GapMind for catabolism of small carbon sources

 

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

Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate 350322 BT0794 D-xylose-proton symporter (D-xylose transporter) (NCBI ptt file)

Query= TCDB::P15729
         (468 letters)



>FitnessBrowser__Btheta:350322
          Length = 484

 Score =  303 bits (775), Expect = 1e-86
 Identities = 189/489 (38%), Positives = 272/489 (55%), Gaps = 60/489 (12%)

Query: 16  FVLLISGVAALGGFLFGFDTAVINGAVAALQ------KHFQTDSLLTGLSVSLALLGSAL 69
           ++  I+ VA LGG LFG+DTAVI+GA   L+        FQ + ++ G++ S AL+G  L
Sbjct: 12  YLYSITSVAILGGLLFGYDTAVISGAEKGLEAFFLSASDFQYNKVMHGITSSSALIGCVL 71

Query: 70  GAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIW------------DFIFWRVLG 117
           G   +G  A R GR  ++ LAAVLF LS++GS  P  ++             F  +RVLG
Sbjct: 72  GGALSGVFASRLGRRNSLRLAAVLFFLSALGSYYPEVLFFEYGKPNMDLLIAFNLYRVLG 131

Query: 118 GIGVGAASVIAPAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNP 177
           GIGVG AS + P YIAE++P+++RG L S  Q AI+ G+ +    N+ I     G  QNP
Sbjct: 132 GIGVGLASAVCPMYIAEIAPSNIRGTLVSCNQFAIIFGMLVVYFVNYLIM----GDHQNP 187

Query: 178 WLFGAAA-----------------WRWMFWTELIPALLYGVCAFLIPESPRYLVAQGQGE 220
            +   AA                 WR+MF +E  PA  +G+  F +P++PRYLV   Q E
Sbjct: 188 IILKDAAGVLSVSAESDMWTVQEGWRYMFGSEAFPAAFFGLLLFFVPKTPRYLVLVQQEE 247

Query: 221 KAAAILWKVEGGDVPSRI-EEIQATVSLDHKPRFSDLLSRRGGLLPIVWIGMGLSALQQF 279
           KA  IL K+ G      I  +I+AT     +  F+  ++       ++ IG+ LS  QQ 
Sbjct: 248 KAYTILEKINGKKKAQEILNDIKATAQEKTEKLFTYGVT-------VIVIGILLSVFQQA 300

Query: 280 VGINVIFYYSSVLWRSVGFTEEKSLLITVITGFINILTTLVAIAFVDKFGRKPLLLMGSI 339
           +GIN + YY+  ++ + G  E   ++ TVI G +NI+ TLVAI  VD+FGRKPLL++GSI
Sbjct: 301 IGINAVLYYAPRIFENAG-AEGGGMMQTVIMGIVNIIFTLVAIFTVDRFGRKPLLIIGSI 359

Query: 340 GMTITLGILSVVFGGATVVNGQPTLTGAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMF 399
           GM +  G  +V    +  + G         ++ +++  +Y   F  SWGPI WVL+ E+F
Sbjct: 360 GMAV--GAFAVAMCDSMAIKG---------VLPVLSIIVYAAFFMMSWGPICWVLISEIF 408

Query: 400 NNKIRAAALSVAAGVQWIANFIISTTFPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKE 459
            N IR  A+++A   QWI N+I+S+TFP L D   +  AY LY      +  F+W +V E
Sbjct: 409 PNTIRGKAVAIAVAFQWIFNYIVSSTFPALYDFSPMF-AYSLYGIICVAAAIFVWRWVPE 467

Query: 460 TKGKTLEQM 468
           TKGKTLE M
Sbjct: 468 TKGKTLEDM 476


Lambda     K      H
   0.325    0.140    0.430 

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: 574
Number of extensions: 25
Number of successful extensions: 8
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: 468
Length of database: 484
Length adjustment: 33
Effective length of query: 435
Effective length of database: 451
Effective search space:   196185
Effective search space used:   196185
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 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