイヌナズナ以外の全植物のたんぱく質データです.

ダウンロードが終わったら,FTPサーバーからログアウトします.

ftp > quit

HMMERによる検索

検索クエリーのプロファイルHMMと検索対象のたんぱく質データが用意できたら,いよいよHMMERを実行します.

HMMERの検索にはhmmsearchコマンドを使い,引数として検索クエリー(プロファイルHMM)と検索対象(たんぱく質データ)を指定します.

$ hmmsearch PF00452 At_GB_all_prot.gz

すると,次のような実行結果が得られます.

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.0 (March 2010); http://hmmer.org/
# Copyright (C) 2010 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  PF00452
# target sequence database:        At_GB_all_prot.gz
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       Bcl-2  [M=101]
Accession:   PF00452.12
Description: Apoptosis regulator proteins, Bcl-2 family
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each sequence (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (101 nodes)
Target sequences:                     160839  (62392833 residues)
Passed MSV filter:                      5198  (0.032318); expected 3216.8 (0.02)
Passed bias filter:                     4482  (0.0278664); expected 3216.8 (0.02)
Passed Vit filter:                       286  (0.00177818); expected 160.8 (0.001)
Passed Fwd filter:                         0  (0); expected 1.6 (1e-05)
Initial search space (Z):             160839  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 2.20u 0.06s 00:00:02.26 Elapsed: 00:00:02.00
# Mc/sec: 3135.16
//

つまり,シロイヌナズナのたんぱく質データの中にはBcl-2ファミリーは見つかりません.

ちなみに,全植物からシロイヌナズナを抜いたたんぱく質データに対して検索すると次のような結果が得られます.

$ hmmsearch PF00452 gp_GB_all_prot.gz
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.0 (March 2010); http://hmmer.org/
# Copyright (C) 2010 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  PF00452
# target sequence database:        gp_GB_all_prot.gz
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       Bcl-2  [M=101]
Accession:   PF00452.12
Description: Apoptosis regulator proteins, Bcl-2 family
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
  ------ inclusion threshold ------
        3.4   13.9   0.0        8.5   12.7   0.0    1.7  1  gi|21616905|gb|AAM66415.1|           NBS-LRR protein [Oryza sativa (i
        3.5   13.9   0.0         16   11.8   0.0    2.1  2  gi|218200452|gb|EEC82879.1|          hypothetical protein OsI_27759 [
        3.8   13.8   0.0         19   11.5   0.0    2.2  2  gi|125602143|gb|EAZ41468.1|          hypothetical protein OsJ_024951 
        3.9   13.8   0.0         18   11.6   0.0    2.1  2  gi|222639889|gb|EEE68021.1|          hypothetical protein OsJ_25992 [
        4.2   13.7   0.0        5.2   13.3   0.0    1.0  1  gi|157328291|emb|CAO17778.1|         unnamed protein product [Vitis v
        4.2   13.6   0.1        8.7   12.6   0.1    1.5  1  gi|116055559|emb|CAL58227.1|         peroxisomal membrane 22 kDa fami
        4.3   13.6   0.0         20   11.5   0.0    2.1  2  gi|113622936|dbj|BAF22881.1|         Os08g0139700 [Oryza sativa (japo
        4.3   13.6   0.0         20   11.5   0.0    2.1  2  gi|115474741|ref|NP_001060967.1|     Os08g0139700 [Oryza sativa (japo
        4.8   13.5   0.0         21   11.4   0.0    2.1  1  gi|115607548|gb|ABJ16553.1|          (E)-beta-caryophyllene/beta-elem
        4.8   13.5   0.0         21   11.4   0.0    2.1  1  gi|38636781|dbj|BAD03024.1|          putative sesquiterpene cyclase 1
        4.8   13.5   0.0         21   11.4   0.0    2.1  1  gi|42761322|dbj|BAD11575.1|          putative sesquiterpene cyclase 1
        5.3   13.3   0.1         85    9.4   0.0    2.8  3  gi|145282028|gb|ABP49617.1|          ubiquitin-protein ligase-like pr
        6.9   12.9   0.1         16   11.7   0.1    1.6  1  gi|162687831|gb|EDQ74211.1|          predicted protein [Physcomitrell
        6.9   12.9   0.1         16   11.7   0.1    1.6  1  gi|168016571|ref|XP_001760822.1|     predicted protein [Physcomitrell
        8.1   12.7   0.1         87    9.4   0.0    2.2  2  gi|116782627|gb|ABK22581.1|          unknown [Picea sitchensis]
        8.3   12.7   0.1         20   11.5   0.1    1.6  1  gi|162692330|gb|EDQ78687.1|          predicted protein [Physcomitrell
        8.3   12.7   0.1         20   11.5   0.1    1.6  1  gi|168007190|ref|XP_001756291.1|     predicted protein [Physcomitrell
        8.4   12.7   0.1    3.1e+02    7.7   0.0    2.5  2  gi|222847830|gb|EEE85377.1|          predicted protein [Populus trich
        8.4   12.7   0.1    3.1e+02    7.7   0.0    2.5  2  gi|224061623|ref|XP_002300572.1|     predicted protein [Populus trich


