Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_012276800.1 SHAL_RS08815 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >NCBI__GCF_000019185.1:WP_012276800.1 Length = 650 Score = 985 bits (2546), Expect = 0.0 Identities = 462/644 (71%), Positives = 536/644 (83%) Query: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 MS SLY V E+AA+ L ++ YK MYQ+S+VNP+GFWRE R+DWIKPFT VK+TSF Sbjct: 1 MSTQSLYKVPSEIAANALVNDEQYKKMYQESIVNPEGFWREHGNRIDWIKPFTKVKKTSF 60 Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120 DDH++ IKWF DGTLN S NCLDRHL D++AIIWEGDD + R +TY +LH +VCKF Sbjct: 61 DDHNLFIKWFYDGTLNASANCLDRHLENNADKLAIIWEGDDAKDQRTLTYGQLHTQVCKF 120 Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 ANALR Q V RGDVVTIYMPM+PEA VAMLAC RIGAIHSVVFGGFSP+++A R+ID S Sbjct: 121 ANALRSQGVRRGDVVTIYMPMVPEAAVAMLACARIGAIHSVVFGGFSPDSIASRVIDGNS 180 Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240 KVVITADEGVRAG+ IPLKAN+D+AL++P+ + ++KVIV KRT G+I W + RDIW++ L Sbjct: 181 KVVITADEGVRAGRIIPLKANIDEALSHPDVNCVEKVIVMKRTGGDINWVEGRDIWWDSL 240 Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300 M A C +EMGAE+ LF+LYTSGSTG PKGV HTT GY++YAA+THE VFDYK EV Sbjct: 241 MDTASEHCIAEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYMVYAAMTHEYVFDYKENEV 300 Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360 YWCTADVGW+TGHSY+VYGPLANGAT L+ EGVPNYP R+ +++D+HKV+ILYTAPT Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATVLIHEGVPNYPSPARLGEMVDRHKVNILYTAPTL 360 Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420 IRA+MA G G DGSSLR++GSVGEPINPEAW WY +G E+CPIVDTWWQTETGG Sbjct: 361 IRALMAEGKEQFAGFDGSSLRIMGSVGEPINPEAWRWYNDVIGHEKCPIVDTWWQTETGG 420 Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480 +LISPLPGAT KPGSATRPFFGV PALVDN+GN+++GA+EGNLVILDSWPGQ RT++GD Sbjct: 421 ILISPLPGATDTKPGSATRPFFGVQPALVDNMGNIVDGASEGNLVILDSWPGQMRTVFGD 480 Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 HDRFV TYFKTF GMYFTGDGA+RDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+VAH Sbjct: 481 HDRFVLTYFKTFRGMYFTGDGAKRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHE 540 Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600 VAEAAVVG PHDIKGQGIY YVTL G +E LR EL+ WVRKEIG +A+PD+IQWA Sbjct: 541 FVAEAAVVGYPHDIKGQGIYAYVTLTKGSVETEELRQELRQWVRKEIGALATPDLIQWAG 600 Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIET 644 GLPKTRSGKIMRR LRKIA E LGD STLADP V+ LIET Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEVSNLGDSSTLADPAVIDTLIET 644 Lambda K H 0.318 0.135 0.418 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: 1457 Number of extensions: 52 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: 651 Length of database: 650 Length adjustment: 38 Effective length of query: 613 Effective length of database: 612 Effective search space: 375156 Effective search space used: 375156 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_012276800.1 SHAL_RS08815 (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.1191233.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 1024.1 0.1 0 1023.9 0.1 1.0 1 NCBI__GCF_000019185.1:WP_012276800.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000019185.1:WP_012276800.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1023.9 0.1 0 0 3 628 .. 20 643 .. 18 644 .. 