Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_045580972.1 AL072_RS06780 acetate--CoA ligase
Query= reanno::pseudo3_N2E3:AO353_03060 (651 letters) >NCBI__GCF_001305595.1:WP_045580972.1 Length = 646 Score = 932 bits (2408), Expect = 0.0 Identities = 439/643 (68%), Positives = 515/643 (80%), Gaps = 3/643 (0%) Query: 1 MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 M+ S +PV+PE+AA + Y MY+QSV +P+ FW E KR+DWIKP++ VK F Sbjct: 1 MTDNSFFPVKPEIAATAHVNAEAYARMYEQSVNDPEAFWGEHGKRIDWIKPYSKVKDVDF 60 Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKF 120 + V I+WF DGTLNVS NC+DRHLA RGDQ AI++EGDDP S+ ITY+ELHE+V + Sbjct: 61 NGD-VHIRWFHDGTLNVSANCIDRHLATRGDQTAILFEGDDPGVSKAITYKELHEKVSRL 119 Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 AN L+ V +GD VTIY+PMIPEA AMLACTRIGAIHS+VFGGFSP++L RI+DC S Sbjct: 120 ANVLKKNGVRKGDRVTIYLPMIPEAAYAMLACTRIGAIHSIVFGGFSPDSLKDRIVDCDS 179 Query: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240 VIT+DEGLR G+K+ LKAN D A+ ++ V+V K TGGN+ W + RD+WY + Sbjct: 180 HFVITSDEGLRGGRKVPLKANADKAVAG--APMVRHVLVVKHTGGNVAWTEGRDLWYHEE 237 Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300 M+ C P+EM AE+ LFILYTSGSTGKPKGV HTTGGYL+YA++THE VFDY+ GE+ Sbjct: 238 MESVSADCPPEEMSAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHEYVFDYKQGEV 297 Query: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360 YWCTADVGWVTGH+YIVYGPLANGATTL+FEGVP YPD++R ++IDKHKVNI YTAPTA Sbjct: 298 YWCTADVGWVTGHSYIVYGPLANGATTLMFEGVPTYPDVSRFWQVIDKHKVNIFYTAPTA 357 Query: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420 IR++M +G V+ +SLR+LGSVGEPINPEAW WYY VG +RCPIVDTWWQTETG Sbjct: 358 IRSLMREGEGPVKTTSRASLRVLGSVGEPINPEAWLWYYNVVGDARCPIVDTWWQTETGG 417 Query: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGD 480 L++PL GA G KPGSA +PFFGV P +VDN G ++EG EGNL I D+WPG RT+YGD Sbjct: 418 ILITPLIGAIGQKPGSATKPFFGVQPVVVDNEGQVLEGETEGNLCIADAWPGMMRTVYGD 477 Query: 481 HDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 H+RFV TYF TF G YFTGDG RRDADGY+WITGRVDDV+NVSGHRMGTAE+ESA+VAHP Sbjct: 478 HERFVQTYFSTFAGKYFTGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHP 537 Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAP 600 KVAEAAVVG PHD+KGQGIY YVTLN GE P+E LR EL WVRKEIGPIASPD+IQWAP Sbjct: 538 KVAEAAVVGYPHDLKGQGIYAYVTLNAGETPTEELRKELVAWVRKEIGPIASPDLIQWAP 597 Query: 601 GLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLID 643 GLPKTRSGKIMRRILRKIA E+D LGD STLADPGVV LID Sbjct: 598 GLPKTRSGKIMRRILRKIAANEHDALGDTSTLADPGVVTDLID 640 Lambda K H 0.319 0.136 0.425 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: 1474 Number of extensions: 66 Number of successful extensions: 3 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: 651 Length of database: 646 Length adjustment: 38 Effective length of query: 613 Effective length of database: 608 Effective search space: 372704 Effective search space used: 372704 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate WP_045580972.1 AL072_RS06780 (acetate--CoA ligase)
