GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0549 in Sinorhizobium meliloti 1021

Align ABC transporter for Xylitol, permease component 2 (characterized)
to candidate SMc01498 SMc01498 sorbitol/mannitol transport inner membrane protein

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



>FitnessBrowser__Smeli:SMc01498
          Length = 276

 Score =  185 bits (470), Expect = 8e-52
 Identities = 95/273 (34%), Positives = 161/273 (58%), Gaps = 2/273 (0%)

Query: 1   MTSTRSLFSQIALLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIF-EPTLSNYREAL 59
           +++ R L + +    + I +  FP  W   TS KT+  A+ +PPV++F + T  NY E  
Sbjct: 5   VSTGRKLITTVVAWTIGILI-FFPILWTFLTSFKTEAQAIASPPVFLFFDWTTENYSEVQ 63

Query: 60  FEDGVLRTLINSLIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVL 119
                L+  +NS++++  +T L L++ +P+A+A+A    +  KD+  W ++ +M+ P+ +
Sbjct: 64  SRSDYLKHFMNSVVVSFGSTLLGLLIAIPSAWAMAFSPTKRTKDVLMWMLSTKMMPPVGV 123

Query: 120 ALPFFLIARNLGLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFT 179
            +P +LI RN GLLD    L+++    NLPI+IW++   F+ IP ++ EAAR++GAS   
Sbjct: 124 LVPMYLIFRNWGLLDTRTGLVIVLTLINLPIIIWMLYTYFKEIPGEILEAARMDGASLTK 183

Query: 180 IMRKICLPLAMPGVAVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYGK 239
            +  +  P+A+PG+A + + + I +WNE  + L L+ ++A    A   S+     L Y K
Sbjct: 184 EIIYVLTPMAIPGIASTLLLNIILAWNEAFWTLNLSAAKAAPLTAFIASYSSPEGLFYAK 243

Query: 240 IMATSTLIVIPVLIFALIASKQLVRGLTMGAVK 272
           + A ST+ + P+LI    + KQLVRGLT GAVK
Sbjct: 244 LSAASTMAIAPILILGWFSQKQLVRGLTFGAVK 276


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: 261
Number of extensions: 12
Number of successful extensions: 2
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: 276
Length adjustment: 25
Effective length of query: 247
Effective length of database: 251
Effective search space:    61997
Effective search space used:    61997
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 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