GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Echinicola vietnamensis KMM 6221, DSM 17526

Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Echvi_1626 Echvi_1626 branched-chain amino acid aminotransferase, group II

Query= BRENDA::P54691
         (305 letters)



>FitnessBrowser__Cola:Echvi_1626
          Length = 355

 Score = 94.4 bits (233), Expect = 4e-24
 Identities = 84/274 (30%), Positives = 135/274 (49%), Gaps = 37/274 (13%)

Query: 16  PFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSAKFLHYDIS 75
           P+E   +S     LHYG   F GL+     +D  TI +FRL RH +R+++S + +     
Sbjct: 48  PYEQLVLSPLAMCLHYGQTVFEGLKAYRQEDD--TISIFRLARHHERINQSLRRMAMPEI 105

Query: 76  AEKIKEV----IVDFVK---KNQPDKSFYIRPLVYSSG--LGIAPRLHNLEKDFLVYGLE 126
            E++ E     +VD  +   +     S YIRP V ++   LG++     L   F+V    
Sbjct: 106 PEELFETGIRELVDLEQEWIRGGEGNSLYIRPFVIATEARLGVSISTDYL---FMVVCTP 162

Query: 127 MGDYLAADGVSCRISSWYRQEDRSFP-------LRGKISAAYITSALAKTEAVESGFDEA 179
           M  Y A   +  ++   Y    R+ P         G   AAY  + LA+    ++GFD+ 
Sbjct: 163 MAAYYAKP-LKVKVERHYT---RAVPGGVGAAKNGGNYGAAYYPAHLAQ----QAGFDQV 214

Query: 180 ILMNSQGK--VCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTCQRP 237
           I  +++    V E+  MN+  + +G ++TP   + +L G+TRDS+L+IA D+G P  +RP
Sbjct: 215 IWTDARDHQFVEESGTMNLMFIIDGVLLTPPAGETVLAGVTRDSLLSIARDMGWPVEERP 274

Query: 238 IDKSELMIA------DEVFLSGTAAKITPVKRIE 265
           I   EL  A       E F +GTAA + P++ I+
Sbjct: 275 ISLKELEEAFSTGKKVEAFGAGTAAVVAPLELIQ 308


Lambda     K      H
   0.320    0.138    0.406 

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: 231
Number of extensions: 13
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: 305
Length of database: 355
Length adjustment: 28
Effective length of query: 277
Effective length of database: 327
Effective search space:    90579
Effective search space used:    90579
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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