Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate 351439 BT1911 7-alpha-hydroxysteroid dehydrogenase (NCBI ptt file)
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__Btheta:351439 Length = 259 Score = 97.1 bits (240), Expect = 3e-25 Identities = 80/256 (31%), Positives = 122/256 (47%), Gaps = 24/256 (9%) Query: 12 VAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVT----S 67 V VITG A G+G AT R+V +G V+ DL + +A KL A ADV S Sbjct: 8 VVVITGAAGGIGEATTRRIVSEGGKVVIADL----SQERADKLAAELTQAGADVRPIYFS 63 Query: 68 EKDVQTALAL---AKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMG 124 ++Q+ L A ++G++DV +N G + N++K ++ F V +NL Sbjct: 64 ATELQSCKELVDFAMKEYGQIDVLINNVGGTDPKRDLNIEKLD---IDYFDEVFHLNLCC 120 Query: 125 TFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIAR 184 T + + V M + GG G I+N AS++ Y ASK G++ +T IA Sbjct: 121 TMYLSQQVIPIMTTH----GG--GNIVNVASISGLTADANGTLYGASKAGVINLTKYIAT 174 Query: 185 DLAPIGIRVMTIAPGLFGTP-LLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIEN 243 + IR +APGL TP L +L E+V N Q P LG+P + A + + N Sbjct: 175 QMGKKNIRCNAVAPGLVLTPAALDNLNEEVRNIFLGQCATP-YLGEPEDVAATIAFLASN 233 Query: 244 P--FLNGEVIRLDGAI 257 ++ G+ I +DG + Sbjct: 234 DARYITGQTIVVDGGL 249 Lambda K H 0.318 0.135 0.385 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: 155 Number of extensions: 7 Number of successful extensions: 1 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: 261 Length of database: 259 Length adjustment: 24 Effective length of query: 237 Effective length of database: 235 Effective search space: 55695 Effective search space used: 55695 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