Align BadK (characterized)
to candidate PP_2217 PP_2217 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Putida:PP_2217 Length = 257 Score = 254 bits (649), Expect = 1e-72 Identities = 130/258 (50%), Positives = 176/258 (68%), Gaps = 1/258 (0%) Query: 1 MSSNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRA 60 M+ IL + G+VG+ITLNRP LNALN ++ + AL + D IG +V+ G+ +A Sbjct: 1 MAFETILLDIHGKVGLITLNRPQALNALNAQIVGEINQALDQLERDPNIGCVVLTGSAKA 60 Query: 61 FAAGADIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIV 120 FAAGADI MA Y +Y + + + + I RKP++AAV+G A GGGCELA+ CD + Sbjct: 61 FAAGADIKEMAELQYPQIYVDDLFS-DADRIANRRKPIIAAVSGFALGGGCELAMMCDFI 119 Query: 121 IAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRV 180 +A +AKF PEI LG+LPG GGTQRL RA+GKAKAM++CL+ R + AEEA+R GLV+R+ Sbjct: 120 LAADNAKFGQPEINLGVLPGMGGTQRLTRAVGKAKAMELCLTGRLMGAEEAERAGLVARI 179 Query: 181 VDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADA 240 V L +E + +A TIA+ S P M +KES+NRAFE TL+EG+ FERR HA F++ D Sbjct: 180 VPQAELVEEALKVAATIASKSIPVSMMVKESVNRAFEVTLSEGVRFERRVFHAAFSTEDQ 239 Query: 241 REGIQAFLEKRAPCFSHR 258 +EG+ AF+ KR F R Sbjct: 240 KEGMAAFIAKREAQFKDR 257 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: 171 Number of extensions: 6 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: 258 Length of database: 257 Length adjustment: 24 Effective length of query: 234 Effective length of database: 233 Effective search space: 54522 Effective search space used: 54522 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