GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylT in Bacteroides thetaiotaomicron VPI-5482

Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate 353132 BT3606 sugar-proton symporter (NCBI ptt file)

Query= SwissProt::P0AE24
         (472 letters)



>lcl|FitnessBrowser__Btheta:353132 BT3606 sugar-proton symporter
           (NCBI ptt file)
          Length = 468

 Score =  265 bits (676), Expect = 3e-75
 Identities = 153/463 (33%), Positives = 258/463 (55%), Gaps = 24/463 (5%)

Query: 23  MFVSVAAAVAGLLFGLDIGVIAGALPFITDHFVLTSRLQEWVVSSMMLGAAIGALFNGWL 82
           +F+SV AA+ G LFG D  VI+G +  +T  F L +  Q W V   ++G+ +G LF+G L
Sbjct: 11  IFLSVVAALGGFLFGYDTAVISGTIAQVTHLFQLDTLQQGWYVGCALIGSIVGVLFSGIL 70

Query: 83  SFRLGRKYSLMAGAILFVLGSIGSAFATSVEMLIAARVVLGIAVGIASYTAPLYLSEMAS 142
           S  +GRK +++  AILF   +IG AF      L+  R++ GI +G+ S  +PLY+SE++ 
Sbjct: 71  SDSIGRKRTMILSAILFSTSAIGCAFCIDFNQLVVYRIIGGIGIGVVSIVSPLYISEVSV 130

Query: 143 ENVRGKMISMYQLMVTLGIVLAFLSD---TAFSYSGN---------------WRAMLGVL 184
              RG+M+S+YQL VT+G + A+L +    A+S SGN               WR MLG+ 
Sbjct: 131 AQFRGRMVSLYQLAVTVGFLGAYLVNYQLLAYSESGNHLPIAWLEKIVVTEVWRGMLGME 190

Query: 185 ALPAVLLIILVVFLPNSPRWLAEKGRHIEAEEVLRMLRDTSEKAREELNEIRESLKLK-Q 243
            LPA++  I++ F+P SPRWL  KG+  +A  +L  + ++ ++A  +LNE +  L  + +
Sbjct: 191 TLPAIIFFIIIFFIPESPRWLIVKGQERKATYILEKIYNSFKEADFQLNETKSVLVSETR 250

Query: 244 GGWALFKINRNVRRAVFLGMLLQAMQQFTGMNIIMYYAPRIFKMAGFTTTEQQMIATLVV 303
             W++  +   + +AV +G+ +  + QF G+N ++YY P IF+ AG +  +  +   ++V
Sbjct: 251 SEWSIL-LKPGILKAVIIGVCIAILGQFMGVNAVLYYGPSIFENAGLSGGD-SLFYQVLV 308

Query: 304 GLTFMFATFIAVFTVDKAGRKPALKIGFSVMALGTLVLGYCLMQFDNGTASSGLSWLSVG 363
           GL     T +A+  +DK GRK  +  G S M +  +++G   + F N    S L  L+  
Sbjct: 309 GLVNTLTTILALLIIDKVGRKKLIYYGVSGMVVSLILIGSYFL-FGNAWNISSLFLLAFF 367

Query: 364 MTMMCIAGYAMSAAPVVWILCSEIQPLKCRDFGITCSTTTNWVSNMIIGATFLTLLDSIG 423
           +  +     A+S   V+++L SE+ P K R   ++ +    W+   +IG     +L ++ 
Sbjct: 368 LCYVFCC--AISICAVIFVLLSEMYPTKIRGLAMSIAGFALWIGTYLIGQLTPWMLQNLT 425

Query: 424 AAGTFWLYTALNIAFVGITFWLIPETKNVTLEHIERKLMAGEK 466
            AGTF+L+  + + ++ I + L+PET   +LE IER     E+
Sbjct: 426 PAGTFFLFAIMCVPYMLIVWKLVPETTGKSLEEIERYWTRSER 468


Lambda     K      H
   0.327    0.138    0.409 

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: 535
Number of extensions: 29
Number of successful extensions: 5
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: 472
Length of database: 468
Length adjustment: 33
Effective length of query: 439
Effective length of database: 435
Effective search space:   190965
Effective search space used:   190965
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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 paper from 2022 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