GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Bacteroides faecis MAJ27

Align Glucose transporter GlcP; Glucose/H(+) symporter (characterized)
to candidate WP_010537714.1 KCY_RS0114120 MFS transporter

Query= SwissProt::A0A0H2VG78
         (446 letters)



>NCBI__GCF_000226135.1:WP_010537714.1
          Length = 309

 Score =  199 bits (505), Expect = 1e-55
 Identities = 114/301 (37%), Positives = 174/301 (57%), Gaps = 22/301 (7%)

Query: 6   YLIF--ILGALGGLLYGYDNGVISGALLFIHKDIPLNSTTEGIVVSSMLIGAIVGAGSSG 63
           YLIF  ++ ALGG L+GYD  VISG +  + +   L++  +G  V   LIG+IVG   +G
Sbjct: 9   YLIFLSVVAALGGFLFGYDTAVISGTIAQVSQLFQLDALQQGWYVGCALIGSIVGVLFAG 68

Query: 64  PLADKLGRRRLVMLIAIVFIIGALILAASTNLALLIIGRLIIGLAVGGSMSTVPVYLSEM 123
            L+DKLGR+  +++ A++F   AL  A S +   L+I R+I G+ +G      P+Y+SE+
Sbjct: 69  ILSDKLGRKLTMVISAVLFSTSALGCAISADFTQLVIYRIIGGVGIGVVSIVSPLYISEV 128

Query: 124 APTEYRGSLGSLNQLMITIGILAAYLVNYAFAD------------------IEGWRWMLG 165
           +  +YRG L SL QL +T+G L AYLVNY                       E WR MLG
Sbjct: 129 SVAQYRGRLVSLYQLAVTVGFLGAYLVNYQLLGYAQSGSQLSIDWLNKIFVTEVWRGMLG 188

Query: 166 LAVVPSVILLVGIYFMPESPRWLLENRNEEAARQVMKITYDD-SEIDKELKEMKEI-NAI 223
           + ++P+V+  + I+F+PESPRWL+    EE A  +++  Y+  SE   +L E K +  + 
Sbjct: 189 MEMLPAVLFFIIIFFIPESPRWLIVKGKEEKAVNILEKIYNSVSEATSQLNETKSVLTSE 248

Query: 224 SESTWTVIKSPWLGRILIVGCIFAIFQQFIGINAVIFYSSSIFAKAGLGEAASILGSVGI 283
           ++S W ++  P + + +I+G   AI  QF+G+NAV++Y  SIF  AGL    S+   V +
Sbjct: 249 TKSEWALLMKPGIFKAVIIGVCIAILGQFMGVNAVLYYGPSIFENAGLSGGDSLFYQVLV 308

Query: 284 G 284
           G
Sbjct: 309 G 309



 Score = 28.9 bits (63), Expect = 2e-04
 Identities = 28/100 (28%), Positives = 47/100 (47%), Gaps = 20/100 (20%)

Query: 241 IVGCIFA-IFQQFIGINAVIFYSSSIFAKAGLGEAAS----------ILGSVGIGTINVL 289
           IVG +FA I    +G    +  S+ +F+ + LG A S          I+G VGIG    +
Sbjct: 61  IVGVLFAGILSDKLGRKLTMVISAVLFSTSALGCAISADFTQLVIYRIIGGVGIG----V 116

Query: 290 VTIVAIFVVDKIDRKKLLVGGNIGMIASLLIMAILIWTIG 329
           V+IV+   + ++      V    G + SL  +A+ +  +G
Sbjct: 117 VSIVSPLYISEVS-----VAQYRGRLVSLYQLAVTVGFLG 151


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: 406
Number of extensions: 23
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 446
Length of database: 309
Length adjustment: 30
Effective length of query: 416
Effective length of database: 279
Effective search space:   116064
Effective search space used:   116064
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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