Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_028951249.1 Q385_RS0108465 acetate--CoA ligase
Query= BRENDA::Q2XNL6 (634 letters) >NCBI__GCF_000619805.1:WP_028951249.1 Length = 630 Score = 707 bits (1824), Expect = 0.0 Identities = 353/633 (55%), Positives = 461/633 (72%), Gaps = 9/633 (1%) Query: 5 TSVLLEEKRVFKPHYTVVEEAHIKNWEAELEKG-KDHENYWAEKAERLEWFRKWDRVLDE 63 + +LL+ + P +V++A +K++E ++ +D E ++++ AE LEWF+KWD+VL E Sbjct: 4 SDLLLKVDEKYYPPEDIVQQAWVKDYEYLYKQSIEDREGFYSKIAEELEWFQKWDKVL-E 62 Query: 64 SNRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTA 123 + P+ +WFVNGK N+TYN +DR + KRN+VA + V+E G+E+K+TY EL VSR A Sbjct: 63 WDYPYAKWFVNGKTNITYNCIDRHVKNGKRNKVAFISVDEEGNEKKVTYGELLYLVSRLA 122 Query: 124 NALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAK 183 N LKSLGIKKGD V++Y+P E ++MLACA+IGA+HSV+++G S GAL R++DA+AK Sbjct: 123 NGLKSLGIKKGDRVSIYMPNTVEAAIAMLACARIGAIHSVVFAGFSEGALKIRVDDAKAK 182 Query: 184 IIITADGTYRRGGVIKLKPIVDEAILQCPTIETTVVVKHTDIDIEMSDISGREMLFD--K 241 +ITA T RRG I L P V EAI +E ++ D D E+SD + D K Sbjct: 183 AVITATYTKRRGKKIPLFPTVKEAIKDLDFVEKIIL---WDRDNELSDEYEEHNVVDFYK 239 Query: 242 LIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNGD 301 LI+ C E DAEDPLFILYTSG+TGKPKGVLHTTGGYMV T + FD+ D Sbjct: 240 LIKNSSKECPPEIQDAEDPLFILYTSGTTGKPKGVLHTTGGYMVNTYMTSKYVFDLKEND 299 Query: 302 LWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAPT 361 ++WCTAD+GWITGHSY+VYGPL G T+++ EG P YP PG+WW VEKYGV FYTAPT Sbjct: 300 IYWCTADVGWITGHSYIVYGPLANGVTSIMMEGVPVYPHPGIWWEYVEKYGVNVFYTAPT 359 Query: 362 AIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTETG 421 AIR LMRFG++ P +Y++ SLK+LG+VGEPINPEAW+WYY+NIGR K I+DTWWQTETG Sbjct: 360 AIRMLMRFGEEIPAKYDISSLKVLGSVGEPINPEAWLWYYKNIGRGKAVIVDTWWQTETG 419 Query: 422 MHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFND 481 H+I +P P KPG KP+ GIE VVD+ G+P+P + G LVI+ PWP+M RT + + Sbjct: 420 AHMITTVPSYPAKPGKAGKPMFGIEVAVVDKQGNPMPPNQVGHLVIKNPWPSMLRTCWGE 479 Query: 482 EQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVAH 541 +RY + YW +IP G Y+AGD+A DE+GY + GR+DDVL++AGHRIGTAEVES V + Sbjct: 480 PERY-EKYWNEIP-GYYSAGDLAAIDEEGYIMVVGRADDVLSVAGHRIGTAEVESAIVEN 537 Query: 542 PAVAEAAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQV 601 AVAEAAVIGK + IKGE IKAF+ILK+G++ + L E +K +R LGP+AV E+ V Sbjct: 538 HAVAEAAVIGKPNEIKGESIKAFVILKEGYEPSEELKERIKDTVRDVLGPIAVPDEIEFV 597 Query: 602 DSLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634 D LPKTRSGKIMRR+L+ARE G ++GDTSTLEE Sbjct: 598 DKLPKTRSGKIMRRLLKARELGLEIGDTSTLEE 630 Lambda K H 0.319 0.138 0.428 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: 1239 Number of extensions: 43 Number of successful extensions: 4 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: 634 Length of database: 630 Length adjustment: 38 Effective length of query: 596 Effective length of database: 592 Effective search space: 352832 Effective search space used: 352832 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_028951249.1 Q385_RS0108465 (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.1181063.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-267 874.1 1.7 2.9e-267 873.9 1.7 1.0 1 NCBI__GCF_000619805.1:WP_028951249.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000619805.1:WP_028951249.