GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1B in Cupriavidus basilensis 4G11

Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate RR42_RS04400 RR42_RS04400 ABC transporter permease

Query= TCDB::A1VZQ3
         (250 letters)



>FitnessBrowser__Cup4G11:RR42_RS04400
          Length = 219

 Score =  139 bits (349), Expect = 6e-38
 Identities = 67/199 (33%), Positives = 120/199 (60%)

Query: 45  INGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIFFLF 104
           + G + T++ ++L+++   + GT+  +M  S   + +A  R YV + +  PL++QIF ++
Sbjct: 15  LQGMLLTIKFALLSMIFGLVLGTVVALMGISHQPVPKAVARAYVSIMRGTPLLVQIFVVY 74

Query: 105 YALPVLGIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQQMRY 164
           Y LP +GI L+    GVL +    GAY+SE +R  IL +PRGQ+ A+ S G T  Q +RY
Sbjct: 75  YGLPGIGIALEPTPAGVLTLSLNVGAYLSESMRGAILGIPRGQWLAAYSLGLTQGQALRY 134

Query: 165 IIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAPAYIFAAVL 224
           +I PQ +R+ +P ++N +++LIK+TS++ ++   EL+ +A    A      P Y+  A +
Sbjct: 135 VIGPQALRLAVPSLSNSLISLIKDTSLVSVITVTELLRTAQEVIAATYQPLPLYLAVAAI 194

Query: 225 YFIICYPLAYFAKAYENKL 243
           Y+++   LA+  +  E +L
Sbjct: 195 YWMLSTALAHMQRLLERRL 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: 130
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: 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