Domain annotation for each sequence (and alignments):
>> gi|21616905|gb|AAM66415.1|  NBS-LRR protein [Oryza sativa (indica cultivar-group)]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013       8.5       2      80 ..      45     123 ..      40     134 .. 0.73

  Alignments for each domain:
  == domain 1    score: 12.7 bits;  conditional E-value: 0.00013
                                 HHHHHHHHHHHHHHCHHHCTTS---SHHH.HHHHHHHHHHHHHHH.-------HHHHHHH--HHHHHCCCHTCCHHHHCHH CS
                       Bcl-2   2 rslgdeleqeheelfenlleqlnietpee.aselfaevaeelfsd.gginWGRivallafagalakklveqgeeelvkriv 80 
                                 +++++e+ +e +++  n+    +i  +e+ +s+ f  v +++ +d   + W ++va l f+++ +k+l  +++e++v+ + 
  gi|21616905|gb|AAM66415.1|  45 KKVIQEITREGTNV-TNFNTLQEI-VRENlKSKKFLLVFDDVWNDeRRPDWEKLVAPLKFGQKGSKNLLTTRMESVVDIVE 123
                                 55556666655553.344444455.344448899***********99*******************999999977655443 PP

>> gi|218200452|gb|EEC82879.1|  hypothetical protein OsI_27759 [Oryza sativa Indica Group]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       8.9   5.6e+05       9      29 ..      41      61 ..      39      69 .. 0.73
   2 ?   11.8   0.0   0.00025        16      33      88 ..     376     435 ..     350     439 .. 0.79

  Alignments for each domain:
  == domain 1    score: -2.8 bits;  conditional E-value: 8.9
                                 HHHHHHHCHHHCTTS---SHH CS
                        Bcl-2  9 eqeheelfenlleqlnietpe 29
                                 ++ +e+++en+l++++ e+++
  gi|218200452|gb|EEC82879.1| 41 DYHYEKEIENVLRRVHEEEDD 61
                                 567888999999988875554 PP

  == domain 2    score: 11.8 bits;  conditional E-value: 0.00025
                                  HHHHHHHHHHHHH------....-HHHHHHH--HHHHHCCCHTCCHHHHCHHHHHHHHHH CS
                        Bcl-2  33 elfaevaeelfsdgginWG....Rivallafagalakklveqgeeelvkrivellseyle 88 
                                   +f ++++++ +d+ inWG    +i++  +++g+l++++ ++++e+  +  ++++ + ++
  gi|218200452|gb|EEC82879.1| 376 YAFVAMGNDVTTDDAINWGmaypKIITSSCIVGRLLNDIASHEREQGSSSSSSTVEACMR 435
                                  46999**************99999******************998776655555555555 PP

>> gi|125602143|gb|EAZ41468.1|  hypothetical protein OsJ_024951 [Oryza sativa (japonica cultivar-group)]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       9.6   6.1e+05       9      29 ..      59      79 ..      57      86 .. 0.72
   2 ?   11.5   0.0    0.0003        19      33      86 ..     394     451 ..     368     458 .. 0.77

