GapMind for catabolism of small carbon sources

 

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

Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate 349961 BT0433 putative xylose repressor (NCBI ptt file)

Query= metacyc::MONOMER-19002
         (326 letters)



>lcl|FitnessBrowser__Btheta:349961 BT0433 putative xylose repressor
           (NCBI ptt file)
          Length = 402

 Score =  149 bits (377), Expect = 9e-41
 Identities = 102/321 (31%), Positives = 152/321 (47%), Gaps = 16/321 (4%)

Query: 6   EKPYVVGIDIGGTNTVFGIVDARGTIIASGAVKTQVYPTVEEYADEVCKNLLPLIIANG- 64
           E  Y +G+DI       G+++ +G ++         +    E  +E+CK +L  I     
Sbjct: 83  ESGYFIGVDIKRFAVNIGLINFKGDMVELKMNIPYKFENSIEGMNELCKLILNFIKKLPI 142

Query: 65  GVDKIKGIGIGA-----PNGNYYTGTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDAN 119
             +KI  I +       P   Y      F          PLA +  E+LG    + ND  
Sbjct: 143 NKEKILNINVNVSGWVNPESGYSFSQFNFEER-------PLADVLSEKLGHKVTIDNDTR 195

Query: 120 AAAVGEMTYGAARGMKDFIMITLGTGVGSGIVINGQVVYGHDGFAGELGHVIVRRDGRIC 179
           A   GE   G  +G KD I + +  GVG GI+I+G+V  G  GF+GE GHV    +  IC
Sbjct: 196 AMTYGEYMQGCVKGEKDIIFVNVSWGVGIGIIIDGKVYTGKSGFSGEFGHVNAYDNEIIC 255

Query: 180 GCGRKGCLETYCSATGVARTAREFLAARTDASLLRNIPAES--IVSKDVYDAAVQGDKLA 237
            CG+KGCLET  S + + R   E + +   + L   I  E   I   ++  A  + D L 
Sbjct: 256 HCGKKGCLETEASGSALHRILLERIKSGESSILSTRISGEEDPITLDEIITAVNKEDLLC 315

Query: 238 QEIFEFTGNILGEALADAIAFSSPEAIILFGGLAKSGDYIMKPIMKAMENNLLNIYKGKA 297
            EI E  G  LG+ +A  I   +PE +I+ G L+ +GDYI +PI  A+    LN+    +
Sbjct: 316 IEIVEEIGQKLGKQIAGLINIFNPELVIIGGTLSLTGDYITQPIKTAVRKYSLNLVNKDS 375

Query: 298 KLLVSELKDSDAAVLGASALA 318
            ++ S+LKD  A ++GA  LA
Sbjct: 376 AIITSKLKDK-AGIVGACMLA 395


Lambda     K      H
   0.318    0.138    0.399 

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: 331
Number of extensions: 22
Number of successful extensions: 3
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: 326
Length of database: 402
Length adjustment: 29
Effective length of query: 297
Effective length of database: 373
Effective search space:   110781
Effective search space used:   110781
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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, 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