GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Shewanella amazonensis SB2B

Align Glucose/galactose porter (characterized)
to candidate 6936095 Sama_0292 glucose/galactose transporter (RefSeq)

Query= TCDB::P0C105
         (412 letters)



>FitnessBrowser__SB2B:6936095
          Length = 389

 Score =  451 bits (1161), Expect = e-131
 Identities = 231/385 (60%), Positives = 291/385 (75%), Gaps = 7/385 (1%)

Query: 28  LTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVKRISY 87
           +T LFF+WGFIT LNDILIPHLK  F+L+YTQ+ML+QFCFFGAYFIVS  AG+L+++I Y
Sbjct: 1   MTTLFFIWGFITALNDILIPHLKAAFELSYTQAMLVQFCFFGAYFIVSPFAGKLIEKIGY 60

Query: 88  KRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILGKPET 147
            RGIV GL   A GC LF PAA   VYALFL  LFVLASG+TILQV+ANPYV ILG   T
Sbjct: 61  IRGIVTGLCTMATGCLLFYPAAEVSVYALFLLGLFVLASGITILQVSANPYVAILGAERT 120

Query: 148 AASRLTLTQAFNSLGTTVAPVFGAVLILSAATDATVNAEADAVRFPYLLLALAFTVLAII 207
           AASRL+L QA NSLG T+AP+FGA LI  AA++A       AV+ PYL+LA A  + A+ 
Sbjct: 121 AASRLSLAQAINSLGHTLAPLFGAALIFGAASNA------HAVQLPYLILAGAVLLTAVG 174

Query: 208 FAILKPPDVQEDEPALSDKKEGSAWQYRHLVLGAIGIFVYVGAEVSVGSFLVNFLSDPTV 267
           F  LK P +Q D        + S WQ++HLVLGA+ IF+YVGAEVSVGSFLVN+ S+  +
Sbjct: 175 FVFLKLPTLQTDHETQVSHSD-SIWQHKHLVLGALAIFLYVGAEVSVGSFLVNYFSESHI 233

Query: 268 AGLSETDAAHHVAYFWGGAMVGRFIGSAAMRYIDDGKALAFNAFVAIILLFITVATTGHI 327
           A LSE +A+  V+Y+WGGAMVGRF+GSA  R +     LA NA +AI+LL +T+ ++G +
Sbjct: 234 AALSEQEASRMVSYYWGGAMVGRFVGSALTRILQPTYVLATNALMAILLLVLTMNSSGAL 293

Query: 328 AMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGILCLAIVGGAIVPLIQGALADAIG 387
           AMWSVLA+G FNSIMFPTIF+LA+ GLG  TS+GSG+LC AIVGGAI+PL+QG +AD+  
Sbjct: 294 AMWSVLAVGFFNSIMFPTIFTLAIRGLGPLTSRGSGLLCQAIVGGAILPLLQGVVADSSS 353

Query: 388 IHLAFLMPIICYAYIAFYGLIGSKS 412
           +  +F++P++ Y YI +Y L GSK+
Sbjct: 354 VQFSFVIPMVAYLYIGWYALRGSKA 378


Lambda     K      H
   0.328    0.141    0.420 

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: 568
Number of extensions: 14
Number of successful extensions: 2
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: 412
Length of database: 389
Length adjustment: 31
Effective length of query: 381
Effective length of database: 358
Effective search space:   136398
Effective search space used:   136398
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 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