GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Bacteroides thetaiotaomicron VPI-5482

Align prephenate dehydratase (EC 4.2.1.51) (characterized)
to candidate 353462 BT3936 prephenate dehydratase (NCBI ptt file)

Query= BRENDA::P57472
         (385 letters)



>FitnessBrowser__Btheta:353462
          Length = 282

 Score =  135 bits (341), Expect = 1e-36
 Identities = 84/276 (30%), Positives = 147/276 (53%), Gaps = 10/276 (3%)

Query: 110 GPKGSYSHIAAYKYADLNFQKCITNECSTFEEVVLSVENNQSDYAVLPIENTCSGSINEV 169
           G  GSY  IAA+KY +    + I   C+ FE+V  S+  +     +L IENT +GS+   
Sbjct: 8   GTLGSYHDIAAHKYFEGEEIELIC--CANFEDVFTSIRKDSQVIGMLAIENTIAGSLLHN 65

Query: 170 FDILKKTNLFIIGEINIFINHNLLTLKKIELNKIKTIYSHPQPFQQCSDFIKKFPEWKIK 229
            ++L+++   IIGE  + I+H+ + L +     +  + SHP    QC DF+ + P+ K+ 
Sbjct: 66  NELLRQSGTQIIGEYKLRISHSFVCLPEESWEDLTEVNSHPIALMQCRDFLNQHPQLKVV 125

Query: 230 YTKSTADAMKKIKKYNDVTNAALGSEIGSKIYGLEILMKNLANKENNITRFILLNRNPKK 289
             + TA + + IKK N   +AA+ S+  ++ YG+++L + +   ++N TRF+++  +P +
Sbjct: 126 EGEDTARSAEIIKKENLKGHAAICSKTAAERYGMKVLQEGIETNKHNFTRFLVV-ADPWQ 184

Query: 290 ISK------NIPTTTTLIFTTGQEAGSLSKVLSILQEKKLIMKKLTSQKIYKNPWEEMFY 343
           + +            +++FT     GSLS+VLSIL    + + K+ S  I    WE  FY
Sbjct: 185 VDELRQHHAKATNKASMVFTLPHTEGSLSQVLSILSFYNINLTKIQSLPIIGREWEYQFY 244

Query: 344 IDIQVNLSSTLMQDALEKIKKITRFIKILGCYPSEK 379
           +D+  N      + ++  I  +T+ +KILG Y   K
Sbjct: 245 VDVSFN-DYLRYKQSIAAITPLTKELKILGEYAEGK 279


Lambda     K      H
   0.318    0.134    0.374 

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: 270
Number of extensions: 6
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: 385
Length of database: 282
Length adjustment: 28
Effective length of query: 357
Effective length of database: 254
Effective search space:    90678
Effective search space used:    90678
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 Aug 03 2021. The underlying query database was built on Aug 03 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