GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17600 in Desulfovibrio vulgaris Hildenborough

Align ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale)
to candidate 209325 DVU0389 amino acid ABC tranporter, permease protein, His/Glu/Gln/Arg/opine family

Query= uniprot:A0A1N7U128
         (237 letters)



>MicrobesOnline__882:209325
          Length = 224

 Score =  104 bits (259), Expect = 2e-27
 Identities = 62/192 (32%), Positives = 97/192 (50%), Gaps = 10/192 (5%)

Query: 22  GVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVEVYTYLFRGTPLYIQLLICYTG 81
           G+  ++ L + S  LG    I +   RV    W+R   ++YT  FRG PL +QL+I Y G
Sbjct: 18  GLITSMMLIVPSATLGLLFGIIVGTGRVFGPAWVRKAGDIYTATFRGVPLVVQLMIIYFG 77

Query: 82  LYSLEIVQDNALLNQFFRNALNCTLLAFVLNTCAYTVEIFAGAIRNIPHGEIEAARAYGL 141
           L ++ I          +       +L FVL + AY  E   GA+ +I  G+++AA+A G 
Sbjct: 78  LPNIGI----------YLEPFPAAVLGFVLCSAAYNSEYVRGALLSIRQGQLKAAQALGF 127

Query: 142 HGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLAFTATVADILKVARDANAETFLTFQ 201
              +  LF+VVP A+RRALP   NE+I ++  +SLA+  T  ++    +   A +F   +
Sbjct: 128 SKLKTVLFIVVPQAVRRALPGCGNEIIYLIKYSSLAYVITCIELTGEGKVVAARSFRFTE 187

Query: 202 AFGIAALLYMLL 213
            F      Y+ L
Sbjct: 188 VFLFVGAYYLFL 199


Lambda     K      H
   0.332    0.143    0.443 

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: 167
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: 237
Length of database: 224
Length adjustment: 23
Effective length of query: 214
Effective length of database: 201
Effective search space:    43014
Effective search space used:    43014
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 (22.0 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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