Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate BPHYT_RS27780 BPHYT_RS27780 acetyl-CoA synthetase
Query= SwissProt::P31638 (660 letters) >FitnessBrowser__BFirm:BPHYT_RS27780 Length = 658 Score = 1028 bits (2657), Expect = 0.0 Identities = 477/631 (75%), Positives = 555/631 (87%) Query: 25 AIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQSNAPFYKWFEDGELNAS 84 AI M+AY+AL EAE D++ FWAR ARE L W +PFTK+LD SNAPFYKWFEDGELNAS Sbjct: 23 AISGMDAYRALVAEAETDHQAFWARLAREHLQWRRPFTKILDDSNAPFYKWFEDGELNAS 82 Query: 85 YNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFANGLKALGIRKGDRVVIY 144 YNCLDRNL G ADK AIVFEADDG+VTR+TY+ L+ +VCR AN L+A G+ +GDRVVIY Sbjct: 83 YNCLDRNLAKGLADKTAIVFEADDGTVTRITYQALYHRVCRLANALRARGVTRGDRVVIY 142 Query: 145 MPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVALITADEQMRGGKALPL 204 MPMS+EG+ AM ACAR+GA HSVVFGGFSAKSL ERLV+VGAVA++TADEQ+RGGK LPL Sbjct: 143 MPMSIEGIAAMLACARIGAPHSVVFGGFSAKSLHERLVNVGAVAVMTADEQVRGGKTLPL 202 Query: 205 KAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDVSAGQPDTCEAEPVSAEHP 264 KAI D+ALA+GG AV+ V+VYRRTGG++ W RD W+ ++ Q DTCE E V AEHP Sbjct: 203 KAIVDEALAMGGTVAVKTVVVYRRTGGRIPWITQRDAWLHELEHAQSDTCEPEWVGAEHP 262 Query: 265 LFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFWCTADIGWVTGHTYIAY 324 LFVLYTSGSTG PKGVQHSTGGYLLWA +TMKWTFDIKPDD+FWCTADIGW+TGHTYI Y Sbjct: 263 LFVLYTSGSTGAPKGVQHSTGGYLLWAAVTMKWTFDIKPDDVFWCTADIGWITGHTYICY 322 Query: 325 GPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIRSLIKAAEADEKIHPKQ 384 GP A GATQV+FEGVPTYP+AGRFW MI RHKVSIFYTAPTAIRSLIKAA+A+E +HP+ Sbjct: 323 GPTAVGATQVIFEGVPTYPDAGRFWQMIERHKVSIFYTAPTAIRSLIKAADANEAVHPRS 382 Query: 385 YDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTETGGHMITPLPGATPLVP 444 +DLSSLR+LGTVGEPINP AW WY +++G RCP++DTFWQTETGGHMI+PLPG TPLVP Sbjct: 383 FDLSSLRILGTVGEPINPSAWTWYAQHVGGGRCPVLDTFWQTETGGHMISPLPGVTPLVP 442 Query: 445 GSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIWGDPERFRKSYFPEELG 504 GSCTLP+PGI AAIVDETGH+VPNG+GG+LV+++PWP+MIRTIWG+PERFR Y+P++LG Sbjct: 443 GSCTLPMPGIDAAIVDETGHEVPNGHGGVLVIRKPWPSMIRTIWGNPERFRHGYYPDDLG 502 Query: 505 GKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESALVSNPLVAEAAVVGRP 564 GKLYLAGDG+IRD+DTGYFTI GRIDDVLNVSGHR+GTMEIESAL ++P VAEAAVVGRP Sbjct: 503 GKLYLAGDGAIRDRDTGYFTITGRIDDVLNVSGHRLGTMEIESALSAHPSVAEAAVVGRP 562 Query: 565 DDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAKPKDIRFGDNLPKTRSG 624 D+ GEAI AFVVLK +RP+G +A ++A ELR WVGKEIGPIAKPKDIRFGD +PKTRSG Sbjct: 563 DETCGEAIVAFVVLKTARPSGPDAKRVADELRAWVGKEIGPIAKPKDIRFGDAMPKTRSG 622 Query: 625 KIMRRLLRSLAKGEEITQDTSTLENPAILEQ 655 K++RRLLRS+AKGE ITQDTS++ENP ++ Q Sbjct: 623 KVVRRLLRSVAKGEAITQDTSSVENPTVISQ 653 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: 1574 Number of extensions: 77 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: 658 Length adjustment: 38 Effective length of query: 622 Effective length of database: 620 Effective search space: 385640 Effective search space used: 385640 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 BPHYT_RS27780 BPHYT_RS27780 (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.6595.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-288 941.7 0.0 9.5e-288 941.6 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS27780 BPHYT_RS27780 acetyl-CoA synthet Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS27780 BPHYT_RS27780 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 941.6 0.0 9.5e-288 9.5e-288 2 626 .. 