GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Slc2a5 in Sphingomonas koreensis DSMZ 15582

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 Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family

Query= TCDB::Q9XIH7
         (511 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1777 Ga0059261_1777 MFS
           transporter, sugar porter (SP) family
          Length = 458

 Score =  200 bits (508), Expect = 1e-55
 Identities = 135/458 (29%), Positives = 229/458 (50%), Gaps = 40/458 (8%)

Query: 33  ASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLVGSGAAGRTSDWLGR 92
           A++  ++ G+D  V+SGA+  ++    L+D  L   +    I +++GS  AG  +D  GR
Sbjct: 29  AALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADRFGR 88

Query: 93  RYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAPVYTAEVAPASSRGF 152
           +  ++     +   +L  G A +    +V RF+ G+ +G A ++ P+Y AEV+PA  RG 
Sbjct: 89  KGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGR 148

Query: 153 LTSFPEIFINIGILLGYVSNYFFSKLPEH-LGWRFMLGVGAVPSVFLAIGVLAMPESPRW 211
           L +  ++ I +GIL+ ++SNY  + L ++ + WR+M G+ AVPS    +  L +PESPRW
Sbjct: 149 LVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTLLLPESPRW 208

Query: 212 LVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIPD---DMTDDVIVVPNKKSAGKG 268
           L + G+                    R  D+ + +G  D   ++    +    +++AGK 
Sbjct: 209 LAIHGQ------------------ADRARDVMQRLGFADPRAELARIELAEAREEAAGK- 249

Query: 269 VWKDLLVRPTPSVRHILIAC-LGIHFAQQASGIDAVVLYSPTIFSKAGLKSKNDQLLATV 327
                  R         +AC + I    Q SGI+A++ Y+P IF  AG    +  LL ++
Sbjct: 250 ------PRLFQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAG-AGADSALLQSI 302

Query: 328 AVGVVKTLFIVVGTCVVDRFGRRALLLTSMGGMFLSLTALGTSLTVINRNPGQTLKWAIG 387
           AVG    +F V    ++DRFGRR LL   +G +  + T L     + +  P  T      
Sbjct: 303 AVGGTNLVFTVAALFLIDRFGRRPLLF--VGSVICAATLLLVGWQLESAKPDGT------ 354

Query: 388 LAVTTVMTFVATFSIGAGPVTWVYCSEIFPVRLRAQGASLGVMLNRLMSGIIGMTFLSLS 447
           L +  ++ F+A F++  G V WV+ SE+FP  +R +G +LG   + +M+  I   F   +
Sbjct: 355 LILFGLLGFIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFA 414

Query: 448 KGLTIGGAFLLFAGVAAAAWVFFFTFLPETRGIPLEEM 485
             +  G  F  F  +     ++ + F+PET GI LE+M
Sbjct: 415 ASVG-GWVFAFFGAMMLLQLLWTWKFMPETNGIALEDM 451


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: 602
Number of extensions: 38
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 511
Length of database: 458
Length adjustment: 34
Effective length of query: 477
Effective length of database: 424
Effective search space:   202248
Effective search space used:   202248
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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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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