Align Probable enoyl-CoA hydratase; EC 4.2.1.17 (uncharacterized)
to candidate PP_3283 PP_3283 1,2-epoxyphenylacetyl-CoA isomerase
Query= curated2:P24162 (257 letters) >FitnessBrowser__Putida:PP_3283 Length = 263 Score = 231 bits (588), Expect = 1e-65 Identities = 122/263 (46%), Positives = 169/263 (64%), Gaps = 6/263 (2%) Query: 1 MSYHTIRYEISEGLAVITLDRPEVMNALNAAMRHELTAALHRAR--GEARAIVLTGSGRA 58 M++ I + I +G+A ++L+RPE +N+ N AM E+ AL + R +AR ++LT GR Sbjct: 1 MTFQHILFSIEDGVAFLSLNRPEQLNSFNTAMHLEVREALRQVRQSSDARVLLLTAEGRG 60 Query: 59 FCSGQDLGDG----AAEGLNLETVLREEYEPLLQAIYSCPLPVLAAVNGAAAGAGANLAL 114 FC+GQDL D AE +L + + Y PL++ + PLPV+ AVNG AAGAGAN+ L Sbjct: 61 FCAGQDLSDRNVAPGAEMPDLGQSIDKFYNPLVRTLRDLPLPVICAVNGVAAGAGANIPL 120 Query: 115 AADVVIAAQSAAFMQAFTRIGLMPDAGGTWWLPRQVGMARAMGMALFAEKIGAEEAARMG 174 A D+V+AA+SA+F+QAF +IGL+PD+GGTW LPR VGMARA +A+ E++GAE+A + G Sbjct: 121 ACDLVLAARSASFIQAFCKIGLVPDSGGTWLLPRLVGMARAKALAMLGERLGAEQAEQWG 180 Query: 175 LIWEAVPDVDFEHHWRARAAHLARGPSAAFAAVKKAFHAGLSNPLPAQLALEARLQGELG 234 LI+ V D A HLA P+ +K++ +A N AQL LE LQ G Sbjct: 181 LIYRVVDDAALRDEALTLARHLAAQPTYGLTLIKRSLNASFDNGFEAQLELERDLQRLAG 240 Query: 235 QSADFREGVQAFLEKRPPHFTGR 257 +S D+REGV AF+ KR P F GR Sbjct: 241 RSEDYREGVNAFMNKRTPAFKGR 263 Lambda K H 0.321 0.133 0.397 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: 159 Number of extensions: 7 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: 257 Length of database: 263 Length adjustment: 24 Effective length of query: 233 Effective length of database: 239 Effective search space: 55687 Effective search space used: 55687 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 (21.9 bits) S2: 47 (22.7 bits)
Align candidate PP_3283 PP_3283 (1,2-epoxyphenylacetyl-CoA isomerase)
to HMM TIGR02280 (paaB: phenylacetate degradation probable enoyl-CoA hydratase PaaB (EC 4.2.1.17))
# 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/TIGR02280.hmm # target sequence database: /tmp/gapView.3704.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02280 [M=256] Accession: TIGR02280 Description: PaaB1: phenylacetate degradation probable enoyl-CoA hydratase PaaB 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-129 416.9 0.7 1.7e-129 416.8 0.7 1.0 1 lcl|FitnessBrowser__Putida:PP_3283 PP_3283 1,2-epoxyphenylacetyl-Co Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_3283 PP_3283 1,2-epoxyphenylacetyl-CoA isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 416.8 0.7 1.7e-129 1.7e-129 1 256 [] 6 263 .] 6 263 .] 0.99 Alignments for each domain: == domain 1 score: 416.8 bits; conditional E-value: 1.7e-129 TIGR02280 1 illelekgvlrltlnrpdklnsfteemhaelaealerverdd.vrallltGaGrGfcaGqdlsernvtkg.aapd 73 il+++e+gv+ l+lnrp++lnsf+ mh e++eal +v++ + +r+lllt GrGfcaGqdls+rnv +g ++pd lcl|FitnessBrowser__Putida:PP_3283 6 ILFSIEDGVAFLSLNRPEQLNSFNTAMHLEVREALRQVRQSSdARVLLLTAEGRGFCAGQDLSDRNVAPGaEMPD 80 899***********************************98766***************************99*** PP TIGR02280 74 lGetvekfynplvrrlaalpkpvvvavnGvaaGaGanlalagdivlaaesakfiqafaklGlipdsGGtwllprl 148 lG++++kfynplvr l+ lp+pv++avnGvaaGaGan+ la+d+vlaa+sa+fiqaf+k+Gl+pdsGGtwllprl lcl|FitnessBrowser__Putida:PP_3283 81 LGQSIDKFYNPLVRTLRDLPLPVICAVNGVAAGAGANIPLACDLVLAARSASFIQAFCKIGLVPDSGGTWLLPRL 155 *************************************************************************** PP TIGR02280 149 vGrarakglallgekldaetaaewGliwqvvddealadevqalaahlakqptrglalikralqaaetnsldtqld 223 vG arak+la+lge+l ae+a++wGli++vvdd+al de+ +la+hla+qpt gl+likr+l+a+ n +++ql+ lcl|FitnessBrowser__Putida:PP_3283 156 VGMARAKALAMLGERLGAEQAEQWGLIYRVVDDAALRDEALTLARHLAAQPTYGLTLIKRSLNASFDNGFEAQLE 230 *************************************************************************** PP TIGR02280 224 lerdlqrelGrsadyaeGvaafldkrepefkGk 256 lerdlqr +Grs dy+eGv+af++kr+p fkG+ lcl|FitnessBrowser__Putida:PP_3283 231 LERDLQRLAGRSEDYREGVNAFMNKRTPAFKGR 263 *******************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (263 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: 00:00:00.00 # Mc/sec: 8.96 // [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