GapMind for catabolism of small carbon sources

 

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

Align Sodium/glucose cotransporter; Na(+)/glucose symporter (characterized)
to candidate 349883 BT0355 Na+/glucose cotransporter (NCBI ptt file)

Query= SwissProt::P96169
         (543 letters)



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

 Score =  296 bits (757), Expect = 2e-84
 Identities = 172/522 (32%), Positives = 296/522 (56%), Gaps = 43/522 (8%)

Query: 11  IDIMVFAIYVAIIIGVGLWVSRDKKGTQKSTEDYFLAGKSLPWWAVGASLIAANISAEQF 70
           +D +V  ++   +IG+ +WV R K   Q  + DYFL G+   W A+GAS+ A+NI +E  
Sbjct: 4   LDWLVIGVFFLALIGIIVWVVRQK---QNDSADYFLGGRDATWLAIGASIFASNIGSEHL 60

Query: 71  IGMSGSGYSIGLAIASYE---WMSAITLIIVGKYFLPIFIEKGIYTIPEFVEKRFNKKLK 127
           IG++G+G S G+A+A +E   WM    ++I+G  F+P +    +YT+PEF+E+R+N + +
Sbjct: 61  IGLAGAGASSGMAMAHWEIQGWM----ILILGWVFVPFYSRSMVYTMPEFLERRYNPQSR 116

Query: 128 TILAVFWISLYIFVNLTSVLYLGGLALETILGIPLMYSI-------LGLALFALVYSIYG 180
           TIL+V  +  Y+   +   +Y GGL  + + GI  ++ I       +GL +   +Y+I+G
Sbjct: 117 TILSVISLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYTIFG 176

Query: 181 GLSAVVWTDVIQVFFLVLGGFMTTYMAVSFIGGTDGWFAGVSKMVDAAPGHFEMILDQSN 240
           G+ +V++T V+Q   L+LG  +   +    +GG D        +     G     L +SN
Sbjct: 177 GMKSVLYTSVLQTPILLLGSLIILVLGFKELGGWDEMMRVCGAVTVNDYGDTMTNLIRSN 236

Query: 241 PQYMNLPGIAVLIGGLWVANLYYWGFNQYIIQRTLAAKSVSEAQKGIVFAAFLKLIVPFL 300
               N P +  LIG   +   +YW  +Q+I+QR L+ K+  EA++G +F A+LKL+  FL
Sbjct: 237 DD-ANFPWLGALIGSA-IIGFWYWCTDQFIVQRVLSGKNEKEARRGTIFGAYLKLLPVFL 294

Query: 301 VVLPGIAAYVITSDPQLMASLGDIAATNLPS-AANADKAYPWL-TQFLPVGVKGVVFAAL 358
            ++PG+ A+ +    + + + G+     L +  ANAD A+P L  + LP GVKG+V   +
Sbjct: 295 FLIPGMIAFAL--HQKYIGAGGEGFLPMLANGTANADAAFPTLVAKLLPAGVKGLVVCGI 352

Query: 359 AAAIVSSLASMLNSTATIFTMDIYKEYISPDSGDHKLVNVGRTAAVVALIIACLIAPMLG 418
            AA++SSLAS+ NS+A +FT+D YK +  P++ + KLV +G+ A VV +I+  L  P++ 
Sbjct: 353 LAALMSSLASLFNSSAMLFTIDFYKRF-RPETPEKKLVGIGQIATVVIVILGILWIPIMR 411

Query: 419 GIGQA-FQYIQEYTGLVSPGILAVFLLGLFWKKTTSKGAIIGVVASIPFAL--------- 468
            +G   + Y+Q+   +++PGI A FLLG+ WK+T+++G + G++A +   L         
Sbjct: 412 SVGDVLYTYLQDVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGLTRLGAKVYY 471

Query: 469 ---------FLKFMPLSMPFMDQMLYTLLFTMVVIAFTSLST 501
                      K++   M ++    +  LF ++V+   SL+T
Sbjct: 472 SNAGEVADSTFKYLFYDMNWLFFCGWMFLFCIIVVIVVSLAT 513


Lambda     K      H
   0.326    0.141    0.421 

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: 973
Number of extensions: 61
Number of successful extensions: 7
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: 543
Length of database: 564
Length adjustment: 36
Effective length of query: 507
Effective length of database: 528
Effective search space:   267696
Effective search space used:   267696
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