Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_065401082.1 BBI00_RS22490 3-oxoadipyl-CoA thiolase
Query= uniprot:B2SYZ2 (400 letters) >NCBI__GCF_001684965.1:WP_065401082.1 Length = 401 Score = 494 bits (1271), Expect = e-144 Identities = 245/401 (61%), Positives = 311/401 (77%), Gaps = 1/401 (0%) Query: 1 MNDAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQA 60 MN+ +I D +RTPI + G L +VRADDL A+ IK ++ RNP V ++DVI+GCANQA Sbjct: 1 MNNVYIIDYVRTPISKLQGGLSEVRADDLAAIVIKEVVARNPEVPVEEIEDVIFGCANQA 60 Query: 61 GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120 GEDNRNVARM LLAGLP + G T+NRLC SGM AV A R+I +GE + IAGGVE M Sbjct: 61 GEDNRNVARMGLLLAGLPYKIGGETVNRLCASGMSAVANAFRSIASGEGEIYIAGGVEHM 120 Query: 121 TRAPFVMGKATSAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRAD 180 TR+P+VM K +AF R + ++DTT GWRFINP MK YGVD M ETAEN+A +SR D Sbjct: 121 TRSPYVMSKPGAAFGRDSQMFDTTFGWRFINPKMKEMYGVDGMGETAENLADMHHISRED 180 Query: 181 QDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPRE-TSLESLGKLKG 239 QD FAL SQQKA +AQ+ G LA+EIV VEI Q+KG+PV DE + +S+E LGKL+ Sbjct: 181 QDKFALWSQQKATKAQESGRLAEEIVKVEIPQRKGEPVIFEKDEFIKPGSSMEGLGKLRP 240 Query: 240 VVRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPA 299 R +G+VTAGNASG+NDGA AL+LA+++A +YGL+ +AR++G + AGVEPRIMGIGP Sbjct: 241 AFRKEGTVTAGNASGMNDGAAALILASEEAVKKYGLKPKARILGSSVAGVEPRIMGIGPV 300 Query: 300 PATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLG 359 ATQKLLK+L ++LE +D+IELNEAFA+Q LAV RTLGL+DDD R+NPNGGAIA+GHPLG Sbjct: 301 EATQKLLKRLDLSLEDMDIIELNEAFAAQALAVTRTLGLKDDDSRINPNGGAIAIGHPLG 360 Query: 360 ASGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400 SGAR+I +A +L++ N ++ALCT+CIGVGQG A+VIE++ Sbjct: 361 VSGARIIGSAAMELQKQNKKYALCTLCIGVGQGYAMVIEKV 401 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: 478 Number of extensions: 18 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: 400 Length of database: 401 Length adjustment: 31 Effective length of query: 369 Effective length of database: 370 Effective search space: 136530 Effective search space used: 136530 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 WP_065401082.1 BBI00_RS22490 (3-oxoadipyl-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.3032045.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-198 644.2 1.5 4.6e-198 644.1 1.5 1.0 1 NCBI__GCF_001684965.1:WP_065401082.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001684965.1:WP_065401082.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 644.1 1.5 4.6e-198 4.6e-198 2 400 .] 3 401 .] 2 401 .] 1.00 Alignments for each domain: == domain 1 score: 644.1 bits; conditional E-value: 4.6e-198 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 +vyi+d +rtpi + G+ls+vraddlaa+ +k+++arnp++ ++ i+dvi+GcanqaGednrnvarm +lla NCBI__GCF_001684965.1:WP_065401082.1 3 NVYIIDYVRTPISKLQGGLSEVRADDLAAIVIKEVVARNPEVPVEEIEDVIFGCANQAGEDNRNVARMGLLLA 75 89*********************************************************************** PP TIGR02430 75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147 Glp ++ g tvnrlc+sg+ a++ a+r+i++Ge ++ iaGGve m+r+p+v+ k +af+r+ +++dtt+Gwr NCBI__GCF_001684965.1:WP_065401082.1 76 GLPYKIGGETVNRLCASGMSAVANAFRSIASGEGEIYIAGGVEHMTRSPYVMSKPGAAFGRDSQMFDTTFGWR 148 ************************************************************************* PP TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220 f+npk+k++yGvd m+etaen+a+ + +sredqd+fal sqq++++aq++G +aeeiv+vei+q+kGe+++++ NCBI__GCF_001684965.1:WP_065401082.1 149 FINPKMKEMYGVDGMGETAENLADMHHISREDQDKFALWSQQKATKAQESGRLAEEIVKVEIPQRKGEPVIFE 221 ************************************************************************* PP TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293 kde ++ +++e+l kl++ +r++gtvtaGnasG+ndGaaal+laseeavk++gl+p+aril+++ aGvepr+ NCBI__GCF_001684965.1:WP_065401082.1 222 KDEFIKPGSSMEGLGKLRPAFRKEGTVTAGNASGMNDGAAALILASEEAVKKYGLKPKARILGSSVAGVEPRI 294 ************************************************************************* PP TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366 mG+gpv a++kll+r++lsled+d+ielneafaaqalav+r lgl+ddd+r+npnGGaia+GhplG+sGar++ NCBI__GCF_001684965.1:WP_065401082.1 295 MGIGPVEATQKLLKRLDLSLEDMDIIELNEAFAAQALAVTRTLGLKDDDSRINPNGGAIAIGHPLGVSGARII 367 ************************************************************************* PP TIGR02430 367 ltalkqleksggryalatlciGvGqGialvierv 400 +a +l+k++++yal+tlciGvGqG a+vie+v NCBI__GCF_001684965.1:WP_065401082.1 368 GSAAMELQKQNKKYALCTLCIGVGQGYAMVIEKV 401 ********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (400 nodes) Target sequences: 1 (401 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: 13.16 // [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