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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 //
