Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_011771371.1 PING_RS16055 acetate--CoA ligase
Query= SwissProt::Q8ZKF6 (652 letters) >NCBI__GCF_000015285.1:WP_011771371.1 Length = 649 Score = 998 bits (2580), Expect = 0.0 Identities = 465/646 (71%), Positives = 547/646 (84%) Query: 1 MSQTHKHAIPANIADRCLINPEQYETKYKQSINDPDTFWGEQGKILDWITPYQKVKNTSF 60 MS+ H + + N+A L+ E+Y T+Y+ SI+DP FWGE+GKILDWI PY KVKN+SF Sbjct: 1 MSEEHIYPVTDNLAKNSLLTNEEYLTQYQASISDPSAFWGEKGKILDWIKPYTKVKNSSF 60 Query: 61 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDTSQSKHISYRELHRDVCRF 120 G+VSIKW+EDG LN++ANC+DRHL GD+ AI+WEGD + + I+Y++LH+ VC+F Sbjct: 61 DSGHVSIKWFEDGKLNVSANCIDRHLATKGDQVAILWEGDTADKDEKITYKQLHQRVCQF 120 Query: 121 ANTLLDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSS 180 AN L G++KGDVV +YMPM PEAAVAMLAC RIGAVHS++FGGFSP+A+AGRI+DSS+ Sbjct: 121 ANVLKSQGVRKGDVVCLYMPMTPEAAVAMLACTRIGAVHSIVFGGFSPDAIAGRIVDSSA 180 Query: 181 RLVITADEGVRAGRSIPLKKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDL 240 ++VITADEG R GR +PLK NVD+AL V+ VIV K TG +++W GRDL W + Sbjct: 181 KIVITADEGRRGGRVVPLKANVDEALTKDGTDCVKSVIVFKNTGGEVNWVVGRDLDWESV 240 Query: 241 IEKASPEHQPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDI 300 S E +PEAMNAEDPLFILYTSGSTG PKGVLHTTGGYLVYAA TFKYVFDY GDI Sbjct: 241 CADESSECEPEAMNAEDPLFILYTSGSTGTPKGVLHTTGGYLVYAAMTFKYVFDYQEGDI 300 Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTA 360 YWCTADVGW+TGH+Y +YGPLA GAT+L+FEGVPN+PTPARM +VVDKH+V+ILYTAPTA Sbjct: 301 YWCTADVGWITGHTYSVYGPLANGATSLIFEGVPNYPTPARMSEVVDKHKVSILYTAPTA 360 Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGG 420 IRALMA+GD+AIEGT RSSLRILGSVGEPINPEAWEWY+ KIG E+CP+VDTWWQTETGG Sbjct: 361 IRALMAKGDQAIEGTHRSSLRILGSVGEPINPEAWEWYYNKIGDERCPIVDTWWQTETGG 420 Query: 421 FMITPLPGAIELKAGSATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFGD 480 +I+PLPGA +LK GSATRPFFGVQPA+VD+EG EG GNLV+ DSWPGQ RTL+ + Sbjct: 421 ILISPLPGATDLKPGSATRPFFGVQPAIVDSEGVVLEGEAAGNLVMLDSWPGQMRTLYNN 480 Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540 H+RFEQTYFSTFK MYF+GDGARRD DGYYWITGRVDDVLNVSGHR+GTAEIESALV+HP Sbjct: 481 HDRFEQTYFSTFKGMYFTGDGARRDSDGYYWITGRVDDVLNVSGHRMGTAEIESALVSHP 540 Query: 541 KIAEAAVVGIPHAIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600 KIAEAAVVG+PH IKGQ IYAYVTLN GE PSPELYAEV+ WVRKEIG +ATPD+LHW + Sbjct: 541 KIAEAAVVGVPHEIKGQGIYAYVTLNEGEYPSPELYAEVKQWVRKEIGAIATPDILHWAE 600 Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646 LPKTRSGKIMRRILRKIA G++ +LGD STLADP VVE+L++E + Sbjct: 601 GLPKTRSGKIMRRILRKIATGESDSLGDISTLADPSVVEQLIKENR 646 Lambda K H 0.317 0.135 0.423 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: 1567 Number of extensions: 61 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: 652 Length of database: 649 Length adjustment: 38 Effective length of query: 614 Effective length of database: 611 Effective search space: 375154 Effective search space used: 375154 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate WP_011771371.1 PING_RS16055 (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.1176599.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1019.0 0.1 0 1018.8 0.1 1.0 1 NCBI__GCF_000015285.1:WP_011771371.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000015285.1:WP_011771371.