GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc2a5 in Methanobacterium lacus AL-21

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_013644894.1 METBO_RS06515 sugar porter family MFS transporter

Query= TCDB::Q9XIH7
         (511 letters)



>NCBI__GCF_000191585.1:WP_013644894.1
          Length = 453

 Score =  283 bits (723), Expect = 1e-80
 Identities = 164/466 (35%), Positives = 265/466 (56%), Gaps = 32/466 (6%)

Query: 25  YAFACAILASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLVGSGAAG 84
           +    A + S+  ++ GYD GV+SGA +FI++D  LS    E+ +  + I +++G+  +G
Sbjct: 13  FVILVAAITSIGGLLFGYDTGVISGAILFIREDFLLSTTAQEVTVSAVLIGAVIGASISG 72

Query: 85  RTSDWLGRRYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAPVYTAEV 144
             +D  GR+  IVLA   F  GA+    + N   +++ R V GI +G A  I P+Y AEV
Sbjct: 73  ILADRYGRKIMIVLASIIFGIGAIFSSVSPNVNALIISRVVVGIAIGMASFIVPLYIAEV 132

Query: 145 APASSRGFLTSFPEIFINIGILLGYVSNYFFSKLPEHLGWRFMLGVGAVPSVFLAIGVLA 204
           AP + RG L S  ++ I +GI++ Y+ + +F+    +  WR+MLG+  +PS+ LA+G+  
Sbjct: 133 APINIRGALVSLNQLAITLGIVISYMVDLYFA---PNGSWRWMLGLAVIPSLILALGMFF 189

Query: 205 MPESPRWLVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIPDDMTDDVIVVPNKKS 264
           MP SPRWL+ +G    A  VL K        I  +D++ + V    +  +  +++ N   
Sbjct: 190 MPPSPRWLISKGFESKAVAVLKK--------IRGIDNVDKEV----NEIEQTLLLEN--- 234

Query: 265 AGKGVWKDLLVRPTPSVRHILIACLGIHFAQQASGIDAVVLYSPTIFSKAGLKSKNDQLL 324
             +G W DLL    P +R  LI  +G+   QQ +GI+ V+ Y+PTI   AGL++    + 
Sbjct: 235 --EGKWSDLL---EPKIRSALIIGIGLAAFQQLTGINTVIYYAPTILEFAGLQTATVTIF 289

Query: 325 ATVAVGVVKTLFIVVGTCVVDRFGRRALLLTSMGGMFLSLTALGTSLTVINRNPGQT--L 382
           ATV +GVV  L  VV   ++DR GRR LLL  + GM +SL  +G +  +    PG T  L
Sbjct: 290 ATVGIGVVNVLLTVVSILLIDRLGRRPLLLAGITGMIVSLGIMGLAFII----PGLTSSL 345

Query: 383 KWAIGLAVTTVMTFVATFSIGAGPVTWVYCSEIFPVRLRAQGASLGVMLNRLMSGIIGMT 442
            W   LAV  +M +V +F+I  GP+ W+  +EI+P+R+R +  S+  M+N   + ++ +T
Sbjct: 346 GW---LAVICLMLYVGSFAISLGPIFWLMIAEIYPLRIRGRAMSIVTMINWATNLVVAIT 402

Query: 443 FLSLSKGLTIGGAFLLFAGVAAAAWVFFFTFLPETRGIPLEEMETL 488
           FL++ + L   G F L+  +A  + +F +  +PET+G  LEE+E L
Sbjct: 403 FLTIIELLGASGTFWLYGVIAVLSLLFVYYRVPETKGKSLEEIERL 448


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: 649
Number of extensions: 41
Number of successful extensions: 6
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: 453
Length adjustment: 34
Effective length of query: 477
Effective length of database: 419
Effective search space:   199863
Effective search space used:   199863
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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