GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msdC2 in Azospirillum brasilense Sp245

Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate AZOBR_RS00065 AZOBR_RS00065 glycerol-3-phosphate transporter membrane protein

Query= uniprot:A3DHA2
         (303 letters)



>FitnessBrowser__azobra:AZOBR_RS00065
          Length = 276

 Score =  124 bits (310), Expect = 3e-33
 Identities = 66/202 (32%), Positives = 116/202 (57%), Gaps = 5/202 (2%)

Query: 101 LMFLNSAIMTIPIVIIQVIVGVFAAYAFAKLRFPLRDKLFFVFIVVMLMPLQVTLVPNYI 160
           +M  NS +M + I + ++ + + +AYA A  RFPLR   F++  + +++P++V ++P Y 
Sbjct: 70  IMMWNSLVMALVIALGKIAISIISAYAVAFFRFPLRMVFFWMIFITLMLPVEVRIIPTYE 129

Query: 161 LLRKLDMIGSFLSVILPGGFSAFGVVLLRQYMRGIPDECCEAAMIDGAGYLKTFTKIILP 220
           ++  L +I S+  + +P   SA   +L RQ+   IPDE  EAA IDGAG L+ F  ++LP
Sbjct: 130 VVANLGLIDSYAGLTIPLIASATATLLFRQFFLTIPDELVEAAKIDGAGALRFFLDVVLP 189

Query: 221 QCKSIIASLAILAFIDNWNMVEQPLIFLSDSAKYPLSVYLA-YINEG----DLGLAFASG 275
             ++ IA+L ++ FI  WN    PL+  + +    + + +   I  G    D  L  A+ 
Sbjct: 190 LSRTNIAALFVILFIYGWNQYLWPLLITNSAEMETVVIGITKMIGNGEAATDWNLIMATT 249

Query: 276 VLYMIPTVLIYLYGEKYFVEGI 297
           VL M+P V + +  +++FV+G+
Sbjct: 250 VLAMLPPVAVVVLMQRWFVKGL 271


Lambda     K      H
   0.331    0.147    0.425 

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: 198
Number of extensions: 11
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: 303
Length of database: 276
Length adjustment: 26
Effective length of query: 277
Effective length of database: 250
Effective search space:    69250
Effective search space used:    69250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 48 (23.1 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