GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctQ in Pseudovibrio axinellae Ad2

Align TRAP transporter, subunit DctQ (characterized, see rationale)
to candidate WP_068004173.1 PsAD2_RS05440 TRAP transporter small permease

Query= uniprot:I7EY26
         (225 letters)



>NCBI__GCF_001623255.1:WP_068004173.1
          Length = 210

 Score =  107 bits (268), Expect = 1e-28
 Identities = 74/213 (34%), Positives = 113/213 (53%), Gaps = 23/213 (10%)

Query: 11  LINTLEETLIALLLGLMTLITFANVVARFVFNSNILWALELTVFLFAWLVLLGASYAVKV 70
           +I+  EE  IA +L +MTL+TF  VV R+ FNS    AL+ T  LFAWL+L G SY +K+
Sbjct: 7   IIDAFEEGFIATILAVMTLVTFWQVVMRYGFNSGWGGALQFTRVLFAWLILFGMSYGLKI 66

Query: 71  HAHLGVDAILNMVSPGARRVIGLISVGCCLVFSLLLLKGAYDYWAVFADLPPTSGRWFPT 130
            +HLGVDA + +      R  GLI     L+++ LL    +  W +  D   +SG     
Sbjct: 67  GSHLGVDAFIRLFPKPVFRTFGLIGALVTLLYAALLFDADWFGWVLGLDNRGSSG----G 122

Query: 131 GFDMKARSQSFYEVQDVPMVAIFGFLEDLINYGDSY-------EKLPKVVPYVVLPLSML 183
            FD  +R   +Y+   +P+      +EDL  + + Y       E++P+   YV+LP+ + 
Sbjct: 123 AFDYVSR---YYK---LPI-----GMEDL-KFPEWYQEMFGVKERVPRWWGYVILPIGLG 170

Query: 184 LMLLRFAQAAMQILRGDVDRLVASHEVEDEIAE 216
           L+  R  Q    IL G  D ++A+HE E+ + E
Sbjct: 171 LLAFRSLQMCWLILTGQRDTMIAAHEAEELVEE 203


Lambda     K      H
   0.327    0.142    0.427 

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: 113
Number of extensions: 4
Number of successful extensions: 1
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: 225
Length of database: 210
Length adjustment: 22
Effective length of query: 203
Effective length of database: 188
Effective search space:    38164
Effective search space used:    38164
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: 45 (21.9 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