Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_109940435.1 DLD82_RS07210 acetate--CoA ligase
Query= BRENDA::Q2XNL6 (634 letters) >NCBI__GCF_003173335.1:WP_109940435.1 Length = 630 Score = 690 bits (1780), Expect = 0.0 Identities = 327/629 (51%), Positives = 452/629 (71%), Gaps = 5/629 (0%) Query: 7 VLLEEKRVFKPHYTVVEEAHIKNW-EAELEKGKDHENYWAEKAERLEWFRKWDRVLDESN 65 VL +++V+ P + A I+++ E E KD + +W A L WF++WD V + Sbjct: 6 VLKPDQKVYYPDPSYQNSALIRDYDELYREFEKDPDAFWRRIASDLLWFKQWDTVRTWDH 65 Query: 66 RPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTANA 125 P WF N ++N+TYN ++R ++ D+RN+VAI + E G ER LTYY+LY++V R NA Sbjct: 66 -PHASWFTNAELNITYNCLERHVNNDRRNKVAIFWAGENGKERILTYYQLYKDVMRMGNA 124 Query: 126 LKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKII 185 LKSLG++KGD V +YLP PELVVSMLACA+IGAVH+V+++G AL ER+ A AKI+ Sbjct: 125 LKSLGVRKGDRVCIYLPGIPELVVSMLACARIGAVHTVVFAGYGAKALNERITGAGAKIV 184 Query: 186 ITADGTYRRGGVIKLKPIVDEAILQCPTIETTVVVKHTDIDIEMSDISGREMLFDKLIEG 245 ITAD + RRGG I LKPIV+EA++ PT+E ++++ + + + D E+ +++LI Sbjct: 185 ITADASVRRGGSIPLKPIVEEALIHAPTVEKVIILRTQEPKVGLLD--DFELDYEELISQ 242 Query: 246 EGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNGDLWWC 305 C+ E +++EDPLFILYTSG+TG PKG++HT GGYMVG T + + D++WC Sbjct: 243 ADRNCEPEHVNSEDPLFILYTSGTTGAPKGIVHTAGGYMVGAYYTTKYVLTLRENDVYWC 302 Query: 306 TADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAPTAIRH 365 TAD GWITGH+Y +YGPLL+G T L E PDYPD G+WW ++E+YGVT FYTAPTAIR Sbjct: 303 TADPGWITGHTYGIYGPLLVGGTIFLTEYTPDYPDAGIWWKLIEEYGVTIFYTAPTAIRM 362 Query: 366 LMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTETGMHLI 425 MR G++ ++Y+L SL++LG+VGEP+NPEA+ W+Y++IG++ CPI+DTWWQTETGMH+I Sbjct: 363 FMRMGEEWSEKYDLSSLRLLGSVGEPLNPEAFEWFYKHIGKKNCPILDTWWQTETGMHMI 422 Query: 426 APLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFNDEQRY 485 + P+KPG KP+PG+ A VV+E GDPVP G GFL I++PWP+M +T++ +++RY Sbjct: 423 TTMVGLPMKPGFAGKPIPGVVATVVNEEGDPVPPGTNGFLAIKEPWPSMMKTVYQNDERY 482 Query: 486 IDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVAHPAVA 545 YW G Y++ D+A DEDGY + GRSDD++ +AGH +GTAE+ES V+H AVA Sbjct: 483 RQ-YWNFGKYGYYSSNDIAMMDEDGYIMLLGRSDDIIIVAGHNVGTAEIESALVSHSAVA 541 Query: 546 EAAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQVDSLP 605 EAA IGK DP+KG +IKAF+IL+ G LI +LK H+R LGP++V E+ VD+LP Sbjct: 542 EAAAIGKPDPLKGNIIKAFVILRNGVSPTPKLIHDLKYHVRIMLGPISVPAELDFVDNLP 601 Query: 606 KTRSGKIMRRILRAREEGEDLGDTSTLEE 634 KTRSGKIMRR+L+A+E G D GD STL+E Sbjct: 602 KTRSGKIMRRVLKAQEMGIDPGDVSTLDE 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: 1286 Number of extensions: 62 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_109940435.1 DLD82_RS07210 (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.2499816.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-252 825.7 0.0 1.3e-252 825.5 0.0 1.0 1 NCBI__GCF_003173335.1:WP_109940435.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003173335.1:WP_109940435.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 825.5 0.0 1.3e-252 1.3e-252 4 618 .. 26 629 .. 23 630 .] 