Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_084200888.1 C0029_RS18225 acetate--CoA ligase
Query= reanno::pseudo3_N2E3:AO353_03060 (651 letters) >NCBI__GCF_002869505.1:WP_084200888.1 Length = 643 Score = 834 bits (2154), Expect = 0.0 Identities = 412/643 (64%), Positives = 485/643 (75%), Gaps = 6/643 (0%) Query: 1 MSAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTS 59 MS +PV P + D TYKAMYQ+S+ +PDGF+ + A L W +P+ V + Sbjct: 1 MSEFPTHPV-PANFKDAHIDADTYKAMYQRSIDDPDGFFSQMANDFLSWDQPWDKVME-- 57 Query: 60 FDDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCK 119 +D + WFA G LNVSYNC+DRHL ER DQ A+IWEGDDPA+S++ITY EL + VCK Sbjct: 58 YDFIKGEAAWFAGGKLNVSYNCVDRHLPERADQTALIWEGDDPADSKHITYAELKDHVCK 117 Query: 120 FANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCK 179 ANAL+ + V +GD V IYMPMIPEA AMLACTRIGA+HS+VFGGFSPEAL RI+D Sbjct: 118 LANALKARGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSIVFGGFSPEALKDRILDSD 177 Query: 180 SKVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYED 239 + VITADEG+R G+K+ LK N D AL ++ +V +RT G++ WN RD+WY + Sbjct: 178 CQTVITADEGVRGGRKVPLKVNADKALE--ACPNVHTCLVVERTSGDVAWNADRDVWYHE 235 Query: 240 LMKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGE 299 L+ T C P+ M AE+ LFILYTSGSTGKPKGV HTTGGYLL AA+T + VFDYR GE Sbjct: 236 LVDGQSTDCEPESMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVFDYRDGE 295 Query: 300 IYWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPT 359 IYWCTADVGWVTGHTYIVYGPLANGA +L+FEGVP YPD R +++DKH+VN YTAPT Sbjct: 296 IYWCTADVGWVTGHTYIVYGPLANGAISLMFEGVPTYPDAGRCWEVVDKHQVNTFYTAPT 355 Query: 360 AIRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETG 419 AIRA+ A G V A SLRLLG+VGEPINPEAWEWY++ VG RCPI+DTWWQTETG Sbjct: 356 AIRALQAVGDEPVTRASRVSLRLLGTVGEPINPEAWEWYHRVVGDGRCPIIDTWWQTETG 415 Query: 420 ATLMSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYG 479 A +++PLPGA LKPGSA PFFGV AL++ G+ IEG G LV+ SWP Q RT++G Sbjct: 416 AHMITPLPGAVPLKPGSATFPFFGVELALLNEDGSEIEGPGAGYLVVKRSWPSQIRTVFG 475 Query: 480 DHDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAH 539 DH R +DTYF+ + G YFTGDGA RD DGY+WITGRVDDVLNVSGHRMGTAE+ESA+V H Sbjct: 476 DHKRLIDTYFRNYPGYYFTGDGATRDEDGYYWITGRVDDVLNVSGHRMGTAEVESALVLH 535 Query: 540 PKVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWA 599 ++AEAAVVG PHDIKGQGIY YVT G EP+E LR EL KEIGPIA PD+IQWA Sbjct: 536 EEIAEAAVVGFPHDIKGQGIYAYVTPMQGVEPNEELRQELIALCVKEIGPIAKPDIIQWA 595 Query: 600 PGLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLI 642 PGLPKTRSGKIMRRILRKIA E D LGD STLADP VV +L+ Sbjct: 596 PGLPKTRSGKIMRRILRKIAENELDSLGDTSTLADPSVVDNLV 638 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: 1458 Number of extensions: 72 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: 643 Length adjustment: 38 Effective length of query: 613 Effective length of database: 605 Effective search space: 370865 Effective search space used: 370865 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_084200888.1 C0029_RS18225 (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.1678905.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 1027.7 0.0 0 1027.5 0.0 1.0 1 NCBI__GCF_002869505.1:WP_084200888.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002869505.1:WP_084200888.