Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate HSERO_RS20640 HSERO_RS20640 enoyl-CoA hydratase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__HerbieS:HSERO_RS20640 Length = 263 Score = 152 bits (384), Expect = 7e-42 Identities = 92/260 (35%), Positives = 145/260 (55%), Gaps = 5/260 (1%) Query: 1 MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA 60 M+ +IL+E R + ++TLNRP LN+ A+ EL A+ AD ++ +++TG+ + Sbjct: 1 MSSPSILLENRDGIAVITLNRPDKLNSFTVAMHLELRDAIATLQADPSVRVLLLTGAGRG 60 Query: 61 FAAGADIGMMSTYTYMD-VYKGDYITRNW----ETVRSIRKPIIAAVAGFALGGGCELAM 115 F AG D+G + D V G+ I + + +++R++ P+I AV G A G G L + Sbjct: 61 FCAGQDLGDRAVKPGDDGVDLGESIDKYYGPLVKSLRALPFPVICAVNGVAAGAGANLPL 120 Query: 116 MCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAG 175 CDI+ AA +A F + KLG++P GGT LPR V A+AM + L + A +AER G Sbjct: 121 ACDIVLAARSASFVEVFCKLGLIPDTGGTYFLPRLVGTARAMGMALLGEKISAEQAERWG 180 Query: 176 LVSRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLF 235 L+ + + L++EA A AA A P+ + K ++ + TL E + ER +L Sbjct: 181 LIWKCVDDDQLMEEAHAMAAHFARAPTKGLAATKATLYASPAHTLPEQLDLERDTMRALG 240 Query: 236 ATEDQKEGMAAFVEKRKPVF 255 + D +EG+ AF+EKR P F Sbjct: 241 RSRDYREGVTAFLEKRAPQF 260 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: 150 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: 263 Length adjustment: 25 Effective length of query: 233 Effective length of database: 238 Effective search space: 55454 Effective search space used: 55454 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