0.97 Alignments for each domain: == domain 1 score: 825.5 bits; conditional E-value: 1.3e-252 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkva 75 +++y ely+e ++dp++fw++ a++ l w+k++++v++++ +p++ Wf+++eln++ync++rhv++ r++kva NCBI__GCF_003173335.1:WP_109940435.1 26 IRDYDELYREFEKDPDAFWRRIASD-LLWFKQWDTVRTWD-HPHASWFTNAELNITYNCLERHVNNdRRNKVA 96 578*********************6.*************9.779*********************99****** PP TIGR02188 76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148 i w g++ + +r ltY++l+++v r+ n+lk+lGv+kgdrv+iYlp ipe+v+ mlacaRiGavh+vvfaG+ NCBI__GCF_003173335.1:WP_109940435.1 97 IFWAGENGK--ERILTYYQLYKDVMRMGNALKSLGVRKGDRVCIYLPGIPELVVSMLACARIGAVHTVVFAGY 167 ******665..6************************************************************* PP TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221 a+al+eRi+ a ak+vitad ++R+g +i+lk iv+eal +a+ +vekv++++ ++ +v + ++ ++ +ee NCBI__GCF_003173335.1:WP_109940435.1 168 GAKALNERITGAGAKIVITADASVRRGGSIPLKPIVEEALIHAP-TVEKVIILRTQEPKVG-LLDDFELDYEE 238 *******************************************9.7*******99998866.999******** PP TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvt 294 l+++ a+++cepe+++sedplfiLYtsG+tG PkG++ht+gGy++ a++t+kyv ++++d++wCtaD GW+t NCBI__GCF_003173335.1:WP_109940435.1 239 LISQ-ADRNCEPEHVNSEDPLFILYTSGTTGAPKGIVHTAGGYMVGAYYTTKYVLTLRENDVYWCTADPGWIT 310 ***6.******************************************************************** PP TIGR02188 295 GhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlg 367 Gh+Y +ygPL++G t +l e +p+ypda+ +w++ie+y+vtifYtaPtaiR++m++gee+ +k+dlsslr+lg NCBI__GCF_003173335.1:WP_109940435.1 311 GHTYGIYGPLLVGGTIFLTEYTPDYPDAGIWWKLIEEYGVTIFYTAPTAIRMFMRMGEEWSEKYDLSSLRLLG 383 ************************************************************************* PP TIGR02188 368 svGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkev 440 svGep+npea+eW+y+++Gk++cpi dtwWqtetG ++it++ g +++kpg a +P++G+ a+vv+eeg++v NCBI__GCF_003173335.1:WP_109940435.1 384 SVGEPLNPEAFEWFYKHIGKKNCPILDTWWQTETGMHMITTMVG--LPMKPGFAGKPIPGVVATVVNEEGDPV 454 ********************************************..5************************** PP TIGR02188 441 eeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg.lyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512 ++++ g+L+ik+pwPsm++t+y+++er+ + Y++ k +y + D a++d+dGyi++lGR Dd+i v+Gh++ NCBI__GCF_003173335.1:WP_109940435.1 455 PPGTN-GFLAIKEPWPSMMKTVYQNDERYRQ-YWNFGKYgYYSSNDIAMMDEDGYIMLLGRSDDIIIVAGHNV 525 **999.8**********************86.6664444389999**************************** PP TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585 gtaeiesalvsh+avaeaa++g+pd +kg++i afv+l++gv+++ +l ++lk +vr ++gpi+ p+++ +v NCBI__GCF_003173335.1:WP_109940435.1 526 GTAEIESALVSHSAVAEAAAIGKPDPLKGNIIKAFVILRNGVSPTP-KLIHDLKYHVRIMLGPISVPAELDFV 597 **********************************************.5************************* PP TIGR02188 586 eelPktRsGkimRRllrkiaegeellgdvstle 618 ++lPktRsGkimRR+l++ g + gdvstl+ NCBI__GCF_003173335.1:WP_109940435.1 598 DNLPKTRSGKIMRRVLKAQEMGID-PGDVSTLD 629 ****************98766655.56****97 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: 32.02 // [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