Align Putative enoyl-CoA hydratase protein; EC 4.2.1.17 (characterized, see rationale)
to candidate GFF1019 PGA1_c10360 putative enoyl-CoA hydratase
Query= uniprot:Q92VJ6 (261 letters) >FitnessBrowser__Phaeo:GFF1019 Length = 260 Score = 283 bits (724), Expect = 3e-81 Identities = 149/259 (57%), Positives = 174/259 (67%) Query: 3 FDTIRCAIDQRGVARVTLARSEKHNALSATMIGELTAVVGRLATDASIRAVILDAEGKSF 62 ++TI AID RGVA +TL R EKHNA+S M+ EL A LA D ++R V+L GKSF Sbjct: 2 YNTITLAIDDRGVATLTLNRPEKHNAMSGEMLQELKAAAAALAKDRTVRVVVLTGAGKSF 61 Query: 63 CAGGDLDWMRQQFSADRPTRIAEATRLAMMLKALNDLPKPLIARVHGNAFGGGVGLISVC 122 CAGGDL WM+ Q AD TR EA LA ML A+N LP+P+I + GNAFGGGVG+ SVC Sbjct: 62 CAGGDLGWMQAQMEADAETRGREARVLAEMLMAINTLPQPVIGAIQGNAFGGGVGMASVC 121 Query: 123 DTVIAASGAQFGLTETRLGLIPATISPYVIARTGEARARPLFMSARVFGAEEAKVAGFVT 182 D I A + GLTETRLGLIPATI PYV+AR GEARAR +FMSAR+FGA EA G + Sbjct: 122 DVAIGADHIKMGLTETRLGLIPATIGPYVVARMGEARARRVFMSARLFGAAEAVDLGILA 181 Query: 183 TVVDGTMLDGAVEAAVTAYLVAAPGAAGRAKRLARSLGLPITDAVIAATIEQLADTWETD 242 VV LD A+EA V YL AP A G AK L R LG I DAVI TI L D WE Sbjct: 182 RVVPAADLDAAIEAEVIPYLSCAPEAVGAAKALVRDLGPKIDDAVIDHTIAALVDRWEGS 241 Query: 243 EAREGVSAFFERRNPSWRQ 261 EA EG++AFF + PSW++ Sbjct: 242 EAPEGIAAFFAKEKPSWQR 260 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: 208 Number of extensions: 9 Number of successful extensions: 1 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: 260 Length adjustment: 25 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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