GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc2a5 in Escherichia coli BW25113

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 17022 b2943 D-galactose transporter (NCBI)

Query= TCDB::Q9XIH7
         (511 letters)



>FitnessBrowser__Keio:17022
          Length = 464

 Score =  226 bits (577), Expect = 1e-63
 Identities = 140/468 (29%), Positives = 241/468 (51%), Gaps = 28/468 (5%)

Query: 19  RGNRSRYAFACAILASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLV 78
           R N++   F C  LA++  ++ G DIGV++GA  FI D+ +++    E ++  +   + V
Sbjct: 9   RSNKAMTFFVC-FLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVSSMMFGAAV 67

Query: 79  GSGAAGRTSDWLGRRYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAP 138
           G+  +G  S  LGR+ ++++    F  G+L    A N   +++ R + G+ VG A   AP
Sbjct: 68  GAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAP 127

Query: 139 VYTAEVAPASSRGFLTSFPEIFINIGILLGYVSNYFFSKLPEHLGWRFMLGVGAVPSVFL 198
           +Y +E+AP   RG + S  ++ I IGIL  Y+S+  FS       WR+MLGV  +P++ L
Sbjct: 128 LYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYTG---AWRWMLGVIIIPAILL 184

Query: 199 AIGVLAMPESPRWLVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIPDDMTDDVIV 258
            IGV  +P+SPRW   + R  DA +VL +  +T  EA   LD+I+ ++ +          
Sbjct: 185 LIGVFFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLQV---------- 234

Query: 259 VPNKKSAGKGVWKDLLVRPTPSVRHILIACLGIHFAQQASGIDAVVLYSPTIFSKAGLKS 318
               K +G  ++K+       + R  +   + +   QQ +G++ ++ Y+P IF  AG  +
Sbjct: 235 ----KQSGWALFKE-----NSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTN 285

Query: 319 KNDQLLATVAVGVVKTLFIVVGTCVVDRFGRRALLLTSMGGMFLSLTALGTSLTVINRNP 378
             +Q+  TV VG+   L   +   +VDR+GR+  L      M   +  LGT + +   +P
Sbjct: 286 TTEQMWGTVIVGLTNVLATFIAIGLVDRWGRKPTLTLGFLVMAAGMGVLGTMMHIGIHSP 345

Query: 379 GQTLKWAIGLAVTTVMTFVATFSIGAGPVTWVYCSEIFPVRLRAQGASLGVMLNRLMSGI 438
                 A   A+  ++ F+  F++ AGP+ WV CSEI P++ R  G +     N + + I
Sbjct: 346 S-----AQYFAIAMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMI 400

Query: 439 IGMTFLSLSKGLTIGGAFLLFAGVAAAAWVFFFTFLPETRGIPLEEME 486
           +G TFL++   L     F ++A +     +     +PET+ + LE +E
Sbjct: 401 VGATFLTMLNTLGNANTFWVYAALNVLFILLTLWLVPETKHVSLEHIE 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: 679
Number of extensions: 32
Number of successful extensions: 4
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: 464
Length adjustment: 34
Effective length of query: 477
Effective length of database: 430
Effective search space:   205110
Effective search space used:   205110
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