GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Azospirillum brasilense Sp245

Align Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized)
to candidate AZOBR_RS18775 AZOBR_RS18775 3-oxoacyl-ACP reductase

Query= SwissProt::Q92RN6
         (256 letters)



>FitnessBrowser__azobra:AZOBR_RS18775
          Length = 259

 Score =  145 bits (365), Expect = 1e-39
 Identities = 95/259 (36%), Positives = 143/259 (55%), Gaps = 17/259 (6%)

Query: 10  DLRDRGVLVTGGGSGIGAALVEAFARQGARVAFVDI----AAESSLALCEKVAAQTGQAP 65
           D RD+ VLVTG   GIGAA+ +AFA +GA VA   +    AAE+  A C  +  + G   
Sbjct: 2   DFRDKTVLVTGASRGIGAAIAKAFAAEGAAVAVNYLQNAEAAEAVAAACRDLGREAGGDA 61

Query: 66  HFIQADLRNVEAVRAAADEAVAKLGSVRVLVNNAARD---DRQALEAVTEESWDE---SL 119
             +QAD+ + EAV    +    + G + V+VNNA R    D +  +   +  W +    +
Sbjct: 62  WAVQADVTDAEAVNRMVERTAEEFGKIDVVVNNAFRPYAFDPEKRKLFWDTDWADYRGQV 121

Query: 120 SVNLRHLFFMCQAVAPHMQRQGGGSIVNFSSIAFLLNMPEIPA--YSTAKAGIIGLTKSL 177
              L   + +C+AV P M+R+ GGSIVN ++   L+  P +P   Y+TAKA ++G +++L
Sbjct: 122 DGALLGTYNVCRAVLPVMRRRPGGSIVNMATD--LVARPTVPYHDYTTAKAALVGFSRNL 179

Query: 178 AGKLGPDNIRVNAILPGMIVTERQRRLWLTEESIARMQERQC-LKRMLVADDLVGPCLFL 236
           A +LGP  IRVN + PG++      R   T+E +      Q  L+R+   +D+ GP LFL
Sbjct: 180 AAELGPLGIRVNCVAPGLVYPTDASR--ATKEDVKDAIVAQTPLRRIATPEDVTGPVLFL 237

Query: 237 ASDSSAAMTAQAMIIDGGV 255
           AS  S  MT Q + +DGG+
Sbjct: 238 ASGWSRFMTGQVLYVDGGL 256


Lambda     K      H
   0.321    0.133    0.377 

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: 10
Number of successful extensions: 5
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: 256
Length of database: 259
Length adjustment: 24
Effective length of query: 232
Effective length of database: 235
Effective search space:    54520
Effective search space used:    54520
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: 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