Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Ac3H11_2775 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2775 Length = 279 Score = 170 bits (430), Expect = 3e-47 Identities = 104/251 (41%), Positives = 141/251 (56%), Gaps = 3/251 (1%) Query: 8 VETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EKAFAAGAD 66 VE RG VG + LNRP +NA+ND + + AAL E D+D ++ IV+ G+ + F AGAD Sbjct: 26 VERRGGVGWIVLNRPDQINAINDDIRRGVPAALAELDSDPSVRVIVIRGAGARGFCAGAD 85 Query: 67 IG-MMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFAADT 125 I + T + V + +R E + KP+IAA+ G+ +GGG ELA+ CD+ FAA Sbjct: 86 IKERRAAETSVQVRRRMQKSRWIEALDRTEKPVIAAIHGYCMGGGMELALACDLRFAASD 145 Query: 126 AKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPAA- 184 A F PE LG++PG GGTQRL V +A+DL LT +DA A GL++R+ +A Sbjct: 146 AVFALPETGLGLIPGGGGTQRLGAVVGPGRALDLLLTGDRVDARRAFDIGLITRMADSAD 205 Query: 185 SLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKEGM 244 SL+ E A A IA+ P A + K++ A L G+ E LF L D KE Sbjct: 206 SLLAEVTALAERIAQKPPTATLFAKQAARAACHLDLKSGLDLELDLFAMLVPMNDVKEAA 265 Query: 245 AAFVEKRKPVF 255 AF EKR P F Sbjct: 266 LAFREKRAPCF 276 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: 193 Number of extensions: 8 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: 279 Length adjustment: 25 Effective length of query: 233 Effective length of database: 254 Effective search space: 59182 Effective search space used: 59182 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