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; rKST1; Sodium/myo-inositol transporter 2; SMIT2; Solute carrier family 5 member 11 (characterized)
to candidate 349869 BT0341 Na+/glucose cotransporter (NCBI ptt file)

Query= SwissProt::Q28728
         (674 letters)



>lcl|FitnessBrowser__Btheta:349869 BT0341 Na+/glucose cotransporter
           (NCBI ptt file)
          Length = 523

 Score =  265 bits (677), Expect = 4e-75
 Identities = 162/530 (30%), Positives = 285/530 (53%), Gaps = 46/530 (8%)

Query: 24  LEPGDIAVLVLYFLFVLAVGLWSTVKTKRDTVKGYFLAGGDMVWWPVGASLFASNVGSGH 83
           L+  D  +L+ YFL ++A+G+W++ K K+ +    FLA   + W  +G S++ +NVG   
Sbjct: 6   LDTLDWGILIAYFLILIAIGIWASSKRKKGS--SLFLAEHSLRWHHIGFSMWGTNVGPSM 63

Query: 84  FVGLAGSGAATGISVAAYEFNGMFSVLMLAWIFLPIYIAGQVTTMPEYLRRRFGGSRIAI 143
            +  A +G  TGI    Y +     + +LA++F P Y+  +V+T+PE++ +RFG S   I
Sbjct: 64  LIASASAGFTTGIVSGNYAWYAFVFICLLAFVFAPRYLGSRVSTLPEFMGKRFGQSTRNI 123

Query: 144 TLAVLYLFIYIFTKISVDMYAGAIFIQQSLHLDLYLSVVGLLAVTALYTVAGGLAAVIYT 203
            LA   +   + + +++ ++AG + I+Q   + ++ S + LL ++A +T+ GGL AV YT
Sbjct: 124 -LAWYTIVTILISWLALTLFAGGVLIRQVFDIPMWQSALILLIISAFFTMLGGLKAVAYT 182

Query: 204 DALQTLIMLVGALTLMGYSFAAVGGMEGLQEKYFLALPSNRSENSSCGLPREDAFHLFRD 263
           +  Q +++++ +  L       VGG+  L +    A+P+             D ++LFR 
Sbjct: 183 NVYQMILLILVSAALAIVGIYKVGGISALTD----AVPA-------------DFWNLFRP 225

Query: 264 PLTSDLPWPGILFGMSIPSLWYWCTDQVIVQRSLAAKNLSHAKGGSLMAAYLKVLPLFIM 323
              +  PW  I+ G  +  +W+WCTDQ +VQ  LAAK+L   + G+    +LK+L + + 
Sbjct: 226 NDDTAFPWLPIILGYPVMGVWFWCTDQSMVQPVLAAKSLKEGQLGTNFTGWLKILDVPLY 285

Query: 324 VFPGMVSRILFPDQVACADPETCQRVCNNPSGCSDIAYPKLVLELLPTGLRGLMMAVMVA 383
           + PG++   LFP                NP    D AY  +V  L P G+ GL++AV+ A
Sbjct: 286 ILPGIICLALFPQ-------------LENP----DEAYMTMVTHLFPVGMVGLVLAVLTA 328

Query: 384 ALMSSLTSIFNSASTIFTMDLW-NHVRPRASEKELMIVGRVFVLLLVLVSVLWIPVVQAS 442
           AL+S++ S  N+ ST+FTMD++   +RP+A +KE++ VG+V  +   L+SV+    + + 
Sbjct: 329 ALVSTIGSALNALSTVFTMDIYVKKIRPQAKQKEIIRVGQVVTVAGALISVIITIAIDSI 388

Query: 443 QGGQLFVYIQAISSYLQPPVAMVFVLGCFWKRANEKGAFWGLVLGLLLGFIRLILDFIYV 502
            G  LF   Q++  ++ PP+A VF+ G FWKR     A   L +G +   I + + +++V
Sbjct: 389 HGLNLFNVFQSVLGFIAPPMAAVFLFGVFWKRTTTLAANAALTVGTVFS-IGVGVLYLWV 447

Query: 503 EPACHQPDERPSVVKNVHYLYFSMILSSVTVLTVTVMSLLTEPPSKEMIS 552
            PA  Q    P      H++  S  L  +  + + V+ LL + P   +++
Sbjct: 448 FPA-DQYSAWP------HFMLLSFYLFVIIGIGMVVVGLLDKTPQTAILN 490


Lambda     K      H
   0.325    0.138    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: 754
Number of extensions: 37
Number of successful extensions: 5
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: 674
Length of database: 523
Length adjustment: 37
Effective length of query: 637
Effective length of database: 486
Effective search space:   309582
Effective search space used:   309582
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