Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_007152037.1 MDG893_RS01990 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >NCBI__GCF_000170835.1:WP_007152037.1 Length = 648 Score = 963 bits (2489), Expect = 0.0 Identities = 459/642 (71%), Positives = 530/642 (82%) Query: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 M+ +YPV P+VA L + Y+ MYQQSV +P+ FW E KRLDWIKPF+ VK T++ Sbjct: 1 MTDKQVYPVSPDVAKRALLNRDQYEKMYQQSVEDPETFWAEHGKRLDWIKPFSKVKNTTY 60 Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120 D ++ IKWF DG LN + NCLDRHL +RGDQ AII+EGDDP++SRN+TYREL+EE CKF Sbjct: 61 DYDNLSIKWFEDGQLNAAANCLDRHLEKRGDQTAIIFEGDDPADSRNVTYRELYEETCKF 120 Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 AN L+ Q V +GDVVTIYMPMI E VAMLAC RIGAIHSVVFGGFSPEAL RI + KS Sbjct: 121 ANVLKDQGVKKGDVVTIYMPMIVETGVAMLACARIGAIHSVVFGGFSPEALGARIANGKS 180 Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240 + V+TADEGVR G+KIPLK NVD AL+ + + + KVIV KRT G++ W RD YE+L Sbjct: 181 RFVVTADEGVRGGRKIPLKKNVDAALSKEDGADVDKVIVVKRTGGDVPWKDGRDQSYEEL 240 Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300 MKVA + C + M AE+ LF+LYTSGSTG PKGV HTT GY++Y ++THE VFDY+ G+V Sbjct: 241 MKVASSDCPAEPMNAEDPLFMLYTSGSTGAPKGVLHTTGGYMVYTSMTHEYVFDYQDGDV 300 Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360 YWCTAD GWVTGHSYI+YGPLANGA T+LFEGVPNYPD +R+ +V+DKHKV+ILYTAPTA Sbjct: 301 YWCTADFGWVTGHSYILYGPLANGAVTVLFEGVPNYPDTSRMGQVVDKHKVNILYTAPTA 360 Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420 IRA+MA G + + G SLRLLGSVGEPINPEAW+WY++ +G +CPIVDTWWQTETGG Sbjct: 361 IRALMAEGESCMNGTTRDSLRLLGSVGEPINPEAWEWYHRVIGNSKCPIVDTWWQTETGG 420 Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480 +LISPLPGA LKPGSAT PFFGV PALVDN GN++EG EGNLVILDSWPGQ RT+YGD Sbjct: 421 ILISPLPGAIDLKPGSATVPFFGVKPALVDNDGNILEGKTEGNLVILDSWPGQMRTIYGD 480 Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 H+RF TYF T+ GMYFTGDGARRDEDGYYWITGRVDDVLNVSGHR+GTAE+ESA+VAH Sbjct: 481 HERFKQTYFSTYKGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVAHD 540 Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600 KVAEAAVVG PH+IKGQGIYVYVTL GEE S+ L+ EL WVRKEIGPIASPDVIQWAP Sbjct: 541 KVAEAAVVGYPHEIKGQGIYVYVTLVHGEEPSDELKKELVQWVRKEIGPIASPDVIQWAP 600 Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642 GLPKTRSGKIMRRILRKIA+ E+D LGD STLADPGVV LI Sbjct: 601 GLPKTRSGKIMRRILRKIASNEHDQLGDTSTLADPGVVDDLI 642 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: 1480 Number of extensions: 57 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: 648 Length adjustment: 38 Effective length of query: 613 Effective length of database: 610 Effective search space: 373930 Effective search space used: 373930 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_007152037.1 MDG893_RS01990 (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.1609341.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 1027.6 0.0 0 1027.4 0.0 1.0 1 NCBI__GCF_000170835.1:WP_007152037.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000170835.1:WP_007152037.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1027.4 0.0 0 0 3 627 .. 20 642 .. 18 644 .. 