GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Pantoea rwandensis LMG 26275

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_084933739.1 HA51_RS07065 urea ABC transporter ATP-binding protein UrtD

Query= uniprot:A0A165KC86
         (260 letters)



>NCBI__GCF_002095475.1:WP_084933739.1
          Length = 263

 Score =  137 bits (344), Expect = 3e-37
 Identities = 90/254 (35%), Positives = 143/254 (56%), Gaps = 13/254 (5%)

Query: 6   NEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGT 65
           ++ VL++  I+  F G +AL+D+ + I  G++  +IGPNGAGKTT  +VITG   PD G 
Sbjct: 19  SDPVLQLEKINVSFDGFRALTDLSLKIGVGELRCVIGPNGAGKTTLMDVITGKTRPDNGQ 78

Query: 66  FELAGKPYEPTAVH--EVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAV-F 122
             +  +  + T +   E+A+AGI R FQ   +F  +T  EN+ +   ++    ++ ++  
Sbjct: 79  V-IYDQDTDLTRMSPVEIARAGIGRKFQKPTVFEALTVSENLEIA--LKNDKSVWASLRA 135

Query: 123 RTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALD 182
           R  G + +      R  E+L  + +G     KA  LS+G ++ LEI   L  DP L+ LD
Sbjct: 136 RLNGEQQD------RIDEVLKLLRLGGERQRKAGLLSHGQKQFLEIGMLLVQDPHLLLLD 189

Query: 183 EPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPA 242
           EPAAGM   E     EL  R      +++++EHD+  V  + D VTVL  G+ +AEG+  
Sbjct: 190 EPAAGMTDAETEYTAELF-RSLAGKHSLMVVEHDMGFVETIADHVTVLHQGQVLAEGSLR 248

Query: 243 EVQKNEKVIEAYLG 256
           +VQ +++VI+ YLG
Sbjct: 249 QVQADDRVIDVYLG 262


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: 186
Number of extensions: 9
Number of successful extensions: 4
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: 263
Length adjustment: 25
Effective length of query: 235
Effective length of database: 238
Effective search space:    55930
Effective search space used:    55930
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 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