Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_046010587.1 OLEAN_RS19275 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >NCBI__GCF_000967895.1:WP_046010587.1 Length = 656 Score = 892 bits (2304), Expect = 0.0 Identities = 424/656 (64%), Positives = 504/656 (76%), Gaps = 5/656 (0%) Query: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 MS ++YPV P L + Y+ MYQ S+ +PD FW +QA+RL WI PFT VK SF Sbjct: 1 MSEQTVYPVSPAQREKALLTKEQYQVMYQHSLESPDEFWAQQAQRLTWITPFTKVKNVSF 60 Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGD-----DPSESRNITYRELHE 115 D + I+WF DG LNVS NC+DRHL ERG + AI+WE D + E+R ITY++L Sbjct: 61 DKQDLHIRWFEDGFLNVSENCIDRHLVERGHETAILWEPDGENVGEKDEARRITYQQLSS 120 Query: 116 EVCKFANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRI 175 EV + AN L+ + +GD+VT+Y+PM+PEA +AMLAC RIGA+HSVVF GFSPEALAGRI Sbjct: 121 EVNRLANGLKSLGIKKGDIVTLYLPMVPEATMAMLACARIGAVHSVVFAGFSPEALAGRI 180 Query: 176 IDCKSKVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDI 235 D + VITADEG+R GK +PLK NVD+A+ + VIV T G + RDI Sbjct: 181 EDGDCRYVITADEGLRGGKHVPLKQNVDEAIALCPAEQVNNVIVLNHTGGEVNHQVGRDI 240 Query: 236 WYEDLMKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDY 295 Y DL+ VC P+ M AE+ LFILYTSGSTGKPKGV HTT GYLLYA++THE VFDY Sbjct: 241 DYHDLISQQSDVCPPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLLYASMTHEYVFDY 300 Query: 296 KPGEVYWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILY 355 +PG++YWC ADVGW+TGHSYIVYGPL NGAT ++FEG+P YPDI R A++I+K+K++ILY Sbjct: 301 RPGDIYWCAADVGWITGHSYIVYGPLCNGATVVMFEGIPTYPDIGRAARLIEKYKINILY 360 Query: 356 TAPTAIRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQ 415 APTAIR++MA+G AA + +D SSLRLLG+VGEPINP+ W WY++ G+ CPIVDTWWQ Sbjct: 361 VAPTAIRSLMAAGDAATKNSDLSSLRLLGTVGEPINPDVWRWYHQAFGRGECPIVDTWWQ 420 Query: 416 TETGGVLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQAR 475 TETG +I+PLPGAT LKPGSAT P FGV PALVD G + GA GNL+I DSWPGQ R Sbjct: 421 TETGAAMIAPLPGATDLKPGSATLPMFGVQPALVDEKGIELHGATHGNLIIKDSWPGQMR 480 Query: 476 TLYGDHDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESA 535 +++GDH RF+DTYF T+ G YFTGDGARRDEDGYYW+TGRVDDVLNVSGHRMGTAEIE+A Sbjct: 481 SVFGDHQRFIDTYFSTYEGSYFTGDGARRDEDGYYWLTGRVDDVLNVSGHRMGTAEIENA 540 Query: 536 MVAHPKVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDV 595 +VAH V EAAVVGVPHDIKG+GIYVYVTL G E SEALRLEL WVRKEIGPIA+PD+ Sbjct: 541 LVAHDSVTEAAVVGVPHDIKGEGIYVYVTLGHGFEESEALRLELIKWVRKEIGPIATPDL 600 Query: 596 IQWAPGLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651 IQWAP LPKTRSGKIMRRILRKIAT E+D +GD STLADP VV LI H M+ A Sbjct: 601 IQWAPALPKTRSGKIMRRILRKIATNEFDSIGDTSTLADPSVVDDLIVVHNKMHAA 656 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: 1400 Number of extensions: 63 Number of successful extensions: 2 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: 656 Length adjustment: 38 Effective length of query: 613 Effective length of database: 618 Effective search space: 378834 Effective search space used: 378834 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_046010587.1 OLEAN_RS19275 (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.3696019.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-302 989.4 0.0 3.6e-302 989.2 0.0 1.0 1 NCBI__GCF_000967895.1:WP_046010587.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000967895.1:WP_046010587.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 989.2 0.0 3.6e-302 3.6e-302 4 627 .. 