GapMind for catabolism of small carbon sources

 

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

Align Glucosamine-6-phosphate deaminase; EC 3.5.99.6; GlcN6P deaminase; GNPDA; Glucosamine-6-phosphate isomerase (uncharacterized)
to candidate 353113 BT3587 glucosamine-6-phosphate isomerase (NCBI ptt file)

Query= curated2:B7H945
         (262 letters)



>lcl|FitnessBrowser__Btheta:353113 BT3587 glucosamine-6-phosphate
           isomerase (NCBI ptt file)
          Length = 261

 Score =  139 bits (351), Expect = 5e-38
 Identities = 76/215 (35%), Positives = 123/215 (57%), Gaps = 6/215 (2%)

Query: 22  EVVKTKENPTLGMATGSSPLGIYAEMRKNK-LDTSRVTTVNLDEYVNLPHEDKNSYHYFM 80
           E++K K    +  A   S     + +  +K +D SR+   ++DEY+ +  E   S+  F+
Sbjct: 41  ELLKEKAEINMIFAAAPSQNEFLSHLIHSKQIDWSRINAFHMDEYIGIHPEAPQSFGNFL 100

Query: 81  QEQLFDHLPFKQTYVPNGMASDLEEECKRYESILAANPVDLQILGIGENGHIGFNEPGTP 140
           ++++FD +PFK     NG A +LEEECKRY  +L  +PVD+  LGIGENGHI FN+P   
Sbjct: 101 RQRIFDKVPFKTVNYLNGQAENLEEECKRYSELLLRHPVDIVCLGIGENGHIAFNDPDVA 160

Query: 141 FNSPTNIVELTE-----STRQANLRFFEKEEDVPTHAITMGIGSIMKAKQVLLVAMGSKK 195
             + +++V++ E       +Q N + FE  + VP  A+T+ I +++KA  +  +     K
Sbjct: 161 NFNDSHLVKVVELDPICRQQQVNEKCFEAFDLVPAKALTLTIPALLKADWMFCIVPFKNK 220

Query: 196 AEAVKELLQGEYSEECPATVLQRHPNVTVIADQEA 230
           A AV   L GE SE+CPA++L++  N  +  D E+
Sbjct: 221 ANAVYNTLYGEISEKCPASILRKKENSCLYLDPES 255


Lambda     K      H
   0.313    0.130    0.363 

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: 156
Number of extensions: 6
Number of successful extensions: 2
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: 262
Length of database: 261
Length adjustment: 25
Effective length of query: 237
Effective length of database: 236
Effective search space:    55932
Effective search space used:    55932
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 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