Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_017223156.1 A923_RS0118350 acetate--CoA ligase
Query= SwissProt::P27550 (652 letters) >NCBI__GCF_000276805.1:WP_017223156.1 Length = 648 Score = 959 bits (2478), Expect = 0.0 Identities = 449/646 (69%), Positives = 531/646 (82%) Query: 1 MSQIHKHTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSF 60 MS + +PA A L+N Y+AMY+ SI P+ FWGEQG I+DWIKPY +VK+TSF Sbjct: 1 MSDTKLYPVPAEFAQNSLLNDSAYQAMYKHSITDPEAFWGEQGHIVDWIKPYSQVKSTSF 60 Query: 61 APGNVSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRF 120 PG+V IKW++DG LN++ANCLDRHL++N ++TAIIWEGD+ S+ ++Y++++ VC+F Sbjct: 61 QPGSVDIKWFQDGQLNVSANCLDRHLKDNANKTAIIWEGDNPEDSEKLTYQDVYEKVCQF 120 Query: 121 ANTLLELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNS 180 +N L GIKKGDVV +YMPMVPEAA+AMLAC RIGAVH+++F GFS EA+A RI + + Sbjct: 121 SNALKAQGIKKGDVVCLYMPMVPEAAIAMLACTRIGAVHTIVFAGFSAEALADRIDNCGA 180 Query: 181 RLVITSDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDL 240 +LVIT+DEGVRAGR LK VD AL P VT+V +V+V RT I W EGRDLWWHD+ Sbjct: 181 KLVITADEGVRAGRITRLKDCVDTALAKPQVTTVNNVIVFARTKADIAWHEGRDLWWHDV 240 Query: 241 VEQASDQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDI 300 V+ + E MNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYA +TFKYVFD+ D+ Sbjct: 241 VKDQPTECVPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYATMTFKYVFDHQDTDV 300 Query: 301 YWCTADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTA 360 +WCTADVGW+TGHSYL+YGPLA ATT++FEGVPN+P ARM+QVVDKHQV LYTAPTA Sbjct: 301 FWCTADVGWITGHSYLVYGPLANAATTVLFEGVPNYPDTARMSQVVDKHQVTTLYTAPTA 360 Query: 361 IRALMAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGG 420 IRALMA+GD AI+GT R+SLR++GSVGEPINPEAW+WY+ IGN P+VDTWWQTETGG Sbjct: 361 IRALMAKGDDAIKGTKRTSLRLMGSVGEPINPEAWQWYYNTIGNASTPIVDTWWQTETGG 420 Query: 421 FMITPLPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGD 480 +ITPLPGAT LK GSATRPFFG+ PALVDNEGN LEGA EG+LVI DSWPGQ R ++GD Sbjct: 421 ILITPLPGATMLKPGSATRPFFGISPALVDNEGNILEGANEGNLVILDSWPGQMRGIYGD 480 Query: 481 HERFEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHP 540 +RFE+ YFSTF NMY +GDGA+RD DGYYWITGRVDDVLNVSGHR+GTAEIESALV+H Sbjct: 481 EDRFEEAYFSTFPNMYCTGDGAKRDLDGYYWITGRVDDVLNVSGHRMGTAEIESALVSHS 540 Query: 541 KIAEAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTD 600 KIAEAAVVG+PH+IKGQ IYAYVTLN GEEP L AEV+ WVR EIG +ATPD LHWT Sbjct: 541 KIAEAAVVGVPHDIKGQGIYAYVTLNAGEEPDAALLAEVKQWVRSEIGAIATPDTLHWTQ 600 Query: 601 SLPKTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646 +LPKTRSGKIMRRILRK+A DT +LGDTSTLADP VV+ L+ EKQ Sbjct: 601 ALPKTRSGKIMRRILRKVATNDTDSLGDTSTLADPSVVDTLIAEKQ 646 Lambda K H 0.317 0.135 0.421 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: 1418 Number of extensions: 42 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: 648 Length adjustment: 38 Effective length of query: 614 Effective length of database: 610 Effective search space: 374540 Effective search space used: 374540 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_017223156.1 A923_RS0118350 (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.107498.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 1011.3 0.6 0 1011.1 0.6 1.0 1 NCBI__GCF_000276805.1:WP_017223156.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000276805.1:WP_017223156.