GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Phaeobacter inhibens BS107

Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate GFF3147 PGA1_c31980 short chain dehydrogenase

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



>FitnessBrowser__Phaeo:GFF3147
          Length = 253

 Score =  121 bits (303), Expect = 2e-32
 Identities = 83/271 (30%), Positives = 136/271 (50%), Gaps = 32/271 (11%)

Query: 5   LNIAGKTVIVTGASSGIGKAIVDELLSLKVKVANFDL---------TDNGEKH--ENLLF 53
           + +AGK  IVTG +SG G  IV + L+   +V   D+         +D  E +  +  + 
Sbjct: 1   MRLAGKCAIVTGGASGFGAGIVTKFLTEGARVMIADINADAAAAAASDVCETYGPDRAIA 60

Query: 54  QKVDVTSREQVEASVAAVVEHFGTVDAVVNNAGIN-IPRLLVDPKDPHGQYELDDATFEK 112
           Q VDV+ R  V+    A + HFG +D +VNNAG++ +P  L D         + +  F++
Sbjct: 61  QTVDVSDRASVDQMAQAALNHFGQIDILVNNAGVSHLPTPLED---------VSEEDFDR 111

Query: 113 ITMINQKGLYLVSQAVGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSW 172
           +  +N K +YL ++A+   + +++ G I+N+AS AG+      + Y  +K  + + TR+ 
Sbjct: 112 VVAVNMKSVYLTARALVPHMKSRQSGAILNVASTAGVSPRPNLNWYNASKGWMITATRTM 171

Query: 173 AKELGKYGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSG 232
           A EL   GVRV  I P   E   L+T           G+   E+RA + S  T P+GR  
Sbjct: 172 AVELAPAGVRVNAINPVAGETPLLKTF---------MGEDTPEVRAKFLS--TIPIGRFS 220

Query: 233 KLSEVADLVAYYISDRSSYITGITTNVAGGK 263
              ++ +   Y  SD +S +TG+   V GG+
Sbjct: 221 TPEDMGNAACYLCSDEASMVTGVALEVDGGR 251


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: 150
Number of extensions: 5
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: 266
Length of database: 253
Length adjustment: 24
Effective length of query: 242
Effective length of database: 229
Effective search space:    55418
Effective search space used:    55418
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 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