Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate RR42_RS13880 RR42_RS13880 AMP-dependent synthetase
Query= SwissProt::P31638 (660 letters) >FitnessBrowser__Cup4G11:RR42_RS13880 Length = 660 Score = 1286 bits (3327), Expect = 0.0 Identities = 619/660 (93%), Positives = 645/660 (97%) Query: 1 MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60 MSAIESVMQEHR+FNPPE FA QAAIPSMEAYQALCDEAERDYEGFWARHARE LHWTKP Sbjct: 1 MSAIESVMQEHRIFNPPESFAKQAAIPSMEAYQALCDEAERDYEGFWARHAREQLHWTKP 60 Query: 61 FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120 FTKVLD+SNAPFYKWFEDGELNAS+NCLDRNL NGNA+KVAIVFEADDG+VTRVTYR+LH Sbjct: 61 FTKVLDESNAPFYKWFEDGELNASFNCLDRNLDNGNAEKVAIVFEADDGTVTRVTYRQLH 120 Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180 KVC+FANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER Sbjct: 121 AKVCQFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180 Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240 LVDVGAVALITADEQMRGGKALPLKAIAD+ALALGGCEAV++VIVYRRTGGKV W EGRD Sbjct: 181 LVDVGAVALITADEQMRGGKALPLKAIADEALALGGCEAVKSVIVYRRTGGKVNWAEGRD 240 Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300 RWM+DV+AGQP TCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKW+FD Sbjct: 241 RWMDDVAAGQPQTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWSFD 300 Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360 IKPDD+FWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF Sbjct: 301 IKPDDMFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360 Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420 YTAPTAIRSLIKAAEADEKIHP+QYDLSSLRLLGTVGEPINPEAWMWYY+NIG ERCP+V Sbjct: 361 YTAPTAIRSLIKAAEADEKIHPRQYDLSSLRLLGTVGEPINPEAWMWYYQNIGGERCPVV 420 Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGI+AAIVDETG DVPNG+GGILVVKRPW Sbjct: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIIAAIVDETGQDVPNGSGGILVVKRPW 480 Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540 P+MIRTIWGDPERF+KSYFPEELGGKLYLAGDGSIRDK+TGYFTIMGRIDDVLNVSGHRM Sbjct: 481 PSMIRTIWGDPERFKKSYFPEELGGKLYLAGDGSIRDKETGYFTIMGRIDDVLNVSGHRM 540 Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600 GTMEIESALVSNP+VAEAAVVGRPDDMTGEAICAFVVLKRSRP EEA +IA +LRNWVG Sbjct: 541 GTMEIESALVSNPIVAEAAVVGRPDDMTGEAICAFVVLKRSRPNEEEAKQIAADLRNWVG 600 Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQAQ 660 KEIGPIAKP+DIRFGDNLPKTRSGKIMRRLLRSLAK EEITQDTSTLENPAILEQLKQAQ Sbjct: 601 KEIGPIAKPRDIRFGDNLPKTRSGKIMRRLLRSLAKNEEITQDTSTLENPAILEQLKQAQ 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: 1661 Number of extensions: 69 Number of successful extensions: 3 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 RR42_RS13880 RR42_RS13880 (AMP-dependent 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.7176.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-300 982.4 0.0 4.7e-300 982.2 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS13880 RR42_RS13880 AMP-dependent synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS13880 RR42_RS13880 AMP-dependent synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 982.2 0.0 4.7e-300 4.7e-300 3 628 .. 28 658 .. 26 659 .. 