GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Kocuria flava HO-9041

Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate WP_058857809.1 AS188_RS04270 acetoin reductase

Query= CharProtDB::CH_091826
         (259 letters)



>NCBI__GCF_001482365.1:WP_058857809.1
          Length = 259

 Score =  109 bits (272), Expect = 7e-29
 Identities = 78/255 (30%), Positives = 124/255 (48%), Gaps = 3/255 (1%)

Query: 3   QVAVVIGGGQTLGAFLCEGLAQAGYHVAVADLNESNANRLADTINSRYGAGRAYGFKVDA 62
           +VA+V G G+ +G  +   LAQ G+ V + DL +     +   I +     RA     D 
Sbjct: 6   RVALVTGAGRGIGKAIALRLAQDGFDVGLVDLRDELTREVLGEIEAT--GRRACAVTADV 63

Query: 63  TDEASVEALARAVDETFGRADLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLCSRE 122
           +D  SV A  + V E  GR D++V +AG+A+  PI +    + +   +VN+ G     + 
Sbjct: 64  SDRDSVRAAVQEVAERLGRLDVMVNNAGIAQVQPILEVTPDEVETIERVNINGVLWGIQA 123

Query: 123 FSKLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHSL 182
            +   +  G +G+II   S +G  G      YSA KF   GLTQ+ A +LA +GITV++ 
Sbjct: 124 AAARFLEQGTRGKIINAASIAGHEGFAVLGVYSATKFAVRGLTQAAAKELAPHGITVNAY 183

Query: 183 MLGNLLKSPMFQSLLPQYAEKLGITPEEVEPYYVDKVPLKRGCDYQDVLNVLLFYASDKA 242
             G ++ + M+  +  ++AE  G         YV  + L R    +DV   + + A   A
Sbjct: 184 CPG-VVGTDMWVEIDERFAELTGAEKGATYEQYVGGIALGRAQTPEDVAAFVSYLAGPDA 242

Query: 243 AYCTGQSINVTGGQV 257
            Y TGQ+  + GG V
Sbjct: 243 DYMTGQAPLIDGGLV 257


Lambda     K      H
   0.319    0.136    0.387 

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: 168
Number of extensions: 9
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: 259
Length of database: 259
Length adjustment: 24
Effective length of query: 235
Effective length of database: 235
Effective search space:    55225
Effective search space used:    55225
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 (21.7 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