Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_028311754.1 H566_RS0112785 3-oxoadipyl-CoA thiolase
Query= uniprot:D8ITH5 (401 letters) >NCBI__GCF_000482785.1:WP_028311754.1 Length = 401 Score = 603 bits (1554), Expect = e-177 Identities = 306/398 (76%), Positives = 340/398 (85%) Query: 3 ALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGED 62 A +CDAIRTPFGRYGG+L VRADDL A PIR+LM RNP VDW+ ++D++YGCANQAGED Sbjct: 4 AYLCDAIRTPFGRYGGSLSGVRADDLGAVPIRALMARNPSVDWAALDDVIYGCANQAGED 63 Query: 63 NRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRA 122 NRNV RM+ LLAGLP VPG+TVNRLCGSSLDA AARAI++GEVQL+IAGGVESM+RA Sbjct: 64 NRNVGRMSALLAGLPPEVPGTTVNRLCGSSLDATASAARAIRAGEVQLVIAGGVESMSRA 123 Query: 123 PFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQDA 182 PFVMGKA AF+RSA + DTTIGWRFVNPLMKA +G+DSMPETAENVATDF + RADQDA Sbjct: 124 PFVMGKATEAFSRSAKVEDTTIGWRFVNPLMKAMHGVDSMPETAENVATDFDVARADQDA 183 Query: 183 FALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVVR 242 FALRSQQR AAAQAAG + EI P+TI QK+GD LVV+ DEH RP+TTLA LAKLKGVVR Sbjct: 184 FALRSQQRAAAAQAAGRLSQEITPVTIAQKRGDALVVSADEHLRPETTLAALAKLKGVVR 243 Query: 243 PDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPAV 302 PDGTVTAGNASGVNDGA ALLLAS A + LKPRAR++ A AGVAPRIMGFGPAPA+ Sbjct: 244 PDGTVTAGNASGVNDGAAALLLASEAGAARHGLKPRARIVASAVAGVAPRIMGFGPAPAI 303 Query: 303 RKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGASG 362 KVLA L L Q+DVIELNEAFAAQ LAV R GL DD A VNPNGGAIA+GHPLGASG Sbjct: 304 TKVLALAKLRLDQIDVIELNEAFAAQALAVTRAHGLADDDARVNPNGGAIALGHPLGASG 363 Query: 363 ARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400 ARLV A+++LER+GGRY LCTMCIGVGQGIALVIERV Sbjct: 364 ARLVIAALHELERTGGRYGLCTMCIGVGQGIALVIERV 401 Lambda K H 0.320 0.135 0.394 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: 562 Number of extensions: 13 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: 401 Length of database: 401 Length adjustment: 31 Effective length of query: 370 Effective length of database: 370 Effective search space: 136900 Effective search space used: 136900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
Align candidate WP_028311754.1 H566_RS0112785 (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.1897357.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-223 726.8 15.1 3.8e-223 726.7 15.1 1.0 1 NCBI__GCF_000482785.1:WP_028311754.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000482785.1:WP_028311754.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 726.7 15.1 3.8e-223 3.8e-223 2 400 .] 3 401 .] 2 401 .] 1.00 Alignments for each domain: == domain 1 score: 726.7 bits; conditional E-value: 3.8e-223 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 ++y++dairtp+GrygGsls vraddl+avp++al+arnps+d+aa+ddvi+GcanqaGednrnv+rm+alla NCBI__GCF_000482785.1:WP_028311754.1 3 HAYLCDAIRTPFGRYGGSLSGVRADDLGAVPIRALMARNPSVDWAALDDVIYGCANQAGEDNRNVGRMSALLA 75 89*********************************************************************** PP TIGR02430 75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147 Glp +vpgttvnrlcgs+lda + aarai+aGe +lviaGGvesmsrapfv+Gka afsrsak+edttiGwr NCBI__GCF_000482785.1:WP_028311754.1 76 GLPPEVPGTTVNRLCGSSLDATASAARAIRAGEVQLVIAGGVESMSRAPFVMGKATEAFSRSAKVEDTTIGWR 148 ************************************************************************* PP TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220 fvnp +ka++Gvdsmpetaenva++f+v+r+dqdafalrsqqr+aaaqa+G +++ei+pv+i+qk+G++ vv+ NCBI__GCF_000482785.1:WP_028311754.1 149 FVNPLMKAMHGVDSMPETAENVATDFDVARADQDAFALRSQQRAAAAQAAGRLSQEITPVTIAQKRGDALVVS 221 ************************************************************************* PP TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293 +dehlr+ettl alaklk+vvr+dgtvtaGnasGvndGaaalllase ++rhgl+prari+a+a aGv+pr+ NCBI__GCF_000482785.1:WP_028311754.1 222 ADEHLRPETTLAALAKLKGVVRPDGTVTAGNASGVNDGAAALLLASEAGAARHGLKPRARIVASAVAGVAPRI 294 ************************************************************************* PP TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366 mG+gp+pa+ k+la a+l+l+++dvielneafaaqalav+r+ gladddarvnpnGGaialGhplGasGarlv NCBI__GCF_000482785.1:WP_028311754.1 295 MGFGPAPAITKVLALAKLRLDQIDVIELNEAFAAQALAVTRAHGLADDDARVNPNGGAIALGHPLGASGARLV 367 ************************************************************************* PP TIGR02430 367 ltalkqleksggryalatlciGvGqGialvierv 400 ++al++le++ggry+l+t+ciGvGqGialvierv NCBI__GCF_000482785.1:WP_028311754.1 368 IAALHELERTGGRYGLCTMCIGVGQGIALVIERV 401 *********************************8 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 28.92 // [ok]
This GapMind analysis is from Apr 09 2024. 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