*はじめに [#y0a46a75]
「[[HMMER:http://hmmer.janelia.org/]]」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 [#u1910b30]
-make
-gcc
*ダウンロード [#yd2147b9]
-HMMER~
http://hmmer.janelia.org/
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 [#aa3c836d]
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．
#geshi(bash){{
./configure
make
make check
sudo make install
}}
*実行 [#vd2ad01b]
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 [#cf7af770]
[[Pfam:http://pfam.sanger.ac.uk/]]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:http://pfam.sanger.ac.uk/family?acc=PF00452]]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:http://pfam.sanger.ac.uk/family?acc=PF00452#tabview=tab5]]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 [#u08aeeea]
[[TAIR:http://www.arabidopsis.org/]]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．
#geshi(bash){{
$ 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．
#geshi(bash){{
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．
#geshi(text){{
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．
#geshi(bash){{
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．
#geshi(bash){{
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．
#geshi(bash){{
ftp > quit
}}
**HMMERによる検索 [#g91b0787]
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．
#geshi(bash){{
$ 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．
#geshi(bash){{
# 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．
#geshi(bash){{
$ 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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