GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:349883
          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:

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