Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_072784733.1 BUA36_RS11840 acetate--CoA ligase
Query= SwissProt::P31638 (660 letters) >NCBI__GCF_900143065.1:WP_072784733.1 Length = 661 Score = 1111 bits (2874), Expect = 0.0 Identities = 520/651 (79%), Positives = 586/651 (90%) Query: 9 QEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQS 68 QE RVF P FA+QA + M+AY ALC EA DYEGFW+R A+E + W +PFT+ L++ Sbjct: 10 QESRVFAPSPAFAAQATVSGMDAYNALCAEAAADYEGFWSRLAKEHIEWQQPFTRTLNED 69 Query: 69 NAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFAN 128 NAPFYKWFEDG+LN SYNCLDRNLQNGNADK AI+FEADDG TRV+Y+ELH KVC+FAN Sbjct: 70 NAPFYKWFEDGKLNVSYNCLDRNLQNGNADKTAIIFEADDGKTTRVSYKELHEKVCKFAN 129 Query: 129 GLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVA 188 GLKA GI+KGDRV+IYM MSVEGV AMQACAR+GATHSVVFGGFSAKSLQER++D GAVA Sbjct: 130 GLKARGIKKGDRVIIYMSMSVEGVAAMQACARIGATHSVVFGGFSAKSLQERIIDAGAVA 189 Query: 189 LITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDVSA 248 +ITADEQ+RGGK LPLKAI D+ALALGGC+ +++VIVY+RTGG +A+ EGRD W+ D+ Sbjct: 190 VITADEQLRGGKNLPLKAIVDEALALGGCDTIKDVIVYQRTGGNIAFKEGRDLWLHDLVE 249 Query: 249 GQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFW 308 GQ CE E V AEHPLF+LYTSGSTG PKGVQHS+GGYLLWA +TMKW+FDIKP D++W Sbjct: 250 GQSAECEPEWVEAEHPLFILYTSGSTGTPKGVQHSSGGYLLWAALTMKWSFDIKPSDVYW 309 Query: 309 CTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIR 368 CTADIGWVTGH+YIAYGP A GATQVVFEGVPTYPNAGRFW+ IA+HKV+IFYTAPTAIR Sbjct: 310 CTADIGWVTGHSYIAYGPTAVGATQVVFEGVPTYPNAGRFWETIAKHKVNIFYTAPTAIR 369 Query: 369 SLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTET 428 SLIKA++ D K+HPK YDLSSLRLLGTVGEPINPEAWMWYY +G E+CPIVDTFWQTET Sbjct: 370 SLIKASDVDAKVHPKNYDLSSLRLLGTVGEPINPEAWMWYYTQVGGEKCPIVDTFWQTET 429 Query: 429 GGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIW 488 GGHMITPLPGATP+VPGSCTLPLPGIMAAIVDE+GHDVPNG GGILVVKRPWP+MIRTIW Sbjct: 430 GGHMITPLPGATPMVPGSCTLPLPGIMAAIVDESGHDVPNGQGGILVVKRPWPSMIRTIW 489 Query: 489 GDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESA 548 +P+RF+ SYFPEELGGK+YLAGDG+IR+KDTGYFTI GRIDDVLNVSGHRMGTMEIESA Sbjct: 490 NNPDRFKTSYFPEELGGKMYLAGDGAIRNKDTGYFTITGRIDDVLNVSGHRMGTMEIESA 549 Query: 549 LVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAK 608 LV+NPLVAEAAVVG+PDD TGE+ICAFVVLK++RPTG++A K+A ELRNWV KEIGPIAK Sbjct: 550 LVANPLVAEAAVVGKPDDTTGESICAFVVLKQARPTGDDAKKLALELRNWVAKEIGPIAK 609 Query: 609 PKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQA 659 PK+IRFGDNLPKTRSGKIMRRLLR LAKGE ITQD STLENPAILEQLK+A Sbjct: 610 PKEIRFGDNLPKTRSGKIMRRLLRVLAKGEVITQDVSTLENPAILEQLKEA 660 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: 1565 Number of extensions: 67 Number of successful extensions: 1 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: 661 Length adjustment: 38 Effective length of query: 622 Effective length of database: 623 Effective search space: 387506 Effective search space used: 387506 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_072784733.1 BUA36_RS11840 (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.2679797.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-299 978.2 0.0 9e-299 978.0 0.0 1.0 1 NCBI__GCF_900143065.1:WP_072784733.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900143065.1:WP_072784733.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 978.0 0.0 9e-299 9e-299 2 628 .. 