GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc2a5 in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_883 Major myo-inositol transporter IolT

Query= TCDB::Q9XIH7
         (511 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_883
          Length = 472

 Score =  230 bits (586), Expect = 1e-64
 Identities = 149/488 (30%), Positives = 246/488 (50%), Gaps = 25/488 (5%)

Query: 1   MNSSGVEQGVVIAESEPPRGNRSRYAFACAILASMTSIILGYDIGVMSGASIFIKDDLKL 60
           +NS G       A   P +    RY      +A+   ++ G+D GV++GA +++KDDL L
Sbjct: 3   INSYGNTADTSAAYVSPEKHQAQRYLQKITWIATFGGLLFGFDTGVINGALLYMKDDLGL 62

Query: 61  SDVQLEILMGILNIYSLVGSGAAGRTSDWLGRRYTIVLAGAFFFCGALLMGFATNYPFIM 120
           +     ++   L I +++G+  +GR SD  GRR  I+     FF GAL    A     ++
Sbjct: 63  TPFTEGLVASALLIGAMMGALFSGRLSDLKGRRRIILFLAVVFFLGALACALAPTLDVMV 122

Query: 121 VGRFVAGIGVGYAMMIAPVYTAEVAPASSRGFLTSFPEIFINIGILLGYVSNYFFSKLPE 180
             RF  G+ VG A ++ P Y +E+AP+S RG + +  E+ I  G  L + +N     L  
Sbjct: 123 AARFTLGLAVGGASVVVPAYLSEMAPSSIRGRIITRNELMIVTGQFLAFTTNATLGNLFS 182

Query: 181 HLG--WRFMLGVGAVPSVFLAIGVLAMPESPRWLVLQGRLGDAFKVLDKTSNTKEEAISR 238
            L   WR+ML +  +P+V L +G+L MPESPRWL  +GR  +  +VL K    +  A + 
Sbjct: 183 DLDGVWRWMLALATLPAVALWLGMLYMPESPRWLATKGRFREGLEVL-KLVREEYYAKAE 241

Query: 239 LDDIKRAVGIPDDMTDDVIVVPNKKSAGKGVWKDLLVRPTPSVRHILIACLGIHFAQQAS 298
           ++ I + +              N++   KG W+DL  +     R I +  +GI    Q +
Sbjct: 242 MEAITQQIS-------------NERFIKKGGWRDLSQK---GARRIFLIGIGIAVTSQLT 285

Query: 299 GIDAVVLYSPTIFSKAGLKSKNDQLLATVAVGVVKTLFIVVGTCVVDRFGRRALLLTSMG 358
           G+++++ +   I ++AGL+ ++  L+A V  G++      VG  ++DR GRR ++L    
Sbjct: 286 GVNSIMYFGTQILTEAGLEQRS-ALIANVVNGIISIGATFVGIALLDRVGRRPMMLLGFT 344

Query: 359 GMFLSLTALGTSLTVINRNPGQTLKWAIGLAVTTVMTFVATFSIGAGPVTWVYCSEIFPV 418
           G  LSL  +G     ++ +  + +     L +  +  F+A+     GP  WV  +EIFP+
Sbjct: 345 GTTLSLLLIGLVSVFVDPSVTRAM-----LILGAMAMFLASMQGLIGPAFWVLLAEIFPM 399

Query: 419 RLRAQGASLGVMLNRLMSGIIGMTFLSLSKGLTIGGAFLLFAGVAAAAWVFFFTFLPETR 478
           R+R     + +    L + +IGM F SL   + IG  F +F G    +  F   ++PETR
Sbjct: 400 RIRGGCMGMAIAAFWLTNVMIGMFFPSLVAMIGIGQTFFVFVGAGLLSLTFVAVWVPETR 459

Query: 479 GIPLEEME 486
           G  LEE+E
Sbjct: 460 GSTLEEIE 467


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: 665
Number of extensions: 47
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: 472
Length adjustment: 34
Effective length of query: 477
Effective length of database: 438
Effective search space:   208926
Effective search space used:   208926
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:

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