Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_109939574.1 DLD82_RS02360 acetate--CoA ligase
Query= BRENDA::Q2XNL6 (634 letters) >NCBI__GCF_003173335.1:WP_109939574.1 Length = 629 Score = 680 bits (1754), Expect = 0.0 Identities = 322/596 (54%), Positives = 433/596 (72%), Gaps = 5/596 (0%) Query: 39 DHENYWAEKAERLEWFRKWDRVLDESNRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAI 98 D + +WA+KA L+W + WD++ D P RWF GK+N++ N +DR + +RN++A+ Sbjct: 39 DPDGFWAKKARELDWIKPWDKIRDWE-WPQARWFCGGKLNVSANCLDRHVKNGRRNKLAL 97 Query: 99 LYVNERGDERKLTYYELYREVSRTANALKSLGIKKGDAVALYLPMCPELVVSMLACAKIG 158 ++ ERG E TY +LYR V R ANALK+LG+KKGD V LY+P+ PE V++MLAC +IG Sbjct: 98 IWKGERGKEEIYTYRQLYRAVMRFANALKNLGVKKGDCVCLYMPLVPEHVIAMLACTRIG 157 Query: 159 AVHSVIYSGLSVGALVERLNDARAKIIITADGTYRRGGVIKLKPIVDEAILQCPTIETTV 218 AVHS++++G AL R+ DA AK++ITAD RRG I L+ IVDEA+ P++E V Sbjct: 158 AVHSIVFAGFGAEALHTRIRDADAKVVITADVGIRRGKFIPLRSIVDEAVKNAPSVEKIV 217 Query: 219 VVKHTDIDIEMSDISGREMLFDKLIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLH 278 V+ +E+ S E+ F + EG + C EEMD+EDPLFILYTSG+TG+PKG++H Sbjct: 218 VLSRERCPVEL--YSEMEVDFYAIQEGVSEECPPEEMDSEDPLFILYTSGTTGQPKGIVH 275 Query: 279 TTGGYMVGVASTLEMTFDIHNGDLWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDY 338 TTGGY+VG T + FD+ D+ WCTAD GWITGHSY+VYGPL +G T ++ E DY Sbjct: 276 TTGGYLVGTHYTSKYIFDLKENDVHWCTADTGWITGHSYIVYGPLSVGATVVITETTLDY 335 Query: 339 PDPGVWWSIVEKYGVTKFYTAPTAIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWM 398 PDPGVWW I+E++GVT FYTAPTAIR MR G++ P +YNL SL+I+G+VGEP+NPEA+ Sbjct: 336 PDPGVWWKIIEEFGVTIFYTAPTAIRMFMRVGEEWPNKYNLSSLRIIGSVGEPLNPEAFE 395 Query: 399 WYYRNIGREKCPIIDTWWQTETGMHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVP 458 WYYR IG+ +CPI+DTWWQTETG+H+I P+KPG P+PG+ ADVVD+ G PVP Sbjct: 396 WYYRVIGKNQCPILDTWWQTETGIHMITTPLGQPMKPGFAGVPIPGVVADVVDKEGKPVP 455 Query: 459 LGKGGFLVIRKPWPAMFRTLFNDEQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRS 518 G+GG LVI++PWP+M RT+ +++RY+ YW QI YT GD+A +DEDGY + GRS Sbjct: 456 AGQGGLLVIKEPWPSMMRTVHKNKERYLQ-YWNQI-NHWYTVGDLAVRDEDGYIMVLGRS 513 Query: 519 DDVLNIAGHRIGTAEVESVFVAHPAVAEAAVIGKADPIKGEVIKAFLILKKGHKLNAALI 578 DD++ +AGH +GTAEVES VAH A+AEAAVIG D +KG+ +KAF++L +G++ + LI Sbjct: 514 DDIIIVAGHNLGTAEVESALVAHEAIAEAAVIGVPDDMKGQAVKAFVVLCQGYEPSQKLI 573 Query: 579 EELKRHLRHELGPVAVVGEMVQVDSLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634 EL H+R +GP+A+ + +D LPKTRSGKIMRR+L+A+E G D GD STLEE Sbjct: 574 SELIYHVRMTIGPIAMPSGIEFMDKLPKTRSGKIMRRVLKAKEMGVDPGDISTLEE 629 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: 1240 Number of extensions: 60 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: 629 Length adjustment: 38 Effective length of query: 596 Effective length of database: 591 Effective search space: 352236 Effective search space used: 352236 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_109939574.1 DLD82_RS02360 (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.4141478.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-269 878.9 0.1 1.1e-268 878.6 0.1 1.0 1 NCBI__GCF_003173335.1:WP_109939574.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003173335.1:WP_109939574.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 878.6 0.1 1.1e-268 1.1e-268 4 619 .. 