GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1B in Paraburkholderia bryophila 376MFSha3.1

Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate H281DRAFT_00741 H281DRAFT_00741 amino acid ABC transporter membrane protein, PAAT family

Query= TCDB::A1VZQ3
         (250 letters)



>FitnessBrowser__Burk376:H281DRAFT_00741
          Length = 219

 Score =  137 bits (344), Expect = 2e-37
 Identities = 68/197 (34%), Positives = 116/197 (58%)

Query: 47  GFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIFFLFYA 106
           G + T++ ++L++    I G +  +M  S  + +    RIYV + +  PL++QIF ++Y 
Sbjct: 17  GAVLTVKFAVLSMFFGLIAGAMLALMGVSHSRTLNWIARIYVSVMRGTPLLVQIFVIYYG 76

Query: 107 LPVLGIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQQMRYII 166
           LP  GI LD    GV+ + A   AY+SE +R  IL + +GQ+ A+ S G +  Q +RY+I
Sbjct: 77  LPSFGISLDPTPAGVIALSANVAAYLSESMRGAILGIHQGQWLAAYSLGLSRRQTLRYVI 136

Query: 167 VPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAPAYIFAAVLYF 226
            PQ +RI +P ++N +++LIK+TS++ ++   EL+ SA    A      P Y+ AA +Y+
Sbjct: 137 APQALRIAVPSLSNSLISLIKDTSLVSVITVTELLRSAQEIIASTYQPLPLYLAAAAVYW 196

Query: 227 IICYPLAYFAKAYENKL 243
           ++C  L    + YE +L
Sbjct: 197 VLCQILELLQRWYERRL 213


Lambda     K      H
   0.328    0.143    0.422 

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: 123
Number of extensions: 7
Number of successful extensions: 1
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: 250
Length of database: 219
Length adjustment: 23
Effective length of query: 227
Effective length of database: 196
Effective search space:    44492
Effective search space used:    44492
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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