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_28995 AO356_28995 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28995
          Length = 258

 Score =  190 bits (483), Expect = 2e-53
 Identities = 106/242 (43%), Positives = 151/242 (62%), Gaps = 8/242 (3%)

Query: 11  LLQVNGVETYY-GNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQA-----R 64
           LL V  +E  Y G I A+AGV + V +G+IV+L+GANGAGKST +  I G  QA      
Sbjct: 14  LLAVQDIEVIYDGAILAVAGVSLRVGQGDIVALLGANGAGKSTTLKAISGLVQADRAQVS 73

Query: 65  TGSVVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGL--DNLKHFAED 122
            G +VF+G+D   +  + +AR  I    EGR +F  +T+ +NL+ G  L     +    D
Sbjct: 74  RGRIVFQGQDTAGVAANLLARRGIVHVLEGRHVFAHLTIEDNLRSGGFLRKPTRRELEHD 133

Query: 123 VEKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGI 182
           +E+I+  FPRLK +   + G  SGGEQQML+IGRALM +P+L+LLDEPS+GLAP++V+ I
Sbjct: 134 LERIYAWFPRLKTKRKTQAGLTSGGEQQMLAIGRALMTQPRLVLLDEPSMGLAPILVEEI 193

Query: 183 FEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242
           F  + +LN  EG++  + EQN   ALR +  AY++ NG+V   G   EL A  +++  YL
Sbjct: 194 FAIVAQLNAQEGVSFLVAEQNINVALRHASYAYILENGRVVGEGDATELAAREDLQHFYL 253

Query: 243 EG 244
            G
Sbjct: 254 GG 255


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: 202
Number of extensions: 10
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: 258
Length adjustment: 24
Effective length of query: 223
Effective length of database: 234
Effective search space:    52182
Effective search space used:    52182
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