GapMind for catabolism of small carbon sources

 

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

Align Sodium/glucose cotransporter 1; Na(+)/glucose cotransporter 1; High affinity sodium-glucose cotransporter; Solute carrier family 5 member 1 (characterized)
to candidate 349869 BT0341 Na+/glucose cotransporter (NCBI ptt file)

Query= SwissProt::P11170
         (662 letters)



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

 Score =  261 bits (668), Expect = 4e-74
 Identities = 159/532 (29%), Positives = 277/532 (52%), Gaps = 53/532 (9%)

Query: 20  YERIRNAADISVIVIYFLVVMAVGLWAMFSTNRGTVGGFFLAGRSMVWWPIGASLFASNI 79
           + +  +  D  +++ YFL+++A+G+WA     +G+    FLA  S+ W  IG S++ +N+
Sbjct: 2   HAKFLDTLDWGILIAYFLILIAIGIWASSKRKKGS--SLFLAEHSLRWHHIGFSMWGTNV 59

Query: 80  GSGHFVGLAGTGAASGIATGGFEWNALIMVVVLGWVFVPIYIRAGVVTMPEYLQKRFGGK 139
           G    +  A  G  +GI +G + W A + + +L +VF P Y+ + V T+PE++ KRFG  
Sbjct: 60  GPSMLIASASAGFTTGIVSGNYAWYAFVFICLLAFVFAPRYLGSRVSTLPEFMGKRFGQS 119

Query: 140 RIQIYLSILSLLLYIFTKISADIFSGAIFIQLTLGLDIYVAIIILLVITGLYTITGGLAA 199
              I L+  +++  + + ++  +F+G + I+    + ++ + +ILL+I+  +T+ GGL A
Sbjct: 120 TRNI-LAWYTIVTILISWLALTLFAGGVLIRQVFDIPMWQSALILLIISAFFTMLGGLKA 178

Query: 200 VIYTDTLQTAIMMVGSVILTGFAFHEVGGYEAFTEKYMRAIPSQISYGNTSIPQKCYTPR 259
           V YT+  Q  ++++ S  L     ++VGG  A T+    A+P+                 
Sbjct: 179 VAYTNVYQMILLILVSAALAIVGIYKVGGISALTD----AVPA----------------- 217

Query: 260 EDAFHIFRDAITGDIPWPGLVFGMSILTLWYWCTDQVIVQRCLSAKNLSHVKAGCILCGY 319
            D +++FR       PW  ++ G  ++ +W+WCTDQ +VQ  L+AK+L   + G    G+
Sbjct: 218 -DFWNLFRPNDDTAFPWLPIILGYPVMGVWFWCTDQSMVQPVLAAKSLKEGQLGTNFTGW 276

Query: 320 LKVMPMFLIVMMGMVSRILYTDKVACVVPSECERYCGTRVGCTNIAFPTLVVELMPNGLR 379
           LK++ + L ++ G++   L+        P E              A+ T+V  L P G+ 
Sbjct: 277 LKILDVPLYILPGIICLALFPQ---LENPDE--------------AYMTMVTHLFPVGMV 319

Query: 380 GLMLSVMMASLMSSLTSIFNSASTLFTMDIYT-KIRKKASEKELMIAGRLFMLFLIGISI 438
           GL+L+V+ A+L+S++ S  N+ ST+FTMDIY  KIR +A +KE++  G++  +    IS+
Sbjct: 320 GLVLAVLTAALVSTIGSALNALSTVFTMDIYVKKIRPQAKQKEIIRVGQVVTVAGALISV 379

Query: 439 AWVPIVQSAQSGQLFDYIQSITSYLGPPIAAVFLLAIFWKRVNEPGAFWGLVLGFLIGIS 498
                + S     LF+  QS+  ++ PP+AAVFL  +FWKR     A   L +G      
Sbjct: 380 IITIAIDSIHGLNLFNVFQSVLGFIAPPMAAVFLFGVFWKRTTTLAANAALTVG------ 433

Query: 499 RMITEFAYGTGSC-MEPSNCPTIICGVHYLYFAIILFVISIITVVVVSLFTK 549
              T F+ G G   +            H++  +  LFVI  I +VVV L  K
Sbjct: 434 ---TVFSIGVGVLYLWVFPADQYSAWPHFMLLSFYLFVIIGIGMVVVGLLDK 482


Lambda     K      H
   0.327    0.141    0.434 

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: 839
Number of extensions: 42
Number of successful extensions: 6
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: 662
Length of database: 523
Length adjustment: 37
Effective length of query: 625
Effective length of database: 486
Effective search space:   303750
Effective search space used:   303750
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 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