GapMind for catabolism of small carbon sources

 

Aligments for a candidate for MFS-glucose in Sphingomonas koreensis DSMZ 15582

Align Glucose/galactose transporter (characterized, see rationale)
to candidate Ga0059261_3850 Ga0059261_3850 Fucose permease

Query= uniprot:A0KXM0
         (423 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_3850 Ga0059261_3850 Fucose
           permease
          Length = 423

 Score =  255 bits (651), Expect = 2e-72
 Identities = 150/400 (37%), Positives = 217/400 (54%), Gaps = 6/400 (1%)

Query: 23  RFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCFFGAYFLVSIPAGQL 82
           R A  ++ +LFF WGF+   ND LI  ++ VF L++T+A+L    FF A+  VS+PA  L
Sbjct: 9   RAAFAAVAALFFAWGFVCANNDPLIAAVRHVFRLSWTEALLTHIVFFFAFATVSLPAAAL 68

Query: 83  VKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASGITILQVAANPYVNA 142
           + R G  + I+  L     GC +         +G+ LG LF+LA+G+  LQVAANP   A
Sbjct: 69  LARAGATRTILIALGSMLAGCLVIQAVRWVPAFGVVLGGLFLLAAGVATLQVAANPLAAA 128

Query: 143 LGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAASVSSELAQANAEAEVVKLPYLL 202
           LG       RL L  + N+LG      FG+  +L+      +  A   A A  +   +L+
Sbjct: 129 LGPPGQRHFRLTLAHSLNSLGMVCGAHFGAQFLLAEVNLTPAMPASRVAGAPTIAHAFLV 188

Query: 203 LAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKTSALQSMHLVLGAVGIFVYVGAE 262
           +      LA++        +R   + AA       G   AL+S   + GA  I +YVGAE
Sbjct: 189 IGGLTFGLALLTL-----AVRRTIERAAPAPAPGGGLGDALRSRWAIAGAAAIGLYVGAE 243

Query: 263 VSIGSFLVNFLGEAHIVGMPEEQAAHYIA-YYWGGAMVGRFIGSAVMQKIPAGTVLAFNA 321
           VSIGS L+ FL     +G+P   A  Y+A  YWGGA+ GRF+GS  ++ IPA  +LA  A
Sbjct: 244 VSIGSVLIPFLSSPDTLGLPAAVAGAYVANLYWGGALAGRFLGSWALRFIPAARLLALFA 303

Query: 322 FMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSLALRDLGPHTSQGSGILCLAIV 381
             AA L L A+   G  A W +L +GLFNSI+FPT+F L L   G   +  SG+LC+AI 
Sbjct: 304 GSAAALCLAALVLPGPAAAWCVLAIGLFNSILFPTVFGLTLERSGVSEAATSGLLCVAIG 363

Query: 382 GGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFYGAKGS 421
            GA++P L G +AD  G+   F++P++ Y +IL +  + +
Sbjct: 364 AGAVLPFLVGRIADLAGLGWTFVIPMIGYVYILGFAFRAA 403


Lambda     K      H
   0.326    0.138    0.402 

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: 477
Number of extensions: 22
Number of successful extensions: 4
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: 423
Length of database: 423
Length adjustment: 32
Effective length of query: 391
Effective length of database: 391
Effective search space:   152881
Effective search space used:   152881
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 (21.7 bits)
S2: 50 (23.9 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 (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 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