GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Pseudomonas fluorescens FW300-N2C3

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AO356_28370 AO356_28370 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28370
          Length = 265

 Score =  194 bits (494), Expect = 1e-54
 Identities = 107/244 (43%), Positives = 153/244 (62%), Gaps = 8/244 (3%)

Query: 7   TGQPLLQVNGVETYYGN-IRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQART 65
           T  P+LQ++ +E  Y   I A+  V + V KG++V L+GANGAGKST +       +A  
Sbjct: 3   TNVPILQIDDIEVLYEQTILAVRSVSLEVEKGQVVVLLGANGAGKSTTLKAASNLVRAER 62

Query: 66  GSVV-----FEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNL--KH 118
           G VV     ++G+D+TR   H +A   + Q  EGR  F ++TV ENL  GA    +  + 
Sbjct: 63  GEVVRGRIVYQGKDVTRSAPHTLAASGLVQVLEGRHCFAQLTVEENLLAGALARQVPRRQ 122

Query: 119 FAEDVEKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLI 178
              D+E ++  FPRLK R     G  SGGEQQM++IGRALMARP+L+LLDEPS+GLAP I
Sbjct: 123 LLADLELVYGHFPRLKLRRKSLAGYTSGGEQQMIAIGRALMARPQLVLLDEPSMGLAPQI 182

Query: 179 VKGIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVR 238
           V+ IFE +R+LN+ +G++  + EQN   ALR +H  YV+ +G+V   GS ++L A  +++
Sbjct: 183 VEEIFEIVRQLNQRDGVSFLIAEQNINVALRYAHHGYVLESGRVVSEGSAEQLAARSDLQ 242

Query: 239 AAYL 242
             YL
Sbjct: 243 DFYL 246


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: 191
Number of extensions: 5
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: 247
Length of database: 265
Length adjustment: 24
Effective length of query: 223
Effective length of database: 241
Effective search space:    53743
Effective search space used:    53743
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: 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