Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_016853633.1 UYS_RS0201040 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >NCBI__GCF_000265245.1:WP_016853633.1 Length = 649 Score = 941 bits (2432), Expect = 0.0 Identities = 442/638 (69%), Positives = 523/638 (81%) Query: 6 LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65 +YPV + AA D+ATY+AMYQ+S+ +P+GFW EQA+ LDW K + +K T FD V Sbjct: 7 VYPVPDDFAAKAWADKATYQAMYQRSLDDPEGFWAEQAECLDWFKAPSKIKHTVFDPQDV 66 Query: 66 DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALR 125 DI+WF DG LNVS NCLDRHL RGDQ AIIWEGDDP +S+ +TYR+LHE C+ ANAL+ Sbjct: 67 DIRWFEDGRLNVSSNCLDRHLETRGDQTAIIWEGDDPEDSKTLTYRQLHERTCQLANALK 126 Query: 126 GQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 185 G V RGD VT+YMPMIPEA +AMLAC RIGA+HSVVFGGFSP+ALA R+ D S+VVIT Sbjct: 127 GMGVKRGDTVTLYMPMIPEAAMAMLACARIGAVHSVVFGGFSPDALAQRVKDAGSRVVIT 186 Query: 186 ADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG 245 ADE VR GK++PLK NVD ALT + +KV+V +RT G I W++ RD+W+ + + Sbjct: 187 ADESVRGGKQVPLKDNVDAALTREGSDVCEKVLVVQRTGGEIDWHEGRDLWFHEQVDPQS 246 Query: 246 TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTA 305 T C +EMGAE+ LFILYTSGSTG PKG++HTT GYLL+AALTH VFDY G++YWCTA Sbjct: 247 TDCPAEEMGAEDPLFILYTSGSTGAPKGLKHTTGGYLLHAALTHRYVFDYHDGDIYWCTA 306 Query: 306 DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMM 365 DVGWVTGHSYIVYGPLANGATTL+FEGVP+YP R+ +++DKH+V+ILYTAPTA+RA+M Sbjct: 307 DVGWVTGHSYIVYGPLANGATTLMFEGVPSYPTNGRMGEIVDKHRVNILYTAPTAVRALM 366 Query: 366 ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP 425 A G ++ + SLRLLGSVGEPINPEAW+W+++ +G ERCPIVDTWWQTETGG++I+P Sbjct: 367 AHGDDVMDSSSRDSLRLLGSVGEPINPEAWEWFHRVIGNERCPIVDTWWQTETGGIMIAP 426 Query: 426 LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV 485 LPGAT LKPGSAT PFFGV PALVDN GN++EGA EGNLV+LD+WPGQAR+++ +H+RF+ Sbjct: 427 LPGATDLKPGSATLPFFGVQPALVDNEGNILEGATEGNLVMLDAWPGQARSIWNNHERFL 486 Query: 486 DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA 545 TYF T+ GMYFTGDG RRDEDGYYWITGRVDDVLNVSGHRMGTAEIES++VAH VAEA Sbjct: 487 QTYFSTYKGMYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRMGTAEIESSLVAHESVAEA 546 Query: 546 AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT 605 AVVG PHDIKGQGIY+YVTL E S+ L+ L WVRK+IGPIASPDVIQWAPGLPKT Sbjct: 547 AVVGFPHDIKGQGIYIYVTLADDVEPSDELKKALTQWVRKDIGPIASPDVIQWAPGLPKT 606 Query: 606 RSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643 RSGKIMRRILRKIA E DGLGD STLADP VV LIE Sbjct: 607 RSGKIMRRILRKIAANECDGLGDTSTLADPSVVDDLIE 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: 1463 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: 649 Length adjustment: 38 Effective length of query: 613 Effective length of database: 611 Effective search space: 374543 Effective search space used: 374543 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_016853633.1 UYS_RS0201040 (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.1681164.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 1013.1 0.0 0 1012.9 0.0 1.0 1 NCBI__GCF_000265245.1:WP_016853633.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000265245.1:WP_016853633.