Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_041098567.1 SUTH_RS08545 enoyl-CoA hydratase
Query= reanno::psRCH2:GFF2389 (257 letters) >NCBI__GCF_000828635.1:WP_041098567.1 Length = 264 Score = 149 bits (375), Expect = 7e-41 Identities = 91/257 (35%), Positives = 134/257 (52%), Gaps = 6/257 (2%) Query: 2 TFETLLVDIQERVALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGSAKAF 61 T L+ + +E VA +TLNRP N+L+ +++ EL AL + AD + +V+ G+ KAF Sbjct: 7 TLPILMREDREGVATLTLNRPTQFNSLSEEMLGELQAALNAIAADKTVRAVVIAGAGKAF 66 Query: 62 AAGADIKEMAELTYPQIYLDDFFADADR----IATRRKPLIAAVAGYALGGGCELALLCD 117 AG D+K+M + + Y+ F + I +P+IA + G A GC+L +CD Sbjct: 67 CAGHDLKQM-RANHSKTYMQKLFKQCGKVMMSIVEMPQPVIARIHGIATAAGCQLVAMCD 125 Query: 118 MIFAADNARFGQPEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVA 177 + AA+ ARF +N+G+ L RA+G+ +AM+M LTG +DAAEA+R GL+ Sbjct: 126 LAVAAEGARFAVSGINVGLFCSTPSV-ALGRAMGRKEAMEMLLTGDFIDAAEAQRRGLIN 184 Query: 178 RVFPAESLLEETLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATA 237 RV P E L E K I KS A M K+ + E L + Sbjct: 185 RVVPLEQLDAEVKKLTDSICAKSAVAVGMGKQMFYKQLEMGLDGAYQLAVETMACNMMAD 244 Query: 238 DQKEGMAAFSEKRKPEF 254 D EG+ AF +KRKPE+ Sbjct: 245 DAAEGIDAFMQKRKPEW 261 Lambda K H 0.321 0.135 0.375 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: 163 Number of extensions: 12 Number of successful extensions: 4 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: 257 Length of database: 264 Length adjustment: 25 Effective length of query: 232 Effective length of database: 239 Effective search space: 55448 Effective search space used: 55448 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 Apr 09 2024. 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