Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_091288310.1 BLV57_RS09725 acetate--CoA ligase
Query= SwissProt::P9WQD1 (651 letters) >NCBI__GCF_900107045.1:WP_091288310.1 Length = 656 Score = 883 bits (2281), Expect = 0.0 Identities = 427/654 (65%), Positives = 511/654 (78%), Gaps = 16/654 (2%) Query: 1 MSESTPEV------SSSYPPPAHFAEHANARAELYREAEEDRLAFWAKQANRLSWTTPFT 54 M+E +P + S ++PP +F+ ANA+A+LY EA+ DR FWA QA RLSW T ++ Sbjct: 1 MTEQSPALDNLLTESRTFPPNENFSAQANAKADLYAEADADREGFWAAQAERLSWDTKWS 60 Query: 55 EVLDWSGAPFAKWFVGGELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLA 114 +VLDW+ APFAKWFVGG+LNVAYNCVDRHVE+GHGD++AIHW GEP GD R +TY++L Sbjct: 61 QVLDWTNAPFAKWFVGGKLNVAYNCVDRHVESGHGDQIAIHWVGEP-GDSRDITYAELKD 119 Query: 115 EVSKAANALTDLGLVAGDRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARI 174 EVSKAAN L +G+ AGDRVAI P+IPEA++AMLACAR+G +HSVVFGGF+ AL++R+ Sbjct: 120 EVSKAANGLASIGVGAGDRVAIQCPMIPEAIVAMLACARIGALHSVVFGGFSPTALRSRV 179 Query: 175 VDAQAKLLITADGQFRRGKPSPLKAAADEALAAIPDCSVEHVLVVRRTGIEMAWSEGRDL 234 D +AK++IT+DGQ+RRGK +P+K DEAL SVE VLV+RRTG E+ EGRDL Sbjct: 180 DDQEAKVVITSDGQYRRGKAAPMKVNVDEALEGAE--SVEKVLVIRRTGDEIPLIEGRDL 237 Query: 235 WWHHVVGSASPAHTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDV 294 WWH +V S HTPE FDSEHPLF+LYTSGTTGKPKGI+HTSGGYLTQ YT +FD Sbjct: 238 WWHELVDGQSAEHTPEAFDSEHPLFILYTSGTTGKPKGILHTSGGYLTQAAYTHHNVFDH 297 Query: 295 KPDSDVFWCTADIGWVTGHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQIIEKYGVTIY 354 K DV+WCTADIGW+TGH+Y VYGPL N T+V+YEGTP+TP RH++II+KY V+IY Sbjct: 298 KAGEDVYWCTADIGWITGHSYIVYGPLANRTTQVVYEGTPNTPHEGRHWEIIQKYKVSIY 357 Query: 355 YTAPTLIRMFMKWGREIPDSHDLSSLRLLGSVGEPINPEAWRWYRDVIGGGRTPLVDTWW 414 YTAPTLIR FMKWG EIP +D+SSLR+LGSVGEPINPEAW WYR+ IG G+ P+VDTWW Sbjct: 358 YTAPTLIRTFMKWGNEIPQKYDISSLRVLGSVGEPINPEAWIWYRENIGAGQAPIVDTWW 417 Query: 415 QTETGSAMISPLPGIAAAKPGSAMTPLPGISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQ 474 QTETG MISPLPG+ + KPGSA LPGISAKIVDD + E + GYLVLD+ Sbjct: 418 QTETGGIMISPLPGVTSTKPGSAQRALPGISAKIVDDQAN------EVGKGGGGYLVLDK 471 Query: 475 PWPSMLRGIWGDPARYWHSYWSKFSDKGYYFAGDGARIDPDGAIWVLGRIDDVMNVSGHR 534 PWP MLRGIWGD AR+ +YWS+F+++GYYFAGDGA+ D DG IW+LGR+DDVMNVSGHR Sbjct: 472 PWPGMLRGIWGDEARFKETYWSRFAEQGYYFAGDGAKYDADGDIWLLGRVDDVMNVSGHR 531 Query: 535 ISTAEVESALVAHSGVAEAAVVGVTDETTTQAICAFVVLRANYAP-HDRTAEELRTEVAR 593 IST EVESALV+H VAEAAVVG TD TT Q I AFV+LR N D +ELR VA+ Sbjct: 532 ISTTEVESALVSHPTVAEAAVVGATDPTTGQGIVAFVILRGNAVDGGDAAVQELRNHVAK 591 Query: 594 VISPIARPRDVHVVPELPKTRSGKIMRRLLRDVAENRELGDTSTLLDPTVFDAI 647 I PIA+PR + VV ELPKTRSGKIMRRLLRDVAENR +GD +TL D +V D I Sbjct: 592 EIGPIAKPRQILVVQELPKTRSGKIMRRLLRDVAENRAVGDVTTLADSSVMDLI 645 Lambda K H 0.319 0.136 0.433 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: 1428 Number of extensions: 70 Number of successful extensions: 6 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: 656 Length adjustment: 38 Effective length of query: 613 Effective length of database: 618 Effective search space: 378834 Effective search space used: 378834 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 (21.8 bits) S2: 54 (25.4 bits)
