GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Flavobacterium sp. LM5

Align Sorbitol dehydrogenase; SDH; Galactitol 2-dehydrogenase; L-iditol 2-dehydrogenase; Polyol dehydrogenase; EC 1.1.1.-; EC 1.1.1.16; EC 1.1.1.14 (characterized)
to candidate WP_078210695.1 BXU11_RS01105 SDR family NAD(P)-dependent oxidoreductase

Query= SwissProt::Q59787
         (256 letters)



>NCBI__GCF_002017945.1:WP_078210695.1
          Length = 250

 Score = 97.8 bits (242), Expect = 2e-25
 Identities = 66/186 (35%), Positives = 97/186 (52%), Gaps = 4/186 (2%)

Query: 6   KTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEIGP--AACAIALDVTDQ 63
           KTALITG+  GIG+A A    +   ++ +     +   A   E+    A   +  DV D+
Sbjct: 3   KTALITGATSGIGKATATLLAQNNFKIVLCGRRKDRLEALEKELSAFTAVHTLCFDVRDK 62

Query: 64  ASIDRCVAELLDRWGSIDILVNNAA-LFDLAPIVEITRESYDRLFAINVSGTLFMMQAVA 122
            ++   +A L + +  IDILVNNA     L  I     + +D +  INV G L++ +A+ 
Sbjct: 63  KAVFESIASLPEAFSDIDILVNNAGNAHGLDSIQNGDMDDWDAMIDINVKGLLYISKAII 122

Query: 123 RAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAP 182
             MIA    G IIN+ S AG+       VYCA+K AV +L QS  ++L  +GI V  I P
Sbjct: 123 PKMIAK-ESGHIINIGSIAGKEVYPNGNVYCASKYAVDALNQSMRMDLNPYGIRVGGIHP 181

Query: 183 GVVDGE 188
           G+V+ E
Sbjct: 182 GMVETE 187


Lambda     K      H
   0.321    0.135    0.392 

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: 130
Number of extensions: 7
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: 256
Length of database: 250
Length adjustment: 24
Effective length of query: 232
Effective length of database: 226
Effective search space:    52432
Effective search space used:    52432
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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