GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Echinicola vietnamensis KMM 6221, DSM 17526

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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