GapMind for catabolism of small carbon sources

 

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

Align Proton myo-inositol cotransporter; H(+)-myo-inositol cotransporter; Hmit; H(+)-myo-inositol symporter; Solute carrier family 2 member 13 (characterized)
to candidate 350322 BT0794 D-xylose-proton symporter (D-xylose transporter) (NCBI ptt file)

Query= SwissProt::Q921A2
         (637 letters)



>lcl|FitnessBrowser__Btheta:350322 BT0794 D-xylose-proton symporter
           (D-xylose transporter) (NCBI ptt file)
          Length = 484

 Score =  147 bits (372), Expect = 8e-40
 Identities = 113/373 (30%), Positives = 180/373 (48%), Gaps = 56/373 (15%)

Query: 69  FVYAAAAFSALGGFLFGYDTGVVSGAMLLLRRQMRLGAMWQELLVSGAV--GAAAVAALA 126
           ++Y+  + + LGG LFGYDT V+SGA   L       + +Q   V   +   +A +  + 
Sbjct: 12  YLYSITSVAILGGLLFGYDTAVISGAEKGLEAFFLSASDFQYNKVMHGITSSSALIGCVL 71

Query: 127 GGALNGA----LGRRSAILLA------SALCTVGSAVLA---AAANKETLLAG---RLVV 170
           GGAL+G     LGRR+++ LA      SAL +    VL       N + L+A    R++ 
Sbjct: 72  GGALSGVFASRLGRRNSLRLAAVLFFLSALGSYYPEVLFFEYGKPNMDLLIAFNLYRVLG 131

Query: 171 GLGIGIASMTVPVYIAEVSPPNLRGRLVTINTLFITGGQFFASVVD-------------- 216
           G+G+G+AS   P+YIAE++P N+RG LV+ N   I  G      V+              
Sbjct: 132 GIGVGLASAVCPMYIAEIAPSNIRGTLVSCNQFAIIFGMLVVYFVNYLIMGDHQNPIILK 191

Query: 217 ---GAFS-------YLQKDGWRYMLGLAAIPAVIQFLGFLFLPESPRWLIQKGQTQKARR 266
              G  S       +  ++GWRYM G  A PA    L   F+P++PR+L+   Q +KA  
Sbjct: 192 DAAGVLSVSAESDMWTVQEGWRYMFGSEAFPAAFFGLLLFFVPKTPRYLVLVQQEEKAYT 251

Query: 267 ILSQMRGNQTIDEEYDSIRNSIEEEEKEASAAGPIICRMLSYPPTRRALAVGCGLQMFQQ 326
           IL ++ G +   E  + I+ + +E+ +          ++ +Y  T   + +G  L +FQQ
Sbjct: 252 ILEKINGKKKAQEILNDIKATAQEKTE----------KLFTYGVT--VIVIGILLSVFQQ 299

Query: 327 LSGINTIMYYSATILQMSGVEDDRLAIWLASITAFTNFIFTLVGVWLVEKVGRRKLTFGS 386
             GIN ++YY+  I + +G E     +    I    N IFTLV ++ V++ GR+ L    
Sbjct: 300 AIGINAVLYYAPRIFENAGAEGG--GMMQTVIMGIVNIIFTLVAIFTVDRFGRKPLLIIG 357

Query: 387 LAGTTVALTILAL 399
             G  V    +A+
Sbjct: 358 SIGMAVGAFAVAM 370



 Score = 67.8 bits (164), Expect = 1e-15
 Identities = 34/100 (34%), Positives = 54/100 (54%), Gaps = 1/100 (1%)

Query: 499 LVGLVLYLVFFAPGMGPMPWTVNSEIYPLWARSTGNACSAGINWIFNVLVSLTFLHTAEY 558
           ++ +++Y  FF    GP+ W + SEI+P   R    A +    WIFN +VS TF    ++
Sbjct: 382 VLSIIVYAAFFMMSWGPICWVLISEIFPNTIRGKAVAIAVAFQWIFNYIVSSTFPALYDF 441

Query: 559 LTYYGAFFLYAGFAAVGLLFVYGCLPETKGKKLEEIESLF 598
              + A+ LY        +FV+  +PETKGK LE++  L+
Sbjct: 442 SPMF-AYSLYGIICVAAAIFVWRWVPETKGKTLEDMSKLW 480


Lambda     K      H
   0.322    0.136    0.410 

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: 594
Number of extensions: 26
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 637
Length of database: 484
Length adjustment: 36
Effective length of query: 601
Effective length of database: 448
Effective search space:   269248
Effective search space used:   269248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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