GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:349961
          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 (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