21 647 .. 18 649 .. 0.98 Alignments for each domain: == domain 1 score: 989.2 bits; conditional E-value: 3.6e-302 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 e+y+ +y+++ e+p++fwa++a+ +l+w++pf+kv++ s+++ +++Wfedg lnvs nc+drh+ +r ++ NCBI__GCF_000967895.1:WP_046010587.1 21 KEQYQVMYQHSLESPDEFWAQQAQ-RLTWITPFTKVKNVSFDKqdlHIRWFEDGFLNVSENCIDRHLVERGHE 92 789*********************.5*************99887789************************** PP TIGR02188 74 vaiiwegd....eegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhs 142 +ai we d e++++r++tY++l +ev+rlan lk+lG+kkgd v++Ylpm+pea++amlacaRiGavhs NCBI__GCF_000967895.1:WP_046010587.1 93 TAILWEPDgenvGEKDEARRITYQQLSSEVNRLANGLKSLGIKKGDIVTLYLPMVPEATMAMLACARIGAVHS 165 ******997654233489******************************************************* PP TIGR02188 143 vvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkeg 214 vvfaGfs+eala Ri+d ++++vitadeglRggk+++lk++vdea++ +++ +v++v+v+++tg ev+ + g NCBI__GCF_000967895.1:WP_046010587.1 166 VVFAGFSPEALAGRIEDGDCRYVITADEGLRGGKHVPLKQNVDEAIALCPAeQVNNVIVLNHTGGEVN-HQVG 237 *************************************************999**************66.999* PP TIGR02188 215 rDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCt 287 rD+ +++l+++ +s+ c+pe++++edplfiLYtsGstGkPkGvlhttgGyll+a++t++yvfd++++di+wC+ NCBI__GCF_000967895.1:WP_046010587.1 238 RDIDYHDLISQ-QSDVCPPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLLYASMTHEYVFDYRPGDIYWCA 309 **********6.************************************************************* PP TIGR02188 288 aDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdl 360 aDvGW+tGhsYivygPL+nGat ++feg+ptypd +r +++iekyk++i+Y+aPtaiR+lm++g++++k+ dl NCBI__GCF_000967895.1:WP_046010587.1 310 ADVGWITGHSYIVYGPLCNGATVVMFEGIPTYPDIGRAARLIEKYKINILYVAPTAIRSLMAAGDAATKNSDL 382 ************************************************************************* PP TIGR02188 361 sslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevv 433 sslr+lg+vGepinp+ w+Wy++ +G+++cpivdtwWqtetG+++i+plpg at+lkpgsatlP+fG+++++v NCBI__GCF_000967895.1:WP_046010587.1 383 SSLRLLGTVGEPINPDVWRWYHQAFGRGECPIVDTWWQTETGAAMIAPLPG-ATDLKPGSATLPMFGVQPALV 454 ***************************************************.6******************** PP TIGR02188 434 deegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvin 506 de+g e++ ++ g L+ik++wP+++r+++gd++rf++tYf++++g yftGDgarrd+dGy+w++GRvDdv+n NCBI__GCF_000967895.1:WP_046010587.1 455 DEKGIELHGATH-GNLIIKDSWPGQMRSVFGDHQRFIDTYFSTYEGSYFTGDGARRDEDGYYWLTGRVDDVLN 526 *******97777.79********************************************************** PP TIGR02188 507 vsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakp 579 vsGhr+gtaeie+alv+h++v+eaavvgvp++ikge i+++v+l +g ee+e +l+ el+k+vrkeigpia+p NCBI__GCF_000967895.1:WP_046010587.1 527 VSGHRMGTAEIENALVAHDSVTEAAVVGVPHDIKGEGIYVYVTLGHGFEESE-ALRLELIKWVRKEIGPIATP 598 *************************************************999.6******************* PP TIGR02188 580 dkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627 d i+++++lPktRsGkimRR+lrkia++e +++gd+stl+dpsvv++l+ NCBI__GCF_000967895.1:WP_046010587.1 599 DLIQWAPALPKTRSGKIMRRILRKIATNEfDSIGDTSTLADPSVVDDLI 647 *********************************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (656 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: 00:00:00.01 # Mc/sec: 28.59 // [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