Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate HSERO_RS07770 HSERO_RS07770 acetyl-CoA synthetase
Query= SwissProt::P31638 (660 letters) >FitnessBrowser__HerbieS:HSERO_RS07770 Length = 660 Score = 1112 bits (2877), Expect = 0.0 Identities = 518/657 (78%), Positives = 592/657 (90%) Query: 4 IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63 IE+ QE+RVF PP AAI M+AY AL E +DYEG WAR A++ L W KPFT+ Sbjct: 4 IETFKQENRVFAPPAELVKHAAISGMDAYHALNAEFAKDYEGTWARLAKDNLKWHKPFTQ 63 Query: 64 VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123 LD+SNAPFYKWF DG++N SYNCLD NL+NGNADK A++FE+DDG VTRV+YRELH KV Sbjct: 64 TLDESNAPFYKWFADGQVNVSYNCLDVNLENGNADKTAVIFESDDGKVTRVSYRELHQKV 123 Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183 C+FANGLK+LGI+KGDRVVIYMPMSVEGV AMQACAR+GATHSVVFGGFSAKSL ER++D Sbjct: 124 CQFANGLKSLGIKKGDRVVIYMPMSVEGVAAMQACARIGATHSVVFGGFSAKSLHERVID 183 Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243 GAVA++TAD Q+RGGK LPLK+I D+AL +GGC+ +++V+VY+R G ++ W EGRD W+ Sbjct: 184 AGAVAVLTADYQVRGGKQLPLKSIVDEALDMGGCDTLKHVVVYKRAGAEINWVEGRDLWL 243 Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303 DV A Q DTCE E V AEHPLF+LYTSGSTGKPKGVQH++ GYLLWA++TMKWTFDIKP Sbjct: 244 SDVVANQSDTCEPEWVDAEHPLFILYTSGSTGKPKGVQHASAGYLLWAVLTMKWTFDIKP 303 Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363 DD++WCTADIGW+TGHTYIAYGPLA GATQ+VFEGVPTYPNAGRFWDM+ARHK +IFYTA Sbjct: 304 DDVYWCTADIGWITGHTYIAYGPLAVGATQIVFEGVPTYPNAGRFWDMVARHKATIFYTA 363 Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423 PTAIRSLIKAA+ADEK+HPKQYDLSSLR+LG+VGEPINPEAWMWYYKN+G+E CPIVDTF Sbjct: 364 PTAIRSLIKAADADEKVHPKQYDLSSLRILGSVGEPINPEAWMWYYKNVGHENCPIVDTF 423 Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAM 483 WQTETGGHMI+PLPGATP VPGSCTLPLPGI AAIVDETG+D+PNGNGGILVVKRPWP+M Sbjct: 424 WQTETGGHMISPLPGATPQVPGSCTLPLPGITAAIVDETGNDIPNGNGGILVVKRPWPSM 483 Query: 484 IRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTM 543 IRTIW DPERF+KSYFPEELGGK+YLAGDG++R+K+TGYFTI GRIDDVLNVSGHRMGTM Sbjct: 484 IRTIWNDPERFKKSYFPEELGGKIYLAGDGAVRNKETGYFTITGRIDDVLNVSGHRMGTM 543 Query: 544 EIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEI 603 EIESALV+N +VAEAAVVG+PD+ TGE+ICAFVVLKR RPTG+EA +IA ELR+WV KEI Sbjct: 544 EIESALVANSIVAEAAVVGKPDETTGESICAFVVLKRPRPTGDEAKQIAKELRDWVAKEI 603 Query: 604 GPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQAQ 660 GPIAKPK+IRFGDNLPKTRSGKIMRRLLR LAKGE ITQD STLENPAIL+QLK+AQ Sbjct: 604 GPIAKPKEIRFGDNLPKTRSGKIMRRLLRVLAKGEAITQDVSTLENPAILDQLKEAQ 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: 1529 Number of extensions: 64 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: 660 Length adjustment: 38 Effective length of query: 622 Effective length of database: 622 Effective search space: 386884 Effective search space used: 386884 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 HSERO_RS07770 HSERO_RS07770 (acetyl-CoA synthetase)
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.2199.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.4e-297 971.3 0.0 1.1e-296 971.1 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS07770 HSERO_RS07770 acetyl-CoA synthet Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS07770 HSERO_RS07770 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 971.1 0.0 1.1e-296 1.1e-296 2 628 .. 27 658 .. 26 659 .. 