Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_012673534.1 SULAZ_RS07040 acetate--CoA ligase
Query= BRENDA::Q2XNL6 (634 letters) >NCBI__GCF_000021545.1:WP_012673534.1 Length = 630 Score = 710 bits (1833), Expect = 0.0 Identities = 354/631 (56%), Positives = 460/631 (72%), Gaps = 9/631 (1%) Query: 7 VLLEEKRVFKPHYTVVEEAHIKNWEAELEKG-KDHENYWAEKAERLEWFRKWDRVLDESN 65 +LL+ + P +VE+A IK++E+ ++ +D E ++++ AE LEWF+KWD+VL E N Sbjct: 6 LLLKVDEKYYPPQEIVEQAWIKDYESLYKQSIEDREGFYSKIAEELEWFQKWDKVL-EWN 64 Query: 66 RPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTANA 125 P+ +WF+NGK N+TYN +DR + KRN+VA + ++E G+E+K+TY EL VSR AN Sbjct: 65 YPYAKWFINGKTNITYNCIDRHVKNGKRNKVAFISIDEEGNEKKVTYGELLDLVSRLANG 124 Query: 126 LKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKII 185 LKSLGIKKGD V++Y+P E ++MLACA+IGA+HSV+++G S GAL R++DA+AK + Sbjct: 125 LKSLGIKKGDRVSIYMPNTVEAAIAMLACARIGAIHSVVFAGFSEGALKIRIDDAKAKAV 184 Query: 186 ITADGTYRRGGVIKLKPIVDEAILQCPTIETTVVVKHTDIDIEMSDISGREMLFD--KLI 243 ITA T RRG I L P V EAI +E ++ D D E+S+ + D KLI Sbjct: 185 ITATYTKRRGKKIPLFPTVKEAIKDLDFVEKVIL---WDRDNELSEEYEEHNVVDFYKLI 241 Query: 244 EGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNGDLW 303 + C E DAEDPLFILYTSG+TGKPKGVLHTTGGYMV T + FD+ D++ Sbjct: 242 KNSSKDCPPEIQDAEDPLFILYTSGTTGKPKGVLHTTGGYMVNTYMTSKYVFDLKENDIY 301 Query: 304 WCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAPTAI 363 WCTAD+GWITGHSY+VYGPL G T+++ EG P YP PG+WW VEKYGV FYTAPTAI Sbjct: 302 WCTADVGWITGHSYIVYGPLANGVTSIMMEGVPVYPHPGIWWEYVEKYGVNVFYTAPTAI 361 Query: 364 RHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTETGMH 423 R LMRFGD+ P +Y+L SLK+LG+VGEPINPEAW+WYY+NIGR K I+DTWWQTETG H Sbjct: 362 RMLMRFGDEIPAKYDLSSLKVLGSVGEPINPEAWLWYYKNIGRGKAVIVDTWWQTETGAH 421 Query: 424 LIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFNDEQ 483 +I +P P KPG KP+ GIE VVD+ G+P+P + G LVI+ PWP+M RT + + + Sbjct: 422 MITTVPSYPAKPGKAGKPMFGIEVAVVDKQGNPMPPNQVGHLVIKNPWPSMLRTCWGEPE 481 Query: 484 RYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVAHPA 543 RY + YW +IP G Y+AGD+A DE+GY + GR+DDVL++AGHRIGTAEVES V + A Sbjct: 482 RY-EKYWNEIP-GYYSAGDLAAIDEEGYIMVVGRADDVLSVAGHRIGTAEVESAIVENHA 539 Query: 544 VAEAAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQVDS 603 V EAAVIGK + IKGE IKAF+ILK+G++ + L E +K +R LGP+AV E+ VD Sbjct: 540 VTEAAVIGKPNEIKGESIKAFVILKEGYQPSEELKERIKDTVREVLGPIAVPDEIEFVDK 599 Query: 604 LPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634 LPKTRSGKIMRR+L+ARE G ++GDTSTLEE Sbjct: 600 LPKTRSGKIMRRLLKARELGLEIGDTSTLEE 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: 1237 Number of extensions: 39 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_012673534.1 SULAZ_RS07040 (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.4513.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-268 876.4 1.2 5.9e-268 876.2 1.2 1.0 1 lcl|NCBI__GCF_000021545.1:WP_012673534.1 SULAZ_RS07040 acetate--CoA ligas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021545.1:WP_012673534.1 SULAZ_RS07040 acetate--CoA ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 876.2 1.2 5.9e-268 5.9e-268 4 619 .. 26 630 .] 23 630 .] 