Align BadK (characterized)
to candidate WP_156424864.1 AQZ52_RS04030 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >NCBI__GCF_001519075.1:WP_156424864.1 Length = 277 Score = 159 bits (401), Expect = 8e-44 Identities = 103/262 (39%), Positives = 141/262 (53%), Gaps = 9/262 (3%) Query: 2 SSNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAF 61 S I E +GRV ITL RP VLNA+N + + L A AF ADDG V+ G R F Sbjct: 20 SMEHITVEQRGRVTRITLARPAVLNAINARMHEELEEAFNAFAADDGQWVAVVTGQGRGF 79 Query: 62 AAGADIASMAAWSYSD--VYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDI 119 AG+D+ ++AA + +G + ++ KP++AAV GLA GGG E+ALACD+ Sbjct: 80 CAGSDLKAVAAEGFRSYPAHGYAGLIERFDC----DKPIIAAVNGLALGGGFEVALACDL 135 Query: 120 VIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSR 179 +IA SA+F LPE ++G + GG RL R IG +AM M LSARP++A E +R G V+ Sbjct: 136 IIAAESARFGLPEPRVGAVALGGGLHRLARQIGLKRAMGMILSARPVDAAEGERLGFVTE 195 Query: 180 VVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFER---RELHARFA 236 VV D L I + ++ A K+++ R + + + A A Sbjct: 196 VVPDTDLESAVERWVEAILLGAPLSIRASKQAVMRGLDEAGVAAAMAAQPGYPAFAAWSA 255 Query: 237 SADAREGIQAFLEKRAPCFSHR 258 SAD REG AF EKR P + R Sbjct: 256 SADLREGTTAFAEKRPPVWQGR 277 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: 146 Number of extensions: 6 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: 277 Length adjustment: 25 Effective length of query: 233 Effective length of database: 252 Effective search space: 58716 Effective search space used: 58716 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 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