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 6937507 Sama_1663 glucose/galactose transporter (RefSeq)

Query= uniprot:A0KXM0
         (423 letters)



>FitnessBrowser__SB2B:6937507
          Length = 415

 Score =  593 bits (1530), Expect = e-174
 Identities = 307/422 (72%), Positives = 347/422 (82%), Gaps = 13/422 (3%)

Query: 1   MASSINTSSHTSSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQ 60
           MAS +  ++     SE G   Y FAL SLT+LFFMWGFITCLNDILIPHLKAVFSLNY Q
Sbjct: 1   MASGVPVTARHEGASEGGR--YGFALTSLTTLFFMWGFITCLNDILIPHLKAVFSLNYAQ 58

Query: 61  AMLIQFCFFGAYFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLG 120
           AMLIQFCFFGAYFLVS+PAG LVKRLGYQKGIV GL+ A++GCGLFYPAA  ATYG+FLG
Sbjct: 59  AMLIQFCFFGAYFLVSVPAGVLVKRLGYQKGIVVGLLTAALGCGLFYPAAVSATYGVFLG 118

Query: 121 ALFVLASGITILQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAA 180
           ALFVLASGIT+LQVAANPYV ALG  +TASSRL LTQAFN+LGTT+AP FGS+LILSVA 
Sbjct: 119 ALFVLASGITVLQVAANPYVTALGPVQTASSRLTLTQAFNSLGTTIAPAFGSVLILSVAV 178

Query: 181 SVSSELAQANAEAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKT 240
             S+E     AEA+ VKLPYLLL   L VLA++FA L LP I +     A   Q      
Sbjct: 179 GASAE-----AEADAVKLPYLLLCGMLIVLAVVFALLKLPHIHDQEDEVAATGQ------ 227

Query: 241 SALQSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVG 300
           SAL   HLVLGA+GIFVYVG EV+IGSFLVNFLGE+H+ GM E  AAHYIA+YWGGAMVG
Sbjct: 228 SALAHRHLVLGAIGIFVYVGGEVAIGSFLVNFLGESHVAGMAEADAAHYIAFYWGGAMVG 287

Query: 301 RFIGSAVMQKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSL 360
           RFIG+AVMQK+ AG VL FNA MAALLVLVAM +SG++AMWAIL VGLFNSIMFPTIFSL
Sbjct: 288 RFIGAAVMQKVDAGKVLGFNATMAALLVLVAMNSSGALAMWAILAVGLFNSIMFPTIFSL 347

Query: 361 ALRDLGPHTSQGSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFYGAKG 420
           AL++LGP T+QGSGILCLAIVGGA+VPLLQG+LAD++G+  +FILPV+CYG+ILFYG KG
Sbjct: 348 ALKNLGPATAQGSGILCLAIVGGALVPLLQGLLADSVGLSASFILPVLCYGYILFYGLKG 407

Query: 421 SK 422
            K
Sbjct: 408 CK 409


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: 635
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