  Alignments for each domain:
  == domain 1    score: -2.9 bits;  conditional E-value: 9.6
                                 HHHHHHHCHHHCTTS---SHH CS
                        Bcl-2  9 eqeheelfenlleqlnietpe 29
                                 ++ +e+++en+l++++ e+++
  gi|125602143|gb|EAZ41468.1| 59 DYHYEKEIENVLRRVHEEEDD 79
                                 567888999999988875554 PP

  == domain 2    score: 11.5 bits;  conditional E-value: 0.0003
                                  HHHHHHHHHHHHH------....-HHHHHHH--HHHHHCCCHTCCHHHHCHHHHHHHH CS
                        Bcl-2  33 elfaevaeelfsdgginWG....Rivallafagalakklveqgeeelvkrivellsey 86 
                                   +f ++++++ +d+ inWG    +i++  +++g+l++++ ++++e+  +  ++ ++e+
  gi|125602143|gb|EAZ41468.1| 394 YAFVAMGNDVTTDDAINWGmaypKIITSSCIVGRLLNDIASHEREQGSSSSSSSTVEA 451
                                  46999**************99999******************9977655544444444 PP

>> gi|222639889|gb|EEE68021.1|  hypothetical protein OsJ_25992 [Oryza sativa Japonica Group]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       8.9   5.7e+05       9      29 ..      41      61 ..      39      69 .. 0.73
   2 ?   11.6   0.0   0.00028        18      33      86 ..     376     433 ..     350     440 .. 0.77

  Alignments for each domain:
  == domain 1    score: -2.8 bits;  conditional E-value: 8.9
                                 HHHHHHHCHHHCTTS---SHH CS
                        Bcl-2  9 eqeheelfenlleqlnietpe 29
                                 ++ +e+++en+l++++ e+++
  gi|222639889|gb|EEE68021.1| 41 DYHYEKEIENVLRRVHEEEDD 61
                                 567888999999988875554 PP

  == domain 2    score: 11.6 bits;  conditional E-value: 0.00028
                                  HHHHHHHHHHHHH------....-HHHHHHH--HHHHHCCCHTCCHHHHCHHHHHHHH CS
                        Bcl-2  33 elfaevaeelfsdgginWG....Rivallafagalakklveqgeeelvkrivellsey 86 
                                   +f ++++++ +d+ inWG    +i++  +++g+l++++ ++++e+  +  ++ ++e+
  gi|222639889|gb|EEE68021.1| 376 YAFVAMGNDVTTDDAINWGmaypKIITSSCIVGRLLNDIASHEREQGSSSSSSSTVEA 433
                                  46999**************99999******************9977655544444444 PP

>> gi|157328291|emb|CAO17778.1|  unnamed protein product [Vitis vinifera]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.2e-05       5.2      48      99 ..       4      53 ..       2      53 .. 0.73

  Alignments for each domain:
  == domain 1    score: 13.3 bits;  conditional E-value: 8.2e-05
                                  -----HHHHHHH--HHHHHCCCHTCCHHHHCHHHHHHHHHHHH...HHHH-- CS
                         Bcl-2 48 inWGRivallafagalakklveqgeeelvkrivellseyleeelasWikeqG 99
                                  i+WGR+v + +  g  +++ ++++++     ++  + ++l++  ++++ +qG
  gi|157328291|emb|CAO17778.1|  4 ISWGRVVLVQC-TGGNCQETRNSNHAT-APSLIYNTLAFLKGLPEAFFTSQG 53
                                  89***996555.555688888888854.577888888888888888877776 PP

>> gi|116055559|emb|CAL58227.1|  peroxisomal membrane 22 kDa family protein (ISS) [Ostreococcus tauri]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00014       8.7      27      64 ..      91     128 ..      64     137 .. 0.80

  Alignments for each domain:
  == domain 1    score: 12.6 bits;  conditional E-value: 0.00014
                                   SHHHHHHHHHHHHHHHHHH-------HHHHHHH--HHH CS
                         Bcl-2  27 tpeeaselfaevaeelfsdgginWGRivallafagala 64 
                                   ++  as++f +++ e  s +++ W+R++++++++ +++
  gi|116055559|emb|CAL58227.1|  91 SKCVASDVFVQIVVEERSANDLDWNRVLSFFVLGVTYV 128
                                   33448899999999999999*************99876 PP

