Align BadK (characterized)
to candidate AO353_03780 AO353_03780 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03780 Length = 249 Score = 120 bits (300), Expect = 4e-32 Identities = 89/256 (34%), Positives = 121/256 (47%), Gaps = 25/256 (9%) Query: 3 SNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFA 62 +N IL E + + + LNRPD NAL A+ L ALL DAD I AI+I G F Sbjct: 2 TNAILLERERGLLTLRLNRPDKKNALTRAMYSQLADALLQADADPEINAILITGTRECFT 61 Query: 63 AGADIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIA 122 AG DIA SD+ F + + + RKPV+AAVAG A G G L L CD+V Sbjct: 62 AGNDIADFLEEPPSDLTSPVF--QFMRNLLECRKPVIAAVAGAAVGIGTTLLLHCDLVYI 119 Query: 123 GRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVD 182 AK +P + LGL P G + LPR +G+AKA ++ L N E+A +G+ Sbjct: 120 SADAKLRMPFVNLGLCPEFGSSLILPRLLGQAKAAELLLLGEGFNGEQAAAWGIA----- 174 Query: 183 DDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADARE 242 T AL T AA + MAL+ FE+ E + + + A RE Sbjct: 175 -------TQALPTGEAALAKAREMALR------FETLAPEAV-----RISKQLMKAPDRE 216 Query: 243 GIQAFLEKRAPCFSHR 258 ++ +E+ F R Sbjct: 217 QLRKAIEEEGNLFVQR 232 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: 107 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: 249 Length adjustment: 24 Effective length of query: 234 Effective length of database: 225 Effective search space: 52650 Effective search space used: 52650 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