Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_043920361.1 jaqu_RS17800 enoyl-CoA hydratase
Query= metacyc::MONOMER-13469 (259 letters) >NCBI__GCF_000877395.1:WP_043920361.1 Length = 262 Score = 130 bits (326), Expect = 4e-35 Identities = 82/255 (32%), Positives = 131/255 (51%), Gaps = 12/255 (4%) Query: 6 IILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGA 65 ++ E DG + +TLN P LNAL+ L + A+ IA + V++ G+AF AG Sbjct: 5 LLQEVDGEIVRLTLNDPGTLNALSDEMLAALGGALERIAVSE-AGVVVLRAEGRAFCAGH 63 Query: 66 DIAEMKDLTAVEGRKFSVLGN------KIFRKLENLEKPVIAAINGFALGGGCELSLSCD 119 +A+M+ + + G+ + R + L +PVIA ++G A GC+L +CD Sbjct: 64 HLAQMQAMRQAPDGGAAAFGDLFDRCAAVMRAIRELPQPVIAQVHGLATAAGCQLVATCD 123 Query: 120 IRIASSKAKFGQPEVGLGITPGFGGTQRLA--RAIGVGMAKELIYTGKVINAEEALRIGL 177 + +AS +A+FG V +G+ F T +A R +G A E++ TG+ ++A EA GL Sbjct: 124 MAVASDEARFGVNGVDIGL---FCSTPMVALSRNVGRKRAFEMLATGRFLSASEAEEAGL 180 Query: 178 VNKVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFA 237 VN+VV D L ++ L + P AVR+ K A + + ++ A E + A Sbjct: 181 VNRVVHADHLADDVDNLARTVASKLPAAVRIGKGAFHAQAERPVEEAYALAREAMVQNLA 240 Query: 238 TEDRVEGMTAFVEKR 252 D EG+ AF+EKR Sbjct: 241 DADTAEGIQAFLEKR 255 Lambda K H 0.318 0.136 0.376 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: 165 Number of extensions: 8 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: 259 Length of database: 262 Length adjustment: 25 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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