28 659 .. 27 660 .. 0.97 Alignments for each domain: == domain 1 score: 978.0 bits; conditional E-value: 9e-299 TIGR02188 2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdk 73 + +++y++l++ea++d+e fw++lake++ew++pf+++l+e+++p++kWfedg+lnvsync+dr++++ ++dk NCBI__GCF_900143065.1:WP_072784733.1 28 SGMDAYNALCAEAAADYEGFWSRLAKEHIEWQQPFTRTLNEDNAPFYKWFEDGKLNVSYNCLDRNLQNgNADK 100 56899******************************************************************** PP TIGR02188 74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146 +aii+e+d+ + + +++Y+el+++vc++an lk+ G+kkgdrv+iY+ m +e v+am+acaRiGa+hsvvf+ NCBI__GCF_900143065.1:WP_072784733.1 101 TAIIFEADDGK--TTRVSYKELHEKVCKFANGLKARGIKKGDRVIIYMSMSVEGVAAMQACARIGATHSVVFG 171 ********775..699********************************************************* PP TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218 Gfsa++l+eRi+da a vitade+lRggk+++lk+ivdeal+ + ++++v+v++rtg ++a +kegrD+w NCBI__GCF_900143065.1:WP_072784733.1 172 GFSAKSLQERIIDAGAVAVITADEQLRGGKNLPLKAIVDEALALGGCdTIKDVIVYQRTGGNIA-FKEGRDLW 243 ******************************************9988889*************77.******** PP TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291 +++lve ++saecepe++++e+plfiLYtsGstG+PkGv+h++gGyll+aalt+k+ fdik++d++wCtaD+G NCBI__GCF_900143065.1:WP_072784733.1 244 LHDLVE-GQSAECEPEWVEAEHPLFILYTSGSTGTPKGVQHSSGGYLLWAALTMKWSFDIKPSDVYWCTADIG 315 ******.6***************************************************************** PP TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklg....eelvkkhdl 360 WvtGhsYi ygP a+Gat+++fegvptyp+a+rfwe+i k+kv+ifYtaPtaiR+l+k++ + ++k++dl NCBI__GCF_900143065.1:WP_072784733.1 316 WVTGHSYIAYGPTAVGATQVVFEGVPTYPNAGRFWETIAKHKVNIFYTAPTAIRSLIKASdvdaKVHPKNYDL 388 **********************************************************97443356899**** PP TIGR02188 361 sslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevv 433 sslr+lg+vGepinpeaw+Wyy++vG ekcpivdt+WqtetGg++itplpg at++ pgs+tlPl+Gi+a++v NCBI__GCF_900143065.1:WP_072784733.1 389 SSLRLLGTVGEPINPEAWMWYYTQVGGEKCPIVDTFWQTETGGHMITPLPG-ATPMVPGSCTLPLPGIMAAIV 460 ***************************************************.6******************** PP TIGR02188 434 deegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkd.GyiwilGRvDd 503 de+g++v ++++ g+Lv+k+pwPsm+rti+++++rf ++Yf + g +y++GDga r+kd Gy++i+GR+Dd NCBI__GCF_900143065.1:WP_072784733.1 461 DESGHDVPNGQG-GILVVKRPWPSMIRTIWNNPDRFKTSYFPEELGgkMYLAGDGAIRNKDtGYFTITGRIDD 532 *********999.8***************************9876567***********999*********** PP TIGR02188 504 vinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee..elekelkklvrkeig 574 v+nvsGhr+gt+eiesalv+++ vaeaavvg+pd+++ge+i+afvvlk+++ + ++ +l+ el+++v+keig NCBI__GCF_900143065.1:WP_072784733.1 533 VLNVSGHRMGTMEIESALVANPLVAEAAVVGKPDDTTGESICAFVVLKQARPTGDDakKLALELRNWVAKEIG 605 *************************************************9987665569************** PP TIGR02188 575 piakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelke 628 piakp++i++ ++lPktRsGkimRRllr +a+ge +++dvstle+p+++e+lke NCBI__GCF_900143065.1:WP_072784733.1 606 PIAKPKEIRFGDNLPKTRSGKIMRRLLRVLAKGEVITQDVSTLENPAILEQLKE 659 ***************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (661 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 16.33 // [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