GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Cupriavidus basilensis 4G11

Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate RR42_RS34980 RR42_RS34980 oxidoreductase

Query= uniprot:B2T9V3
         (247 letters)



>FitnessBrowser__Cup4G11:RR42_RS34980
          Length = 251

 Score =  324 bits (830), Expect = 1e-93
 Identities = 169/251 (67%), Positives = 199/251 (79%), Gaps = 4/251 (1%)

Query: 1   MTQRLAGKTALITAAGQGIGLATAELFAREGARVIATDIR---IDGLAGKP-VEARKLDV 56
           MTQRLAGK AL+TAAGQGIG ATAE + REGARVIA DI    ++ LAG+P     +LDV
Sbjct: 1   MTQRLAGKLALVTAAGQGIGRATAEAYLREGARVIAADIDARLLEALAGQPGCTTLRLDV 60

Query: 57  RDDAAIKALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIRAFLPA 116
            D AA++A A + GA+D+LFN AGFVH G ILEC E  +DF+ +LNV+AMY M+RAFLPA
Sbjct: 61  TDGAAVQAAAKQAGALDILFNGAGFVHHGTILECDEAAFDFSMNLNVRAMYSMMRAFLPA 120

Query: 117 MLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNAICPGT 176
           M+ +  GSI+NM+S A S+KG PNRF Y A+KAAVIG+TKSVAAD+I  G+RCNAICPGT
Sbjct: 121 MVARRRGSIVNMASVAGSIKGAPNRFVYGATKAAVIGMTKSVAADYIGHGIRCNAICPGT 180

Query: 177 VASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDESSFTTG 236
           V SPSL QRI  QA+  G +L  V+AAFVARQPMGRIG   EIAALA+YLGSDES+FTTG
Sbjct: 181 VESPSLRQRIADQARDGGRSLAEVEAAFVARQPMGRIGSAAEIAALAVYLGSDESAFTTG 240

Query: 237 HAHVIDGGWSN 247
            A VIDGGWSN
Sbjct: 241 TAQVIDGGWSN 251


Lambda     K      H
   0.320    0.133    0.381 

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: 236
Number of extensions: 6
Number of successful extensions: 2
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: 247
Length of database: 251
Length adjustment: 24
Effective length of query: 223
Effective length of database: 227
Effective search space:    50621
Effective search space used:    50621
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 (21.8 bits)
S2: 46 (22.3 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