Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_053937296.1 WG78_RS08045 acetate--CoA ligase
Query= SwissProt::P31638 (660 letters) >NCBI__GCF_001294205.1:WP_053937296.1 Length = 655 Score = 951 bits (2457), Expect = 0.0 Identities = 455/657 (69%), Positives = 547/657 (83%), Gaps = 6/657 (0%) Query: 1 MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60 MS I+SV++E+R+F P E F +A + ME Y ALC++A DYEGFWA REL+ W +P Sbjct: 1 MSTIDSVLKENRLFPPSEDFRVKANVSGMEGYNALCEQANNDYEGFWADLGRELVSWKQP 60 Query: 61 FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120 FTKVL+ + APFYKWFEDG LN SYNCLDR+L G+ DK AI+FEADDG+ T VTYRELH Sbjct: 61 FTKVLNSTEAPFYKWFEDGTLNVSYNCLDRHLA-GSGDKPAIIFEADDGTSTPVTYRELH 119 Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180 +VC+FANGL++LG++KGDRVV+YMPM VE VVAMQACAR+GA HSVVFGGFSAKSLQER Sbjct: 120 QRVCQFANGLRSLGVKKGDRVVVYMPMGVEAVVAMQACARIGAIHSVVFGGFSAKSLQER 179 Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240 + D A +ITA+E +RGGK++PL+A+ DDALALGGCE++++++V++RT A + R+ Sbjct: 180 IGDARASLVITANEGLRGGKSVPLQAVVDDALALGGCESIQHIVVFQRTQTAPAQWDARN 239 Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300 W +++A QP CE E ++AE PLF+LYTSGSTGKPKG+QHS+GGYLL L+TMKW FD Sbjct: 240 VWWHELTAQQPTECEPEWMNAEDPLFILYTSGSTGKPKGIQHSSGGYLLGTLVTMKWVFD 299 Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360 KPDD+FWCTAD+GW+TGH+Y+ YGPLA GATQVVFEG+PTYP+A RFW MIARHKV+ F Sbjct: 300 YKPDDVFWCTADVGWITGHSYVCYGPLAIGATQVVFEGIPTYPDANRFWSMIARHKVTTF 359 Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420 YTAPTAIRSLIK AD P Q+DLSSLRLLGTVGEPINPEAW+WY++ +G RCPIV Sbjct: 360 YTAPTAIRSLIKLG-AD---LPGQHDLSSLRLLGTVGEPINPEAWIWYHEVVGGGRCPIV 415 Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480 DT+WQTETG HMI PLPGA PGSCTLPLPGI+A IVDE+G V G GG LV+K+PW Sbjct: 416 DTWWQTETGAHMIAPLPGAVATKPGSCTLPLPGILADIVDESGAPVEPGKGGALVIKKPW 475 Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540 P+M+RTIWGDP+RF+K+YFPEE G+LYLAGD + D + GY IMGRIDDVLNVSGHR+ Sbjct: 476 PSMVRTIWGDPDRFKKTYFPEEFNGQLYLAGDSAHTD-ENGYIWIMGRIDDVLNVSGHRL 534 Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600 GTMEIESALV+NPLVAEAAVVGRP ++ GEA+ AFVVLK++RP GE+A +IA ELR WV Sbjct: 535 GTMEIESALVANPLVAEAAVVGRPHEIKGEAVVAFVVLKQNRPEGEDAKRIARELREWVA 594 Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLK 657 EIG IA+P +IRFG+NLPKTRSGKIMRRLLR +AKGEEITQD STLENPAILEQL+ Sbjct: 595 HEIGKIAQPDEIRFGENLPKTRSGKIMRRLLRVIAKGEEITQDVSTLENPAILEQLR 651 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: 1477 Number of extensions: 57 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: 660 Length of database: 655 Length adjustment: 38 Effective length of query: 622 Effective length of database: 617 Effective search space: 383774 Effective search space used: 383774 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_053937296.1 WG78_RS08045 (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.978599.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-303 994.2 0.0 1.3e-303 993.9 0.0 1.0 1 NCBI__GCF_001294205.1:WP_053937296.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001294205.1:WP_053937296.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 993.9 0.0 1.3e-303 1.3e-303 3 627 .. 28 651 .. 26 653 .. 