Align candidate WP_091288310.1 BLV57_RS09725 (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.1907654.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-292 957.9 0.4 1.2e-292 957.7 0.4 1.0 1 NCBI__GCF_900107045.1:WP_091288310.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900107045.1:WP_091288310.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 957.7 0.4 1.2e-292 1.2e-292 3 627 .. 27 646 .. 25 648 .. 0.98 Alignments for each domain: == domain 1 score: 957.7 bits; conditional E-value: 1.2e-292 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkv 74 ++++ ++ly+ea +d+e fwa +a+ +l+w++++++vld++++p++kWf++g+lnv+yncvdrhve+ + d++ NCBI__GCF_900107045.1:WP_091288310.1 27 QANAKADLYAEADADREGFWAAQAE-RLSWDTKWSQVLDWTNAPFAKWFVGGKLNVAYNCVDRHVESgHGDQI 98 5678899*****************9.5********************************************** PP TIGR02188 75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147 ai+w g+ +g dsr +tYael++ev+++an l ++Gv gdrvai pmipea++amlacaRiGa+hsvvf+G NCBI__GCF_900107045.1:WP_091288310.1 99 AIHWVGE-PG-DSRDITYAELKDEVSKAANGLASIGVGAGDRVAIQCPMIPEAIVAMLACARIGALHSVVFGG 169 ******9.77.59************************************************************ PP TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220 fs+ al++R+ d eak+vit+d+++R+gk+ ++k +vdeale ae svekvlv++rtg+e+ + egrD+ww+ NCBI__GCF_900107045.1:WP_091288310.1 170 FSPTALRSRVDDQEAKVVITSDGQYRRGKAAPMKVNVDEALEGAE-SVEKVLVIRRTGDEIP-LIEGRDLWWH 240 ******************************************998.8*************66.********** PP TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik.dedifwCtaDvGW 292 elv+ ++sae++pe++dse+plfiLYtsG+tGkPkG+lht+gGyl++aa+t++ vfd+k ed++wCtaD+GW NCBI__GCF_900107045.1:WP_091288310.1 241 ELVD-GQSAEHTPEAFDSEHPLFILYTSGTTGKPKGILHTSGGYLTQAAYTHHNVFDHKaGEDVYWCTADIGW 312 ****.6*****************************************************668*********** PP TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365 +tGhsYivygPLan t++++eg+p++p+++r+we+i+kykv+i+YtaPt+iR++mk+g+e+++k+d+sslrv NCBI__GCF_900107045.1:WP_091288310.1 313 ITGHSYIVYGPLANRTTQVVYEGTPNTPHEGRHWEIIQKYKVSIYYTAPTLIRTFMKWGNEIPQKYDISSLRV 385 ************************************************************************* PP TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438 lgsvGepinpeaw Wy+e++G +++pivdtwWqtetGgi+i+plpg +t++kpgsa++ l+Gi+a++vd++++ NCBI__GCF_900107045.1:WP_091288310.1 386 LGSVGEPINPEAWIWYRENIGAGQAPIVDTWWQTETGGIMISPLPG-VTSTKPGSAQRALPGISAKIVDDQAN 457 **********************************************.5************************* PP TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkdGyiwilGRvDdvinvsG 509 ev ++ + g+Lv++kpwP+mlr+i+gde rf etY++++ + +yf+GDga+ d+dG+iw+lGRvDdv+nvsG NCBI__GCF_900107045.1:WP_091288310.1 458 EVGKGGG-GYLVLDKPWPGMLRGIWGDEARFKETYWSRFAEqgYYFAGDGAKYDADGDIWLLGRVDDVMNVSG 529 ***9988.8*****************************98777****************************** PP TIGR02188 510 hrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdki 582 hr++t+e+esalvsh++vaeaavvg++d ++g+ ivafv+l+ ++ ++ +el+++v+keigpiakp++i NCBI__GCF_900107045.1:WP_091288310.1 530 HRISTTEVESALVSHPTVAEAAVVGATDPTTGQGIVAFVILRGNAVDGGDAAVQELRNHVAKEIGPIAKPRQI 602 *******************************************99998889********************** PP TIGR02188 583 lvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627 lvv+elPktRsGkimRRllr++ae++ +gdv+tl+d+sv++ ++ NCBI__GCF_900107045.1:WP_091288310.1 603 LVVQELPKTRSGKIMRRLLRDVAENRA-VGDVTTLADSSVMDLIS 646 ***********************9765.67**********99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (656 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: 21.18 // [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