0.97 Alignments for each domain: == domain 1 score: 982.2 bits; conditional E-value: 4.7e-300 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.r 70 ++e+y++l++ea++d+e fwa++a+e+l+w+kpf+kvldes++p++kWfedgeln+s+nc+dr++ + + lcl|FitnessBrowser__Cup4G11:RR42_RS13880 28 SMEAYQALCDEAERDYEGFWARHAREQLHWTKPFTKVLDESNAPFYKWFEDGELNASFNCLDRNLDNgN 96 6899***************************************************************9* PP TIGR02188 71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGa 139 ++kvai++e+d+ + + ++tY++l+++vc++an lk+lG++kgdrv+iY+pm +e v+am+acaR+Ga lcl|FitnessBrowser__Cup4G11:RR42_RS13880 97 AEKVAIVFEADDGT--VTRVTYRQLHAKVCQFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGA 163 ***********664..89*************************************************** PP TIGR02188 140 vhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgee 207 +hsvvf+Gfsa++l+eR+vd+ a +itade++Rggk+++lk+i+deal+ + +v++v+v++rtg + lcl|FitnessBrowser__Cup4G11:RR42_RS13880 164 THSVVFGGFSAKSLQERLVDVGAVALITADEQMRGGKALPLKAIADEALALGGCeAVKSVIVYRRTGGK 232 *************************************************9988779************* PP TIGR02188 208 vaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvf 276 v+ w egrD w++++ + +++++ce+e++++e+plf+LYtsGstGkPkGv+h+tgGyll+a +t+k+ f lcl|FitnessBrowser__Cup4G11:RR42_RS13880 233 VN-WAEGRDRWMDDVAA-GQPQTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWSF 299 66.**************.6************************************************** PP TIGR02188 277 dikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiR 345 dik++d+fwCtaD+GWvtGh+Yi ygPLa+Gat+++fegvptyp+a+rfw++i ++kv+ifYtaPtaiR lcl|FitnessBrowser__Cup4G11:RR42_RS13880 300 DIKPDDMFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIR 368 ********************************************************************* PP TIGR02188 346 almklgee....lvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplp 410 +l+k++e+ +++++dlsslr+lg+vGepinpeaw+Wyy+++G e+cp+vdt+WqtetGg++itplp lcl|FitnessBrowser__Cup4G11:RR42_RS13880 369 SLIKAAEAdekiHPRQYDLSSLRLLGTVGEPINPEAWMWYYQNIGGERCPVVDTFWQTETGGHMITPLP 437 ****985422337899***************************************************** PP TIGR02188 411 gvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg 479 g at+l pgs+tlPl+Gi a++vde+g++v ++++ g+Lv+k+pwPsm+rti+gd+erf ++Yf + g lcl|FitnessBrowser__Cup4G11:RR42_RS13880 438 G-ATPLVPGSCTLPLPGIIAAIVDETGQDVPNGSG-GILVVKRPWPSMIRTIWGDPERFKKSYFPEELG 504 *.6*****************************999.8***************************98765 PP TIGR02188 480 ..lyftGDgarrdkd.GyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaiv 545 ly++GDg+ rdk+ Gy++i+GR+Ddv+nvsGhr+gt+eiesalvs++ vaeaavvg+pd+++geai+ lcl|FitnessBrowser__Cup4G11:RR42_RS13880 505 gkLYLAGDGSIRDKEtGYFTIMGRIDDVLNVSGHRMGTMEIESALVSNPIVAEAAVVGRPDDMTGEAIC 573 67***********988***************************************************** PP TIGR02188 546 afvvlkegveedee..elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellg 612 afvvlk+++ ++ee +++++l+++v keigpiakp++i++ ++lPktRsGkimRRllr++a++ee+++ lcl|FitnessBrowser__Cup4G11:RR42_RS13880 574 AFVVLKRSRPNEEEakQIAADLRNWVGKEIGPIAKPRDIRFGDNLPKTRSGKIMRRLLRSLAKNEEITQ 642 *******9987776669**************************************************** PP TIGR02188 613 dvstledpsvveelke 628 d+stle+p+++e+lk+ lcl|FitnessBrowser__Cup4G11:RR42_RS13880 643 DTSTLENPAILEQLKQ 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 0.02s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 10.29 // [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