Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_013518028.1 ALIDE2_RS18585 acetate--CoA ligase
Query= SwissProt::P31638 (660 letters) >NCBI__GCF_000204645.1:WP_013518028.1 Length = 665 Score = 1069 bits (2764), Expect = 0.0 Identities = 508/660 (76%), Positives = 581/660 (88%), Gaps = 5/660 (0%) Query: 2 SAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPF 61 SAIESV+ E+RVF PPEG A I M Y+ALC EA++D+EGFWAR ARE L WT+PF Sbjct: 6 SAIESVLIENRVFPPPEGLVKTARISGMAGYEALCAEADKDFEGFWARLARENLQWTRPF 65 Query: 62 TKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHG 121 TK LD+SNAPFY+WF DGELNAS NCLDR++ K AI+FEADDG+VT+VTY+EL Sbjct: 66 TKTLDESNAPFYQWFADGELNASANCLDRHMGTPVESKTAIIFEADDGAVTKVTYKELLA 125 Query: 122 KVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERL 181 +V +FAN LKA G++KGDRV+IYMPM++EGVVAMQACAR+GATHSVVFGGFSAK++QER+ Sbjct: 126 RVAQFANALKAQGVKKGDRVLIYMPMTIEGVVAMQACARIGATHSVVFGGFSAKAVQERI 185 Query: 182 VDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWT--EGR 239 +D GAVA+ITA+ Q+RGGK LPLKAI D+ +A+GGCE++++V+VY RT AW +GR Sbjct: 186 IDAGAVAVITANYQLRGGKELPLKAIVDEGIAMGGCESIKSVLVYERT--PTAWNRVDGR 243 Query: 240 DRWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTF 299 D+ + AGQ C V AEHPLF+LYTSGSTGKPKGVQHSTGGYLLWA +TM WTF Sbjct: 244 DKSFAEALAGQSTECVPVAVEAEHPLFILYTSGSTGKPKGVQHSTGGYLLWAKLTMDWTF 303 Query: 300 DIKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSI 359 D++PDD+FWCTADIGWVTGHTYIAYGPLAAG TQV+FEG+PTYPNAGRFW MI RHKVSI Sbjct: 304 DLRPDDVFWCTADIGWVTGHTYIAYGPLAAGGTQVMFEGIPTYPNAGRFWQMIERHKVSI 363 Query: 360 FYTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPI 419 FYTAPTAIRSLIKAA++DEK+HPK +DLSSLR+LG+VGEPINPEAWMWYYKN+G ERCPI Sbjct: 364 FYTAPTAIRSLIKAADSDEKVHPKNWDLSSLRILGSVGEPINPEAWMWYYKNVGGERCPI 423 Query: 420 VDTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRP 479 VDT+WQTE GGH+ITPLPGATPLVPGSCTLPLPGI AAIVDETG DVPNG+GG+LV+KRP Sbjct: 424 VDTWWQTENGGHLITPLPGATPLVPGSCTLPLPGIAAAIVDETGKDVPNGSGGMLVIKRP 483 Query: 480 WPAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHR 539 WP+MIRTIW DPERF+KSYFPEE+GGK+YLAGDG++RD T YF + GRIDDVLNVSGHR Sbjct: 484 WPSMIRTIWNDPERFKKSYFPEEMGGKIYLAGDGAVRDAKTAYFRVTGRIDDVLNVSGHR 543 Query: 540 MGTMEIESALVS-NPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNW 598 MGTMEIESALV+ + LVAEAAVVGRPDD+TGEAICAFVVLKR+RPTGEEA +IA ELRNW Sbjct: 544 MGTMEIESALVAKSDLVAEAAVVGRPDDLTGEAICAFVVLKRARPTGEEAKQIAAELRNW 603 Query: 599 VGKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQ 658 V KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGE ITQDTSTLENPAIL+QL Q Sbjct: 604 VAKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEAITQDTSTLENPAILDQLAQ 663 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: 1552 Number of extensions: 69 Number of successful extensions: 2 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: 665 Length adjustment: 38 Effective length of query: 622 Effective length of database: 627 Effective search space: 389994 Effective search space used: 389994 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_013518028.1 ALIDE2_RS18585 (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.3993558.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-288 943.1 0.0 3.6e-288 942.9 0.0 1.0 1 NCBI__GCF_000204645.1:WP_013518028.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000204645.1:WP_013518028.