GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Bacteroides clarus YIT 12056

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_009120431.1 BUB52_RS15230 SDR family oxidoreductase

Query= SwissProt::Q59787
         (256 letters)



>NCBI__GCF_900129655.1:WP_009120431.1
          Length = 253

 Score = 91.3 bits (225), Expect = 2e-23
 Identities = 62/194 (31%), Positives = 95/194 (48%), Gaps = 16/194 (8%)

Query: 3   LDGKTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEIGPA----ACAIAL 58
           ++ K  LITG++ GIG   A  +   G R+ +   N+E   A   E+        C +  
Sbjct: 1   MEKKIVLITGASSGIGEGCARKFAMNGYRLILNGRNMEKLTAVKRELETEYRADVCLLPF 60

Query: 59  DVTDQASIDRCVAELLDRWGSIDILVNNAALFDLAPIVEITRE------SYDRLFAINVS 112
           DV D+ +    +  L + W +IDILVNNA L     ++ + +E       +D +   NV 
Sbjct: 61  DVRDRGAAKAALDSLPEEWKAIDILVNNAGL-----VIGVDKEHEGNLDEWDIVLDTNVK 115

Query: 113 GTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIR 172
             L M + V   M+  GRG  +INM S AG        VYCA+KAAV +L+    ++L+ 
Sbjct: 116 SLLAMTRLVVPGMVERGRG-HVINMGSIAGDYAYPGGSVYCASKAAVKALSDGLRIDLVD 174

Query: 173 HGINVNAIAPGVVD 186
             + V  I PG+V+
Sbjct: 175 TPVRVTNIKPGLVE 188


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: 144
Number of extensions: 10
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: 256
Length of database: 253
Length adjustment: 24
Effective length of query: 232
Effective length of database: 229
Effective search space:    53128
Effective search space used:    53128
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: 47 (22.7 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