GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HP1174 in Bacteroides thetaiotaomicron VPI-5482

Align Glucose/galactose porter (characterized)
to candidate 353115 BT3589 glucose/galactose transporter (NCBI ptt file)

Query= TCDB::P0C105
         (412 letters)



>lcl|FitnessBrowser__Btheta:353115 BT3589 glucose/galactose
           transporter (NCBI ptt file)
          Length = 438

 Score =  221 bits (562), Expect = 4e-62
 Identities = 131/432 (30%), Positives = 235/432 (54%), Gaps = 40/432 (9%)

Query: 15  TSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIV 74
           ++ +K Y  +L  L  +FF++GF++ +N ILIP+ +   +L + +S  + F F+ AYF++
Sbjct: 7   SARKKTYYISLAILAGMFFIFGFVSWVNSILIPYFRISCELTHFESYFVAFAFYIAYFVM 66

Query: 75  SLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVA 134
           ++P+G L+K++ +K+GI+ G ++ A+G  +F+PAA  R + +FL  LF + +G+ ILQ A
Sbjct: 67  AIPSGILLKKVGFKKGIMYGFMLTALGAFIFVPAALARQFEIFLIGLFSIGTGLAILQTA 126

Query: 135 ANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLIL-----------------SA 177
           ANPYVTI+G  ++AA R+++    N +   ++P+  A LIL                  A
Sbjct: 127 ANPYVTIIGPIDSAARRISIMGICNKVAGIISPLIFAALILKANDSELFALIESGALDEA 186

Query: 178 ATDATVNAEADAVRFPYLLLA--LAFTVLAIIFAILKPPDVQEDEPALSDKKEG------ 229
             +A +N     V  PY++L   L  T + I +++L  P++  DE   +D+++       
Sbjct: 187 TKNAMLNELIQRVIIPYIILGIILLLTGIGIRYSVL--PEINTDEQNATDEQDNKHTDKK 244

Query: 230 SAWQYRHLVLGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVG 289
           S   + +L+LGA+ IF +VG +V     ++N+ +     G+   +A    +Y  G  M+G
Sbjct: 245 SILDFPYLILGALAIFFHVGTQVIAIDTIINYANS---MGMDLLEAKVFPSYTLGCTMIG 301

Query: 290 RFIGSAAM-RYIDDGKALAFNAFVAIILLF------ITVATTGHIAMWSVL---AIGLFN 339
             +G   + +YI    AL     + + L F        +   GH A  S+    A+G  N
Sbjct: 302 YILGIILIPKYISQKNALIGCTLLGLALSFGVVWADFDMTLFGHQANASIFFLNALGFPN 361

Query: 340 SIMFPTIFSLALHGLGSHTSQGSGILCLAIVGGAIVPLIQGALADAIGIHLAFLMPIICY 399
           ++++  I+ L++HGLG  T  GS +L + + G AI+PL+ G  AD   + + + + I C+
Sbjct: 362 ALIYAGIWPLSIHGLGKFTKTGSSLLIMGLCGNAILPLVYGHFADQYSLRIGYWVLIPCF 421

Query: 400 AYIAFYGLIGSK 411
            Y+ F+ + G K
Sbjct: 422 IYLVFFAIKGHK 433


Lambda     K      H
   0.328    0.141    0.420 

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: 546
Number of extensions: 30
Number of successful extensions: 4
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: 412
Length of database: 438
Length adjustment: 32
Effective length of query: 380
Effective length of database: 406
Effective search space:   154280
Effective search space used:   154280
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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