Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate GFF12 HP15_12 enoyl-CoA hydratase/isomerase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__Marino:GFF12 Length = 270 Score = 160 bits (406), Expect = 2e-44 Identities = 100/247 (40%), Positives = 133/247 (53%), Gaps = 3/247 (1%) Query: 12 GRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EKAFAAGADIG-M 69 G VG V LNRPK +NA+ND + + AL +F+ D I IV+ G E+ AGADI Sbjct: 21 GNVGWVILNRPKQINAINDEIRVGVPEALEQFEKDKEIRVIVIRGEGERGLCAGADIKER 80 Query: 70 MSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFAADTAKFG 129 + V K R E++ KP+I A+ G+ +GGG ELA+ CDI +A+ A Sbjct: 81 RGPENSLQVRKRMECARWIESIDQTTKPVIVAIHGYCMGGGLELALACDIRYASPNAVMA 140 Query: 130 QPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPA-ASLVD 188 PE LG++PG GGTQRL R V+ A+D+ L+ +DAA A GLV+RV SL+ Sbjct: 141 LPETGLGLIPGGGGTQRLSRVVAPGHALDMLLSGDRLDAARARSIGLVTRVAETQESLLQ 200 Query: 189 EAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKEGMAAFV 248 E A IA P A VK + + E L G+ E LF L TED +E +AF Sbjct: 201 EVSELAQKIAMKPPLATTYVKRAARASLELELKRGLDLELDLFALLAPTEDAREAASAFS 260 Query: 249 EKRKPVF 255 E+R P F Sbjct: 261 ERRSPNF 267 Lambda K H 0.321 0.134 0.380 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: 152 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: 258 Length of database: 270 Length adjustment: 25 Effective length of query: 233 Effective length of database: 245 Effective search space: 57085 Effective search space used: 57085 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