25 654 .. 24 657 .. 0.97 Alignments for each domain: == domain 1 score: 941.6 bits; conditional E-value: 9.5e-288 TIGR02188 2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.r 70 + +++y++l++ea++d+++fwa+la+e+l+w +pf+k+ld+s++p++kWfedgeln+sync+dr+++k lcl|FitnessBrowser__BFirm:BPHYT_RS27780 25 SGMDAYRALVAEAETDHQAFWARLAREHLQWRRPFTKILDDSNAPFYKWFEDGELNASYNCLDRNLAKgL 94 5789****************************************************************99 PP TIGR02188 71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGav 140 +dk+ai++e+d+ + + ++tY+ l+++vcrlan+l++ Gv +gdrv+iY+pm +e ++amlacaRiGa lcl|FitnessBrowser__BFirm:BPHYT_RS27780 95 ADKTAIVFEADDGT--VTRITYQALYHRVCRLANALRARGVTRGDRVVIYMPMSIEGIAAMLACARIGAP 162 ***********664..89**************************************************** PP TIGR02188 141 hsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeeva 209 hsvvf+Gfsa++l+eR+v++ a v+tade++Rggk+++lk+ivdeal++ + +v++v+v++rtg + lcl|FitnessBrowser__BFirm:BPHYT_RS27780 163 HSVVFGGFSAKSLHERLVNVGAVAVMTADEQVRGGKTLPLKAIVDEALAMGGTvAVKTVVVYRRTGGRIP 232 **************************************************9999**************66 PP TIGR02188 210 ewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik 279 w +rD w++el + +s++cepe++++e+plf+LYtsGstG PkGv+h+tgGyll+aa+t+k++fdik lcl|FitnessBrowser__BFirm:BPHYT_RS27780 233 -WITQRDAWLHELEHA-QSDTCEPEWVGAEHPLFVLYTSGSTGAPKGVQHSTGGYLLWAAVTMKWTFDIK 300 .************995.***************************************************** PP TIGR02188 280 dedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmk 349 ++d+fwCtaD+GW+tGh+Yi+ygP a+Gat+++fegvptypda+rfw++ie++kv+ifYtaPtaiR+l+k lcl|FitnessBrowser__BFirm:BPHYT_RS27780 301 PDDVFWCTADIGWITGHTYICYGPTAVGATQVIFEGVPTYPDAGRFWQMIERHKVSIFYTAPTAIRSLIK 370 ********************************************************************** PP TIGR02188 350 lgee....lvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvate 415 ++++ ++++ dlsslr+lg+vGepinp+aw+Wy ++vG ++cp+ dt+WqtetGg++i+plpg +t+ lcl|FitnessBrowser__BFirm:BPHYT_RS27780 371 AADAneavHPRSFDLSSLRILGTVGEPINPSAWTWYAQHVGGGRCPVLDTFWQTETGGHMISPLPG-VTP 439 9965223357899*****************************************************.5** PP TIGR02188 416 lkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyft 483 l pgs+tlP++Gi+a++vde+g+ev ++++ gvLvi+kpwPsm+rti+g++erf + Y+ + g ly++ lcl|FitnessBrowser__BFirm:BPHYT_RS27780 440 LVPGSCTLPMPGIDAAIVDETGHEVPNGHG-GVLVIRKPWPSMIRTIWGNPERFRHGYYPDDLGgkLYLA 508 ***************************999.8**************************98765557**** PP TIGR02188 484 GDgarrdkd.GyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlke 552 GDga rd+d Gy++i+GR+Ddv+nvsGhrlgt+eiesal +h++vaeaavvg+pde+ geaivafvvlk+ lcl|FitnessBrowser__BFirm:BPHYT_RS27780 509 GDGAIRDRDtGYFTITGRIDDVLNVSGHRLGTMEIESALSAHPSVAEAAVVGRPDETCGEAIVAFVVLKT 578 *******999***********************************************************9 PP TIGR02188 553 gve..edeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledp 620 ++ +d++++++el+++v keigpiakp++i++ +++PktRsGk++RRllr++a+ge +++d+s +e+p lcl|FitnessBrowser__BFirm:BPHYT_RS27780 579 ARPsgPDAKRVADELRAWVGKEIGPIAKPKDIRFGDAMPKTRSGKVVRRLLRSVAKGEAITQDTSSVENP 648 9873356669************************************************************ PP TIGR02188 621 svveel 626 +v+ + lcl|FitnessBrowser__BFirm:BPHYT_RS27780 649 TVISQF 654 **9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (658 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 7.47 // [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