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.3817971.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 1039.1 0.1 0 1038.9 0.1 1.0 1 NCBI__GCF_001305595.1:WP_045580972.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001305595.1:WP_045580972.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1038.9 0.1 0 0 3 628 .. 20 640 .. 18 641 .. 0.98 Alignments for each domain: == domain 1 score: 1038.9 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdk 73 ++e+y+++ye++++dpe+fw++++k +++w+kp++kv+d +++ +++Wf+dg+lnvs+nc+drh+++r d+ NCBI__GCF_001305595.1:WP_045580972.1 20 NAEAYARMYEQSVNDPEAFWGEHGK-RIDWIKPYSKVKDVDFNGdvHIRWFHDGTLNVSANCIDRHLATRGDQ 91 7899*********************.5**************9987899************************* PP TIGR02188 74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146 +ai +egd++g s+++tY+el+++v+rlanvlk+ Gv+kgdrv+iYlpmipea++amlac+RiGa+hs+vf+ NCBI__GCF_001305595.1:WP_045580972.1 92 TAILFEGDDPGV-SKAITYKELHEKVSRLANVLKKNGVRKGDRVTIYLPMIPEAAYAMLACTRIGAIHSIVFG 163 ***********7.************************************************************ PP TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219 Gfs+++l++Rivd+++++vit+deglRgg++++lk+++d+a++ a+ +v++vlvvk+tg +va w+egrD+w+ NCBI__GCF_001305595.1:WP_045580972.1 164 GFSPDSLKDRIVDCDSHFVITSDEGLRGGRKVPLKANADKAVAGAP-MVRHVLVVKHTGGNVA-WTEGRDLWY 234 *********************************************9.7*************77.********* PP TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292 +e++e+ +sa+c+pe++++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd+k+++++wCtaDvGW NCBI__GCF_001305595.1:WP_045580972.1 235 HEEMES-VSADCPPEEMSAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHEYVFDYKQGEVYWCTADVGW 306 *****6.****************************************************************** PP TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365 vtGhsYivygPLanGattl+fegvptypd srfw+vi+k+kv+ifYtaPtaiR+lm++ge vk +++ slrv NCBI__GCF_001305595.1:WP_045580972.1 307 VTGHSYIVYGPLANGATTLMFEGVPTYPDVSRFWQVIDKHKVNIFYTAPTAIRSLMREGEGPVKTTSRASLRV 379 ************************************************************************* PP TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438 lgsvGepinpeaw Wyy+vvG+ +cpivdtwWqtetGgilitpl g a+ +kpgsat+P+fG++++vvd+eg+ NCBI__GCF_001305595.1:WP_045580972.1 380 LGSVGEPINPEAWLWYYNVVGDARCPIVDTWWQTETGGILITPLIG-AIGQKPGSATKPFFGVQPVVVDNEGQ 451 **********************************************.6************************* PP TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhr 511 +e e+e g L+i ++wP+m+rt+ygd+erfv+tYf+++ g yftGDg+rrd+dGy+wi+GRvDdvinvsGhr NCBI__GCF_001305595.1:WP_045580972.1 452 VLEGETE-GNLCIADAWPGMMRTVYGDHERFVQTYFSTFAGKYFTGDGCRRDADGYYWITGRVDDVINVSGHR 523 ***8777.79*************************************************************** PP TIGR02188 512 lgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilv 584 +gtae+esalv+h++vaeaavvg+p+++kg+ i+a+v+l++g++++ee l+kel ++vrkeigpia+pd i++ NCBI__GCF_001305595.1:WP_045580972.1 524 MGTAEVESALVAHPKVAEAAVVGYPHDLKGQGIYAYVTLNAGETPTEE-LRKELVAWVRKEIGPIASPDLIQW 595 *********************************************995.************************ PP TIGR02188 585 veelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 ++ lPktRsGkimRR+lrkia++e ++lgd+stl+dp vv +l++ NCBI__GCF_001305595.1:WP_045580972.1 596 APGLPKTRSGKIMRRILRKIAANEhDALGDTSTLADPGVVTDLID 640 ************************99**************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (646 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 33.61 // [ok]
This GapMind analysis is from Sep 24 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