GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc2a5 in Pedobacter sp. GW460-11-11-14-LB5

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 CA265_RS01275 CA265_RS01275 hypothetical protein

Query= TCDB::Q9XIH7
         (511 letters)



>FitnessBrowser__Pedo557:CA265_RS01275
          Length = 462

 Score =  194 bits (493), Expect = 6e-54
 Identities = 143/482 (29%), Positives = 227/482 (47%), Gaps = 46/482 (9%)

Query: 25  YAFACAILASMTSIILGYDIGVMSGASIFIKDDLKLSDVQLEILMGILNIYSLVGSGAAG 84
           + F   ++A++   + G+D+ V+SG    +K    LS  Q  + +    +  +VG   +G
Sbjct: 9   FIFLITLIAALGGFLFGFDMAVVSGIIEPLKSQYGLSSAQEGLFVSCALLGCIVGVSFSG 68

Query: 85  RTSDWLGRRYTIVLAGAFFFCGALLMGFATNYPFIMVGRFVAGIGVGYAMMIAPVYTAEV 144
             SD +GRR  + LA   F   A+   F+  YP ++  R +AG+GVG A  ++P+Y +EV
Sbjct: 69  YLSDKVGRRKVLFLAAILFLVSAVGFAFSVAYPVLIFFRVLAGMGVGVASNVSPLYISEV 128

Query: 145 APASSRGFLTSFPEIFINIGILLGYVSNYFFSKLPE-HLG--------------WRFMLG 189
           AP+  RG L  F ++ I IGIL  Y+SN F  +    H G              WR M  
Sbjct: 129 APSQKRGRLVVFYQLAITIGILAAYISNLFLQRYATVHAGAGEGILHWLFVENVWRGMFI 188

Query: 190 VGAVPSVFLAIGVLAMPESPRWLVLQGRLGDAFKVLDKTSNTKEEAISRLDDIKRAVGIP 249
           VG VP+    + +L +PESPRWLV  GR  +A   L K  N  E     LD IK      
Sbjct: 189 VGVVPAAAFCLLLLIVPESPRWLVQYGRNEEALNTLIKI-NGAETGRLELDSIKE----- 242

Query: 250 DDMTDDVIVVPNKKSAGKGVWKDLLVRPTPSVRHILIACLGIHFAQQASGIDAVVLYSPT 309
                    + ++KS G   +K+L+  P   +  +L     +    Q SGI+ V+ Y PT
Sbjct: 243 ---------MASQKSGG---YKELMRLP---LSKLLALATILTALSQFSGINGVIFYGPT 287

Query: 310 IFSKAGLKSKNDQLLATVAVGVVKTLFIVVGTCVVDRFGRRALLLTSMGGMFLSLTALGT 369
           I   AG+ + +D L   V +G    LF  +    VD +GRR L +  +G +  +     T
Sbjct: 288 ILKSAGIVT-SDALFYQVILGSANVLFTFIAISKVDTWGRRPLYI--IGSLCAAGALALT 344

Query: 370 SLTVINRNPGQTLKWAIGLAVTTVMTFVATFSIGAGPVTWVYCSEIFPVRLRAQGASLGV 429
               +    G    W     + +++ F+  F+   GP+ +V  +EIFP  +R    S+ +
Sbjct: 345 GFCFLMDITG----W---FMLFSIILFLLFFAFSLGPLKFVISTEIFPTHIRGTALSMCI 397

Query: 430 MLNRLMSGIIGMTFLSLSKGLTIGGAFLLFAGVAAAAWVFFFTFLPETRGIPLEEMETLF 489
           M   +   ++ M F  +  GL I   F +F+     ++++    L ET+G  LEE+E  +
Sbjct: 398 MTMWVSDWVVNMLFPIMRDGLGIATTFFIFSFFCILSFLYAKKKLFETKGKSLEEIEKAW 457

Query: 490 GS 491
            S
Sbjct: 458 NS 459


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: 592
Number of extensions: 33
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: 462
Length adjustment: 34
Effective length of query: 477
Effective length of database: 428
Effective search space:   204156
Effective search space used:   204156
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