0.97 Alignments for each domain: == domain 1 score: 993.9 bits; conditional E-value: 1.3e-303 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvekrkdkva 75 +e y++l+e+a++d+e fwa+l++e ++w++pf+kvl+++++p++kWfedg+lnvsync+drh++ + dk a NCBI__GCF_001294205.1:WP_053937296.1 28 GMEGYNALCEQANNDYEGFWADLGRELVSWKQPFTKVLNSTEAPFYKWFEDGTLNVSYNCLDRHLAGSGDKPA 100 6889********************************************************************* PP TIGR02188 76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148 ii+e+d+ + s +tY+el+++vc++an l++lGvkkgdrv++Y+pm +eav+am+acaRiGa+hsvvf+Gf NCBI__GCF_001294205.1:WP_053937296.1 101 IIFEADDGT--STPVTYRELHQRVCQFANGLRSLGVKKGDRVVVYMPMGVEAVVAMQACARIGAIHSVVFGGF 171 ******765..79************************************************************ PP TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwwe 220 sa++l+eRi da+a lvita+eglRggk+++l+++vd+al+ + s+++++v++rt++ a+w + r+vww+ NCBI__GCF_001294205.1:WP_053937296.1 172 SAKSLQERIGDARASLVITANEGLRGGKSVPLQAVVDDALALGGCeSIQHIVVFQRTQTAPAQW-DARNVWWH 243 ****************************************9988779***********997766.59****** PP TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293 el+++ +++ecepe++++edplfiLYtsGstGkPkG++h++gGyll + +t+k+vfd+k++d+fwCtaDvGW+ NCBI__GCF_001294205.1:WP_053937296.1 244 ELTAQ-QPTECEPEWMNAEDPLFILYTSGSTGKPKGIQHSSGGYLLGTLVTMKWVFDYKPDDVFWCTADVGWI 315 ****6.******************************************************************* PP TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366 tGhsY++ygPLa+Gat+++feg+ptypda+rfw++i ++kvt+fYtaPtaiR+l+klg +l+ +hdlsslr+l NCBI__GCF_001294205.1:WP_053937296.1 316 TGHSYVCYGPLAIGATQVVFEGIPTYPDANRFWSMIARHKVTTFYTAPTAIRSLIKLGADLPGQHDLSSLRLL 388 ************************************************************************* PP TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439 g+vGepinpeaw Wy+evvG ++cpivdtwWqtetG+++i+plpg a+++kpgs+tlPl+Gi a++vde+g + NCBI__GCF_001294205.1:WP_053937296.1 389 GTVGEPINPEAWIWYHEVVGGGRCPIVDTWWQTETGAHMIAPLPG-AVATKPGSCTLPLPGILADIVDESGAP 460 *********************************************.6************************** PP TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkk.lkg.lyftGDgarrdkdGyiwilGRvDdvinvsGh 510 ve++++ g+LvikkpwPsm+rti+gd++rf +tYf + ++g ly++GD+a++d++Gyiwi+GR+Ddv+nvsGh NCBI__GCF_001294205.1:WP_053937296.1 461 VEPGKG-GALVIKKPWPSMVRTIWGDPDRFKKTYFPEeFNGqLYLAGDSAHTDENGYIWIMGRIDDVLNVSGH 532 ***999.8***************************75255579****************************** PP TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee..elekelkklvrkeigpiakpdk 581 rlgt+eiesalv+++ vaeaavvg+p+eikgea+vafvvlk+++ e e+ ++++el+++v++eig+ia+pd+ NCBI__GCF_001294205.1:WP_053937296.1 533 RLGTMEIESALVANPLVAEAAVVGRPHEIKGEAVVAFVVLKQNRPEGEDakRIARELREWVAHEIGKIAQPDE 605 ******************************************9986655559********************* PP TIGR02188 582 ilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627 i++ e+lPktRsGkimRRllr ia+gee+++dvstle+p+++e+l+ NCBI__GCF_001294205.1:WP_053937296.1 606 IRFGENLPKTRSGKIMRRLLRVIAKGEEITQDVSTLENPAILEQLR 651 *******************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (655 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: 32.79 // [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