GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:350322
          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:

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