Align BadK (characterized)
to candidate RR42_RS19805 RR42_RS19805 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Cup4G11:RR42_RS19805 Length = 258 Score = 164 bits (416), Expect = 1e-45 Identities = 104/261 (39%), Positives = 144/261 (55%), Gaps = 9/261 (3%) Query: 3 SNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFA 62 ++P+L V ITLNRPDVLNALN AL+ L A+ D+ + A+V++ N R F Sbjct: 2 TSPVLYHAAEGVATITLNRPDVLNALNSALLLELRAAVERAAQDEAVRAVVLSANGRGFC 61 Query: 63 AGADIASMAAWSYSDVYGSNFITRNWE-----TIRQIRKPVLAAVAGLAYGGGCELALAC 117 AGAD+A + + S + R +R + KPV+ +V G+A G G LALA Sbjct: 62 AGADLAGRG----TGLQDSGTLLRERYHPIILALRNMPKPVITSVNGVAAGAGMSLALAG 117 Query: 118 DIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLV 177 D+V+AGRSA F K+GL+P AG T LPR G+ +A + + A ++AEEA R GLV Sbjct: 118 DVVLAGRSASFLQAFSKIGLVPDAGSTYFLPRYAGEMRARALAILAEKIDAEEAHRIGLV 177 Query: 178 SRVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFAS 237 +V +D+ L ET LA +A A +KE+LN + +S L + E S Sbjct: 178 WKVHEDEALPAETARLAAHLAQMPTFAYGLIKEALNASLQSDLPAQLEREATLQSRASKS 237 Query: 238 ADAREGIQAFLEKRAPCFSHR 258 D +EG+ AFLEKR P F R Sbjct: 238 EDVKEGVAAFLEKRKPAFKGR 258 Lambda K H 0.321 0.135 0.389 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: 134 Number of extensions: 5 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: 258 Length of database: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 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)
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