Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_010961287.1 MCA_RS10000 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >NCBI__GCF_000008325.1:WP_010961287.1 Length = 662 Score = 837 bits (2161), Expect = 0.0 Identities = 402/643 (62%), Positives = 490/643 (76%), Gaps = 5/643 (0%) Query: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTS 59 M +YPV ++A S + Y+ MY +S+ +P+GFW E A+ + W P+ V + + Sbjct: 19 MKTEHVYPVPSDIATSARITDEIYREMYDRSIRDPEGFWAELAQEFISWNTPWQRVARWN 78 Query: 60 FDDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCK 119 F H I+WF+ LNVSYNCLDRHLA+R DQ AI+WEGD+P + R +TY ELH+ VC+ Sbjct: 79 F--HTPSIEWFSGARLNVSYNCLDRHLADRRDQTAILWEGDEPGDQRALTYGELHDRVCR 136 Query: 120 FANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCK 179 FAN L+ V +GD V IY+PMIPEA VAMLAC RIGAIHS+VFGGFS EAL RI+D Sbjct: 137 FANVLKSHGVGKGDRVCIYLPMIPEAAVAMLACARIGAIHSIVFGGFSSEALKDRILDAD 196 Query: 180 SKVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYED 239 +V+I ADEG R GK +PLK NVD AL+ + ++ V+V + T + W RD W+ + Sbjct: 197 CRVLICADEGRRGGKFVPLKRNVDAALS--QCPHVETVLVVRHTGRPVDWTAGRDHWFHE 254 Query: 240 LMKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGE 299 ++ A C P++M AE+ LFILYTSGSTGKPKGV HTT GYLL+AA+TH+ VFDY+ GE Sbjct: 255 AVQSASADCPPEDMDAEDPLFILYTSGSTGKPKGVVHTTGGYLLFAAVTHKYVFDYRDGE 314 Query: 300 VYWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPT 359 VYWCTAD+GW+TGHSY+V+GPL NGATTL+FEGVP YP R+ ++IDK++VSI YTAPT Sbjct: 315 VYWCTADIGWITGHSYVVFGPLCNGATTLMFEGVPTYPTPARLWQIIDKYQVSIFYTAPT 374 Query: 360 AIRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETG 419 IRA+M G V+ AD SLR+LGSVGEPINPEAW+WYY+ VG++RCP++DTWWQTETG Sbjct: 375 VIRALMGLGADWVKQADRHSLRILGSVGEPINPEAWEWYYQEVGEKRCPVLDTWWQTETG 434 Query: 420 GVLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYG 479 G++I+PLPGAT LKPGSATRPFFGVVP ++D GN + G AEG L I SWPGQART++ Sbjct: 435 GIMITPLPGATPLKPGSATRPFFGVVPVILDPQGNELTGPAEGVLAIAASWPGQARTVFR 494 Query: 480 DHDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAH 539 +HDRF +TYF + G YFTGDGARRD DGYYWITGRVDDV+NVSGHRMGTAEIESA+V H Sbjct: 495 NHDRFRETYFALYPGKYFTGDGARRDADGYYWITGRVDDVINVSGHRMGTAEIESALVLH 554 Query: 540 PKVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWA 599 VAEAAVVG PH+IKGQGIY YVTL A SE L+ +L VR+EIG IA+PD+IQW Sbjct: 555 DSVAEAAVVGYPHNIKGQGIYAYVTLVADAVPSEDLKRQLIELVREEIGAIATPDIIQWT 614 Query: 600 PGLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642 P LPKTRSGKIMRRILRKIA E D LGD STLADP VV +I Sbjct: 615 PALPKTRSGKIMRRILRKIAANELDQLGDTSTLADPAVVEDII 657 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: 1388 Number of extensions: 69 Number of successful extensions: 3 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: 662 Length adjustment: 38 Effective length of query: 613 Effective length of database: 624 Effective search space: 382512 Effective search space used: 382512 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_010961287.1 MCA_RS10000 (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.1854.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 1030.1 0.0 0 1029.8 0.0 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010961287.1 MCA_RS10000 acetate--CoA ligase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008325.1:WP_010961287.1 MCA_RS10000 acetate--CoA ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1029.8 0.0 0 0 5 628 .. 40 658 .. 36 659 .. 