Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_054341003.1 Nant_RS07360 3-oxoadipyl-CoA thiolase
Query= uniprot:D8ITH5 (401 letters) >NCBI__GCF_001305295.1:WP_054341003.1 Length = 402 Score = 595 bits (1534), Expect = e-175 Identities = 293/400 (73%), Positives = 339/400 (84%), Gaps = 1/400 (0%) Query: 2 EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61 +A ICDA+RTPFGRYGG L +VR DDL A P+++LMERNP V+W+ VED++YG ANQAGE Sbjct: 3 DAFICDAVRTPFGRYGGGLSSVRPDDLGAIPLKALMERNPDVNWASVEDVIYGNANQAGE 62 Query: 62 DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121 DNRNVARM+ LLAG P++VPG+TVNRLCGS +DA+GMAARAIKSGE +LMIAGG ESM+R Sbjct: 63 DNRNVARMSALLAGFPVSVPGTTVNRLCGSGMDAIGMAARAIKSGETELMIAGGCESMSR 122 Query: 122 APFVMGKAESAFARSA-AIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180 APFVMGKAESAF+R+ ++DTTIGWRF+N MK QYG+DSMPETAENVA +F I+RADQ Sbjct: 123 APFVMGKAESAFSRTPNGLYDTTIGWRFINKKMKEQYGVDSMPETAENVAEEFNISRADQ 182 Query: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV 240 D FA RSQQ+ A A G F EI P+ IPQ+KGDP+VV TDEHPR TTL LAKLK Sbjct: 183 DLFAFRSQQKTAIAMQKGLFNEEIVPVVIPQRKGDPIVVDTDEHPRASTTLEDLAKLKAP 242 Query: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300 R G+VTAGNASGVNDGACALL+AS +AA L P+AR++ MA AG+ PRIMGFGPAP Sbjct: 243 FRAGGSVTAGNASGVNDGACALLIASAEAAKANGLVPKARIVAMAAAGLEPRIMGFGPAP 302 Query: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360 A R VL + GLTL QMDVIELNEAFA+QGLAV+RDLGLPDDAAHVNPNGGAI++GHPLGA Sbjct: 303 ATRNVLKKAGLTLDQMDVIELNEAFASQGLAVLRDLGLPDDAAHVNPNGGAISLGHPLGA 362 Query: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400 SGARLV TA+ QL R+GGRYALCTMCIGVGQGIA++IERV Sbjct: 363 SGARLVMTAMYQLHRTGGRYALCTMCIGVGQGIAMIIERV 402 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: 561 Number of extensions: 14 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: 401 Length of database: 402 Length adjustment: 31 Effective length of query: 370 Effective length of database: 371 Effective search space: 137270 Effective search space used: 137270 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_054341003.1 Nant_RS07360 (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.3138856.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-225 734.6 4.7 1.7e-225 734.4 4.7 1.0 1 NCBI__GCF_001305295.1:WP_054341003.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001305295.1:WP_054341003.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 734.4 4.7 1.7e-225 1.7e-225 1 400 [] 2 402 .] 2 402 .] 1.00 Alignments for each domain: == domain 1 score: 734.4 bits; conditional E-value: 1.7e-225 TIGR02430 1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaall 73 k+++i+da+rtp+GrygG+lssvr ddl+a+plkal++rnp++++a+++dvi+G anqaGednrnvarm+all NCBI__GCF_001305295.1:WP_054341003.1 2 KDAFICDAVRTPFGRYGGGLSSVRPDDLGAIPLKALMERNPDVNWASVEDVIYGNANQAGEDNRNVARMSALL 74 689********************************************************************** PP TIGR02430 74 aGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsak.ledttiG 145 aG+pvsvpgttvnrlcgsg+da+g+aaraik+Ge++l+iaGG esmsrapfv+Gka+safsr+ + l dttiG NCBI__GCF_001305295.1:WP_054341003.1 75 AGFPVSVPGTTVNRLCGSGMDAIGMAARAIKSGETELMIAGGCESMSRAPFVMGKAESAFSRTPNgLYDTTIG 147 ***************************************************************888******* PP TIGR02430 146 wrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetv 218 wrf+n k+k++yGvdsmpetaenvaeef++sr+dqd fa+rsqq+ta a +kG+f+eeivpv+i+q+kG++ v NCBI__GCF_001305295.1:WP_054341003.1 148 WRFINKKMKEQYGVDSMPETAENVAEEFNISRADQDLFAFRSQQKTAIAMQKGLFNEEIVPVVIPQRKGDPIV 220 ************************************************************************* PP TIGR02430 219 vdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGvep 291 vd+deh+ra+ttle laklka++r++g+vtaGnasGvndGa+all+as+ea+k++gl+p+ari+a+a+aG+ep NCBI__GCF_001305295.1:WP_054341003.1 221 VDTDEHPRASTTLEDLAKLKAPFRAGGSVTAGNASGVNDGACALLIASAEAAKANGLVPKARIVAMAAAGLEP 293 ************************************************************************* PP TIGR02430 292 rvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGar 364 r+mG+gp+pa++++l++agl+l+++dvielneafa+q+lavlr+lgl+dd+a+vnpnGGai+lGhplGasGar NCBI__GCF_001305295.1:WP_054341003.1 294 RIMGFGPAPATRNVLKKAGLTLDQMDVIELNEAFASQGLAVLRDLGLPDDAAHVNPNGGAISLGHPLGASGAR 366 ************************************************************************* PP TIGR02430 365 lvltalkqleksggryalatlciGvGqGialvierv 400 lv+ta++ql+++ggryal+t+ciGvGqGia++ierv NCBI__GCF_001305295.1:WP_054341003.1 367 LVMTAMYQLHRTGGRYALCTMCIGVGQGIAMIIERV 402 ***********************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (400 nodes) Target sequences: 1 (402 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: 00:00:00.00 # Mc/sec: 20.77 // [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