>> gi|113622936|dbj|BAF22881.1|  Os08g0139700 [Oryza sativa (japonica cultivar-group)]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0        10   6.4e+05       9      29 ..      77      97 ..      75     104 .. 0.72
   2 ?   11.5   0.0   0.00031        20      33      86 ..     412     469 ..     386     476 .. 0.77

  Alignments for each domain:
  == domain 1    score: -3.0 bits;  conditional E-value: 10
                                  HHHHHHHCHHHCTTS---SHH CS
                         Bcl-2  9 eqeheelfenlleqlnietpe 29
                                  ++ +e+++en+l++++ e+++
  gi|113622936|dbj|BAF22881.1| 77 DYHYEKEIENVLRRVHEEEDD 97
                                  567888999999988875554 PP

  == domain 2    score: 11.5 bits;  conditional E-value: 0.00031
                                   HHHHHHHHHHHHH------....-HHHHHHH--HHHHHCCCHTCCHHHHCHHHHHHHH CS
                         Bcl-2  33 elfaevaeelfsdgginWG....Rivallafagalakklveqgeeelvkrivellsey 86 
                                    +f ++++++ +d+ inWG    +i++  +++g+l++++ ++++e+  +  ++ ++e+
  gi|113622936|dbj|BAF22881.1| 412 YAFVAMGNDVTTDDAINWGmaypKIITSSCIVGRLLNDIASHEREQGSSSSSSSTVEA 469
                                   46999**************99999******************9977655544444444 PP

>> gi|115474741|ref|NP_001060967.1|  Os08g0139700 [Oryza sativa (japonica cultivar-group)]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0        10   6.4e+05       9      29 ..      77      97 ..      75     104 .. 0.72
   2 ?   11.5   0.0   0.00031        20      33      86 ..     412     469 ..     386     476 .. 0.77

  Alignments for each domain:
  == domain 1    score: -3.0 bits;  conditional E-value: 10
                                      HHHHHHHCHHHCTTS---SHH CS
                             Bcl-2  9 eqeheelfenlleqlnietpe 29
                                      ++ +e+++en+l++++ e+++
  gi|115474741|ref|NP_001060967.1| 77 DYHYEKEIENVLRRVHEEEDD 97
                                      567888999999988875554 PP

  == domain 2    score: 11.5 bits;  conditional E-value: 0.00031
                                       HHHHHHHHHHHHH------....-HHHHHHH--HHHHHCCCHTCCHHHHCHHHHHHHH CS
                             Bcl-2  33 elfaevaeelfsdgginWG....Rivallafagalakklveqgeeelvkrivellsey 86 
                                        +f ++++++ +d+ inWG    +i++  +++g+l++++ ++++e+  +  ++ ++e+
  gi|115474741|ref|NP_001060967.1| 412 YAFVAMGNDVTTDDAINWGmaypKIITSSCIVGRLLNDIASHEREQGSSSSSSSTVEA 469
                                       46999**************99999******************9977655544444444 PP

>> gi|115607548|gb|ABJ16553.1|  (E)-beta-caryophyllene/beta-elemene synthase [Oryza sativa (japonica cultivar-group)]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00033        21      33      86 ..     436     493 ..     410     500 .. 0.77

  Alignments for each domain:
  == domain 1    score: 11.4 bits;  conditional E-value: 0.00033
                                  HHHHHHHHHHHHH------....-HHHHHHH--HHHHHCCCHTCCHHHHCHHHHHHHH CS
                        Bcl-2  33 elfaevaeelfsdgginWG....Rivallafagalakklveqgeeelvkrivellsey 86 
                                   +f ++++++ +d+ inWG    +i++  +++g+l++++ ++++e+  +  ++ ++e+
  gi|115607548|gb|ABJ16553.1| 436 YAFVAMGNDVTTDDAINWGmaypKIITSSCIVGRLLNDIASHEREQGSSSSSSSTVEA 493
                                  46999**************99999******************9977655544444444 PP

>> gi|38636781|dbj|BAD03024.1|  putative sesquiterpene cyclase 1 [Oryza sativa Japonica Group]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00033        21      33      86 ..     436     493 ..     410     500 .. 0.77

