GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artQ in Collimonas arenae Ter10

Align arginine/ornithine transport protein (characterized)
to candidate WP_061534023.1 CAter10_RS14915 amino acid ABC transporter permease

Query= CharProtDB::CH_107317
         (229 letters)



>NCBI__GCF_001584165.1:WP_061534023.1
          Length = 219

 Score =  125 bits (313), Expect = 8e-34
 Identities = 73/208 (35%), Positives = 109/208 (52%), Gaps = 12/208 (5%)

Query: 12  GAWLTLQLALLSMLLAIVLGLLGAAFRLSPVRWLAWCGDLYATVVRGIPDLVLILLIFYG 71
           G   TL  A+ SML  ++LG   A  R+ P RW  W    Y +++RG P LV I +I+YG
Sbjct: 17  GVGYTLVFAVASMLGGLLLGFPLAIARIVPSRWAQWPATAYVSLMRGTPLLVQIFVIYYG 76

Query: 72  GQGLLNWVAPQLGYDDYIDLNPFVSGVGTLGFIFGAYLSETFRGAFMAIPKGQGEAGYGY 131
                    P +G    I  +P  +G+  L    GAYLSE+ RGA + +  GQ  A Y  
Sbjct: 77  --------LPSIG----ISFSPLTAGILALSLNAGAYLSESLRGAILGVHNGQWSASYSL 124

Query: 132 GMSHRQVFFRIQVPQMIRLAIPGFTNNWLVLVKATALISVVGLQDMMFKAKQASDATREP 191
           G+++ Q    I +PQ IR+A+P  +N  + L+K T+L+SV+ + ++M   K+    T  P
Sbjct: 125 GLNYGQTLRYIVIPQAIRIAVPSMSNTLISLIKDTSLVSVITVTELMLATKEVIAVTFRP 184

Query: 192 FTYYLAVAGLYLLVTSVSLLLLRLLERR 219
              YLA A +Y  ++     L   LER+
Sbjct: 185 LPLYLAAAAVYWCLSICFERLQIRLERK 212


Lambda     K      H
   0.328    0.144    0.442 

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: 123
Number of extensions: 8
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: 229
Length of database: 219
Length adjustment: 22
Effective length of query: 207
Effective length of database: 197
Effective search space:    40779
Effective search space used:    40779
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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