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1027.5 0.0 0 0 3 627 .. 19 638 .. 17 640 .. 0.99 Alignments for each domain: == domain 1 score: 1027.5 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkv 74 ++++yk++y+++i+dp+ f++++a++ l+w++p++kv++ ++ + +++Wf++g+lnvsyncvdrh+ +r+d++ NCBI__GCF_002869505.1:WP_084200888.1 19 DADTYKAMYQRSIDDPDGFFSQMANDFLSWDQPWDKVMEYDFIKgEAAWFAGGKLNVSYNCVDRHLPERADQT 91 6799*************************************9999**************************** PP TIGR02188 75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147 a+iwegd++ ds+++tYael+++vc+lan+lk+ Gvkkgdrv+iY+pmipea++amlac+RiGavhs+vf+G NCBI__GCF_002869505.1:WP_084200888.1 92 ALIWEGDDPA-DSKHITYAELKDHVCKLANALKARGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSIVFGG 163 *********9.5************************************************************* PP TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220 fs+eal++Ri d+++++vitadeg+Rgg++++lk ++d+ale+++ +v+++lvv+rt +va w+ +rDvw++ NCBI__GCF_002869505.1:WP_084200888.1 164 FSPEALKDRILDSDCQTVITADEGVRGGRKVPLKVNADKALEACP-NVHTCLVVERTSGDVA-WNADRDVWYH 234 ********************************************9.6*************77.********** PP TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293 elv+ ++s++cepe++d+edplfiLYtsGstGkPkGvlhttgGyll+aa+t+kyvfd++d++i+wCtaDvGWv NCBI__GCF_002869505.1:WP_084200888.1 235 ELVD-GQSTDCEPESMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVFDYRDGEIYWCTADVGWV 306 ****.6******************************************************************* PP TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366 tGh+YivygPLanGa +l+fegvptypda+r+wev++k++v++fYtaPtaiRal+++g+e v++ ++ slr+l NCBI__GCF_002869505.1:WP_084200888.1 307 TGHTYIVYGPLANGAISLMFEGVPTYPDAGRCWEVVDKHQVNTFYTAPTAIRALQAVGDEPVTRASRVSLRLL 379 ************************************************************************* PP TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439 g+vGepinpeaweWy++vvG+++cpi+dtwWqtetG+++itplpg a++lkpgsat P+fG+e ++++e+g+e NCBI__GCF_002869505.1:WP_084200888.1 380 GTVGEPINPEAWEWYHRVVGDGRCPIIDTWWQTETGAHMITPLPG-AVPLKPGSATFPFFGVELALLNEDGSE 451 *********************************************.6************************** PP TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512 +e g+Lv+k++wPs++rt++gd++r+++tYf++++g+yftGDga+rd+dGy+wi+GRvDdv+nvsGhr+ NCBI__GCF_002869505.1:WP_084200888.1 452 IEGPGA-GYLVVKRSWPSQIRTVFGDHKRLIDTYFRNYPGYYFTGDGATRDEDGYYWITGRVDDVLNVSGHRM 523 *97666.8***************************************************************** PP TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585 gtae+esalv he++aeaavvg+p++ikg+ i+a+v+ ++gve++ee l++el++l keigpiakpd i+++ NCBI__GCF_002869505.1:WP_084200888.1 524 GTAEVESALVLHEEIAEAAVVGFPHDIKGQGIYAYVTPMQGVEPNEE-LRQELIALCVKEIGPIAKPDIIQWA 595 **********************************************5.************************* PP TIGR02188 586 eelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627 + lPktRsGkimRR+lrkiae+e ++lgd+stl+dpsvv++l NCBI__GCF_002869505.1:WP_084200888.1 596 PGLPKTRSGKIMRRILRKIAENElDSLGDTSTLADPSVVDNLV 638 ****************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (643 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: 23.90 // [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