GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SSS-glucose in Bacteroides thetaiotaomicron VPI-5482

Align Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 (characterized)
to candidate 349883 BT0355 Na+/glucose cotransporter (NCBI ptt file)

Query= SwissProt::Q6R4Q5
         (597 letters)



>FitnessBrowser__Btheta:349883
          Length = 564

 Score =  374 bits (959), Expect = e-108
 Identities = 215/587 (36%), Positives = 343/587 (58%), Gaps = 31/587 (5%)

Query: 17  LTVVDIAIIAVYFALNVAVGIWSSCRASRNTVRGYFLAGRDMTWWPIGASLFASSEGSGL 76
           +  +D  +I V+F   + + +W   R  +N    YFL GRD TW  IGAS+FAS+ GS  
Sbjct: 1   MEALDWLVIGVFFLALIGIIVWV-VRQKQNDSADYFLGGRDATWLAIGASIFASNIGSEH 59

Query: 77  FIGLAGSGAAGGLAVAGFEWNATYVLLALAWVFVPIYLSSEIVTMPEYMQKRYGGQRIRM 136
            IGLAG+GA+ G+A+A +E    +++L L WVFVP Y  S + TMPE++++RY  Q  R 
Sbjct: 60  LIGLAGAGASSGMAMAHWEIQG-WMILILGWVFVPFYSRSMVYTMPEFLERRYNPQS-RT 117

Query: 137 YLSVLSLLLSVFTKISIDLYAGALFVHICLG----WN---FYLSTVIMLAITALYTIAGG 189
            LSV+SL+  V TK+++ +YAG L      G    W    F+++ + ++ +TALYTI GG
Sbjct: 118 ILSVISLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYTIFGG 177

Query: 190 LTAVIYTDALQTLVMVAGAVILTIKAFEQIGGYEQLAEAYAQAVPSRTISNTTCHVPRAD 249
           + +V+YT  LQT +++ G++I+ +  F+++GG++++      AV      +T  ++ R++
Sbjct: 178 MKSVLYTSVLQTPILLLGSLIILVLGFKELGGWDEMMRVCG-AVTVNDYGDTMTNLIRSN 236

Query: 250 AMHMFRDPYTADLPWTGMTFGLTIMAAWYWCTDQVIVQRSLSARDLNHAKGGSILASYLK 309
                     A+ PW G   G  I+  WYWCTDQ IVQR LS ++   A+ G+I  +YLK
Sbjct: 237 D--------DANFPWLGALIGSAIIGFWYWCTDQFIVQRVLSGKNEKEARRGTIFGAYLK 288

Query: 310 MLPMGLMVMPGMISRVLFPDDVGCVVPAECLRACGAEIGCSNIAYPKLVMELMPTGLRGL 369
           +LP+ L ++PGMI+  L    +G       L         ++ A+P LV +L+P G++GL
Sbjct: 289 LLPVFLFLIPGMIAFALHQKYIGAGGEG-FLPMLANGTANADAAFPTLVAKLLPAGVKGL 347

Query: 370 MVAVMMAALMSSLTSIFNSSSTLFTMDIWRRLRPRAGERELLLVGRLVIVVLVGVSVAWI 429
           +V  ++AALMSSL S+FNSS+ LFT+D ++R RP   E++L+ +G++  VV+V + + WI
Sbjct: 348 VVCGILAALMSSLASLFNSSAMLFTIDFYKRFRPETPEKKLVGIGQIATVVIVILGILWI 407

Query: 430 PVLQGSNGGQLFIYMQSVTSSLAPPVTAVFVLGIFWRRANEQGAFWGLMAGLAVGATRLV 489
           P+++ S G  L+ Y+Q V S LAP + A F+LGI W+R + QG  WGL+AG+ +G TRL 
Sbjct: 408 PIMR-SVGDVLYTYLQDVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGLTRLG 466

Query: 490 LEFLHPAPPCGHPDTRPPILHGVHYLHFAVALFLLSGAVVVAGSLLTPHPQGVQIQSLTW 549
            +  +         T   + + +++L F   +FL    VV+  SL T  P   +IQ L +
Sbjct: 467 AKVYYSNAGEVADSTFKYLFYDMNWLFFCGWMFLFCIIVVIVVSLATEAPTAEKIQGLVF 526

Query: 550 WTLAQDLPLGVKTGDGRASQRHAFWARVCGVNAILLMCVNIFFYTYF 596
                    G  T + +A+ R A W     ++ ++++ +   FY YF
Sbjct: 527 ---------GTATKEQKAATR-ASWDHWDIIHTVIILAITGAFYWYF 563


Lambda     K      H
   0.327    0.139    0.437 

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: 745
Number of extensions: 42
Number of successful extensions: 8
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: 597
Length of database: 564
Length adjustment: 36
Effective length of query: 561
Effective length of database: 528
Effective search space:   296208
Effective search space used:   296208
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: 53 (25.0 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