Align Putative enoyl-CoA hydratase protein; EC 4.2.1.17 (characterized, see rationale)
to candidate AZOBR_RS13325 AZOBR_RS13325 enoyl-CoA hydratase
Query= uniprot:Q92VJ6 (261 letters) >FitnessBrowser__azobra:AZOBR_RS13325 Length = 263 Score = 112 bits (280), Expect = 8e-30 Identities = 85/249 (34%), Positives = 117/249 (46%), Gaps = 5/249 (2%) Query: 15 VARVTLARSEKHNALSATMIGELTAVVGRLATDASIRAVILDAEGKS-FCAGGDLDWMRQ 73 VAR+T+ + NA++ M L +V R D +R ++L G + FCAG D+ + Sbjct: 15 VARLTIDNPARRNAMTLDMWAALPELVRRAEVDPEVRVILLRGAGDAAFCAGADISQFSE 74 Query: 74 QFSADRPTRIAEATRLAMMLKALNDLPKPLIARVHGNAFGGGVGLISVCDTVIAASGAQF 133 + S + R+ +A A L KP +A V G FGGGVG+ CD +AA+ A+F Sbjct: 75 KRSGEAEGRVYDAAVEAAQA-TLFAAGKPTVAYVRGACFGGGVGIALSCDLRVAAADARF 133 Query: 134 GLTETRLGLIPATIS--PYVIARTGEARARPLFMSARVFGAEEAKVAGFVTTVVDGTMLD 191 + RLGL T S V AR G + L +AR AEEA G V + D Sbjct: 134 RIPAARLGL-GYTFSNVELVTARLGASTTADLLFTARTVDAEEALRLGLVGRLFGAEEAD 192 Query: 192 GAVEAAVTAYLVAAPGAAGRAKRLARSLGLPITDAVIAATIEQLADTWETDEAREGVSAF 251 AVE VTA AP KR L P + AA + +D+ REG +AF Sbjct: 193 AAVEDLVTAIGGNAPLTLRAVKRALVELAQPAVERDTAAVDALVRACLGSDDYREGQAAF 252 Query: 252 FERRNPSWR 260 E+R P +R Sbjct: 253 KEKREPKFR 261 Lambda K H 0.321 0.133 0.383 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: 177 Number of extensions: 10 Number of successful extensions: 5 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: 261 Length of database: 263 Length adjustment: 25 Effective length of query: 236 Effective length of database: 238 Effective search space: 56168 Effective search space used: 56168 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