GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0549 in Rhodobacter viridis JA737

Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate WP_110804034.1 C8J30_RS01980 carbohydrate ABC transporter permease

Query= reanno::Dino:3607127
         (272 letters)



>NCBI__GCF_003217355.1:WP_110804034.1
          Length = 382

 Score =  115 bits (288), Expect = 1e-30
 Identities = 75/242 (30%), Positives = 130/242 (53%), Gaps = 16/242 (6%)

Query: 38  VALEAPPVWIFEPTLSNYREALFEDGVLRTLINSLIIAISTTFLALVLGVPAAFALARFE 97
           V   APP      T  NY   +  +G+ R  +N++ + I  T + +++   AA+ALA   
Sbjct: 148 VTTVAPP----RLTTGNYARVITAEGIGRAFLNTMTVTIPATVIPILIAAFAAYALAWMR 203

Query: 98  FRGKKDLWFWFITNRMISPIVLAL-PFFLIARNLGLLDKHITLILIYLTFNLPIVIWIVT 156
           F G+  L    I   ++ P+ LAL P   +   +GL   ++ + L +  F LP+ I+++ 
Sbjct: 204 FPGRA-LLVATIVGLLVVPLQLALIPLLKLHNQIGLNQSYLGIWLAHTGFGLPLAIYLLR 262

Query: 157 DQFRGIPYDLDEAARLEGASQFTIMRKICLPLAMPGVAVSAIFSFIFSWNELMFGLIL-- 214
           +   G+P ++ E+AR++GA++F I R+I LPL+ P +A  AIF F++ WN+L+   +   
Sbjct: 263 NYMVGLPREIIESARVDGATEFQIFRRIVLPLSFPALASFAIFQFLWVWNDLLVATVFLG 322

Query: 215 --TRSEAKTAPAMAVSFMEGYNLPYGKIMATSTL--IVIPVLIFALIASKQLVRGLTMGA 270
             T ++  T    A+    G +    +I+A S    I +P+++F  +  K LVRGL  G+
Sbjct: 323 NATDTQVMTGALRALLGSRGGD---WEILAASAFVSIAVPLIVFFAL-QKYLVRGLLAGS 378

Query: 271 VK 272
           VK
Sbjct: 379 VK 380


Lambda     K      H
   0.331    0.143    0.431 

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: 281
Number of extensions: 12
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: 272
Length of database: 382
Length adjustment: 28
Effective length of query: 244
Effective length of database: 354
Effective search space:    86376
Effective search space used:    86376
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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