GapMind for catabolism of small carbon sources

 

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

Align Glucose transporter GlcP; Glucose/H(+) symporter (characterized)
to candidate 353132 BT3606 sugar-proton symporter (NCBI ptt file)

Query= SwissProt::A0A0H2VG78
         (446 letters)



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

 Score =  281 bits (719), Expect = 3e-80
 Identities = 170/457 (37%), Positives = 264/457 (57%), Gaps = 33/457 (7%)

Query: 6   YLIF--ILGALGGLLYGYDNGVISGALLFIHKDIPLNSTTEGIVVSSMLIGAIVGAGSSG 63
           Y+IF  ++ ALGG L+GYD  VISG +  +     L++  +G  V   LIG+IVG   SG
Sbjct: 9   YIIFLSVVAALGGFLFGYDTAVISGTIAQVTHLFQLDTLQQGWYVGCALIGSIVGVLFSG 68

Query: 64  PLADKLGRRRLVMLIAIVFIIGALILAASTNLALLIIGRLIIGLAVGGSMSTVPVYLSEM 123
            L+D +GR+R ++L AI+F   A+  A   +   L++ R+I G+ +G      P+Y+SE+
Sbjct: 69  ILSDSIGRKRTMILSAILFSTSAIGCAFCIDFNQLVVYRIIGGIGIGVVSIVSPLYISEV 128

Query: 124 APTEYRGSLGSLNQLMITIGILAAYLVNY---AFAD---------------IEGWRWMLG 165
           +  ++RG + SL QL +T+G L AYLVNY   A+++                E WR MLG
Sbjct: 129 SVAQFRGRMVSLYQLAVTVGFLGAYLVNYQLLAYSESGNHLPIAWLEKIVVTEVWRGMLG 188

Query: 166 LAVVPSVILLVGIYFMPESPRWLLENRNEEAARQVMKITYDD-SEIDKELKEMKEINAIS 224
           +  +P++I  + I+F+PESPRWL+    E  A  +++  Y+   E D +L E K +  +S
Sbjct: 189 METLPAIIFFIIIFFIPESPRWLIVKGQERKATYILEKIYNSFKEADFQLNETKSV-LVS 247

Query: 225 E--STWTVIKSPWLGRILIVGCIFAIFQQFIGINAVIFYSSSIFAKAGLGEAASILGSVG 282
           E  S W+++  P + + +I+G   AI  QF+G+NAV++Y  SIF  AGL    S+   V 
Sbjct: 248 ETRSEWSILLKPGILKAVIIGVCIAILGQFMGVNAVLYYGPSIFENAGLSGGDSLFYQVL 307

Query: 283 IGTINVLVTIVAIFVVDKIDRKKLLVGGNIGMIASLLIMAILIWTIGIASSAWII--IVC 340
           +G +N L TI+A+ ++DK+ RKKL+  G  GM+ SL    ILI +  +  +AW I  +  
Sbjct: 308 VGLVNTLTTILALLIIDKVGRKKLIYYGVSGMVVSL----ILIGSYFLFGNAWNISSLFL 363

Query: 341 LSLFIVFF---GISWGPVLWVMLPELFPMRARGAATGISALVLNIGTLIVSLFFPILSDA 397
           L+ F+ +     IS   V++V+L E++P + RG A  I+   L IGT ++    P +   
Sbjct: 364 LAFFLCYVFCCAISICAVIFVLLSEMYPTKIRGLAMSIAGFALWIGTYLIGQLTPWMLQN 423

Query: 398 LSTEWVFLIFAFIGVLAMIFVIKFLPETRGRSLEEIE 434
           L+    F +FA + V  M+ V K +PET G+SLEEIE
Sbjct: 424 LTPAGTFFLFAIMCVPYMLIVWKLVPETTGKSLEEIE 460


Lambda     K      H
   0.327    0.144    0.422 

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: 626
Number of extensions: 33
Number of successful extensions: 6
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: 446
Length of database: 468
Length adjustment: 33
Effective length of query: 413
Effective length of database: 435
Effective search space:   179655
Effective search space used:   179655
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 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