GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Pseudomonas fluorescens GW456-L13

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate PfGW456L13_85 Urea ABC transporter, ATPase protein UrtE

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_85
          Length = 232

 Score =  160 bits (405), Expect = 2e-44
 Identities = 91/223 (40%), Positives = 127/223 (56%)

Query: 11  LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70
           +LQV  +  YYG    L G+   V  GE+  L+G NG GK+TL+  + G   A+ G+V +
Sbjct: 1   MLQVEKLHQYYGGSHILRGLTFDVKVGEVTCLLGRNGVGKTTLLKCLMGLLPAKEGAVNW 60

Query: 71  EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTLF 130
           EG+ IT    H+     IA  P+GR IF R+TV ENL MG          E    I+ LF
Sbjct: 61  EGKPITAFKPHQRVHAGIAYVPQGREIFGRLTVEENLLMGLSRFPGSEAKEVPAFIYELF 120

Query: 131 PRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLN 190
           P L +   +RGG LSGG+QQ L+IGRAL +RP+LL+LDEP+ G+ P ++K I   I+KL 
Sbjct: 121 PVLLQMKQRRGGDLSGGQQQQLAIGRALASRPRLLILDEPTEGIQPSVIKEIGAVIKKLA 180

Query: 191 EAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLA 233
               + + LVEQ    A  L+ +  VM  G++   G G+ + A
Sbjct: 181 ARGDMAILLVEQFYDFAAELADQYLVMSRGEIVQQGRGENMEA 223


Lambda     K      H
   0.320    0.137    0.387 

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: 173
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: 247
Length of database: 232
Length adjustment: 23
Effective length of query: 224
Effective length of database: 209
Effective search space:    46816
Effective search space used:    46816
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 (21.8 bits)
S2: 46 (22.3 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