  Alignments for each domain:
  == domain 1    score: 11.4 bits;  conditional E-value: 0.00033
                                  HHHHHHHHHHHHH------....-HHHHHHH--HHHHHCCCHTCCHHHHCHHHHHHHH CS
                        Bcl-2  33 elfaevaeelfsdgginWG....Rivallafagalakklveqgeeelvkrivellsey 86 
                                   +f ++++++ +d+ inWG    +i++  +++g+l++++ ++++e+  +  ++ ++e+
  gi|38636781|dbj|BAD03024.1| 436 YAFVAMGNDVTTDDAINWGmaypKIITSSCIVGRLLNDIASHEREQGSSSSSSSTVEA 493
                                  46999**************99999******************9977655544444444 PP

>> gi|42761322|dbj|BAD11575.1|  putative sesquiterpene cyclase 1 [Oryza sativa Japonica Group]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00033        21      33      86 ..     436     493 ..     410     500 .. 0.77

  Alignments for each domain:
  == domain 1    score: 11.4 bits;  conditional E-value: 0.00033
                                  HHHHHHHHHHHHH------....-HHHHHHH--HHHHHCCCHTCCHHHHCHHHHHHHH CS
                        Bcl-2  33 elfaevaeelfsdgginWG....Rivallafagalakklveqgeeelvkrivellsey 86 
                                   +f ++++++ +d+ inWG    +i++  +++g+l++++ ++++e+  +  ++ ++e+
  gi|42761322|dbj|BAD11575.1| 436 YAFVAMGNDVTTDDAINWGmaypKIITSSCIVGRLLNDIASHEREQGSSSSSSSTVEA 493
                                  46999**************99999******************9977655544444444 PP

>> gi|145282028|gb|ABP49617.1|  ubiquitin-protein ligase-like protein [Pyrus communis]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         4   2.6e+05      67      88 ..      21      42 ..      11      56 .. 0.63
   2 ?   -0.8   0.0         2   1.3e+05      14      45 ..     125     157 ..     119     165 .. 0.72
   3 ?    9.4   0.0    0.0013        85      15      83 ..     215     273 ..     209     281 .. 0.81

  Alignments for each domain:
  == domain 1    score: -1.7 bits;  conditional E-value: 4
                                 CCCHTCCHHHHCHHHHHHHHHH CS
                        Bcl-2 67 lveqgeeelvkrivellseyle 88
                                 ++ ++++e+v+++ e++ +y++
  gi|145282028|gb|ABP49617.1| 21 CEAEKKDEAVNMLKEMVQRYVA 42
                                 4444446666666666666664 PP

  == domain 2    score: -0.8 bits;  conditional E-value: 2
                                  HHCHHHCTTS---SHHHHHHH.HHHHHHHHHHH CS
                        Bcl-2  14 elfenlleqlnietpeeasel.faevaeelfsd 45 
                                  ++++ ++e l  + + e+ e+ f++ +++ ++d
  gi|145282028|gb|ABP49617.1| 125 SAYNPMIEYLCNHGQTEKAEVfFRQLMKKGVQD 157
                                  578889998888777775555488888887777 PP

  == domain 3    score: 9.4 bits;  conditional E-value: 0.0013
                                  HCHHHCTTS---SHHHHHHHHHHHHHHHHHH-------HHHHHHH--HHHHHCCCHTCCHHHHCHHHHH CS
                        Bcl-2  15 lfenlleqlnietpeeaselfaevaeelfsdgginWGRivallafagalakklveqgeeelvkrivell 83 
                                  +++++le  +i  p  + +lf++v+e+lf+d     GR+ +   +   +++k v++++ +lv +i+e+l
  gi|145282028|gb|ABP49617.1| 215 ALDSMLEGGHI--P--EASLFRSVMESLFED-----GRVQTASRVMKSMVEKGVKENM-DLVAKILETL 273
                                  56777777676..3..4689***********.....***9999999999999999998.5788888775 PP

>> gi|162687831|gb|EDQ74211.1|  predicted protein [Physcomitrella patens subsp. patens]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00026        16      17      70 ..     212     265 ..     204     285 .. 0.73

