Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_028989221.1 G579_RS0104490 acetate--CoA ligase
Query= SwissProt::P31638 (660 letters) >NCBI__GCF_000423825.1:WP_028989221.1 Length = 652 Score = 809 bits (2089), Expect = 0.0 Identities = 409/654 (62%), Positives = 488/654 (74%), Gaps = 10/654 (1%) Query: 4 IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63 +ES++ E RVF E FA QA + S E Y ALC AE D GFW AR+ L W KPFT+ Sbjct: 6 LESILTEARVFPVHEDFARQANLNS-EQYAALCRRAEEDPSGFWGDLARQELAWDKPFTQ 64 Query: 64 VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123 VLD S APFY+WF DGELN + NCLDR+L + +K A+++E +DG V TY +LH +V Sbjct: 65 VLDDSRAPFYRWFADGELNVAANCLDRHLSSPTRNKAALIWEGEDGEVRTFTYGQLHREV 124 Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183 RFAN LK LGI GDRV IYMPM E VAM ACARLGA HSVVFGGFSA++L++R+ D Sbjct: 125 SRFANVLKKLGITTGDRVAIYMPMVPEAAVAMLACARLGAIHSVVFGGFSAEALKDRIED 184 Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243 A LITAD R G+ + LK AD AL G +V V+V RRTG +V +GRD W Sbjct: 185 TQAKLLITADGGFRAGRVVHLKQHADQALMRDG-HSVDKVVVLRRTGQEVDMLDGRDLWW 243 Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303 ++ C A V+AEHPLFVLYTSGSTGKPKG+ HS+GGYLLW+ +TM+W FDIKP Sbjct: 244 HELMQDAEPQCPAVSVNAEHPLFVLYTSGSTGKPKGIVHSSGGYLLWSALTMRWVFDIKP 303 Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363 +D++WCTADIGWVTGHTY YGPLA GAT ++FEGVPTYP+AGRFW MI RH VS+FYTA Sbjct: 304 EDVYWCTADIGWVTGHTYALYGPLAVGATVLLFEGVPTYPDAGRFWAMIERHGVSVFYTA 363 Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423 PTA+R+L+K E P +YDLSSLRLLGTVGEPINPEAWMWYY+ IG ERCP+VDT+ Sbjct: 364 PTAVRALMKLGEE----WPGKYDLSSLRLLGTVGEPINPEAWMWYYRVIGKERCPVVDTW 419 Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGN-GGILVVKRPWPA 482 WQTETGGH+I PLPG TPL PGSCT PLPGI IVDE G V GG LVVKRPWP Sbjct: 420 WQTETGGHLIAPLPGVTPLKPGSCTRPLPGIFPDIVDEEGDPVQGTEAGGYLVVKRPWPG 479 Query: 483 MIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGT 542 M+RT+WG+ R+ ++Y+ + + Y+AGD + RD D GY+ IMGRIDDVLNVSGHR+GT Sbjct: 480 MLRTVWGNDARYLETYW-AKFQNRYYVAGDSAHRDAD-GYYWIMGRIDDVLNVSGHRLGT 537 Query: 543 MEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKE 602 MEIESALVS+P VAEAAVVGRP ++ GEAI AFV+L++S ++ ++ LR V + Sbjct: 538 MEIESALVSHPAVAEAAVVGRPHEIKGEAITAFVILRQSH-VQDDRDRLTEALRQHVSEA 596 Query: 603 IGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQL 656 IGPIAKP DIRF DNLPKTRSGKIMRRLLR++A+GEEITQDTSTLEN + QL Sbjct: 597 IGPIAKPDDIRFTDNLPKTRSGKIMRRLLRAIARGEEITQDTSTLENEETVRQL 650 Lambda K H 0.319 0.136 0.422 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: 1406 Number of extensions: 78 Number of successful extensions: 9 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: 660 Length of database: 652 Length adjustment: 38 Effective length of query: 622 Effective length of database: 614 Effective search space: 381908 Effective search space used: 381908 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_028989221.1 G579_RS0104490 (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.3874875.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1025.6 0.0 0 1025.4 0.0 1.0 1 NCBI__GCF_000423825.1:WP_028989221.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000423825.1:WP_028989221.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1025.4 0.0 0 0 3 626 .. 