GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Pseudomonas simiae WCS417

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF2277 PS417_11610 urea ABC transporter ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__WCS417:GFF2277
          Length = 252

 Score =  166 bits (420), Expect = 4e-46
 Identities = 94/248 (37%), Positives = 146/248 (58%), Gaps = 8/248 (3%)

Query: 9   VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68
           VL + G++  F G +A+ ++ + I R +V  +IGPNGAGKTT  ++I G     +G+ + 
Sbjct: 12  VLAIEGLTVSFDGFKAVDNLNLYIDRNEVRVVIGPNGAGKTTVLDLICGKTRATSGSIQF 71

Query: 69  AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128
            G+       + + +AG+ R FQN  ++  +T  EN+ +      G  ++GA+F    FK
Sbjct: 72  DGQELTNMREYNIVRAGVGRKFQNPSIYENLTVFENLEMS--YPAGRKVWGALF----FK 125

Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188
                IA R +E+   + +G     +A  LS+G ++ LEI   L  DP+L+ LDEP AGM
Sbjct: 126 RNAQVIA-RVEEVAREIFLGDLLQQQADLLSHGQKQWLEIGMLLMQDPELLMLDEPVAGM 184

Query: 189 NATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNE 248
           +  E+ Q  EL++RI +  R++L+IEHD++ V  +  +VTVL  GK +AEG+ A VQ N 
Sbjct: 185 SVNERAQTAELLNRI-SQGRSVLVIEHDMEFVKSIAHKVTVLHQGKVLAEGSMASVQSNP 243

Query: 249 KVIEAYLG 256
           KVIE YLG
Sbjct: 244 KVIEVYLG 251


Lambda     K      H
   0.319    0.137    0.384 

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: 152
Number of extensions: 4
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: 260
Length of database: 252
Length adjustment: 24
Effective length of query: 236
Effective length of database: 228
Effective search space:    53808
Effective search space used:    53808
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 (21.7 bits)
S2: 47 (22.7 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