GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SMIT1 in Bacteroides thetaiotaomicron VPI-5482

Align Sodium/myo-inositol cotransporter 2; Na(+)/myo-inositol cotransporter 2; Sodium-dependent glucose cotransporter; Sodium/glucose cotransporter KST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11 (characterized)
to candidate 349883 BT0355 Na+/glucose cotransporter (NCBI ptt file)

Query= SwissProt::Q8K0E3
         (673 letters)



>lcl|FitnessBrowser__Btheta:349883 BT0355 Na+/glucose cotransporter
           (NCBI ptt file)
          Length = 564

 Score =  371 bits (952), Expect = e-107
 Identities = 200/542 (36%), Positives = 321/542 (59%), Gaps = 21/542 (3%)

Query: 24  MEPADIAVLVLYFLFVLAVGLWSTVRTKRDTVKGYFLAGGDMVWWPVGASLFASNVGSGH 83
           ME  D  V+ ++FL ++ + +W  VR K++    YFL G D  W  +GAS+FASN+GS H
Sbjct: 1   MEALDWLVIGVFFLALIGIIVW-VVRQKQNDSADYFLGGRDATWLAIGASIFASNIGSEH 59

Query: 84  FIGLAGSGAAVGISVAAYELNGLFSVLMLAWVFLPIYIAGQVTTMPEYLRRRFGGNRISI 143
            IGLAG+GA+ G+++A +E+ G + +L+L WVF+P Y    V TMPE+L RR+     +I
Sbjct: 60  LIGLAGAGASSGMAMAHWEIQG-WMILILGWVFVPFYSRSMVYTMPEFLERRYNPQSRTI 118

Query: 144 TLAVLYLFIYIFTKISVDMYAGAIFIQQSLHLD-------LYLAIVGLLAITALYTVAGG 196
            L+V+ L  Y+ TK++V +YAG +  QQ   +         ++A +GL+ +TALYT+ GG
Sbjct: 119 -LSVISLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYTIFGG 177

Query: 197 LAAVIYTDALQTVIMLIGAFILMGYSFAAVGGMEGLKDQYFLALASNRSENSSCGLPRED 256
           + +V+YT  LQT I+L+G+ I++   F  +GG + +         ++  +  +       
Sbjct: 178 MKSVLYTSVLQTPILLLGSLIILVLGFKELGGWDEMMRVCGAVTVNDYGDTMT------- 230

Query: 257 AFHIFRDPLTSDLPWPGILFGMSIPSLWYWCTDQVIVQRSLAAKNLSHAKGGSLMAAYLK 316
             ++ R    ++ PW G L G +I   WYWCTDQ IVQR L+ KN   A+ G++  AYLK
Sbjct: 231 --NLIRSNDDANFPWLGALIGSAIIGFWYWCTDQFIVQRVLSGKNEKEARRGTIFGAYLK 288

Query: 317 VLPLFLMVFPGMVSRVLFPDQVACAHPDICQRVCSNPSGCSDIAYPKLVLELLPTGLRGL 376
           +LP+FL + PGM++  L    +          + +N +  +D A+P LV +LLP G++GL
Sbjct: 289 LLPVFLFLIPGMIAFALHQKYIGAGGEGFLPML-ANGTANADAAFPTLVAKLLPAGVKGL 347

Query: 377 MMAVMVAALMSSLTSIFNSASTIFTMDLWNHIRPRASERELMIVGRIFVFALVLVSILWI 436
           ++  ++AALMSSL S+FNS++ +FT+D +   RP   E++L+ +G+I    +V++ ILWI
Sbjct: 348 VVCGILAALMSSLASLFNSSAMLFTIDFYKRFRPETPEKKLVGIGQIATVVIVILGILWI 407

Query: 437 PIVQASQGGQLFIYIQSISSYLQPPVAMVFIMGCFWKRTNEKGAFSGLILGLLLGLVRLI 496
           PI++ S G  L+ Y+Q + S L P +A  F++G  WKRT+ +G   GLI G+++GL RL 
Sbjct: 408 PIMR-SVGDVLYTYLQDVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGLTRLG 466

Query: 497 LDFVYAQPRCDQPDDRPAVVKDVHYLYFSMILSFTTLITVVTVSWFTETPSKEMVSRLTW 556
               Y+            +  D+++L+F   +    +I V+ VS  TE P+ E +  L +
Sbjct: 467 AKVYYSNAGEVADSTFKYLFYDMNWLFFCGWMFLFCIIVVIVVSLATEAPTAEKIQGLVF 526

Query: 557 FT 558
            T
Sbjct: 527 GT 528


Lambda     K      H
   0.325    0.139    0.426 

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: 874
Number of extensions: 40
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: 673
Length of database: 564
Length adjustment: 37
Effective length of query: 636
Effective length of database: 527
Effective search space:   335172
Effective search space used:   335172
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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