Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate Ac3H11_2775 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= SwissProt::Q0AVM1 (260 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2775 Length = 279 Score = 173 bits (439), Expect = 3e-48 Identities = 103/254 (40%), Positives = 145/254 (57%), Gaps = 7/254 (2%) Query: 8 LEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDKSFVAGAD 67 +E+ + + +NRP +NA+N D + A+ ++ DP+V +++I G+G + F AGAD Sbjct: 26 VERRGGVGWIVLNRPDQINAINDDIRRGVPAALAELDSDPSVRVIVIRGAGARGFCAGAD 85 Query: 68 IAFMQNLSAMEAREFGALGQKVFRLIEAM---EKPVIAAVNGFALGGGCELAMCCDFRIA 124 I + +A + + QK R IEA+ EKPVIAA++G+ +GGG ELA+ CD R A Sbjct: 86 IK--ERRAAETSVQVRRRMQKS-RWIEALDRTEKPVIAAIHGYCMGGGMELALACDLRFA 142 Query: 125 ASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGLVNKVV- 183 AS+A F PE GLG+ PG GGTQRL +VGPG A LL T D ++A AF IGL+ ++ Sbjct: 143 ASDAVFALPETGLGLIPGGGGTQRLGAVVGPGRALDLLLTGDRVDARRAFDIGLITRMAD 202 Query: 184 QPEELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSIEADAFGLCFATQDQK 243 + LL EV +A RI K A +K AA D+ + +E D F + D K Sbjct: 203 SADSLLAEVTALAERIAQKPPTATLFAKQAARAACHLDLKSGLDLELDLFAMLVPMNDVK 262 Query: 244 EGMTAFLEKRKANF 257 E AF EKR F Sbjct: 263 EAALAFREKRAPCF 276 Lambda K H 0.319 0.136 0.378 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: 169 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: 260 Length of database: 279 Length adjustment: 25 Effective length of query: 235 Effective length of database: 254 Effective search space: 59690 Effective search space used: 59690 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 (21.8 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