GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1B in Pseudomonas fluorescens FW300-N1B4

Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate Pf1N1B4_1694 Cystine ABC transporter, permease protein

Query= TCDB::A1VZQ3
         (250 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1694
          Length = 221

 Score =  131 bits (329), Expect = 1e-35
 Identities = 68/209 (32%), Positives = 114/209 (54%)

Query: 37  ALDNKDAFINGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPL 96
           ALD+    + G  YT+ +S+  +    + G    +M  SRFK++    RIYV  F+  PL
Sbjct: 8   ALDSAPFLLKGAYYTVILSLGGMFFGLLMGFGLALMRLSRFKLVSWIARIYVSFFRGTPL 67

Query: 97  VIQIFFLFYALPVLGIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGF 156
           ++Q+F ++Y LP LGI LD     ++G      AY  E++R+ I ++ RGQ+EA+AS G 
Sbjct: 68  LVQLFVIYYGLPQLGIELDPLPAALIGFSLNMAAYACEILRAAISSIERGQWEAAASIGM 127

Query: 157 TYIQQMRYIIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAP 216
           T  Q +R  I+PQ  R  LPP+ N  ++L+K+T++   +   EL   A    A       
Sbjct: 128 TRAQTLRRAILPQAARTALPPLGNSFISLVKDTALAATIQVPELFRQAQLITARTFEIFT 187

Query: 217 AYIFAAVLYFIICYPLAYFAKAYENKLKK 245
            Y+ AA++Y+++   L++     E ++ +
Sbjct: 188 MYLAAALIYWVLATVLSHLQNQLEARVNR 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: 146
Number of extensions: 6
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: 221
Length adjustment: 23
Effective length of query: 227
Effective length of database: 198
Effective search space:    44946
Effective search space used:    44946
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