GapMind for catabolism of small carbon sources

 

Aligments for a candidate for MFS-glucose in Bacteroides thetaiotaomicron VPI-5482

Align The glucose uptake porter, GluP (characterized)
to candidate 350322 BT0794 D-xylose-proton symporter (D-xylose transporter) (NCBI ptt file)

Query= TCDB::Q0SE66
         (483 letters)



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

 Score =  314 bits (805), Expect = 4e-90
 Identities = 190/495 (38%), Positives = 282/495 (56%), Gaps = 56/495 (11%)

Query: 16  TAEGTSVPV-RIAVVAALGGLLFGYDSAVINGAVSAIEG------KFQVDSALLGFAIAS 68
           T EG+ + +  I  VA LGGLLFGYD+AVI+GA   +E        FQ +  + G   +S
Sbjct: 5   TNEGSKLYLYSITSVAILGGLLFGYDTAVISGAEKGLEAFFLSASDFQYNKVMHGITSSS 64

Query: 69  ALLGAAAGAMLAGRIADRYGRLVTMRAAAVMFLLSAIGTGFAA---------NVEMLVTF 119
           AL+G   G  L+G  A R GR  ++R AAV+F LSA+G+ +           N+++L+ F
Sbjct: 65  ALIGCVLGGALSGVFASRLGRRNSLRLAAVLFFLSALGSYYPEVLFFEYGKPNMDLLIAF 124

Query: 120 ---RIVGGIGVGLASVIAPAYIAEISPARVRGRLGSLQQLAIVTGIFVSLLVDY------ 170
              R++GGIGVGLAS + P YIAEI+P+ +RG L S  Q AI+ G+ V   V+Y      
Sbjct: 125 NLYRVLGGIGVGLASAVCPMYIAEIAPSNIRGTLVSCNQFAIIFGMLVVYFVNYLIMGDH 184

Query: 171 --------ALAAIAGGSQEELWFGLEAWRWMFLAMCVPALAYGLLSLTIPESPRYLIAQG 222
                   A   ++  ++ ++W   E WR+MF +   PA  +GLL   +P++PRYL+   
Sbjct: 185 QNPIILKDAAGVLSVSAESDMWTVQEGWRYMFGSEAFPAAFFGLLLFFVPKTPRYLVLVQ 244

Query: 223 RLGEARGILAVLLGEKGLDLKIESIRSTLARETQPSIRDLKGSAFGLMPIVWIGIGLSVF 282
           +  +A  IL  + G+K     +  I++T   +T+      K   +G+  IV IGI LSVF
Sbjct: 245 QEEKAYTILEKINGKKKAQEILNDIKATAQEKTE------KLFTYGVTVIV-IGILLSVF 297

Query: 283 QQFVGINVIFYYSSVLWQAVGFDEGSSLQITVITSVVNIATTLIAIAYIDRVGRRPLLII 342
           QQ +GIN + YY+  +++  G + G  +Q TVI  +VNI  TL+AI  +DR GR+PLLII
Sbjct: 298 QQAIGINAVLYYAPRIFENAGAEGGGMMQ-TVIMGIVNIIFTLVAIFTVDRFGRKPLLII 356

Query: 343 GSAGMAVTLATMAFIFGTASTTVVDGVTTPQLTGLQGPIALVAANLFVVAFGMSWGPVVW 402
           GS GMAV         G  +  + D +       ++G + +++  ++   F MSWGP+ W
Sbjct: 357 GSIGMAV---------GAFAVAMCDSMA------IKGVLPVLSIIVYAAFFMMSWGPICW 401

Query: 403 VLLGEAFPNRIRAAALSLAAGAQWAANWLITVTFPSMKDFSLGISYGFYAVCAVLSLVFV 462
           VL+ E FPN IR  A+++A   QW  N++++ TFP++ DFS   +Y  Y +  V + +FV
Sbjct: 402 VLISEIFPNTIRGKAVAIAVAFQWIFNYIVSSTFPALYDFSPMFAYSLYGIICVAAAIFV 461

Query: 463 LRWVKETKGVELEAM 477
            RWV ETKG  LE M
Sbjct: 462 WRWVPETKGKTLEDM 476


Lambda     K      H
   0.324    0.138    0.405 

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: 600
Number of extensions: 27
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: 483
Length of database: 484
Length adjustment: 34
Effective length of query: 449
Effective length of database: 450
Effective search space:   202050
Effective search space used:   202050
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: 52 (24.6 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