GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc2a5 in Pantoea rwandensis LMG 26275

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 WP_084932255.1 HA51_RS04135 sugar porter family MFS transporter

Query= TCDB::Q9XIH7
         (511 letters)



>NCBI__GCF_002095475.1:WP_084932255.1
          Length = 474

 Score =  237 bits (605), Expect = 6e-67
 Identities = 143/474 (30%), Positives = 244/474 (51%), Gaps = 27/474 (5%)

Query: 19  RGNRSRYAFACAILASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLV 78
           +    RY     ++A+   ++ GYD+GV++GA  ++   L L+ +   ++   L + ++ 
Sbjct: 4   QAEHKRYMRKIIVIATFGGLLFGYDVGVINGALPYMAKSLGLNSLSTGLITSALLMGAVF 63

Query: 79  GSGAAGRTSDWLGRRYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAP 138
           G+   G+ SD +GRR  I+     FF   L    A +   +MV RFV G  VG A +  P
Sbjct: 64  GAILGGKLSDLVGRRKNILFLALLFFVSTLGCSIAPDIQTMMVCRFVLGFAVGGASVTVP 123

Query: 139 VYTAEVAPASSRGFLTSFPEIFINIGILLGYVSNYFFSKL---PEHLGWRFMLGVGAVPS 195
            Y AE+APA SRG + ++ E+ I  G+L+ ++SN          EH+ WR+ML +  +P+
Sbjct: 124 TYLAEMAPAQSRGRMVTWNELMIVGGVLIAFISNAVLGITLGENEHV-WRYMLALAMIPA 182

Query: 196 VFLAIGVLAMPESPRWLVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIPDDMTDD 255
           V L  G+L +PESPRWLV QGR  +A  VL++  +     I  L +IK A+         
Sbjct: 183 VCLFFGMLTVPESPRWLVKQGREAEAKSVLERIRDEHTAGI-ELYNIKHAIS-------- 233

Query: 256 VIVVPNKKSAGKGVWKDLLVRPTPSVRHILIACLGIHFAQQASGIDAVVLYSPTIFSKAG 315
                +++  GK  +++L +   P +R I++  + +    Q +G+++++ +   I   AG
Sbjct: 234 -----HEQQLGKVKFRELNI---PWIRRIMLIGIAVAVFSQTTGVNSIMYFGTEILRDAG 285

Query: 316 LKSKNDQLLATVAVGVVKTLFIVVGTCVVDRFGRRALLLTSMGGMFLSLTALGTSLTVIN 375
           L++ +  L+   A G++  L    G  ++DR GRR ++L  + G  + L  +  + +++ 
Sbjct: 286 LET-SAALIGNTAFGLISVLSTFAGIWLLDRAGRRPMMLVGLAGTTVILLVIAIATSMLA 344

Query: 376 RNPGQTLKWAIGLAVTTVMTFVATFSIGAGPVTWVYCSEIFPVRLRAQGASLGVMLNRLM 435
            NP         + +T  + F+A      GPV WV  SEIFP+R+R  G  + V    + 
Sbjct: 345 GNPAMPY-----VVLTLTVIFLAFMQGAIGPVLWVTLSEIFPLRIRGAGMGISVAFLWIT 399

Query: 436 SGIIGMTFLSLSKGLTIGGAFLLFAGVAAAAWVFFFTFLPETRGIPLEEMETLF 489
           +  IG+TF  + +G  + G F  FA +    ++    F PET+G  LEE+E  F
Sbjct: 400 NFFIGLTFPMMLEGFGLSGTFFAFAAIGVVGFIIMKMFFPETKGKSLEEIEESF 453


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: 653
Number of extensions: 43
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: 474
Length adjustment: 34
Effective length of query: 477
Effective length of database: 440
Effective search space:   209880
Effective search space used:   209880
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 24 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