GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1B in Burkholderia phytofirmans PsJN

Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate BPHYT_RS21915 BPHYT_RS21915 ABC transporter permease

Query= TCDB::A1VZQ3
         (250 letters)



>FitnessBrowser__BFirm:BPHYT_RS21915
          Length = 222

 Score =  129 bits (325), Expect = 4e-35
 Identities = 68/201 (33%), Positives = 115/201 (57%), Gaps = 1/201 (0%)

Query: 45  INGFIYTLEVSILALLIATIFGTIGGV-MATSRFKIIRAYTRIYVELFQNVPLVIQIFFL 103
           ++G + T+EV+  +L ++ + G + G+   T + +I+  +   Y+  F+  PL++Q+F L
Sbjct: 16  LHGAVVTVEVTAASLALSCVLGLLIGIGRLTPKRRIVYGFCTAYLTFFRGTPLLVQLFLL 75

Query: 104 FYALPVLGIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQQMR 163
           F+ LP  GI L  F  G+LG+G Y  AYVSE+VR  I +V RGQ EA+ S G +  Q MR
Sbjct: 76  FFGLPQFGILLPAFVCGMLGLGLYSAAYVSEIVRGAIQSVDRGQMEAARSIGMSSGQAMR 135

Query: 164 YIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAPAYIFAAV 223
            II+PQ I  ++PP+ N+ + LIKN++++ ++   +LMH      +        Y+  A+
Sbjct: 136 AIILPQAIVRMIPPLGNEFIALIKNSALVSLLTIDDLMHEGQKIISVSYRSLEVYLAIAL 195

Query: 224 LYFIICYPLAYFAKAYENKLK 244
           +Y ++     Y     E  L+
Sbjct: 196 VYLVLTQATNYALHRVERHLR 216


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: 145
Number of extensions: 4
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: 222
Length adjustment: 23
Effective length of query: 227
Effective length of database: 199
Effective search space:    45173
Effective search space used:    45173
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