Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate RR42_RS35915 RR42_RS35915 beta-ketoadipyl CoA thiolase
Query= uniprot:B2SYZ2 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS35915 Length = 400 Score = 629 bits (1623), Expect = 0.0 Identities = 311/400 (77%), Positives = 352/400 (88%) Query: 1 MNDAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQA 60 M +AFICDAIRTPIGRY G+L VR DDLGAVP+KAL+ RNP +DW +DDVIYG ANQA Sbjct: 1 MTEAFICDAIRTPIGRYAGSLSGVRPDDLGAVPLKALMARNPNLDWSAIDDVIYGNANQA 60 Query: 61 GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120 GEDNRNVARMS LLAGLP PG+TINRLCGSGMDA GTAARAIK+GEA LM+AGGVESM Sbjct: 61 GEDNRNVARMSLLLAGLPQSVPGATINRLCGSGMDATGTAARAIKSGEAGLMLAGGVESM 120 Query: 121 TRAPFVMGKATSAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRAD 180 +RAPFVMGKATSAF+R A I+DTTIGWRFINP M+ YGVDSMPETAENVA ++ +SR D Sbjct: 121 SRAPFVMGKATSAFSRDAQIFDTTIGWRFINPAMRAAYGVDSMPETAENVATDYKISRED 180 Query: 181 QDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPRETSLESLGKLKGV 240 QD AL SQ+KA+RAQ DGTLAQEI V IAQKKGDP+ DEHPR TS+E+LGKL+GV Sbjct: 181 QDLMALRSQEKASRAQADGTLAQEITAVTIAQKKGDPLVVERDEHPRATSMEALGKLRGV 240 Query: 241 VRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPAP 300 VR DG+VTAGNASGVNDGACA+LLA++ AA Q+GL +AR+VGMATAGV PR+MGIGPAP Sbjct: 241 VRADGTVTAGNASGVNDGACAILLASEAAARQHGLTPKARIVGMATAGVAPRVMGIGPAP 300 Query: 301 ATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLGA 360 A+QKLLKQLGMT++Q+DVIELNEAFA+QGLAVLR LG+ DDD RVNPNGGAIALGHPLG Sbjct: 301 ASQKLLKQLGMTIDQMDVIELNEAFAAQGLAVLRELGVADDDARVNPNGGAIALGHPLGM 360 Query: 361 SGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400 SGARL+TTA+YQL RT GR+ALCTMCIGVGQGIA+VIER+ Sbjct: 361 SGARLVTTAMYQLHRTGGRYALCTMCIGVGQGIAMVIERV 400 Lambda K H 0.318 0.135 0.386 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: 588 Number of extensions: 17 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: 400 Length of database: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 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: 50 (23.9 bits)
Align candidate RR42_RS35915 RR42_RS35915 (beta-ketoadipyl CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))
# 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/TIGR02430.hmm # target sequence database: /tmp/gapView.6604.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02430 [M=400] Accession: TIGR02430 Description: pcaF: 3-oxoadipyl-CoA thiolase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-223 726.4 13.2 5.2e-223 726.2 13.2 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS35915 RR42_RS35915 beta-ketoadipyl CoA Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS35915 RR42_RS35915 beta-ketoadipyl CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 726.2 13.2 5.2e-223 5.2e-223 2 400 .] 3 400 .] 2 400 .] 1.00 Alignments for each domain: == domain 1 score: 726.2 bits; conditional E-value: 5.2e-223 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarma 70 e++i+dairtpiGry+Gsls vr ddl+avplkal+arnp+ld++aiddvi+G anqaGednrnvarm+ lcl|FitnessBrowser__Cup4G11:RR42_RS35915 3 EAFICDAIRTPIGRYAGSLSGVRPDDLGAVPLKALMARNPNLDWSAIDDVIYGNANQAGEDNRNVARMS 71 89******************************************************************* PP TIGR02430 71 allaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakl 139 +llaGlp+svpg+t+nrlcgsg+da g+aaraik+Gea l++aGGvesmsrapfv+Gka safsr+a++ lcl|FitnessBrowser__Cup4G11:RR42_RS35915 72 LLLAGLPQSVPGATINRLCGSGMDATGTAARAIKSGEAGLMLAGGVESMSRAPFVMGKATSAFSRDAQI 140 ********************************************************************* PP TIGR02430 140 edttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpve 208 +dttiGwrf+np+++a yGvdsmpetaenva+++++sredqd +alrsq+++++aqa G +a+ei+ v+ lcl|FitnessBrowser__Cup4G11:RR42_RS35915 141 FDTTIGWRFINPAMRAAYGVDSMPETAENVATDYKISREDQDLMALRSQEKASRAQADGTLAQEITAVT 209 ********************************************************************* PP TIGR02430 209 ikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltp 277 i+qkkG++ vv++deh+r t++eal kl++vvr+dgtvtaGnasGvndGa+a+llase a+++hgltp lcl|FitnessBrowser__Cup4G11:RR42_RS35915 210 IAQKKGDPLVVERDEHPR-ATSMEALGKLRGVVRADGTVTAGNASGVNDGACAILLASEAAARQHGLTP 277 ******************.8************************************************* PP TIGR02430 278 rarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvn 346 +ari+++a+aGv+prvmG+gp+pa +kll+++g++++++dvielneafaaq+lavlrelg+adddarvn lcl|FitnessBrowser__Cup4G11:RR42_RS35915 278 KARIVGMATAGVAPRVMGIGPAPASQKLLKQLGMTIDQMDVIELNEAFAAQGLAVLRELGVADDDARVN 346 ********************************************************************* PP TIGR02430 347 pnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400 pnGGaialGhplG+sGarlv+ta++ql+++ggryal+t+ciGvGqGia+vierv lcl|FitnessBrowser__Cup4G11:RR42_RS35915 347 PNGGAIALGHPLGMSGARLVTTAMYQLHRTGGRYALCTMCIGVGQGIAMVIERV 400 *****************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (400 nodes) Target sequences: 1 (400 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: 11.67 // [ok]
This GapMind analysis is from Sep 17 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