GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutA in Azospirillum brasilense Sp245

Align Lactate utilization protein A (characterized)
to candidate AZOBR_RS01615 AZOBR_RS01615 Fe-S oxidoreductase

Query= SwissProt::Q81GA5
         (239 letters)



>FitnessBrowser__azobra:AZOBR_RS01615
          Length = 261

 Score =  234 bits (596), Expect = 2e-66
 Identities = 114/235 (48%), Positives = 152/235 (64%), Gaps = 1/235 (0%)

Query: 2   KVTLFVTCLVDMFETNVGKATVEVLERLGCEIEFPEAQVCCGQPAYNSGHVEAAKEAMKH 61
           +V LFVTCLVD++   VG A V++LE  GC +E P +Q CCGQPA+N+G    A++  + 
Sbjct: 9   RVGLFVTCLVDVYRPTVGFAAVKLLEDAGCTVEVPASQTCCGQPAFNAGDRATARDLARS 68

Query: 62  MIETFEDAEYIVTPSGSCATMFHE-YPHVFKDDPKWAKRAQKVADKTYEFTQFIVDVLKV 120
            I  FE  +++V PSGSCA    + YP +  DDP WA RA+ ++ +T+E   F+ DVL V
Sbjct: 69  TIAAFEGFDHVVVPSGSCAGQIRKHYPELLADDPAWAARARHLSARTHELVSFLTDVLGV 128

Query: 121 TDVGASLPGIATIHKSCHMTRMLGVKEAPGILLSNVKGLTVRDLPNVQNCCGFGGTFSVK 180
           TD GA   G  T H SC   R LGVKE P  LL+ V+GLT+ +LP  + CCGFGGTF VK
Sbjct: 129 TDTGARYDGTITYHDSCSGLRELGVKEQPRRLLAKVEGLTLNELPGAEVCCGFGGTFCVK 188

Query: 181 MTPISEQMVDEKVDSVMETGADYLIGADCGCLLNIGGRIERLGKEVKVMHIAEVL 235
              IS +MV+ K   +  T AD L+  D GCLLN+ G+++R G  V+V H+AEVL
Sbjct: 189 YPDISNRMVEAKTADIAGTKADTLLAGDMGCLLNMAGKLKREGSAVRVRHVAEVL 243


Lambda     K      H
   0.320    0.135    0.407 

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: 220
Number of extensions: 9
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: 239
Length of database: 261
Length adjustment: 24
Effective length of query: 215
Effective length of database: 237
Effective search space:    50955
Effective search space used:    50955
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