GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS17580 BWI76_RS17580 MFS
           transporter
          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 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