Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate 351439 BT1911 7-alpha-hydroxysteroid dehydrogenase (NCBI ptt file)
Query= BRENDA::Q4J9F2 (255 letters) >FitnessBrowser__Btheta:351439 Length = 259 Score = 148 bits (373), Expect = 1e-40 Identities = 89/250 (35%), Positives = 133/250 (53%), Gaps = 5/250 (2%) Query: 7 KNKVVIVTGAGSGIGRAIAKKFALNDSIVVAVELLEDRLNQIVQELRGMGKEVLGVKADV 66 +NKVV++TGA GIG A ++ VV +L ++R +++ EL G +V + Sbjct: 5 ENKVVVITGAAGGIGEATTRRIVSEGGKVVIADLSQERADKLAAELTQAGADVRPIYFSA 64 Query: 67 SKKKDVEEFVRRTFETYSRIDVLCNNAGIMDGVTP--VAEVSDELWERVLAVNLYSAFYS 124 ++ + +E V + Y +IDVL NN G D + ++ + ++ V +NL Y Sbjct: 65 TELQSCKELVDFAMKEYGQIDVLINNVGGTDPKRDLNIEKLDIDYFDEVFHLNLCCTMYL 124 Query: 125 SRAVIPIMLKQGKGVIVNTASIAGIRGGFAGAPYTVAKHGLIGLTRSIAAHYGDQGIRAV 184 S+ VIPIM G G IVN ASI+G+ G Y +K G+I LT+ IA G + IR Sbjct: 125 SQQVIPIMTTHGGGNIVNVASISGLTADANGTLYGASKAGVINLTKYIATQMGKKNIRCN 184 Query: 185 AVLPGTVKTNIGLGSSKPSELGMRTLTKLMSLSSRLAEPEDIANVIVFLASDEASFVNGD 244 AV PG V T L + +R + + L EPED+A I FLAS++A ++ G Sbjct: 185 AVAPGLVLTPAALDNLNEE---VRNIFLGQCATPYLGEPEDVAATIAFLASNDARYITGQ 241 Query: 245 AVVVDGGLTV 254 +VVDGGLT+ Sbjct: 242 TIVVDGGLTI 251 Lambda K H 0.318 0.135 0.369 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: 151 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: 255 Length of database: 259 Length adjustment: 24 Effective length of query: 231 Effective length of database: 235 Effective search space: 54285 Effective search space used: 54285 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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