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1018.8 0.1 0 0 4 628 .. 21 643 .. 18 644 .. 0.98 Alignments for each domain: == domain 1 score: 1018.8 bits; conditional E-value: 0 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 +eey + y+ +i+dp++fw++++k l+w+kp++kv+++s+++ ++kWfedg+lnvs+nc+drh++++ d+ NCBI__GCF_000015285.1:WP_011771371.1 21 NEEYLTQYQASISDPSAFWGEKGK-ILDWIKPYTKVKNSSFDSghvSIKWFEDGKLNVSANCIDRHLATKGDQ 92 789********************9.6**************9988889************************** PP TIGR02188 74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146 vai wegd +++ +k+tY++l+++vc++anvlk++Gv+kgd v++Y+pm+pea++amlac+RiGavhs+vf+ NCBI__GCF_000015285.1:WP_011771371.1 93 VAILWEGDTADK-DEKITYKQLHQRVCQFANVLKSQGVRKGDVVCLYMPMTPEAAVAMLACTRIGAVHSIVFG 164 ********7775.99********************************************************** PP TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218 Gfs++a+a Rivd++ak+vitadeg Rgg+v++lk++vdeal+k + v++v+v+k tg ev+ w+ grD+ NCBI__GCF_000015285.1:WP_011771371.1 165 GFSPDAIAGRIVDSSAKIVITADEGRRGGRVVPLKANVDEALTKDGTdCVKSVIVFKNTGGEVN-WVVGRDLD 236 *******************************************998889*************66.******** PP TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291 we+++++ +s+ecepe++++edplfiLYtsGstG+PkGvlhttgGyl++aa+t+kyvfd++++di+wCtaDvG NCBI__GCF_000015285.1:WP_011771371.1 237 WESVCAD-ESSECEPEAMNAEDPLFILYTSGSTGTPKGVLHTTGGYLVYAAMTFKYVFDYQEGDIYWCTADVG 308 ******7.***************************************************************** PP TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364 W+tGh+Y vygPLanGat+l+fegvp+yp+++r+ ev++k+kv+i+YtaPtaiRalm++g+++++ +++sslr NCBI__GCF_000015285.1:WP_011771371.1 309 WITGHTYSVYGPLANGATSLIFEGVPNYPTPARMSEVVDKHKVSILYTAPTAIRALMAKGDQAIEGTHRSSLR 381 ************************************************************************* PP TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437 +lgsvGepinpeaweWyy+++G+e+cpivdtwWqtetGgili+plpg at+lkpgsat+P+fG+++++vd+eg NCBI__GCF_000015285.1:WP_011771371.1 382 ILGSVGEPINPEAWEWYYNKIGDERCPIVDTWWQTETGGILISPLPG-ATDLKPGSATRPFFGVQPAIVDSEG 453 ***********************************************.6************************ PP TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510 +e e+ g Lv+ ++wP+++rt+y++++rf +tYf+++kg+yftGDgarrd+dGy+wi+GRvDdv+nvsGh NCBI__GCF_000015285.1:WP_011771371.1 454 VVLEGEAA-GNLVMLDSWPGQMRTLYNNHDRFEQTYFSTFKGMYFTGDGARRDSDGYYWITGRVDDVLNVSGH 525 ***98777.89************************************************************** PP TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583 r+gtaeiesalvsh+++aeaavvgvp+eikg+ i+a+v+l+eg+ ++ e l +e+k++vrkeig+ia+pd ++ NCBI__GCF_000015285.1:WP_011771371.1 526 RMGTAEIESALVSHPKIAEAAVVGVPHEIKGQGIYAYVTLNEGEYPSPE-LYAEVKQWVRKEIGAIATPDILH 597 ************************************************5.*********************** PP TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 ++e lPktRsGkimRR+lrkia+ge ++lgd+stl+dpsvve+l++ NCBI__GCF_000015285.1:WP_011771371.1 598 WAEGLPKTRSGKIMRRILRKIATGEsDSLGDISTLADPSVVEQLIK 643 *************************99****************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (649 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 29.41 // [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