  Alignments for each domain:
  == domain 1    score: 11.7 bits;  conditional E-value: 0.00026
                                  HHHCTTS---SHHHHHHHHHHHHHHHHHH.-------HHHHHHH--HHHHHCCCH CS
                        Bcl-2  17 enlleqlnietpeeaselfaevaeelfsd.gginWGRivallafagalakklveq 70 
                                  ++l   lni++  ++ + f +v++++f + ++ nW  iv  laf + l+++ +  
  gi|162687831|gb|EDQ74211.1| 212 QQLKGLLNITNF-TTDTDFVSVMRSVFGHiDEWNWRSIVIGLAFLAFLITTKTMA 265
                                  555555666444.4445599***************************99843333 PP

>> gi|168016571|ref|XP_001760822.1|  predicted protein [Physcomitrella patens subsp. patens]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00026        16      17      70 ..     212     265 ..     204     285 .. 0.73

  Alignments for each domain:
  == domain 1    score: 11.7 bits;  conditional E-value: 0.00026
                                       HHHCTTS---SHHHHHHHHHHHHHHHHHH.-------HHHHHHH--HHHHHCCCH CS
                             Bcl-2  17 enlleqlnietpeeaselfaevaeelfsd.gginWGRivallafagalakklveq 70 
                                       ++l   lni++  ++ + f +v++++f + ++ nW  iv  laf + l+++ +  
  gi|168016571|ref|XP_001760822.1| 212 QQLKGLLNITNF-TTDTDFVSVMRSVFGHiDEWNWRSIVIGLAFLAFLITTKTMA 265
                                       555555666444.4445599***************************99843333 PP

>> gi|116782627|gb|ABK22581.1|  unknown [Picea sitchensis]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.69   4.4e+04      28      50 ..      47      69 ..      21      70 .. 0.77
   2 ?    9.4   0.0    0.0014        87      15      82 ..      76     143 ..      73     153 .. 0.78

  Alignments for each domain:
  == domain 1    score: 0.7 bits;  conditional E-value: 0.69
                                 HHHHHHHHHHHHHHHHHH----- CS
                        Bcl-2 28 peeaselfaevaeelfsdgginW 50
                                  ++ +e++ e+ +++ + +g nW
  gi|116782627|gb|ABK22581.1| 47 YDQLYEAIIEIFKKINEIPGANW 69
                                 34457788888888888899999 PP

  == domain 2    score: 9.4 bits;  conditional E-value: 0.0014
                                  HCHHHCTTS---SHHH.HHHHHHHHHHHHHHH-------HHHHHHH--HHHHHCCCHTCCHHHHCHHHH CS
                        Bcl-2  15 lfenlleqlnietpee.aselfaevaeelfsdgginWGRivallafagalakklveqgeeelvkrivel 82 
                                   + +++++ ++++++e ++e f++ +++  ++   ++GR v+++++a   a  l+++  ++ v ++ +l
  gi|116782627|gb|ABK22581.1|  76 SMVKMIQEYDLDQNKEiDREEFHAFVRKFSRHLVATYGRDVVIVTVAVPAAAILTKKATQS-VPMVGDL 143
                                  56689999999888888999************************99988887777666533.4444444 PP

>> gi|162692330|gb|EDQ78687.1|  predicted protein [Physcomitrella patens subsp. patens]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00031        20      18      77 ..     213     275 ..     205     288 .. 0.71

  Alignments for each domain:
  == domain 1    score: 11.5 bits;  conditional E-value: 0.00031
                                  HHCTTS---SHHHHHHHHHHHHHHHHHH.-------HHHHHHH--HHHH.HCCCHTCCHH..HH CS
                        Bcl-2  18 nlleqlnietpeeaselfaevaeelfsd.gginWGRivallafagalak.klveqgeeel..vk 77 
                                  +l   lni t+ ++ + f +v++++f++ ++ nW  iv  laf   l+  k+  +++++l  v+
  gi|162692330|gb|EDQ78687.1| 213 QLKGLLNI-THFTTDTDFISVMTSVFQNtNEWNWRSIVIGLAFLSFLVLtKILAKKKPKLfwVS 275
                                  44455566.4445556699*********99*************999875366666665554455 PP

>> gi|168007190|ref|XP_001756291.1|  predicted protein [Physcomitrella patens subsp. patens]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00031        20      18      77 ..     213     275 ..     205     288 .. 0.71