0.97 Alignments for each domain: == domain 1 score: 876.2 bits; conditional E-value: 5.9e-268 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rk 71 +++y++ly+++ied+e f++k a+ elew+++++kvl+++ p +kWf +g++n++ync+drhv++ ++ lcl|NCBI__GCF_000021545.1:WP_012673534.1 26 IKDYESLYKQSIEDREGFYSKIAE-ELEWFQKWDKVLEWN-YPYAKWFINGKTNITYNCIDRHVKNgKR 92 689********************9.5*************9.679**********************9** PP TIGR02188 72 dkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGav 140 +kva i +e + ++k+tY ell+ v+rlan lk+lG+kkgdrv+iY+p ++ea+iamlacaRiGa+ lcl|NCBI__GCF_000021545.1:WP_012673534.1 93 NKVAFISIDEEGN--EKKVTYGELLDLVSRLANGLKSLGIKKGDRVSIYMPNTVEAAIAMLACARIGAI 159 *****98777554..7***************************************************** PP TIGR02188 141 hsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeeva 209 hsvvfaGfs al+ Ri da+ak vita + R+gk+i+l +v ea+++ + vekv++ r +e + lcl|NCBI__GCF_000021545.1:WP_012673534.1 160 HSVVFAGFSEGALKIRIDDAKAKAVITATYTKRRGKKIPLFPTVKEAIKDLD-FVEKVILWDRDNELSE 227 ***************************************************8.7************999 PP TIGR02188 210 ewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdi 278 e++e v + +l++ ++s++c+pe d+edplfiLYtsG+tGkPkGvlhttgGy++ +++t kyvfd+ lcl|NCBI__GCF_000021545.1:WP_012673534.1 228 EYEEHNVVDFYKLIK-NSSKDCPPEIQDAEDPLFILYTSGTTGKPKGVLHTTGGYMVNTYMTSKYVFDL 295 ***************.5**************************************************** PP TIGR02188 279 kdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRal 347 k++di+wCtaDvGW+tGhsYivygPLanG+t+++ egvp yp+++ +we +eky+v++fYtaPtaiR+l lcl|NCBI__GCF_000021545.1:WP_012673534.1 296 KENDIYWCTADVGWITGHSYIVYGPLANGVTSIMMEGVPVYPHPGIWWEYVEKYGVNVFYTAPTAIRML 364 ********************************************************************* PP TIGR02188 348 mklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatel 416 m+ g+e+++k+dlssl+vlgsvGepinpeaw Wyy+++G++k+ ivdtwWqtetG+++it++p+ ++ lcl|NCBI__GCF_000021545.1:WP_012673534.1 365 MRFGDEIPAKYDLSSLKVLGSVGEPINPEAWLWYYKNIGRGKAVIVDTWWQTETGAHMITTVPS--YPA 431 ****************************************************************..6** PP TIGR02188 417 kpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGD 485 kpg a +P+fGie++vvd++g+++ +++ g Lvik+pwPsmlrt +g++er+ +Y+++++g+y +GD lcl|NCBI__GCF_000021545.1:WP_012673534.1 432 KPGKAGKPMFGIEVAVVDKQGNPMPPNQV-GHLVIKNPWPSMLRTCWGEPERYE-KYWNEIPGYYSAGD 498 *************************9999.8*********************95.6************* PP TIGR02188 486 garrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegv 554 a+ d++Gyi+++GR+Ddv+ v+Ghr+gtae+esa+v+++av+eaav+g+p+eikge+i afv+lkeg+ lcl|NCBI__GCF_000021545.1:WP_012673534.1 499 LAAIDEEGYIMVVGRADDVLSVAGHRIGTAEVESAIVENHAVTEAAVIGKPNEIKGESIKAFVILKEGY 567 ********************************************************************* PP TIGR02188 555 eedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstled 619 +++ee l++ +k++vr+ +gpia pd+i++v++lPktRsGkimRRll++ g ++gd+stle+ lcl|NCBI__GCF_000021545.1:WP_012673534.1 568 QPSEE-LKERIKDTVREVLGPIAVPDEIEFVDKLPKTRSGKIMRRLLKARELGL-EIGDTSTLEE 630 ****5.*****************************************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.11 # Mc/sec: 3.59 // [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