Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 18097 b4069 acetyl-coenzyme A synthetase (NCBI)
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__Keio:18097 Length = 652 Score = 1347 bits (3487), Expect = 0.0 Identities = 652/652 (100%), Positives = 652/652 (100%) Query: 1 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF Sbjct: 1 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60 Query: 61 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF Sbjct: 61 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120 Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS Sbjct: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180 Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL Sbjct: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240 Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI Sbjct: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300 Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA Sbjct: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360 Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG Sbjct: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420 Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD Sbjct: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480 Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP Sbjct: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540 Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD Sbjct: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600 Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS 652 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS Sbjct: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQAIAMPS 652 Lambda K H 0.317 0.135 0.421 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1730 Number of extensions: 45 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 652 Length of database: 652 Length adjustment: 38 Effective length of query: 614 Effective length of database: 614 Effective search space: 376996 Effective search space used: 376996 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate 18097 b4069 (acetyl-coenzyme A synthetase (NCBI))
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR02188.hmm # target sequence database: /tmp/gapView.13805.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02188 [M=629] Accession: TIGR02188 Description: Ac_CoA_lig_AcsA: acetate--CoA ligase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1039.2 0.0 0 1038.9 0.0 1.0 1 lcl|FitnessBrowser__Keio:18097 b4069 acetyl-coenzyme A syntheta Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:18097 b4069 acetyl-coenzyme A synthetase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1038.9 0.0 0 0 3 628 .. 20 643 .. 18 644 .. 0.99 Alignments for each domain: == domain 1 score: 1038.9 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvaiiw 78 + ++y+++y+++i+ p++fw++++k l+w+kp++kv+++s++p ++kW+edg+ln+++nc+drh++++ d++aiiw lcl|FitnessBrowser__Keio:18097 20 NPQQYEAMYQQSINVPDTFWGEQGK-ILDWIKPYQKVKNTSFAPgnvSIKWYEDGTLNLAANCLDRHLQENGDRTAIIW 97 6799*********************.6***************999899******************************* PP TIGR02188 79 egdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRi 157 egd++++ s++++Y+el+r+vcr+an+l elG+kkgd vaiY+pm+pea++amlacaRiGavhsv+f+Gfs+ea+a Ri lcl|FitnessBrowser__Keio:18097 98 EGDDASQ-SKHISYKELHRDVCRFANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRI 175 ***9996.*********************************************************************** PP TIGR02188 158 vdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelvekeasaecepek 235 +d++++lvit+deg+R g++i+lkk+vd+al++ + sve+v+v+krtg ++ w+egrD+ww++lve+ as+++++e+ lcl|FitnessBrowser__Keio:18097 176 IDSNSRLVITSDEGVRAGRSIPLKKNVDDALKNPNVtSVEHVVVLKRTGGKID-WQEGRDLWWHDLVEQ-ASDQHQAEE 252 *********************************9988**************66.**************6.********* PP TIGR02188 236 ldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfe 314 +++edplfiLYtsGstGkPkGvlhttgGyl++aalt+kyvfd++++di+wCtaDvGWvtGhsY++ygPLa+Gattl+fe lcl|FitnessBrowser__Keio:18097 253 MNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGPLACGATTLMFE 331 ******************************************************************************* PP TIGR02188 315 gvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpiv 393 gvp++p+++r+++v++k++v+i+YtaPtaiRalm++g+++++ +d+sslr+lgsvGepinpeaweWy++++G+ekcp+v lcl|FitnessBrowser__Keio:18097 332 GVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVV 410 ******************************************************************************* PP TIGR02188 394 dtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvet 472 dtwWqtetGg++itplpg atelk+gsat+P+fG+++++vd+eg+++e +e g Lvi+++wP+++rt++gd+erf +t lcl|FitnessBrowser__Keio:18097 411 DTWWQTETGGFMITPLPG-ATELKAGSATRPFFGVQPALVDNEGNPLEGATE-GSLVITDSWPGQARTLFGDHERFEQT 487 ******************.6****************************8888.89************************ PP TIGR02188 473 YfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlk 551 Yf+++k++yf+GDgarrd+dGy+wi+GRvDdv+nvsGhrlgtaeiesalv+h+++aeaavvg+p++ikg+ai+a+v+l+ lcl|FitnessBrowser__Keio:18097 488 YFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAIYAYVTLN 566 ******************************************************************************* PP TIGR02188 552 egveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 +g+e++ e l +e++++vrkeigp+a+pd ++++++lPktRsGkimRR+lrkia+g+ ++lgd+stl+dp vve+l e lcl|FitnessBrowser__Keio:18097 567 HGEEPSPE-LYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAAGDtSNLGDTSTLADPGVVEKLLE 643 *******5.************************************************99***************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (652 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.04 # Mc/sec: 8.58 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory