Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_076478630.1 BW971_RS08810 acetate--CoA ligase
Query= SwissProt::P9WQD1 (651 letters) >NCBI__GCF_900156495.1:WP_076478630.1 Length = 657 Score = 910 bits (2352), Expect = 0.0 Identities = 447/647 (69%), Positives = 512/647 (79%), Gaps = 12/647 (1%) Query: 7 EVSSSYPPPAHFAEHANARAELYREAEEDRLAFWAKQANRLSWTTPFTEVLDWSGAPFAK 66 E S+PP FA+ ANA AELY A+ DRL FWA+QA L W T FT+VLDWS APFAK Sbjct: 14 EAGQSFPPSRDFADQANAGAELYTRADADRLEFWAEQARALDWDTDFTDVLDWSNAPFAK 73 Query: 67 WFVGGELNVAYNCVDRHVEAGHGDRVAIHWEGEPVGDRRTLTYSDLLAEVSKAANALTDL 126 WFVGG+LNVA NCVDRHV AG+GDRVAIHW GEP GD R +TYS LL +VS+AAN + Sbjct: 74 WFVGGKLNVAVNCVDRHVAAGNGDRVAIHWVGEP-GDHRDITYSQLLGDVSRAANYFDSI 132 Query: 127 GLVAGDRVAIYLPLIPEAVIAMLACARLGIMHSVVFGGFTAAALQARIVDAQAKLLITAD 186 GL GDRVAIY+P++PEA++ MLACARLG+ HSVVF GF++ AL++R+ DA+AKL++T D Sbjct: 133 GLRPGDRVAIYMPMVPEAIVTMLACARLGLTHSVVFAGFSSTALRSRVDDAEAKLVVTTD 192 Query: 187 GQFRRGKPSPLKAAADEALAAIPDC--SVEHVLVVRRTGI--EMAWSEGRDLWWHHVVGS 242 GQ+RRGKP+PLKA DEAL D SV+ VLVVRRT E+ W GRD+WW V Sbjct: 193 GQYRRGKPAPLKANVDEALGTGDDAAVSVQTVLVVRRTNHDPELNWVSGRDVWWDDTVAE 252 Query: 243 ASPAHTPEPFDSEHPLFLLYTSGTTGKPKGIMHTSGGYLTQCCYTMRTIFDVKPDSDVFW 302 AS H P+ FDSE PLFLLYTSGTTGKPKGI+HTSGGYLTQ YT +FD K DVFW Sbjct: 253 ASDHHEPDAFDSEQPLFLLYTSGTTGKPKGILHTSGGYLTQVRYTFHNVFDHKEGRDVFW 312 Query: 303 CTADIGWVTGHTYGVYGPLCNGVTEVLYEGTPDTPDRHRHFQIIEKYGVTIYYTAPTLIR 362 C ADIGWVTGH+Y VYGPL NG TEV+YEGTP++P+ HRHF+IIE+YGV+IYY APTLIR Sbjct: 313 CGADIGWVTGHSYLVYGPLSNGATEVVYEGTPNSPNEHRHFEIIERYGVSIYYIAPTLIR 372 Query: 363 MFMKWGREIPDSHDLSSLRLLGSVGEPINPEAWRWYRDVIGGGRTPLVDTWWQTETGSAM 422 FMKWGREIPD+HDLSSLRLLGSVGEPINPEAWRWYR+VIG P+VDTWWQTETG+ M Sbjct: 373 TFMKWGREIPDAHDLSSLRLLGSVGEPINPEAWRWYREVIGHDSCPIVDTWWQTETGAIM 432 Query: 423 ISPLPGIAAAKPGSAMTPLPGISAKIVDDHGDPLPPHTEGAQHVTGYLVLDQPWPSMLRG 482 ISPLPG+ AKPGSAM PLPGISA IVDD P+ A GYLVLD+PWPSMLRG Sbjct: 433 ISPLPGVTDAKPGSAMRPLPGISATIVDDDAAPV------AAGEQGYLVLDKPWPSMLRG 486 Query: 483 IWGDPARYWHSYWSKFSDKGYYFAGDGARIDPDGAIWVLGRIDDVMNVSGHRISTAEVES 542 IWGD R+ +YWS+F+D+G+YFAGDGAR D D A+WVLGRIDDVMNVSGHRIST+EVES Sbjct: 487 IWGDDQRFIDTYWSRFADQGWYFAGDGARYDDDHALWVLGRIDDVMNVSGHRISTSEVES 546 Query: 543 ALVAHSGVAEAAVVGVTDETTTQAICAFVVLRANYA-PHDRTAEELRTEVARVISPIARP 601 ALV H VAEAAV+G D TT Q I AFV+LR D ELR +VA+ ISPIA+P Sbjct: 547 ALVNHHSVAEAAVIGAADATTGQGIVAFVILRGGVEDTGDTLIAELRDQVAKDISPIAKP 606 Query: 602 RDVHVVPELPKTRSGKIMRRLLRDVAENRELGDTSTLLDPTVFDAIR 648 R+V VVPELPKTRSGKIMRRLL+DVAE RELGDTSTL+DPTVF+ IR Sbjct: 607 REVLVVPELPKTRSGKIMRRLLKDVAEGRELGDTSTLVDPTVFEEIR 653 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: 1537 Number of extensions: 93 Number of successful extensions: 6 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: 657 Length adjustment: 38 Effective length of query: 613 Effective length of database: 619 Effective search space: 379447 Effective search space used: 379447 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_076478630.1 BW971_RS08810 (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.3643378.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-285 932.9 0.0 4.5e-285 932.7 0.0 1.0 1 NCBI__GCF_900156495.1:WP_076478630.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900156495.1:WP_076478630.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 932.7 0.0 4.5e-285 4.5e-285 4 627 .. 