GapMind for catabolism of small carbon sources

 

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

Align Glucose/galactose transporter (characterized, see rationale)
to candidate 6937233 Sama_1403 glucose/galactose transporter (RefSeq)

Query= uniprot:A0KXM0
         (423 letters)



>FitnessBrowser__SB2B:6937233
          Length = 415

 Score =  594 bits (1531), Expect = e-174
 Identities = 305/413 (73%), Positives = 345/413 (83%), Gaps = 11/413 (2%)

Query: 9   SHTSSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCF 68
           ++ +    AG  NYRFAL SLT+LFFMWGFITCLNDILIPHLKAVFSLNY QAMLIQFCF
Sbjct: 7   ANANHAGAAGAENYRFALGSLTTLFFMWGFITCLNDILIPHLKAVFSLNYAQAMLIQFCF 66

Query: 69  FGAYFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASG 128
           FGAYFLVS+PAG LVKRLGYQKGIV GL+ A++GCGLFYPAA  ATYG+FLGALFVLASG
Sbjct: 67  FGAYFLVSVPAGVLVKRLGYQKGIVVGLLTAALGCGLFYPAAVSATYGVFLGALFVLASG 126

Query: 129 ITILQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAASVSSELAQ 188
           IT+LQVAANPYV ALG  +TASSRL LTQAFN+LGTT+AP FGS+LILSVA   S+E   
Sbjct: 127 ITVLQVAANPYVTALGPVQTASSRLTLTQAFNSLGTTIAPAFGSVLILSVAVGASAE--- 183

Query: 189 ANAEAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKTSALQSMHL 248
             AEA+ VKLPYLLL   L VLA++FA L LP I +     A   Q      SAL   HL
Sbjct: 184 --AEADAVKLPYLLLCGMLIVLAVVFALLKLPHIHDQEDEVAATGQ------SALAHRHL 235

Query: 249 VLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVGRFIGSAVM 308
           VLGA+GIFVYVG EV+IGSFLVNFLGE+H+ GM E  AAHYIA+YWGGAMVGRFIG+AVM
Sbjct: 236 VLGAIGIFVYVGGEVAIGSFLVNFLGESHVAGMAEADAAHYIAFYWGGAMVGRFIGAAVM 295

Query: 309 QKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSLALRDLGPH 368
           QK+ AG VL FNA MAALLVLVAM +SG++AMWAIL VGLFNSIMFPTIFSLAL++LGP 
Sbjct: 296 QKVDAGKVLGFNATMAALLVLVAMNSSGALAMWAILAVGLFNSIMFPTIFSLALKNLGPA 355

Query: 369 TSQGSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFYGAKGS 421
           T+QGSGILCLAIVGGA+VPLLQG+LAD++G+  +FILPV+CYG+ILFYG KGS
Sbjct: 356 TAQGSGILCLAIVGGALVPLLQGLLADSVGLSASFILPVLCYGYILFYGLKGS 408


Lambda     K      H
   0.326    0.138    0.402 

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: 638
Number of extensions: 28
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: 423
Length of database: 415
Length adjustment: 32
Effective length of query: 391
Effective length of database: 383
Effective search space:   149753
Effective search space used:   149753
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