GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc2a5 in Bacteroides faecis MAJ27

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_010537714.1 KCY_RS0114120 MFS transporter

Query= TCDB::Q9XIH7
         (511 letters)



>NCBI__GCF_000226135.1:WP_010537714.1
          Length = 309

 Score =  143 bits (361), Expect = 8e-39
 Identities = 97/321 (30%), Positives = 160/321 (49%), Gaps = 35/321 (10%)

Query: 25  YAFACAILASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLVGSGAAG 84
           Y    +++A++   + GYD  V+SG    +    +L  +Q    +G   I S+VG   AG
Sbjct: 9   YLIFLSVVAALGGFLFGYDTAVISGTIAQVSQLFQLDALQQGWYVGCALIGSIVGVLFAG 68

Query: 85  RTSDWLGRRYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAPVYTAEV 144
             SD LGR+ T+V++   F   AL    + ++  +++ R + G+G+G   +++P+Y +EV
Sbjct: 69  ILSDKLGRKLTMVISAVLFSTSALGCAISADFTQLVIYRIIGGVGIGVVSIVSPLYISEV 128

Query: 145 APASSRGFLTSFPEIFINIGILLGYVSNY---------------FFSKLPEHLGWRFMLG 189
           + A  RG L S  ++ + +G L  Y+ NY               + +K+     WR MLG
Sbjct: 129 SVAQYRGRLVSLYQLAVTVGFLGAYLVNYQLLGYAQSGSQLSIDWLNKIFVTEVWRGMLG 188

Query: 190 VGAVPSVFLAIGVLAMPESPRWLVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIP 249
           +  +P+V   I +  +PESPRWL+++G+   A  +L+K  N+  EA S+L++ K  +   
Sbjct: 189 MEMLPAVLFFIIIFFIPESPRWLIVKGKEEKAVNILEKIYNSVSEATSQLNETKSVL--- 245

Query: 250 DDMTDDVIVVPNKKSAGKGVWKDLLVRPTPSVRHILIACLGIHFAQQASGIDAVVLYSPT 309
                         S  K  W  LL++P      I+  C+ I    Q  G++AV+ Y P+
Sbjct: 246 -------------TSETKSEWA-LLMKPGIFKAVIIGVCIAI--LGQFMGVNAVLYYGPS 289

Query: 310 IFSKAGLKSKNDQLLATVAVG 330
           IF  AGL S  D L   V VG
Sbjct: 290 IFENAGL-SGGDSLFYQVLVG 309


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: 388
Number of extensions: 25
Number of successful extensions: 3
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: 309
Length adjustment: 31
Effective length of query: 480
Effective length of database: 278
Effective search space:   133440
Effective search space used:   133440
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: 50 (23.9 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