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1012.9 0.0 0 0 4 628 .. 22 644 .. 19 645 .. 0.98 Alignments for each domain: == domain 1 score: 1012.9 bits; conditional E-value: 0 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 +y+++y+++ +dpe fwa++a+ l+w+k +k++++ ++p +++Wfedg+lnvs nc+drh+e+r d+ NCBI__GCF_000265245.1:WP_016853633.1 22 KATYQAMYQRSLDDPEGFWAEQAE-CLDWFKAPSKIKHTVFDPqdvDIRWFEDGRLNVSSNCLDRHLETRGDQ 93 679********************9.6************999887789************************** PP TIGR02188 74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146 +aiiwegd+++ ds++ltY++l++++c+lan+lk +Gvk+gd+v++Y+pmipea++amlacaRiGavhsvvf+ NCBI__GCF_000265245.1:WP_016853633.1 94 TAIIWEGDDPE-DSKTLTYRQLHERTCQLANALKGMGVKRGDTVTLYMPMIPEAAMAMLACARIGAVHSVVFG 165 ********998.6************************************************************ PP TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218 Gfs++ala+R++da +++vitade++Rggk+++lk++vd+al+++ + ekvlvv+rtg e+ w+egrD+w NCBI__GCF_000265245.1:WP_016853633.1 166 GFSPDALAQRVKDAGSRVVITADESVRGGKQVPLKDNVDAALTREGSdVCEKVLVVQRTGGEID-WHEGRDLW 237 *******************************************99996779***********66.******** PP TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291 ++e v+ +s++c++e++++edplfiLYtsGstG PkG+ httgGyll+aalt++yvfd++d+di+wCtaDvG NCBI__GCF_000265245.1:WP_016853633.1 238 FHEQVD-PQSTDCPAEEMGAEDPLFILYTSGSTGAPKGLKHTTGGYLLHAALTHRYVFDYHDGDIYWCTADVG 309 ******.6***************************************************************** PP TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364 WvtGhsYivygPLanGattl+fegvp+yp+++r+ e+++k++v+i+YtaPta+Ralm+ g++++++ +++slr NCBI__GCF_000265245.1:WP_016853633.1 310 WVTGHSYIVYGPLANGATTLMFEGVPSYPTNGRMGEIVDKHRVNILYTAPTAVRALMAHGDDVMDSSSRDSLR 382 ************************************************************************* PP TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437 +lgsvGepinpeaweW+++v+G+e+cpivdtwWqtetGgi+i+plpg at+lkpgsatlP+fG+++++vd+eg NCBI__GCF_000265245.1:WP_016853633.1 383 LLGSVGEPINPEAWEWFHRVIGNERCPIVDTWWQTETGGIMIAPLPG-ATDLKPGSATLPFFGVQPALVDNEG 454 ***********************************************.6************************ PP TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510 + +e +e g Lv+ ++wP+++r+i++++erf +tYf+++kg+yftGDg+rrd+dGy+wi+GRvDdv+nvsGh NCBI__GCF_000265245.1:WP_016853633.1 455 NILEGATE-GNLVMLDAWPGQARSIWNNHERFLQTYFSTYKGMYFTGDGCRRDEDGYYWITGRVDDVLNVSGH 526 ****8777.79************************************************************** PP TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583 r+gtaeies+lv+he+vaeaavvg+p++ikg+ i+++v+l + ve+++e l+k l+++vrk igpia+pd i+ NCBI__GCF_000265245.1:WP_016853633.1 527 RMGTAEIESSLVAHESVAEAAVVGFPHDIKGQGIYIYVTLADDVEPSDE-LKKALTQWVRKDIGPIASPDVIQ 598 ************************************************5.*********************** PP TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 +++ lPktRsGkimRR+lrkia++e + lgd+stl+dpsvv++l+e NCBI__GCF_000265245.1:WP_016853633.1 599 WAPGLPKTRSGKIMRRILRKIAANEcDGLGDTSTLADPSVVDDLIE 644 ******************************************9986 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 18.26 // [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