GapMind for catabolism of small carbon sources

 

Aligments for a candidate for peb1B in Shewanella sp. ANA-3

Align PEP1B, component of Uptake system for glutamate and aspartate (characterized)
to candidate 7023652 Shewana3_0881 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= TCDB::A1VZQ3
         (250 letters)



>lcl|FitnessBrowser__ANA3:7023652 Shewana3_0881 polar amino acid ABC
           transporter, inner membrane subunit (RefSeq)
          Length = 226

 Score =  115 bits (287), Expect = 1e-30
 Identities = 61/202 (30%), Positives = 110/202 (54%), Gaps = 1/202 (0%)

Query: 45  INGFIYTLEVSILALLIATIFGTIGGVMATSRFKIIRAYTRIYVELFQNVPLVIQIFFLF 104
           +NG   TL V+  A+L+  + G    +M  S    IR    +YV + +  P+V+Q+  L+
Sbjct: 25  LNGLKVTLIVTFFAMLLGAVLGVGTTLMKMSSKWYIRFPAELYVGVIRGTPVVVQLVILY 84

Query: 105 YALPVLGIRLDIFTIGVLGVGAYHGAYVSEVVRSGILAVPRGQFEASASQGFTYIQQMRY 164
           + + +    +D  T  ++  G   GAY+SE++R+GI AV +GQ EA+ S G +    M+ 
Sbjct: 85  FIV-LAAFDVDKVTAAIIAFGLNSGAYISEIIRAGIQAVDKGQTEAARSLGLSQAMTMKL 143

Query: 165 IIVPQTIRIILPPMTNQMVNLIKNTSVLLIVGGAELMHSADSYAADYGNYAPAYIFAAVL 224
           II+PQ I+ ILP + N+ + L+K T+V+  +GG +LM + +   +     +      A++
Sbjct: 144 IILPQAIKNILPALGNEFIVLLKETAVIGFIGGVDLMRAGEIIRSRTFEDSIPLFTCALI 203

Query: 225 YFIICYPLAYFAKAYENKLKKA 246
           Y  + Y   +    +E +LK++
Sbjct: 204 YLFLTYSFTFMLSKFEKRLKQS 225


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: 148
Number of extensions: 8
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: 250
Length of database: 226
Length adjustment: 23
Effective length of query: 227
Effective length of database: 203
Effective search space:    46081
Effective search space used:    46081
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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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