GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0549 in Thiothrix lacustris DSM 21227

Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate WP_084260334.1 Q394_RS0103655 carbohydrate ABC transporter permease

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



>NCBI__GCF_000621325.1:WP_084260334.1
          Length = 281

 Score =  189 bits (481), Expect = 4e-53
 Identities = 95/266 (35%), Positives = 154/266 (57%)

Query: 7   LFSQIALLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALFEDGVLR 66
           L S+  L   I  +  FP  +M  T+ KT++ A+  P VW+F PT  N+       G   
Sbjct: 16  LVSRTLLAWAITFIIFFPLLFMFVTAFKTELQAIAVPSVWVFTPTWENFALVQERSGYFD 75

Query: 67  TLINSLIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLI 126
              NS+I ++ +T L L++ VPAA+++A    +  KD+  W ++ +M+  +   LP +++
Sbjct: 76  YAWNSVITSVGSTILGLLIAVPAAYSMAFSPTKRTKDILMWMLSTKMMPAVGALLPIYVL 135

Query: 127 ARNLGLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICL 186
            +  GLLD  I+LI+I+   NLPI++W++   F+ IP ++ EAAR++GAS     R + L
Sbjct: 136 CQTFGLLDNVISLIIIFTMMNLPIMVWMLYSNFKDIPIEILEAARMDGASLSEEFRHVLL 195

Query: 187 PLAMPGVAVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYGKIMATSTL 246
           PLAM G+A + +   + SWNE  + L LT + A T  ++  S+     L + K+ A S L
Sbjct: 196 PLAMGGMASTGLLCLVLSWNEAFWVLNLTAANAGTLASLVASYSSPEGLFWAKLSAVSVL 255

Query: 247 IVIPVLIFALIASKQLVRGLTMGAVK 272
            + P+++F   + KQLV+GLT GAVK
Sbjct: 256 AIAPIVVFGWFSQKQLVQGLTFGAVK 281


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: 262
Number of extensions: 11
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: 272
Length of database: 281
Length adjustment: 25
Effective length of query: 247
Effective length of database: 256
Effective search space:    63232
Effective search space used:    63232
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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