0.99 Alignments for each domain: == domain 1 score: 1029.8 bits; conditional E-value: 0 TIGR02188 5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkd 72 e y+e+y+++i+dpe fwa+la+e ++w +p+++v ++++++ +++Wf++++lnvsync+drh+++r+d lcl|NCBI__GCF_000008325.1:WP_010961287.1 40 EIYREMYDRSIRDPEGFWAELAQEFISWNTPWQRVARWNFHTpSIEWFSGARLNVSYNCLDRHLADRRD 108 679*************************************988************************** PP TIGR02188 73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavh 141 ++ai wegde+g+ +r+ltY el+++vcr+anvlk++Gv kgdrv+iYlpmipea++amlacaRiGa+h lcl|NCBI__GCF_000008325.1:WP_010961287.1 109 QTAILWEGDEPGD-QRALTYGELHDRVCRFANVLKSHGVGKGDRVCIYLPMIPEAAVAMLACARIGAIH 176 ***********95.******************************************************* PP TIGR02188 142 svvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevae 210 s+vf+Gfs+eal++Ri da+++++i+adeg Rggk ++lk++vd+al++++ +ve+vlvv++tg++v lcl|NCBI__GCF_000008325.1:WP_010961287.1 177 SIVFGGFSSEALKDRILDADCRVLICADEGRRGGKFVPLKRNVDAALSQCP-HVETVLVVRHTGRPVD- 243 **************************************************9.7*************66. PP TIGR02188 211 wkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik 279 w+ grD+w++e+v++ asa+c+pe++d+edplfiLYtsGstGkPkGv+httgGyll aa+t+kyvfd++ lcl|NCBI__GCF_000008325.1:WP_010961287.1 244 WTAGRDHWFHEAVQS-ASADCPPEDMDAEDPLFILYTSGSTGKPKGVVHTTGGYLLFAAVTHKYVFDYR 311 **************6.***************************************************** PP TIGR02188 280 dedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalm 348 d++++wCtaD+GW+tGhsY+v+gPL+nGattl+fegvptyp+++r+w++i+ky+v+ifYtaPt+iRalm lcl|NCBI__GCF_000008325.1:WP_010961287.1 312 DGEVYWCTADIGWITGHSYVVFGPLCNGATTLMFEGVPTYPTPARLWQIIDKYQVSIFYTAPTVIRALM 380 ********************************************************************* PP TIGR02188 349 klgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelk 417 lg ++vk+ d++slr+lgsvGepinpeaweWyy++vG+++cp+ dtwWqtetGgi+itplpg at+lk lcl|NCBI__GCF_000008325.1:WP_010961287.1 381 GLGADWVKQADRHSLRILGSVGEPINPEAWEWYYQEVGEKRCPVLDTWWQTETGGIMITPLPG-ATPLK 448 ***************************************************************.6**** PP TIGR02188 418 pgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDg 486 pgsat+P+fG+ ++++d +g+e++ +e gvL+i +wP+++rt++++++rf etYf ++g yftGDg lcl|NCBI__GCF_000008325.1:WP_010961287.1 449 PGSATRPFFGVVPVILDPQGNELTGPAE-GVLAIAASWPGQARTVFRNHDRFRETYFALYPGKYFTGDG 516 ************************8888.8*************************************** PP TIGR02188 487 arrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegve 555 arrd+dGy+wi+GRvDdvinvsGhr+gtaeiesalv h++vaeaavvg+p++ikg+ i+a+v+l + + lcl|NCBI__GCF_000008325.1:WP_010961287.1 517 ARRDADGYYWITGRVDDVINVSGHRMGTAEIESALVLHDSVAEAAVVGYPHNIKGQGIYAYVTLVADAV 585 ********************************************************************* PP TIGR02188 556 edeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvv 623 ++e+ l+++l++lvr+eig+ia+pd i+++++lPktRsGkimRR+lrkia++e ++lgd+stl+dp+vv lcl|NCBI__GCF_000008325.1:WP_010961287.1 586 PSED-LKRQLIELVREEIGAIATPDIIQWTPALPKTRSGKIMRRILRKIAANElDQLGDTSTLADPAVV 653 9995.**************************************************************** PP TIGR02188 624 eelke 628 e++++ lcl|NCBI__GCF_000008325.1:WP_010961287.1 654 EDIIR 658 *9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (662 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 8.16 // [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