GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:350322
          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:

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