GapMind for catabolism of small carbon sources

 

Aligments 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)



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