Alignments for a candidate for SGLT1 in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for SGLT1 in Bacteroides thetaiotaomicron VPI-5482

Align sodium/glucose cotransporter 1 (characterized)
to candidate 349869 BT0341 Na+/glucose cotransporter (NCBI ptt file)

Query= CharProtDB::CH_091086
         (664 letters)



>FitnessBrowser__Btheta:349869
          Length = 523

 Score =  261 bits (668), Expect = 4e-74
 Identities = 160/532 (30%), Positives = 275/532 (51%), Gaps = 53/532 (9%)

Query: 20  HELIRNAADISIIVIYFVVVMAVGLWAMFSTNRGTVGGFFLAGRSMVWWPIGASLFASNI 79
           H    +  D  I++ YF++++A+G+WA     +G+    FLA  S+ W  IG S++ +N+
Sbjct: 2   HAKFLDTLDWGILIAYFLILIAIGIWASSKRKKGS--SLFLAEHSLRWHHIGFSMWGTNV 59

Query: 80  GSGHFVGLAGTGAASGIAIGGFEWNALVLVVVLGWLFVPIYIKAGVVTMPEYLRKRFGGQ 139
           G    +  A  G  +GI  G + W A V + +L ++F P Y+ + V T+PE++ KRF GQ
Sbjct: 60  GPSMLIASASAGFTTGIVSGNYAWYAFVFICLLAFVFAPRYLGSRVSTLPEFMGKRF-GQ 118

Query: 140 RIQVYLSLLSLLLYIFTKISADIFSGAIFINLALGLNLYLAIFLLLAITALYTITGGLAA 199
             +  L+  +++  + + ++  +F+G + I     + ++ +  +LL I+A +T+ GGL A
Sbjct: 119 STRNILAWYTIVTILISWLALTLFAGGVLIRQVFDIPMWQSALILLIISAFFTMLGGLKA 178

Query: 200 VIYTDTLQTVIMLVGSLILTGFAFHEVGGYDAFMEKYMKAIPTIVSDGNTTFQEKCYTPR 259
           V YT+  Q +++++ S  L     ++VGG  A  +    A+P                  
Sbjct: 179 VAYTNVYQMILLILVSAALAIVGIYKVGGISALTD----AVP------------------ 216

Query: 260 ADSFHIFRDPLTGDLPWPGFIFGMSILTLWYWCTDQVIVQRCLSAKNMSHVKGGCILCGY 319
           AD +++FR       PW   I G  ++ +W+WCTDQ +VQ  L+AK++   + G    G+
Sbjct: 217 ADFWNLFRPNDDTAFPWLPIILGYPVMGVWFWCTDQSMVQPVLAAKSLKEGQLGTNFTGW 276

Query: 320 LKLMPMFIMVMPGMISRILYTEKIACVVPSECEKYCGTKVGCTNIAYPTLVVELMPNGLR 379
           LK++ + + ++PG+I   L+ +      P E              AY T+V  L P G+ 
Sbjct: 277 LKILDVPLYILPGIICLALFPQ---LENPDE--------------AYMTMVTHLFPVGMV 319

Query: 380 GLMLSVMLASLMSSLTSIFNSASTLFTMDIYA-KVRKRASEKELMIAGRLFILVLIGISI 438
           GL+L+V+ A+L+S++ S  N+ ST+FTMDIY  K+R +A +KE++  G++  +    IS+
Sbjct: 320 GLVLAVLTAALVSTIGSALNALSTVFTMDIYVKKIRPQAKQKEIIRVGQVVTVAGALISV 379

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

Query: 499 RMITEFAYGTGSC-MEPSNCPTIICGVHYLYFAIILFAISFITIVVISLLTK 549
              T F+ G G   +            H++  +  LF I  I +VV+ LL K
Sbjct: 434 ---TVFSIGVGVLYLWVFPADQYSAWPHFMLLSFYLFVIIGIGMVVVGLLDK 482


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: 759
Number of extensions: 40
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: 664
Length of database: 523
Length adjustment: 37
Effective length of query: 627
Effective length of database: 486
Effective search space:   304722
Effective search space used:   304722
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources