Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_050655293.1 C1M55_RS02775 acetate--CoA ligase
Query= SwissProt::P9WQD1 (651 letters) >NCBI__GCF_002893965.1:WP_050655293.1 Length = 643 Score = 941 bits (2433), Expect = 0.0 Identities = 453/648 (69%), Positives = 530/648 (81%), Gaps = 10/648 (1%) Query: 2 SESTPEVSSSYPPPAHFAEHANARAELYREAEEDRLAFWAKQANRLSWTTPFTEVLDWSG 61 S + +V +YPP A FA ANA EL A+ DRLAFWA QA RL W +T+VLDW+ Sbjct: 3 SAAETDVPQAYPPSAEFAAAANAGPELQAAADTDRLAFWANQAERLHWHEKWTDVLDWTD 62 Query: 62 APFAKWFVGGELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLAEVSKAAN 121 AP AKWFVGG+LNVAYNCVDRHV AG+GDR+AIH+EGEP GD R LTY+DLLAEVS+AAN Sbjct: 63 APVAKWFVGGKLNVAYNCVDRHVLAGNGDRIAIHFEGEP-GDSRDLTYNDLLAEVSRAAN 121 Query: 122 ALTDLGLVAGDRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARIVDAQAKL 181 TDLGLVAGDRVAIY+P+IPEA++ MLACARLG+ HSVVF GF+A AL++RI DAQAKL Sbjct: 122 TFTDLGLVAGDRVAIYMPMIPEAIVTMLACARLGLTHSVVFAGFSATALRSRIDDAQAKL 181 Query: 182 LITADGQFRRGKPSPLKAAADEALAAIPDCSVEHVLVVRRTGIEMAWSEGRDLWWHHVVG 241 ++T DGQ+RRG +P+K A DE++A SV++VLVV RTGI++ W++GRDLWWH V Sbjct: 182 VVTVDGQWRRGAAAPIKTAVDESVAGAE--SVQNVLVVNRTGIDVDWTDGRDLWWHETVA 239 Query: 242 SASPAHTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDVKPDSDVF 301 ASP H + FD+EHPLF+LYTSGTTGKPKGI+HTSGGYLTQ YT +FD K DV+ Sbjct: 240 QASPEHEAQAFDAEHPLFILYTSGTTGKPKGIIHTSGGYLTQASYTHHNVFDHKAGQDVY 299 Query: 302 WCTADIGWVTGHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQIIEKYGVTIYYTAPTLI 361 WCTADIGWVTGH+Y VYGPL NGVT+V+YEGTP++P+ HRHF IIEKYGV+IYYTAPTL+ Sbjct: 300 WCTADIGWVTGHSYIVYGPLSNGVTQVVYEGTPNSPNEHRHFDIIEKYGVSIYYTAPTLV 359 Query: 362 RMFMKWGREIPDSHDLSSLRLLGSVGEPINPEAWRWYRDVIGGGRTPLVDTWWQTETGSA 421 R FMKWGREIPD+HDLSS+RLLGSVGEPINPEAWRW+R+VIGG + P+VDTWWQTETG+ Sbjct: 360 RTFMKWGREIPDAHDLSSIRLLGSVGEPINPEAWRWFREVIGGNKAPIVDTWWQTETGAI 419 Query: 422 MISPLPGIAAAKPGSAMTPLPGISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQPWPSMLR 481 MISPLPGI A KPGSAM PLPGISAKIVDD PL P GYLVLD+PWP+MLR Sbjct: 420 MISPLPGITATKPGSAMAPLPGISAKIVDDDAKPLGPGG------NGYLVLDEPWPAMLR 473 Query: 482 GIWGDPARYWHSYWSKFSDKGYYFAGDGARIDPDGAIWVLGRIDDVMNVSGHRISTAEVE 541 GIWGD RY +YWS+++++G+YFAGDGA+ D DGA+WVLGR+DDVMNVSGHRIST+EVE Sbjct: 474 GIWGDMDRYRDTYWSRYAEEGWYFAGDGAKYDDDGALWVLGRVDDVMNVSGHRISTSEVE 533 Query: 542 SALVAHSGVAEAAVVGVTDETTTQAICAFVVLRANYA-PHDRTAEELRTEVARVISPIAR 600 SALV H GVAEAAVVG DETT Q I AFV+LR D EL+ +V+ ISPIA+ Sbjct: 534 SALVNHHGVAEAAVVGAADETTGQGIVAFVILREGVENTGDVLIAELKAQVSTDISPIAK 593 Query: 601 PRDVHVVPELPKTRSGKIMRRLLRDVAENRELGDTSTLLDPTVFDAIR 648 PR + +VPELPKTRSGKIMRRLLRDVAE R+LGDTSTL+DP VFDAIR Sbjct: 594 PRQITIVPELPKTRSGKIMRRLLRDVAEGRDLGDTSTLVDPKVFDAIR 641 Lambda K H 0.319 0.136 0.433 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: 1524 Number of extensions: 89 Number of successful extensions: 5 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: 643 Length adjustment: 38 Effective length of query: 613 Effective length of database: 605 Effective search space: 370865 Effective search space used: 370865 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 (21.8 bits) S2: 54 (25.4 bits)