  Alignments for each domain:
  == domain 1    score: 11.5 bits;  conditional E-value: 0.00031
                                       HHCTTS---SHHHHHHHHHHHHHHHHHH.-------HHHHHHH--HHHH.HCCCHTCCHH..HH CS
                             Bcl-2  18 nlleqlnietpeeaselfaevaeelfsd.gginWGRivallafagalak.klveqgeeel..vk 77 
                                       +l   lni t+ ++ + f +v++++f++ ++ nW  iv  laf   l+  k+  +++++l  v+
  gi|168007190|ref|XP_001756291.1| 213 QLKGLLNI-THFTTDTDFISVMTSVFQNtNEWNWRSIVIGLAFLSFLVLtKILAKKKPKLfwVS 275
                                       44455566.4445556699*********99*************999875366666665554455 PP

>> gi|222847830|gb|EEE85377.1|  predicted protein [Populus trichocarpa]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0048   3.1e+02      19      55 ..      73     108 ..      67     144 .. 0.71
   2 ?    2.3   0.0      0.23   1.5e+04      47      79 ..     242     274 ..     218     287 .. 0.74

  Alignments for each domain:
  == domain 1    score: 7.7 bits;  conditional E-value: 0.0048
                                  HCTTS---SHHHHHHHHHHHHHHHHHH-------HHH CS
                        Bcl-2  19 lleqlnietpeeaselfaevaeelfsdgginWGRiva 55 
                                  ++++ ++  +  a+++++ev++e +s++g nW  + a
  gi|222847830|gb|EEE85377.1|  73 CSNHNSV-GETAARDTLEEVMAEALSKSGSNWSTVHA 108
                                  5555555.445599******************97744 PP

  == domain 2    score: 2.3 bits;  conditional E-value: 0.23
                                  ------HHHHHHH--HHHHHCCCHTCCHHHHCH CS
                        Bcl-2  47 ginWGRivallafagalakklveqgeeelvkri 79 
                                  +++W Ri al+  +   a+ + +   + lv+ +
  gi|222847830|gb|EEE85377.1| 242 DPSWARIAALVPEVVSCAEACDQVATKILVDAV 274
                                  689*******99888888888877664444433 PP

>> gi|224061623|ref|XP_002300572.1|  predicted protein [Populus trichocarpa]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0048   3.1e+02      19      55 ..      73     108 ..      67     144 .. 0.71
   2 ?    2.3   0.0      0.23   1.5e+04      47      79 ..     242     274 ..     218     287 .. 0.74

  Alignments for each domain:
  == domain 1    score: 7.7 bits;  conditional E-value: 0.0048
                                       HCTTS---SHHHHHHHHHHHHHHHHHH-------HHH CS
                             Bcl-2  19 lleqlnietpeeaselfaevaeelfsdgginWGRiva 55 
                                       ++++ ++  +  a+++++ev++e +s++g nW  + a
  gi|224061623|ref|XP_002300572.1|  73 CSNHNSV-GETAARDTLEEVMAEALSKSGSNWSTVHA 108
                                       5555555.445599******************97744 PP

  == domain 2    score: 2.3 bits;  conditional E-value: 0.23
                                       ------HHHHHHH--HHHHHCCCHTCCHHHHCH CS
                             Bcl-2  47 ginWGRivallafagalakklveqgeeelvkri 79 
                                       +++W Ri al+  +   a+ + +   + lv+ +
  gi|224061623|ref|XP_002300572.1| 242 DPSWARIAALVPEVVSCAEACDQVATKILVDAV 274
                                       689*******99888888888877664444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (101 nodes)
Target sequences:                    1210800  (410418238 residues)
Passed MSV filter:                     33081  (0.0273216); expected 24216.0 (0.02)
Passed bias filter:                    28502  (0.0235398); expected 24216.0 (0.02)
Passed Vit filter:                      1482  (0.00122398); expected 1210.8 (0.001)
Passed Fwd filter:                        23  (1.89957e-05); expected 12.1 (1e-05)
Initial search space (Z):            1210800  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 14.69u 0.41s 00:00:15.10 Elapsed: 00:00:21.93
# Mc/sec: 1890.21
//
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