GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SGLT1 in Shewanella loihica PV-4

Align sodium/glucose cotransporter 1 (characterized)
to candidate 5209833 Shew_2286 SSS family solute/sodium (Na+) symporter (RefSeq)

Query= CharProtDB::CH_091086
         (664 letters)



>lcl|FitnessBrowser__PV4:5209833 Shew_2286 SSS family solute/sodium
           (Na+) symporter (RefSeq)
          Length = 519

 Score =  249 bits (636), Expect = 2e-70
 Identities = 149/471 (31%), Positives = 250/471 (53%), Gaps = 56/471 (11%)

Query: 28  DISIIVIYFVVVMAVGLWAMFSTNRGT--VGGFFLAGRSMVWWPIGASLFASNIGSGHFV 85
           DI I+++Y + ++ + LW      R       +FLAG+++ WW IGASL ASNI +   +
Sbjct: 6   DIGILLVYALGLLGLALWISRQDKRHERDTKDYFLAGKALPWWAIGASLIASNISAEQII 65

Query: 86  GLAGTGAASGIAIGGFEWNALVLVVVLGWLFVPIYIKAGVVTMPEYLRKRFGGQRIQVYL 145
           G++G+G A G+AI  +EW A + ++++G   +PI+IK  + TMP+YL +RF  +R++  L
Sbjct: 66  GMSGSGYAIGLAIASYEWMAAITLILVGKYMLPIFIKNEIYTMPQYLEQRF-DKRVKTTL 124

Query: 146 SLLSLLLYIFTKISADIFSGAIFINLALGLNLYLAIFLLLAITALYTITGGLAAVIYTDT 205
           +L  L +YI   ++A ++ G + I    G++    +  L   +  Y++ GGL AV YTD 
Sbjct: 125 ALFWLSVYILVNLTAVLWLGGLAIETVAGIDWLYGMVFLALFSLAYSLYGGLKAVAYTDI 184

Query: 206 LQTVIMLVGSLILTGFAFHEV-------GGYDAFMEKYMKAIPTIVSDGNTTFQEKCYTP 258
           +Q V+++ G L+L+  A   V        G+D       +    I+S  N  +       
Sbjct: 185 IQVVLLIFGGLLLSYLALDRVADGQGVLAGFDRLSSALPEHFEMILSQSNPHY------- 237

Query: 259 RADSFHIFRDPLTGDLPWPG---FIFGMSILTLWYWCTDQVIVQRCLSAKNMSHVKGGCI 315
                          +  PG    + G+ I+ + YW  +Q I+QR L+AK+++  + G  
Sbjct: 238 ---------------MSLPGISVLVGGLWIMNISYWGFNQYIIQRALAAKSVAEAQKGIA 282

Query: 316 LCGYLKLMPMFIMVMPGMISRILYTEKIACVVPSECEKYCGTKVGCTNIAYPTLVVELMP 375
              YLKL+   I+V+PG+ + +LY                   +   + AYP+++  LMP
Sbjct: 283 FAAYLKLLMPLIVVLPGIAAVLLY-----------------PGLESPDQAYPSMMA-LMP 324

Query: 376 NGLRGLMLSVMLASLMSSLTSIFNSASTLFTMDIYAKVRKRASEKELMIAGRLFILVLIG 435
            G++GL+ + ++A+++SSL S+ NS ST+FTMDIYA +R   SE   ++ GRL  L+ + 
Sbjct: 325 AGVKGLVFAALVAAIVSSLASMTNSISTIFTMDIYAMLRPAKSEGHYVLVGRLSSLISLL 384

Query: 436 ISIAWV-PIVQSAQSGQLFDYIQSITSYLGPPIAAVFLLAIFWKRVNEPGA 485
           I++    P++   +  Q F YIQ  T    P I  +FL  +FW+R    GA
Sbjct: 385 IALVMAQPLL--GEFEQAFQYIQEFTGVFTPGIVVIFLTGMFWRRATSQGA 433


Lambda     K      H
   0.327    0.141    0.436 

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: 731
Number of extensions: 33
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: 664
Length of database: 519
Length adjustment: 37
Effective length of query: 627
Effective length of database: 482
Effective search space:   302214
Effective search space used:   302214
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