GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Dyella japonica UNC79MFTsu3.2

Align Glucose/galactose transporter (characterized, see rationale)
to candidate N515DRAFT_1222 N515DRAFT_1222 MFS transporter, FHS family, L-fucose permease

Query= uniprot:A0KXM0
         (423 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1222
          Length = 422

 Score =  242 bits (618), Expect = 1e-68
 Identities = 146/415 (35%), Positives = 215/415 (51%), Gaps = 15/415 (3%)

Query: 12  SSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCFFGA 71
           SS   AG      AL+   SLFF+WG    LND+LIP  K  F LN  QA L+Q  F+  
Sbjct: 4   SSSRAAGRSPLPLALI--VSLFFLWGVANNLNDVLIPQFKKAFVLNDFQAGLVQSAFYLG 61

Query: 72  YFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASGITI 131
           YFLV++PAG  ++R GY+  +V GL +  +G  LF+PAA   TYG FL ALFV+ASG+  
Sbjct: 62  YFLVAMPAGIYMRRFGYKSAVVFGLALYGLGALLFWPAAQQGTYGFFLFALFVIASGLAF 121

Query: 132 LQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAASVSSELAQANA 191
           L+ +ANP+V  LG  E+A+ RLNL QAFN LG+      G   I S       +LA  +A
Sbjct: 122 LETSANPFVTLLGPRESAARRLNLAQAFNPLGSITGILIGQHFIFSGVEHTPEQLAALSA 181

Query: 192 ---------EAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKTSA 242
                    E   V+LPYL +   +    ++      P +    + A    + H      
Sbjct: 182 AERAAFVAHETAAVQLPYLAIGLVVLAWGLLILLTRFPAVHAVEEGAVP--RDHGALARL 239

Query: 243 LQSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVGRF 302
           L     +      F YVGA+V + S+L+ ++ +A + G P + AA+Y+       M GRF
Sbjct: 240 LGDRRFLATLAAQFFYVGAQVGVWSYLIRYV-QATMPGTPAKLAANYMLVSLACFMAGRF 298

Query: 303 IGSAVMQKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSLAL 362
            GSA+M+ +    +LA  A +   L + A+   G     A++    F S+M+PTIF+L +
Sbjct: 299 AGSALMRYVAPRRLLALFAAVNVALTVFAVAVPGVAGACALVACSFFMSVMYPTIFALGV 358

Query: 363 RDLGPHTSQ-GSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFY 416
              G    + GS +L + I+GGA++    G ++D  GI  A ++P   +  IL +
Sbjct: 359 EGRGDDERKLGSALLVMTIIGGAVLTAAMGAVSDAAGISRAMLVPAASFVVILLF 413


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: 486
Number of extensions: 25
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: 422
Length adjustment: 32
Effective length of query: 391
Effective length of database: 390
Effective search space:   152490
Effective search space used:   152490
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.

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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