26 629 .] 23 629 .] 0.97 Alignments for each domain: == domain 1 score: 878.6 bits; conditional E-value: 1.1e-268 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkva 75 l +yk+ y+e +dp+ fwak+a+e l+w+kp++k++d++ p+++Wf +g+lnvs+nc+drhv++ r++k+a NCBI__GCF_003173335.1:WP_109939574.1 26 LGDYKKAYAEFLSDPDGFWAKKARE-LDWIKPWDKIRDWE-WPQARWFCGGKLNVSANCLDRHVKNgRRNKLA 96 568*********************5.*************9.5699**************************** PP TIGR02188 76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148 +iw g+ + ++ +tY++l+r v r+an+lk+lGvkkgd v++Y+p++pe viamlac+RiGavhs+vfaGf NCBI__GCF_003173335.1:WP_109939574.1 97 LIWKGERGK--EEIYTYRQLYRAVMRFANALKNLGVKKGDCVCLYMPLVPEHVIAMLACTRIGAVHSIVFAGF 167 ******554..699*********************************************************** PP TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221 aeal++Ri da+ak+vitad g+R+gk i+l++ivdea+++a+ svek++v+ r +v+ + ++++v + NCBI__GCF_003173335.1:WP_109939574.1 168 GAEALHTRIRDADAKVVITADVGIRRGKFIPLRSIVDEAVKNAP-SVEKIVVLSRERCPVE-LYSEMEVDFYA 238 *******************************************9.7*************77.88899999999 PP TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvt 294 + e ++s+ec+pe++dsedplfiLYtsG+tG+PkG++httgGyl+ +++t ky+fd+k++d++wCtaD GW+t NCBI__GCF_003173335.1:WP_109939574.1 239 IQE-GVSEECPPEEMDSEDPLFILYTSGTTGQPKGIVHTTGGYLVGTHYTSKYIFDLKENDVHWCTADTGWIT 310 999.6******************************************************************** PP TIGR02188 295 GhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlg 367 GhsYivygPL++Gat ++ e++ +ypd++ +w++ie+++vtifYtaPtaiR++m++gee+++k++lsslr++g NCBI__GCF_003173335.1:WP_109939574.1 311 GHSYIVYGPLSVGATVVITETTLDYPDPGVWWKIIEEFGVTIFYTAPTAIRMFMRVGEEWPNKYNLSSLRIIG 383 ************************************************************************* PP TIGR02188 368 svGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkev 440 svGep+npea+eWyy+v+Gk++cpi dtwWqtetG ++it+ g ++kpg a +P++G+ a+vvd+egk+v NCBI__GCF_003173335.1:WP_109939574.1 384 SVGEPLNPEAFEWYYRVIGKNQCPILDTWWQTETGIHMITTPLG--QPMKPGFAGVPIPGVVADVVDKEGKPV 454 ***************************************99888..6************************** PP TIGR02188 441 eeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlg 513 ++++ g+Lvik+pwPsm+rt+++++er+ + Y++++++ y GD a+rd+dGyi++lGR Dd+i v+Gh+lg NCBI__GCF_003173335.1:WP_109939574.1 455 PAGQG-GLLVIKEPWPSMMRTVHKNKERYLQ-YWNQINHWYTVGDLAVRDEDGYIMVLGRSDDIIIVAGHNLG 525 **999.8**********************85.***************************************** PP TIGR02188 514 taeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvve 586 tae+esalv+hea+aeaav+gvpd++kg+a+ afvvl +g+e+++ +l +el+ +vr +igpia p+ i++++ NCBI__GCF_003173335.1:WP_109939574.1 526 TAEVESALVAHEAIAEAAVIGVPDDMKGQAVKAFVVLCQGYEPSQ-KLISELIYHVRMTIGPIAMPSGIEFMD 597 *********************************************.5************************** PP TIGR02188 587 elPktRsGkimRRllrkiaegeellgdvstled 619 +lPktRsGkimRR+l++ g gd+stle+ NCBI__GCF_003173335.1:WP_109939574.1 598 KLPKTRSGKIMRRVLKAKEMGV-DPGDISTLEE 629 ***************9866655.556*****85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (629 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 23.92 // [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