GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Erythrobacter gangjinensis K7-2

Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate WP_047006347.1 AAW01_RS06205 SDR family NAD(P)-dependent oxidoreductase

Query= metacyc::MONOMER-13092
         (266 letters)



>NCBI__GCF_001010925.1:WP_047006347.1
          Length = 261

 Score = 85.1 bits (209), Expect = 1e-21
 Identities = 82/263 (31%), Positives = 118/263 (44%), Gaps = 32/263 (12%)

Query: 13  IVTGASSGIGKAIVDELLSLKVKVANFDLTDNGEKHENL------LFQKVDVTSREQVEA 66
           IVTG +SG+G+A    L +   KVA FDL  N E+ E +      +F KVDV+    +EA
Sbjct: 10  IVTGGASGLGEATARALAAKGAKVALFDL--NEERGEAVAAEIGGVFCKVDVSDEASIEA 67

Query: 67  SVAAVVEHFGTVDAVVNNAGI-NIPRLLVDPKDPHGQYELDDATFEKITMINQKGLY--L 123
             A   E  G    +VN AGI  + +     ++      L  A FEK   IN  G +  +
Sbjct: 68  GFARAREAHGQERVLVNCAGIATVGKTTKRDRETGAISHLPLAAFEKTIRINLMGTFNCM 127

Query: 124 VSQAVGRLLVAK-----KKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAKELGK 178
              A G + +       ++GVIIN AS A  +G  GQ AYA +KA V   T   A++L  
Sbjct: 128 AKAAAGMITLDTVGEYGERGVIINTASVAAEDGQIGQVAYATSKAGVKGMTLPAARDLMG 187

Query: 179 YGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKLSEVA 238
            G+RV  I PGI     +  L              E+ +   A++   P  R G+  E A
Sbjct: 188 EGIRVNAILPGIFHTPMMDGLP-------------EKAQVALAASVPFP-KRLGRPEEYA 233

Query: 239 DLVAYYISDRSSYITGITTNVAG 261
            L  + +   + Y+   T  + G
Sbjct: 234 KLACFMV--ETEYMNAETVRLDG 254


Lambda     K      H
   0.313    0.131    0.361 

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: 136
Number of extensions: 5
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: 266
Length of database: 261
Length adjustment: 25
Effective length of query: 241
Effective length of database: 236
Effective search space:    56876
Effective search space used:    56876
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (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