Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_079651030.1 B5X82_RS24705 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >NCBI__GCF_900167915.1:WP_079651030.1 Length = 499 Score = 629 bits (1623), Expect = 0.0 Identities = 300/500 (60%), Positives = 373/500 (74%), Gaps = 3/500 (0%) Query: 3 AASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDD 62 A +LYPV AA + A A + S+ +P+ +W ++A RLDW + T ++SFD+ Sbjct: 2 ADNLYPVPASWAAKSRMTAAERAADHGFSLASPERYWLDRAGRLDWFRFPTKADESSFDE 61 Query: 63 HHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSES-RNITYRELHEEVCKFA 121 +KWFADG LNVS NC+DRHLAE GDQ+AI+WE DDP+E+ R TY +LHEEVC+ A Sbjct: 62 ADFQVKWFADGELNVSVNCIDRHLAEHGDQVAIVWEPDDPAEAPRRFTYAQLHEEVCRLA 121 Query: 122 NALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSK 181 N L+ V +G VTIY+PMIPEA A+LAC RIGAIHSVVFGGFSP+ALAGRI DC S Sbjct: 122 NVLKAHGVKKGHRVTIYLPMIPEAAFALLACARIGAIHSVVFGGFSPDALAGRIQDCDSS 181 Query: 182 VVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLM 241 VVITAD G R GK +PLKANVD+AL + +S++ V+V + T G ++ RD+W ++ + Sbjct: 182 VVITADHGRRGGKLVPLKANVDEALK--QCTSVETVVVVRATDGAVEMVPGRDVWLDEAI 239 Query: 242 KVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVY 301 + C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL+A+LTHE FDY+ G+V+ Sbjct: 240 RHVAADCPPERMNAEDPLFILYTSGSTGKPKGVVHTTGGYLLWASLTHELCFDYRRGDVF 299 Query: 302 WCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAI 361 WC+AD+GWVTGHSYIVYGPLANGATTL++EGVPN+P +R+ +V+D+H V L+TAPTA+ Sbjct: 300 WCSADIGWVTGHSYIVYGPLANGATTLIYEGVPNWPSPSRMWEVVDRHGVHTLFTAPTAL 359 Query: 362 RAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGV 421 RA+M G V G SLRLLG+VGEPINPEAW WY++ VG+ RCPI+DTWWQTETG Sbjct: 360 RALMREGDDFVAGTSRKSLRLLGTVGEPINPEAWRWYHEVVGEGRCPIIDTWWQTETGAA 419 Query: 422 LISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDH 481 +I+P+PGATALKPGSAT P GV P LVD G +EG EGNL I SWPGQ RT++GDH Sbjct: 420 MIAPMPGATALKPGSATLPMPGVAPELVDAEGRPVEGTGEGNLCIARSWPGQMRTVWGDH 479 Query: 482 DRFVDTYFKTFSGMYFTGDG 501 RF TYF T+ G YFTGDG Sbjct: 480 ARFFQTYFSTYPGKYFTGDG 499 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: 1088 Number of extensions: 54 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: 499 Length adjustment: 36 Effective length of query: 615 Effective length of database: 463 Effective search space: 284745 Effective search space used: 284745 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: 53 (25.0 bits)
Align candidate WP_079651030.1 B5X82_RS24705 (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.2980803.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-226 736.9 0.0 1e-225 736.7 0.0 1.0 1 NCBI__GCF_900167915.1:WP_079651030.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900167915.1:WP_079651030.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 736.7 0.0 1e-225 1e-225 13 486 .. 29 499 .] 18 499 .] 0.97 Alignments for each domain: == domain 1 score: 736.7 bits; conditional E-value: 1e-225 TIGR02188 13 eaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvaiiwegde 82 + ++pe++w + a +l+w++ +k ++s+++ +vkWf+dgelnvs+nc+drh++++ d+vai+we d+ NCBI__GCF_900167915.1:WP_079651030.1 29 FSLASPERYWLDRAG-RLDWFRFPTKADESSFDEadfQVKWFADGELNVSVNCIDRHLAEHGDQVAIVWEPDD 100 567889********9.5**********99999887889*********************************** PP TIGR02188 83 egedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealae 155 + e r++tYa+l++evcrlanvlk++Gvkkg rv+iYlpmipea++a+lacaRiGa+hsvvf+Gfs++ala NCBI__GCF_900167915.1:WP_079651030.1 101 PAEAPRRFTYAQLHEEVCRLANVLKAHGVKKGHRVTIYLPMIPEAAFALLACARIGAIHSVVFGGFSPDALAG 173 ************************************************************************* PP TIGR02188 156 RivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvekeas 228 Ri+d+++ +vitad+g Rggk ++lk++vdeal++++ sve+v+vv+ t+ v+ ++ grDvw++e++++ + NCBI__GCF_900167915.1:WP_079651030.1 174 RIQDCDSSVVITADHGRRGGKLVPLKANVDEALKQCT-SVETVVVVRATDGAVE-MVPGRDVWLDEAIRH-VA 243 ************************************8.8*************66.**************6.** PP TIGR02188 229 aecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivy 301 a+c+pe++++edplfiLYtsGstGkPkGv+httgGyll+a+lt+++ fd++ +d+fwC+aD+GWvtGhsYivy NCBI__GCF_900167915.1:WP_079651030.1 244 ADCPPERMNAEDPLFILYTSGSTGKPKGVVHTTGGYLLWASLTHELCFDYRRGDVFWCSADIGWVTGHSYIVY 316 ************************************************************************* PP TIGR02188 302 gPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepin 374 gPLanGattl++egvp++p++sr+wev+++++v +++taPta+Ralm++g+++v+ ++++slr+lg+vGepin NCBI__GCF_900167915.1:WP_079651030.1 317 GPLANGATTLIYEGVPNWPSPSRMWEVVDRHGVHTLFTAPTALRALMREGDDFVAGTSRKSLRLLGTVGEPIN 389 ************************************************************************* PP TIGR02188 375 peaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeegg 447 peaw+Wy+evvG+++cpi+dtwWqtetG+++i+p+pg at+lkpgsatlP++G+ +e+vd eg++ve + e g NCBI__GCF_900167915.1:WP_079651030.1 390 PEAWRWYHEVVGEGRCPIIDTWWQTETGAAMIAPMPG-ATALKPGSATLPMPGVAPELVDAEGRPVEGTGE-G 460 *************************************.6****************************7666.7 PP TIGR02188 448 vLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDg 486 L+i ++wP+++rt++gd+ rf++tYf++++g yftGDg NCBI__GCF_900167915.1:WP_079651030.1 461 NLCIARSWPGQMRTVWGDHARFFQTYFSTYPGKYFTGDG 499 8*************************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (499 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 30.66 // [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