Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate AO356_26360 AO356_26360 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_26360 Length = 257 Score = 316 bits (809), Expect = 3e-91 Identities = 161/258 (62%), Positives = 198/258 (76%), Gaps = 1/258 (0%) Query: 1 MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA 60 M+YE IL+E + RVGL+TLNRP+ALNALN ++ EL AL +AD IG IV+TGS+KA Sbjct: 1 MSYETILLEIKDRVGLITLNRPQALNALNAQIVSELNQALDSLEADPKIGCIVLTGSKKA 60 Query: 61 FAAGADIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDII 120 FAAGADI M+ TY +Y D + + + V + RKPIIAAV GFALGGGCELA+MCD I Sbjct: 61 FAAGADIKEMAELTYPQIYLDDLFSDS-DRVANRRKPIIAAVNGFALGGGCELALMCDFI 119 Query: 121 FAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRV 180 A D AKFGQPEI LG++PG GGTQRL RAV KAKAM++CLT RF+DA EAER G+V+R+ Sbjct: 120 LAGDNAKFGQPEINLGVLPGMGGTQRLTRAVGKAKAMEMCLTGRFIDAVEAERCGIVARI 179 Query: 181 IPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQ 240 +PA L+D+A+ AA IA P MMVKESVNRA+E +L+EGV FERR+FH+ FAT+DQ Sbjct: 180 VPADELLDDALKTAALIASKSVPISMMVKESVNRAFEVSLSEGVRFERRVFHAAFATQDQ 239 Query: 241 KEGMAAFVEKRKPVFKHR 258 KEGMAAFV KR F+ + Sbjct: 240 KEGMAAFVAKRAAEFQDK 257 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: 223 Number of extensions: 7 Number of successful extensions: 2 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: 257 Length adjustment: 24 Effective length of query: 234 Effective length of database: 233 Effective search space: 54522 Effective search space used: 54522 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