0.98 Alignments for each domain: == domain 1 score: 1023.9 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkd 72 + e+yk++y+e+i +pe fw+++++ +++w+kpf+kv+++s+++ ++kWf dg+ln+s+nc+drh+e+++d NCBI__GCF_000019185.1:WP_012276800.1 20 NDEQYKKMYQESIVNPEGFWREHGN-RIDWIKPFTKVKKTSFDDhnlFIKWFYDGTLNASANCLDRHLENNAD 91 6799*********************.5*************99877789************************* PP TIGR02188 73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvf 145 k+aiiwegd+++ d+r+ltY +l+++vc++an+l+++Gv++gd v+iY+pm+pea++amlacaRiGa+hsvvf NCBI__GCF_000019185.1:WP_012276800.1 92 KLAIIWEGDDAK-DQRTLTYGQLHTQVCKFANALRSQGVRRGDVVTIYMPMVPEAAVAMLACARIGAIHSVVF 163 *********998.6*********************************************************** PP TIGR02188 146 aGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDv 217 +Gfs++++a+R++d ++k+vitadeg+R g++i+lk+++deal++ + vekv+v+krtg +++ w+egrD+ NCBI__GCF_000019185.1:WP_012276800.1 164 GGFSPDSIASRVIDGNSKVVITADEGVRAGRIIPLKANIDEALSHPDVnCVEKVIVMKRTGGDIN-WVEGRDI 235 *********************************************99889*************66.******* PP TIGR02188 218 wweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDv 290 ww++l+++ as++c +e++++edplf+LYtsGstG+PkGvlhttgGy+++aa+t++yvfd+k+++++wCtaDv NCBI__GCF_000019185.1:WP_012276800.1 236 WWDSLMDT-ASEHCIAEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYMVYAAMTHEYVFDYKENEVYWCTADV 307 *******6.**************************************************************** PP TIGR02188 291 GWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlssl 363 GW+tGhsY+vygPLanGat l++egvp+yp+++r+ e+++++kv+i+YtaPt+iRalm++g+e+++ d ssl NCBI__GCF_000019185.1:WP_012276800.1 308 GWITGHSYMVYGPLANGATVLIHEGVPNYPSPARLGEMVDRHKVNILYTAPTLIRALMAEGKEQFAGFDGSSL 380 ************************************************************************* PP TIGR02188 364 rvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdee 436 r++gsvGepinpeaw+Wy++v+G+ekcpivdtwWqtetGgili+plpg at++kpgsat+P+fG+++++vd+ NCBI__GCF_000019185.1:WP_012276800.1 381 RIMGSVGEPINPEAWRWYNDVIGHEKCPIVDTWWQTETGGILISPLPG-ATDTKPGSATRPFFGVQPALVDNM 452 ************************************************.6*********************** PP TIGR02188 437 gkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsG 509 g+ v+ +e g Lvi ++wP+++rt++gd++rfv tYfk+++g+yftGDga+rd+dGy+wi+GRvDdvinvsG NCBI__GCF_000019185.1:WP_012276800.1 453 GNIVDGASE-GNLVILDSWPGQMRTVFGDHDRFVLTYFKTFRGMYFTGDGAKRDEDGYYWITGRVDDVINVSG 524 *****8777.79************************************************************* PP TIGR02188 510 hrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdki 582 hrlgtae+esalv+he vaeaavvg+p++ikg+ i+a+v+l++g+ e+e el++el+++vrkeig++a+pd i NCBI__GCF_000019185.1:WP_012276800.1 525 HRLGTAEVESALVAHEFVAEAAVVGYPHDIKGQGIYAYVTLTKGSVETE-ELRQELRQWVRKEIGALATPDLI 596 *******************************************999888.5********************** PP TIGR02188 583 lvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 +++ lPktRsGkimRR+lrkia++e ++lgd stl+dp+v+++l+e NCBI__GCF_000019185.1:WP_012276800.1 597 QWAGGLPKTRSGKIMRRFLRKIAANEvSNLGDSSTLADPAVIDTLIE 643 *******************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (650 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: 00:00:00.02 # Mc/sec: 17.75 // [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