Align BadK (characterized)
to candidate Ga0059261_3685 Ga0059261_3685 Enoyl-CoA hydratase/carnithine racemase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Korea:Ga0059261_3685 Length = 257 Score = 253 bits (645), Expect = 4e-72 Identities = 128/251 (50%), Positives = 170/251 (67%), Gaps = 1/251 (0%) Query: 1 MSSNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRA 60 M+ IL E G V ++TLNRP LNALN ++ L A FDAD G V+ G+ +A Sbjct: 1 MNYETILVEQHGAVTLVTLNRPQALNALNSQVLTELLDAFAKFDADPSQGCAVLTGSEKA 60 Query: 61 FAAGADIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIV 120 FAAGADI M A ++D+YG NF W+ + RKP++AAV+G A GGGCELA+ CD + Sbjct: 61 FAAGADIKEMQAQGFADMYGHNFFA-GWDQFTRTRKPIIAAVSGFALGGGCELAMMCDFI 119 Query: 121 IAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRV 180 +A +AKF PEIKL + PG GG+QRL RA+GKAKAM+MCL+ R + AEEA+R GLVSR+ Sbjct: 120 LAADTAKFGQPEIKLAVAPGMGGSQRLTRAVGKAKAMEMCLTGRMMGAEEAERAGLVSRI 179 Query: 181 VDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADA 240 V L D+ + A IA + +++A KE +N AFE+TLA+G+ FERR H F +AD Sbjct: 180 VPAADLLDDALKTAAAIAGMAPLSVLANKEMVNAAFETTLAQGVQFERRLFHGLFGTADQ 239 Query: 241 REGIQAFLEKR 251 +EG+ AF+EKR Sbjct: 240 KEGMAAFVEKR 250 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: 166 Number of extensions: 4 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