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 873.9 1.7 2.9e-267 2.9e-267 4 619 .. 26 630 .] 23 630 .] 0.97 Alignments for each domain: == domain 1 score: 873.9 bits; conditional E-value: 2.9e-267 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkva 75 +++y+ ly+++ied+e f++k a+ elew+++++kvl+++ p +kWf++g++n++ync+drhv++ +++kva NCBI__GCF_000619805.1:WP_028951249.1 26 VKDYEYLYKQSIEDREGFYSKIAE-ELEWFQKWDKVLEWD-YPYAKWFVNGKTNITYNCIDRHVKNgKRNKVA 96 579********************9.5**************.679**********************9****** PP TIGR02188 76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148 i +e + ++k+tY ell v+rlan lk+lG+kkgdrv+iY+p ++ea+iamlacaRiGa+hsvvfaGf NCBI__GCF_000619805.1:WP_028951249.1 97 FISVDEEGN--EKKVTYGELLYLVSRLANGLKSLGIKKGDRVSIYMPNTVEAAIAMLACARIGAIHSVVFAGF 167 *98766554..7************************************************************* PP TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221 s al+ R+ da+ak vita + R+gk+i+l +v ea+++ + vek+++ r +e e++e v + + NCBI__GCF_000619805.1:WP_028951249.1 168 SEGALKIRVDDAKAKAVITATYTKRRGKKIPLFPTVKEAIKDLD-FVEKIILWDRDNELSDEYEEHNVVDFYK 239 *******************************************8.7***********99999*********** PP TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvt 294 l++ ++s+ec+pe d+edplfiLYtsG+tGkPkGvlhttgGy++ +++t kyvfd+k++di+wCtaDvGW+t NCBI__GCF_000619805.1:WP_028951249.1 240 LIK-NSSKECPPEIQDAEDPLFILYTSGTTGKPKGVLHTTGGYMVNTYMTSKYVFDLKENDIYWCTADVGWIT 311 ***.5******************************************************************** PP TIGR02188 295 GhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlg 367 GhsYivygPLanG+t+++ egvp yp+++ +we +eky+v++fYtaPtaiR+lm+ gee+++k+d+ssl+vlg NCBI__GCF_000619805.1:WP_028951249.1 312 GHSYIVYGPLANGVTSIMMEGVPVYPHPGIWWEYVEKYGVNVFYTAPTAIRMLMRFGEEIPAKYDISSLKVLG 384 ************************************************************************* PP TIGR02188 368 svGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkev 440 svGepinpeaw Wyy+++G++k+ ivdtwWqtetG+++it++p+ ++kpg a +P+fGie++vvd++g+++ NCBI__GCF_000619805.1:WP_028951249.1 385 SVGEPINPEAWLWYYKNIGRGKAVIVDTWWQTETGAHMITTVPS--YPAKPGKAGKPMFGIEVAVVDKQGNPM 455 ********************************************..6************************** PP TIGR02188 441 eeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513 +++ g Lvik+pwPsmlrt +g++er+ +Y+++++g+y +GD a+ d++Gyi+++GR+Ddv+ v+Ghr+g NCBI__GCF_000619805.1:WP_028951249.1 456 PPNQV-GHLVIKNPWPSMLRTCWGEPERYE-KYWNEIPGYYSAGDLAAIDEEGYIMVVGRADDVLSVAGHRIG 526 *9999.8*********************95.6***************************************** PP TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvve 586 tae+esa+v+++avaeaav+g+p+eikge+i afv+lkeg+e++ee l++ +k++vr+ +gpia pd+i++v+ NCBI__GCF_000619805.1:WP_028951249.1 527 TAEVESAIVENHAVAEAAVIGKPNEIKGESIKAFVILKEGYEPSEE-LKERIKDTVRDVLGPIAVPDEIEFVD 598 *********************************************5.************************** PP TIGR02188 587 elPktRsGkimRRllrkiaegeellgdvstled 619 +lPktRsGkimRRll++ g ++gd+stle+ NCBI__GCF_000619805.1:WP_028951249.1 599 KLPKTRSGKIMRRLLKARELGL-EIGDTSTLEE 630 ***************9876665.566*****85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (630 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: 20.95 // [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