Align sorbitol-6-phosphate dehydrogenase; EC 1.1.1.140 (characterized)
to candidate Echvi_4411 Echvi_4411 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= CharProtDB::CH_091827 (259 letters) >FitnessBrowser__Cola:Echvi_4411 Length = 292 Score = 102 bits (253), Expect = 1e-26 Identities = 77/257 (29%), Positives = 129/257 (50%), Gaps = 21/257 (8%) Query: 3 QVAVVIGGGQTLGAFLCHGLAAEGYRVAVVDIQSDKAANVAQEINAEYGESMAYGFGADA 62 +VAVV GG +G +C LAA+G V V + DK V EI A G+++ D Sbjct: 47 KVAVVTGGSGAIGRAICCRLAADGALVVVCGMSHDKMQGVVDEIGANGGKAVKRQL--DI 104 Query: 63 TSEQSVLALSRGVDEIFGRVDLLVYSA-GIAKAAF--ISDFQLGDFDRSLQVNLVGYFLC 119 +SE+ ++ + + E +G++D+LV A G A+ A I + + D +L VNL G L Sbjct: 105 SSEEKIIEFYQWLKESYGQLDILVNCAGGSARQASRPIYELETETIDTTLHVNLRGAILV 164 Query: 120 AREFSRLMIRDGIQGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITV 179 RE S++M+ +G I+ + S G+ G S Y+AAK G + T+S+A++L + GIT Sbjct: 165 TREASKIMVA-AKRGTIVSVTSVIGEHGKAKFSEYAAAKAGIIAFTKSIAMELGKLGITA 223 Query: 180 HSLMLGNLLKSPMFQSLLPQYATKLGIKPDQVEQYYIDKVPLKRGCDYQDVLNMLLFYAS 239 + + G + + ++ P KL K + + Y +D+ M+ + Sbjct: 224 NCVSPGIVQRG----TITPAQMAKLK-KTNYMNDYGRP----------EDISEMVAYLTR 268 Query: 240 PKASYCTGQSINVTGGQ 256 + + TGQ+ V GG+ Sbjct: 269 EEGKFITGQNFKVDGGR 285 Lambda K H 0.320 0.137 0.391 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: 166 Number of extensions: 10 Number of successful extensions: 4 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: 259 Length of database: 292 Length adjustment: 25 Effective length of query: 234 Effective length of database: 267 Effective search space: 62478 Effective search space used: 62478 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 (21.8 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