GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc2a5 in Klebsiella michiganensis M5al

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 BWI76_RS17580 BWI76_RS17580 MFS transporter

Query= TCDB::Q9XIH7
         (511 letters)



>FitnessBrowser__Koxy:BWI76_RS17580
          Length = 479

 Score =  204 bits (520), Expect = 4e-57
 Identities = 141/479 (29%), Positives = 236/479 (49%), Gaps = 25/479 (5%)

Query: 31  ILASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLVGSGAAGRTSDWL 90
           ++A+   ++ GYD GV++GA   +K  + L+     ++M +L I + +GS   G+ +D+ 
Sbjct: 20  LVATFGGLLFGYDTGVINGAFSSLKQYMALTPTTEGLVMSVLLIGAALGSVFGGKFADFF 79

Query: 91  GRRYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAPVYTAEVAPASSR 150
           GRR  ++     FF GAL+   A +   +++ RF+ G  VG A + AP + +EVAP   R
Sbjct: 80  GRRKYLLFLSFIFFIGALMSALAPDITVLLISRFILGYAVGGASVTAPTFISEVAPTEMR 139

Query: 151 GFLTSFPEIFINIGILLGYVSNYFFSKLPEHLG--WRFMLGVGAVPSVFLAIGVLAMPES 208
           G LT   E+ I IG L  +  N     L  HL   WR+ML V  +P++ L IG+L  PES
Sbjct: 140 GKLTGLNEVAIVIGQLAAFAINAIIGILWGHLPDVWRYMLMVQTIPAICLFIGMLRSPES 199

Query: 209 PRWLVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIPDDMTDDVIVVPNKKSAGKG 268
           PRWL+ + R  +A ++L            ++  ++RA    +D+T  +    +KK   + 
Sbjct: 200 PRWLISKNRHEEALEIL-----------KQIRPLERATKEFNDITTLIKAEADKKLHSQN 248

Query: 269 VWKDLLVRPTPSVRHILIACLGIHFAQQASGIDAVVLYSPTIFSKAGLKSKNDQLLATVA 328
            +  + +  TP +  +L+  +     QQ +G++ ++ Y   I S AG  S+   L+  V 
Sbjct: 249 AF--ITILQTPWIFKLLLVGVIWAALQQTTGVNVIMYYGTEILSSAGF-SERTSLICNVL 305

Query: 329 VGVVKTLFIVVGTC-VVDRFGRRALLLTSMGGM-FLSLTALGTSLTVINRNPGQTLKWAI 386
            GV     ++ G   +VDRF R+ +++     M  L L   G   T++  +   T  W +
Sbjct: 306 NGVFSVGGMLFGVLFLVDRFKRKTIIIYGFALMATLHLIIAGVDYTLVG-DIKATAIWLL 364

Query: 387 GLAVTTVMTFVATFSIGAGPVTWVYCSEIFPVRLRAQGASLGVMLNRLMSGIIGMTFLSL 446
           G        FV       G +TWV  +E+FP++ R     + V    +M+ I+   F  L
Sbjct: 365 G------AMFVGVMQGTMGFITWVVLAELFPLKFRGLSMGISVFFMWVMNAIVSYLFPLL 418

Query: 447 SKGLTIGGAFLLFAGVAAAAWVFFFTFLPETRGIPLEEMETLFGSYTANKKNNSMSKDN 505
              L +G  FL+FA +   A VF  T LPET    LE++E    +  +    N+ +K++
Sbjct: 419 QAKLGLGPVFLIFAAINYLAIVFVITALPETSNKSLEQLEEELSANKSTAGFNTATKES 477


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: 624
Number of extensions: 40
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: 479
Length adjustment: 34
Effective length of query: 477
Effective length of database: 445
Effective search space:   212265
Effective search space used:   212265
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