0.97 Alignments for each domain: == domain 1 score: 971.1 bits; conditional E-value: 1.1e-296 TIGR02188 2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek 69 + +++y++l +e ++d+e wa+lak++l+w+kpf+++ldes++p++kWf+dg++nvsync+d ++e+ lcl|FitnessBrowser__HerbieS:HSERO_RS07770 27 SGMDAYHALNAEFAKDYEGTWARLAKDNLKWHKPFTQTLDESNAPFYKWFADGQVNVSYNCLDVNLEN 94 57899*************************************************************** PP TIGR02188 70 .rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaR 136 ++dk+a+i+e+d+ + + +++Y+el+++vc++an lk+lG+kkgdrv+iY+pm +e v+am+acaR lcl|FitnessBrowser__HerbieS:HSERO_RS07770 95 gNADKTAVIFESDDGK--VTRVSYRELHQKVCQFANGLKSLGIKKGDRVVIYMPMSVEGVAAMQACAR 160 *************664..89************************************************ PP TIGR02188 137 iGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkr 203 iGa+hsvvf+Gfsa++l+eR++da a v+tad ++Rggk+++lk+ivdeal++ + ++++v+v+kr lcl|FitnessBrowser__HerbieS:HSERO_RS07770 161 IGATHSVVFGGFSAKSLHERVIDAGAVAVLTADYQVRGGKQLPLKSIVDEALDMGGCdTLKHVVVYKR 228 ******************************************************99889********* PP TIGR02188 204 tgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaalt 271 +g+e++ w+egrD+w++++v+ ++s++cepe++d+e+plfiLYtsGstGkPkGv+h+++Gyll+a+lt lcl|FitnessBrowser__HerbieS:HSERO_RS07770 229 AGAEIN-WVEGRDLWLSDVVA-NQSDTCEPEWVDAEHPLFILYTSGSTGKPKGVQHASAGYLLWAVLT 294 ****66.**************.5********************************************* PP TIGR02188 272 vkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYt 339 +k++fdik++d++wCtaD+GW+tGh+Yi ygPLa+Gat+++fegvptyp+a+rfw+++ ++k tifYt lcl|FitnessBrowser__HerbieS:HSERO_RS07770 295 MKWTFDIKPDDVYWCTADIGWITGHTYIAYGPLAVGATQIVFEGVPTYPNAGRFWDMVARHKATIFYT 362 ******************************************************************** PP TIGR02188 340 aPtaiRalmklgee....lvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGg 403 aPtaiR+l+k++++ ++k++dlsslr+lgsvGepinpeaw+Wyy++vG+e+cpivdt+WqtetGg lcl|FitnessBrowser__HerbieS:HSERO_RS07770 363 APTAIRSLIKAADAdekvHPKQYDLSSLRILGSVGEPINPEAWMWYYKNVGHENCPIVDTFWQTETGG 430 **********985422337899********************************************** PP TIGR02188 404 ilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfve 471 ++i+plpg at++ pgs+tlPl+Gi+a++vde+g+++ ++++ g+Lv+k+pwPsm+rti++d+erf + lcl|FitnessBrowser__HerbieS:HSERO_RS07770 431 HMISPLPG-ATPQVPGSCTLPLPGITAAIVDETGNDIPNGNG-GILVVKRPWPSMIRTIWNDPERFKK 496 ********.6*****************************999.8************************ PP TIGR02188 472 tYfkklkg..lyftGDgarrdkd.GyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvp 536 +Yf + g +y++GDga+r+k+ Gy++i+GR+Ddv+nvsGhr+gt+eiesalv+++ vaeaavvg+p lcl|FitnessBrowser__HerbieS:HSERO_RS07770 497 SYFPEELGgkIYLAGDGAVRNKEtGYFTITGRIDDVLNVSGHRMGTMEIESALVANSIVAEAAVVGKP 564 ***9876567*********99877******************************************** PP TIGR02188 537 deikgeaivafvvlkegveedee..elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllr 602 de++ge+i+afvvlk+ + + +e +++kel+++v+keigpiakp++i++ ++lPktRsGkimRRllr lcl|FitnessBrowser__HerbieS:HSERO_RS07770 565 DETTGESICAFVVLKRPRPTGDEakQIAKELRDWVAKEIGPIAKPKEIRFGDNLPKTRSGKIMRRLLR 632 ***************99987776669****************************************** PP TIGR02188 603 kiaegeellgdvstledpsvveelke 628 +a+ge +++dvstle+p+++++lke lcl|FitnessBrowser__HerbieS:HSERO_RS07770 633 VLAKGEAITQDVSTLENPAILDQLKE 658 ***********************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (660 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.04 # Mc/sec: 10.26 // [ok]
This GapMind analysis is from Sep 17 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