0.98 Alignments for each domain: == domain 1 score: 1027.4 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkd 72 + ++y+++y++++edpe+fwa+++k +l+w+kpf+kv++++ + ++kWfedg+ln+++nc+drh+ekr d NCBI__GCF_000170835.1:WP_007152037.1 20 NRDQYEKMYQQSVEDPETFWAEHGK-RLDWIKPFSKVKNTTYDYdnlSIKWFEDGQLNAAANCLDRHLEKRGD 91 679**********************.5***********9987665589************************* PP TIGR02188 73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvf 145 ++aii+egd++ dsr++tY+el++e+c++anvlk++Gvkkgd v+iY+pmi+e+ +amlacaRiGa+hsvvf NCBI__GCF_000170835.1:WP_007152037.1 92 QTAIIFEGDDPA-DSRNVTYRELYEETCKFANVLKDQGVKKGDVVTIYMPMIVETGVAMLACARIGAIHSVVF 163 ***********9.5*********************************************************** PP TIGR02188 146 aGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDv 217 +Gfs+eal Ri + ++++v+tadeg+Rgg++i+lkk+vd+al+k++ +v+kv+vvkrtg +v wk+grD NCBI__GCF_000170835.1:WP_007152037.1 164 GGFSPEALGARIANGKSRFVVTADEGVRGGRKIPLKKNVDAALSKEDGaDVDKVIVVKRTGGDVP-WKDGRDQ 235 ********************************************99988**************66.******* PP TIGR02188 218 wweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDv 290 +eel++ as++c++e++++edplf+LYtsGstG PkGvlhttgGy++++++t++yvfd++d+d++wCtaD NCBI__GCF_000170835.1:WP_007152037.1 236 SYEELMKV-ASSDCPAEPMNAEDPLFMLYTSGSTGAPKGVLHTTGGYMVYTSMTHEYVFDYQDGDVYWCTADF 307 *******5.**************************************************************** PP TIGR02188 291 GWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlssl 363 GWvtGhsYi+ygPLanGa t+lfegvp+ypd+sr+ +v++k+kv+i+YtaPtaiRalm++ge+ ++ + ++sl NCBI__GCF_000170835.1:WP_007152037.1 308 GWVTGHSYILYGPLANGAVTVLFEGVPNYPDTSRMGQVVDKHKVNILYTAPTAIRALMAEGESCMNGTTRDSL 380 ************************************************************************* PP TIGR02188 364 rvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdee 436 r+lgsvGepinpeaweWy++v+G++kcpivdtwWqtetGgili+plpg a++lkpgsat+P+fG+++++vd++ NCBI__GCF_000170835.1:WP_007152037.1 381 RLLGSVGEPINPEAWEWYHRVIGNSKCPIVDTWWQTETGGILISPLPG-AIDLKPGSATVPFFGVKPALVDND 452 ************************************************.6*********************** PP TIGR02188 437 gkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsG 509 g+ +e ++e g Lvi ++wP+++rtiygd+erf +tYf+++kg+yftGDgarrd+dGy+wi+GRvDdv+nvsG NCBI__GCF_000170835.1:WP_007152037.1 453 GNILEGKTE-GNLVILDSWPGQMRTIYGDHERFKQTYFSTYKGMYFTGDGARRDEDGYYWITGRVDDVLNVSG 524 *****8777.79************************************************************* PP TIGR02188 510 hrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdki 582 hrlgtae+esalv+h++vaeaavvg+p+eikg+ i+++v+l +g+e+++e l+kel ++vrkeigpia+pd i NCBI__GCF_000170835.1:WP_007152037.1 525 HRLGTAEVESALVAHDKVAEAAVVGYPHEIKGQGIYVYVTLVHGEEPSDE-LKKELVQWVRKEIGPIASPDVI 596 *************************************************5.********************** PP TIGR02188 583 lvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627 ++++ lPktRsGkimRR+lrkia++e ++lgd+stl+dp vv++l+ NCBI__GCF_000170835.1:WP_007152037.1 597 QWAPGLPKTRSGKIMRRILRKIASNEhDQLGDTSTLADPGVVDDLI 642 **************************9****************987 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: 21.23 // [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