Align candidate WP_050655293.1 C1M55_RS02775 (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.1121992.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-287 939.9 0.2 3.4e-287 939.7 0.2 1.0 1 NCBI__GCF_002893965.1:WP_050655293.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002893965.1:WP_050655293.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 939.7 0.2 3.4e-287 3.4e-287 8 627 .. 27 641 .. 20 643 .] 0.98 Alignments for each domain: == domain 1 score: 939.7 bits; conditional E-value: 3.4e-287 TIGR02188 8 kelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiwe 79 el + a +d+ +fwa++a+ +l+w+++++ vld++ +p +kWf++g+lnv+yncvdrhv + + d++ai++e NCBI__GCF_002893965.1:WP_050655293.1 27 PELQAAADTDRLAFWANQAE-RLHWHEKWTDVLDWTDAPVAKWFVGGKLNVAYNCVDRHVLAgNGDRIAIHFE 98 5778889999*********9.5**************************************999********** PP TIGR02188 80 gdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaea 152 g+ +g dsr ltY++ll+ev+r+an++++lG+ gdrvaiY+pmipea+++mlacaR+G +hsvvfaGfsa a NCBI__GCF_002893965.1:WP_050655293.1 99 GE-PG-DSRDLTYNDLLAEVSRAANTFTDLGLVAGDRVAIYMPMIPEAIVTMLACARLGLTHSVVFAGFSATA 169 **.77.59***************************************************************** PP TIGR02188 153 laeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvek 225 l++Ri da+aklv+t d+++R+g + ++k++vde+++ ae sv++vlvv+rtg +v w++grD+ww+e+v++ NCBI__GCF_002893965.1:WP_050655293.1 170 LRSRIDDAQAKLVVTVDGQWRRGAAAPIKTAVDESVAGAE-SVQNVLVVNRTGIDVD-WTDGRDLWWHETVAQ 240 *************************************998.8*************66.**************6 PP TIGR02188 226 easaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik.dedifwCtaDvGWvtGhs 297 as e+e++++d+e+plfiLYtsG+tGkPkG++ht+gGyl++a++t++ vfd+k +d++wCtaD+GWvtGhs NCBI__GCF_002893965.1:WP_050655293.1 241 -ASPEHEAQAFDAEHPLFILYTSGTTGKPKGIIHTSGGYLTQASYTHHNVFDHKaGQDVYWCTADIGWVTGHS 312 .*****************************************************668**************** PP TIGR02188 298 YivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvG 370 YivygPL+nG+t++++eg+p+ p+++r++++ieky+v+i+YtaPt++R++mk+g+e++++hdlss+r+lgsvG NCBI__GCF_002893965.1:WP_050655293.1 313 YIVYGPLSNGVTQVVYEGTPNSPNEHRHFDIIEKYGVSIYYTAPTLVRTFMKWGREIPDAHDLSSIRLLGSVG 385 ************************************************************************* PP TIGR02188 371 epinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveee 443 epinpeaw+W++ev+G +k+pivdtwWqtetG+i+i+plpg +t++kpgsa+ Pl+Gi+a++vd+++k++ ++ NCBI__GCF_002893965.1:WP_050655293.1 386 EPINPEAWRWFREVIGGNKAPIVDTWWQTETGAIMISPLPG-ITATKPGSAMAPLPGISAKIVDDDAKPLGPG 457 *****************************************.5****************************99 PP TIGR02188 444 eeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkdGyiwilGRvDdvinvsGhrlgt 514 + g+Lv+++pwP+mlr+i+gd +r+ +tY++++ + yf+GDga+ d+dG +w+lGRvDdv+nvsGhr++t NCBI__GCF_002893965.1:WP_050655293.1 458 GN-GYLVLDEPWPAMLRGIWGDMDRYRDTYWSRYAEegWYFAGDGAKYDDDGALWVLGRVDDVMNVSGHRIST 529 88.8*****************************987779********************************** PP TIGR02188 515 aeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvvee 587 +e+esalv+h+ vaeaavvg++de++g+ ivafv+l+egve++ + l +elk++v++ i+piakp++i++v+e NCBI__GCF_002893965.1:WP_050655293.1 530 SEVESALVNHHGVAEAAVVGAADETTGQGIVAFVILREGVENTGDVLIAELKAQVSTDISPIAKPRQITIVPE 602 *******************************************99**************************** PP TIGR02188 588 lPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627 lPktRsGkimRRllr++aeg++l gd+stl dp+v+++++ NCBI__GCF_002893965.1:WP_050655293.1 603 LPKTRSGKIMRRLLRDVAEGRDL-GDTSTLVDPKVFDAIR 641 *******************9875.6***********9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (643 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 38.62 // [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