29 650 .. 27 652 .] 0.98 Alignments for each domain: == domain 1 score: 1025.4 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkv 74 + e+y++l+++a+edp+ fw++la++el+w+kpf++vld+s +p+++Wf+dgelnv++nc+drh+++ +++k+ NCBI__GCF_000423825.1:WP_028989221.1 29 NSEQYAALCRRAEEDPSGFWGDLARQELAWDKPFTQVLDDSRAPFYRWFADGELNVAANCLDRHLSSpTRNKA 101 6799***************************************************************9***** PP TIGR02188 75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147 a+iweg++ ++r++tY +l+rev+r+anvlk+lG+ gdrvaiY+pm+pea++amlacaR+Ga+hsvvf+G NCBI__GCF_000423825.1:WP_028989221.1 102 ALIWEGEDG--EVRTFTYGQLHREVSRFANVLKKLGITTGDRVAIYMPMVPEAAVAMLACARLGAIHSVVFGG 172 *******55..49************************************************************ PP TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220 fsaeal++Ri+d++akl+itad+g+R g+v++lk+ +d+al + +sv+kv+v++rtg+ev + +grD+ww+ NCBI__GCF_000423825.1:WP_028989221.1 173 FSAEALKDRIEDTQAKLLITADGGFRAGRVVHLKQHADQALMRDGHSVDKVVVLRRTGQEVD-MLDGRDLWWH 244 ************************************************************66.********** PP TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293 el+++ a+ +c++ ++++e+plf+LYtsGstGkPkG++h++gGyll+ alt+++vfdik+ed++wCtaD+GWv NCBI__GCF_000423825.1:WP_028989221.1 245 ELMQD-AEPQCPAVSVNAEHPLFVLYTSGSTGKPKGIVHSSGGYLLWSALTMRWVFDIKPEDVYWCTADIGWV 316 ****7.******************************************************************* PP TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366 tGh+Y +ygPLa+Gat llfegvptypda+rfw++ie+++v++fYtaPta+Ralmklgee++ k+dlsslr+l NCBI__GCF_000423825.1:WP_028989221.1 317 TGHTYALYGPLAVGATVLLFEGVPTYPDAGRFWAMIERHGVSVFYTAPTAVRALMKLGEEWPGKYDLSSLRLL 389 ************************************************************************* PP TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439 g+vGepinpeaw+Wyy+v+Gke+cp+vdtwWqtetGg+li+plpg +t+lkpgs+t+Pl+Gi +++vdeeg++ NCBI__GCF_000423825.1:WP_028989221.1 390 GTVGEPINPEAWMWYYRVIGKERCPVVDTWWQTETGGHLIAPLPG-VTPLKPGSCTRPLPGIFPDIVDEEGDP 461 *********************************************.5************************** PP TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg.lyftGDgarrdkdGyiwilGRvDdvinvsGhr 511 v+ +e gg+Lv+k+pwP+mlrt++g++ r+ etY+ k+++ +y +GD+a+rd+dGy+wi+GR+Ddv+nvsGhr NCBI__GCF_000423825.1:WP_028989221.1 462 VQGTEAGGYLVVKRPWPGMLRTVWGNDARYLETYWAKFQNrYYVAGDSAHRDADGYYWIMGRIDDVLNVSGHR 534 **88888*******************************997999***************************** PP TIGR02188 512 lgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee.elekelkklvrkeigpiakpdkil 583 lgt+eiesalvsh+avaeaavvg+p+eikgeai+afv+l++++ +d++ +l++ l+++v++ igpiakpd+i+ NCBI__GCF_000423825.1:WP_028989221.1 535 LGTMEIESALVSHPAVAEAAVVGRPHEIKGEAITAFVILRQSHVQDDRdRLTEALRQHVSEAIGPIAKPDDIR 607 ****************************************9877666549*********************** PP TIGR02188 584 vveelPktRsGkimRRllrkiaegeellgdvstledpsvveel 626 ++++lPktRsGkimRRllr+ia+gee+++d+stle+++ v +l NCBI__GCF_000423825.1:WP_028989221.1 608 FTDNLPKTRSGKIMRRLLRAIARGEEITQDTSTLENEETVRQL 650 **************************************99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (652 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 30.05 // [ok]
This GapMind analysis is from Apr 09 2024. 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