29 653 .. 26 655 .. 0.97 Alignments for each domain: == domain 1 score: 932.7 bits; conditional E-value: 4.5e-285 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkva 75 +++ +ely++a +d+ +fwa++a+ l+w+++f+ vld+s++p++kWf++g+lnv++ncvdrhv++ + d+va NCBI__GCF_900156495.1:WP_076478630.1 29 ANAGAELYTRADADRLEFWAEQAR-ALDWDTDFTDVLDWSNAPFAKWFVGGKLNVAVNCVDRHVAAgNGDRVA 100 5667899*****************.6****************************************9****** PP TIGR02188 76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGf 148 i+w g+ +g d+r +tY++ll +v+r+an + ++G++ gdrvaiY+pm+pea+++mlacaR+G +hsvvfaGf NCBI__GCF_900156495.1:WP_076478630.1 101 IHWVGE-PG-DHRDITYSQLLGDVSRAANYFDSIGLRPGDRVAIYMPMVPEAIVTMLACARLGLTHSVVFAGF 171 *****9.77.59************************************************************* PP TIGR02188 149 saealaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgee.vaewkegrDv 217 s+ al++R+ daeaklv+t+d+++R+gk +lk++vdeal + ++ sv++vlvv+rt+++ +w++grDv NCBI__GCF_900156495.1:WP_076478630.1 172 SSTALRSRVDDAEAKLVVTTDGQYRRGKPAPLKANVDEALGTGDDaavSVQTVLVVRRTNHDpELNWVSGRDV 244 ****************************************987766679**********9752568******* PP TIGR02188 218 wweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikd.edifwCtaD 289 ww+++v++ as+++ep+++dse+plf+LYtsG+tGkPkG+lht+gGyl+++ +t++ vfd+k+ d+fwC aD NCBI__GCF_900156495.1:WP_076478630.1 245 WWDDTVAE-ASDHHEPDAFDSEQPLFLLYTSGTTGKPKGILHTSGGYLTQVRYTFHNVFDHKEgRDVFWCGAD 316 *******6.*****************************************************636******** PP TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362 +GWvtGhsY+vygPL+nGat++++eg+p+ p+++r++e+ie+y+v+i+Y aPt+iR++mk+g+e++++hdlss NCBI__GCF_900156495.1:WP_076478630.1 317 IGWVTGHSYLVYGPLSNGATEVVYEGTPNSPNEHRHFEIIERYGVSIYYIAPTLIRTFMKWGREIPDAHDLSS 389 ************************************************************************* PP TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435 lr+lgsvGepinpeaw+Wy+ev+G+++cpivdtwWqtetG+i+i+plpg +t++kpgsa++Pl+Gi+a++vd+ NCBI__GCF_900156495.1:WP_076478630.1 390 LRLLGSVGEPINPEAWRWYREVIGHDSCPIVDTWWQTETGAIMISPLPG-VTDAKPGSAMRPLPGISATIVDD 461 *************************************************.5********************** PP TIGR02188 436 egkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyftGDgarrdkdGyiwilGRvDdvin 506 ++ +v ++e+ g+Lv++kpwPsmlr+i+gd++rf++tY++++ + yf+GDgar d+d +w+lGR+Ddv+n NCBI__GCF_900156495.1:WP_076478630.1 462 DAAPVAAGEQ-GYLVLDKPWPSMLRGIWGDDQRFIDTYWSRFADqgWYFAGDGARYDDDHALWVLGRIDDVMN 533 *******999.8******************************87779************************** PP TIGR02188 507 vsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakp 579 vsGhr++t+e+esalv+h++vaeaav+g++d ++g+ ivafv+l+ gve + ++l +el+++v+k i+piakp NCBI__GCF_900156495.1:WP_076478630.1 534 VSGHRISTSEVESALVNHHSVAEAAVIGAADATTGQGIVAFVILRGGVEDTGDTLIAELRDQVAKDISPIAKP 606 *************************************************9999******************** PP TIGR02188 580 dkilvveelPktRsGkimRRllrkiaegeellgdvstledpsvveelk 627 +++lvv+elPktRsGkimRRll+++aeg+el gd+stl dp+v+ee++ NCBI__GCF_900156495.1:WP_076478630.1 607 REVLVVPELPKTRSGKIMRRLLKDVAEGREL-GDTSTLVDPTVFEEIR 653 ***************************9875.6************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (657 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: 40.09 // [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