Alignments for a candidate for Slc2a5 in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for Slc2a5 in Dyella japonica UNC79MFTsu3.2

Align The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized)
to candidate N515DRAFT_1228 N515DRAFT_1228 MFS transporter, SP family, galactose:H+ symporter

Query= TCDB::Q9XIH7
         (511 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1228
          Length = 463

 Score =  237 bits (605), Expect = 6e-67
 Identities = 146/457 (31%), Positives = 237/457 (51%), Gaps = 30/457 (6%)

Query: 31  ILASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLVGSGAAGRTSDWL 90
           +LA++  ++ G DIGV+SGAS FIK +  +SD  +E ++  +   + VG+  AG  S  L
Sbjct: 22  VLAALAGLMFGLDIGVISGASQFIKAEFAISDHTIEWIVSSMMFGAAVGALGAGWLSSHL 81

Query: 91  GRRYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAPVYTAEVAPASSR 150
           GR+ +++L    F  G+LL G A +   ++  R + G+ +G A   AP+Y AEVAP   R
Sbjct: 82  GRKRSLILGAILFVIGSLLCGLAWSPETLIAARVILGLAIGIATFTAPLYLAEVAPEHIR 141

Query: 151 GFLTSFPEIFINIGILLGYVSNYFFSKLPEHLGWRFMLGVGAVPSVFLAIGVLAMPESPR 210
           G + S  ++ I IGIL+ ++S+   + L  H  WR+MLGV A+P     +GVL +P+SPR
Sbjct: 142 GAMISTYQLMITIGILVAFLSD---TALSYHGAWRWMLGVIAIPGALFLLGVLGLPDSPR 198

Query: 211 WLVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIPDDMTDDVIVVPNKKSAGKGVW 270
           WL+++GR  +A  VL +    +        DI+  +  P    D                
Sbjct: 199 WLMMRGRRDEAIDVLRRLRGDEVVVAREAADIEEQLKTPQRGWD---------------- 242

Query: 271 KDLLVRPTPSVRHILIACLGIHFAQQASGIDAVVLYSPTIFSKAGLKSKNDQLLATVAVG 330
              L    P+ R  +     +   QQ +G++ V+ Y+P IF + G  +   Q+  T  VG
Sbjct: 243 ---LFAENPNFRRSVFLGALLQIMQQFTGMNVVMYYAPRIFQEMGYDTA-AQMWFTALVG 298

Query: 331 VVKTLFIVVGTCVVDRFGRRALLLTSMGGMFLSLTALGTSLT-VINRNPGQTLKWAIGLA 389
           +   L   +   ++DR+GR+ +L T    M + L  +G  +   IN   GQT ++     
Sbjct: 299 LTNVLATFIAIALIDRWGRKPILYTGFAVMAVGLGVVGALMNGGIN---GQTEQYT---C 352

Query: 390 VTTVMTFVATFSIGAGPVTWVYCSEIFPVRLRAQGASLGVMLNRLMSGIIGMTFLSLSKG 449
           V  ++ F+  F++ AGP+ W  CSEI P++ R  G  +    N + + ++G TFLSL   
Sbjct: 353 VAMLLFFIVGFAMSAGPLVWTLCSEIQPLKGRDFGIGVSTFTNWITNMVVGFTFLSLLNT 412

Query: 450 LTIGGAFLLFAGVAAAAWVFFFTFLPETRGIPLEEME 486
           +     F L+A + A   V  F  +PET+G+ LE++E
Sbjct: 413 IGNASTFWLYAALNAVFIVLTFWLVPETKGVTLEQIE 449


Lambda     K      H
   0.324    0.140    0.415 

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: 695
Number of extensions: 55
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: 511
Length of database: 463
Length adjustment: 34
Effective length of query: 477
Effective length of database: 429
Effective search space:   204633
Effective search space used:   204633
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources