GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldox-small in Azospirillum brasilense Sp245

Align glycolaldehyde oxidoreductase small subunit (characterized)
to candidate AZOBR_RS27485 AZOBR_RS27485 oxidoreductase

Query= metacyc::MONOMER-18073
         (163 letters)



>FitnessBrowser__azobra:AZOBR_RS27485
          Length = 206

 Score =  143 bits (360), Expect = 2e-39
 Identities = 71/151 (47%), Positives = 96/151 (63%)

Query: 7   GEKIKIKVKVNGVLYERYVSPRILLVDFLREELGLTGTKIGCDTTTCGACTVLLNGKSVK 66
           G  + +  +VNG      V  R  L+D LRE LGL G K GCD   CGACTV L+G+ V 
Sbjct: 49  GMTVHLSFRVNGRPTALDVDARASLLDLLRERLGLVGAKKGCDHGQCGACTVHLDGRRVA 108

Query: 67  SCTLFAVQADGAEITTIEGLSVDSKLHPIQEAFKENFALQCGFCTPGMIMQAYFLLKENP 126
           SC   A +ADG ++TTIEG++  + LHP+Q+AF ++ ALQCG+CTPG IM A   +KE  
Sbjct: 109 SCLTMAAKADGRDVTTIEGIAGANGLHPMQQAFIDHDALQCGYCTPGQIMAAIACVKEGH 168

Query: 127 NPSEEEVRDGLHGNICRCTGYQNIVKAVLDA 157
             + E++++ + GNICRC  Y  IV A+  A
Sbjct: 169 ASTPEQIKEYMSGNICRCGAYVGIVAAIEQA 199


Lambda     K      H
   0.322    0.138    0.409 

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: 112
Number of extensions: 5
Number of successful extensions: 1
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: 163
Length of database: 206
Length adjustment: 19
Effective length of query: 144
Effective length of database: 187
Effective search space:    26928
Effective search space used:    26928
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: 44 (21.6 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