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1011.1 0.6 0 0 4 628 .. 21 643 .. 18 644 .. 0.98 Alignments for each domain: == domain 1 score: 1011.1 bits; conditional E-value: 0 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 ++y+++y+++i+dpe+fw+++++ ++w+kp+++v+++s++p ++kWf+dg+lnvs+nc+drh++++++k NCBI__GCF_000276805.1:WP_017223156.1 21 DSAYQAMYKHSITDPEAFWGEQGH-IVDWIKPYSQVKSTSFQPgsvDIKWFQDGQLNVSANCLDRHLKDNANK 92 578*********************.6****************99999************************** PP TIGR02188 74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146 +aiiwegd+++ ds+kltY++++++vc+++n+lk++G+kkgd v++Y+pm+pea+iamlac+RiGavh++vfa NCBI__GCF_000276805.1:WP_017223156.1 93 TAIIWEGDNPE-DSEKLTYQDVYEKVCQFSNALKAQGIKKGDVVCLYMPMVPEAAIAMLACTRIGAVHTIVFA 164 ********998.6************************************************************ PP TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218 Gfsaeala+Ri ++ aklvitadeg+R g++++lk+ vd al+k + +v++v+v+ rt++++a w+egrD+w NCBI__GCF_000276805.1:WP_017223156.1 165 GFSAEALADRIDNCGAKLVITADEGVRAGRITRLKDCVDTALAKPQVtTVNNVIVFARTKADIA-WHEGRDLW 236 ********************************************9988**************77.******** PP TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291 w+++v++ +++ec pe++++edplfiLYtsGstGkPkGvlhttgGyl++a++t+kyvfd++d+d+fwCtaDvG NCBI__GCF_000276805.1:WP_017223156.1 237 WHDVVKD-QPTECVPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYATMTFKYVFDHQDTDVFWCTADVG 308 ******7.***************************************************************** PP TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364 W+tGhsY+vygPLan att+lfegvp+ypd++r+ +v++k++vt++YtaPtaiRalm++g++++k +++ slr NCBI__GCF_000276805.1:WP_017223156.1 309 WITGHSYLVYGPLANAATTVLFEGVPNYPDTARMSQVVDKHQVTTLYTAPTAIRALMAKGDDAIKGTKRTSLR 381 ************************************************************************* PP TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437 ++gsvGepinpeaw+Wyy+++G+ ++pivdtwWqtetGgilitplpg at lkpgsat+P+fGi++++vd+eg NCBI__GCF_000276805.1:WP_017223156.1 382 LMGSVGEPINPEAWQWYYNTIGNASTPIVDTWWQTETGGILITPLPG-ATMLKPGSATRPFFGISPALVDNEG 453 ***********************************************.6************************ PP TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510 + +e +e g Lvi ++wP+++r+iygde+rf e+Yf++++++y tGDga+rd dGy+wi+GRvDdv+nvsGh NCBI__GCF_000276805.1:WP_017223156.1 454 NILEGANE-GNLVILDSWPGQMRGIYGDEDRFEEAYFSTFPNMYCTGDGAKRDLDGYYWITGRVDDVLNVSGH 525 ****7777.78************************************************************** PP TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583 r+gtaeiesalvsh+++aeaavvgvp++ikg+ i+a+v+l++g+e+d+ +l +e+k++vr+eig+ia+pd+++ NCBI__GCF_000276805.1:WP_017223156.1 526 RMGTAEIESALVSHSKIAEAAVVGVPHDIKGQGIYAYVTLNAGEEPDA-ALLAEVKQWVRSEIGAIATPDTLH 597 ************************************************.5*********************** PP TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 ++++lPktRsGkimRR+lrk+a+++ ++lgd+stl+dpsvv++l++ NCBI__GCF_000276805.1:WP_017223156.1 598 WTQALPKTRSGKIMRRILRKVATNDtDSLGDTSTLADPSVVDTLIA 643 *************************99***************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (648 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: 33.35 // [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