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 942.9 0.0 3.6e-288 3.6e-288 3 628 .. 32 663 .. 30 664 .. 0.96 Alignments for each domain: == domain 1 score: 942.9 bits; conditional E-value: 3.6e-288 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkv 74 + y++l++ea +d e fwa+la+e+l+w++pf+k+ldes++p+++Wf+dgeln+s+nc+drh+ + + k+ NCBI__GCF_000204645.1:WP_013518028.1 32 GMAGYEALCAEADKDFEGFWARLARENLQWTRPFTKTLDESNAPFYQWFADGELNASANCLDRHMGTpVESKT 104 56789**************************************************************999*** PP TIGR02188 75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147 aii+e+d+ + k+tY+ell++v+++an+lk++Gvkkgdrv iY+pm++e v+am+acaRiGa+hsvvf+G NCBI__GCF_000204645.1:WP_013518028.1 105 AIIFEADDGA--VTKVTYKELLARVAQFANALKAQGVKKGDRVLIYMPMTIEGVVAMQACARIGATHSVVFGG 175 *******664..8************************************************************ PP TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvww 219 fsa+a++eRi+da a vita+ +lRggk ++lk+ivde +++ + s+++vlv++rt + + ++grD+ + NCBI__GCF_000204645.1:WP_013518028.1 176 FSAKAVQERIIDAGAVAVITANYQLRGGKELPLKAIVDEGIAMGGCeSIKSVLVYERTPTA-WNRVDGRDKSF 247 *****************************************9998889***********99.5599******* PP TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292 e+++ ++s+ec p ++++e+plfiLYtsGstGkPkGv+h+tgGyll+a+lt+ ++fd++++d+fwCtaD+GW NCBI__GCF_000204645.1:WP_013518028.1 248 AEALA-GQSTECVPVAVEAEHPLFILYTSGSTGKPKGVQHSTGGYLLWAKLTMDWTFDLRPDDVFWCTADIGW 319 *****.6****************************************************************** PP TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgee....lvkkhdls 361 vtGh+Yi ygPLa+G t+++feg+ptyp+a+rfw++ie++kv+ifYtaPtaiR+l+k++++ ++k+ dls NCBI__GCF_000204645.1:WP_013518028.1 320 VTGHTYIAYGPLAAGGTQVMFEGIPTYPNAGRFWQMIERHKVSIFYTAPTAIRSLIKAADSdekvHPKNWDLS 392 *********************************************************9954223378899*** PP TIGR02188 362 slrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvd 434 slr+lgsvGepinpeaw+Wyy++vG e+cpivdtwWqte Gg+litplpg at+l pgs+tlPl+Gi a++vd NCBI__GCF_000204645.1:WP_013518028.1 393 SLRILGSVGEPINPEAWMWYYKNVGGERCPIVDTWWQTENGGHLITPLPG-ATPLVPGSCTLPLPGIAAAIVD 464 **************************************************.6********************* PP TIGR02188 435 eegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkd.GyiwilGRvDdv 504 e+gk+v ++++ g+Lvik+pwPsm+rti++d+erf ++Yf + g +y++GDga+rd+ y+ ++GR+Ddv NCBI__GCF_000204645.1:WP_013518028.1 465 ETGKDVPNGSG-GMLVIKRPWPSMIRTIWNDPERFKKSYFPEEMGgkIYLAGDGAVRDAKtAYFRVTGRIDDV 536 ********999.8***************************9877667***********76489********** PP TIGR02188 505 invsGhrlgtaeiesalvsh.eavaeaavvgvpdeikgeaivafvvlkegveedee..elekelkklvrkeig 574 +nvsGhr+gt+eiesalv++ + vaeaavvg+pd+++geai+afvvlk+++ + ee ++++el+++v+keig NCBI__GCF_000204645.1:WP_013518028.1 537 LNVSGHRMGTMEIESALVAKsDLVAEAAVVGRPDDLTGEAICAFVVLKRARPTGEEakQIAAELRNWVAKEIG 609 ******************872579*************************9987666669************** PP TIGR02188 575 piakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelke 628 piakp++i++ ++lPktRsGkimRRllr++a+ge +++d+stle+p+++++l + NCBI__GCF_000204645.1:WP_013518028.1 610 PIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEAITQDTSTLENPAILDQLAQ 663 **************************************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (665 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: 28.93 // [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