GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Sphingomonas koreensis DSMZ 15582

Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Ga0059261_3811 Ga0059261_3811 branched-chain amino acid aminotransferase, group II

Query= BRENDA::P54691
         (305 letters)



>FitnessBrowser__Korea:Ga0059261_3811
          Length = 362

 Score = 99.0 bits (245), Expect = 1e-25
 Identities = 96/318 (30%), Positives = 149/318 (46%), Gaps = 31/318 (9%)

Query: 9   YFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKSAK 68
           + + K V      +  AT  LHY    F GL+      D GT L FR   +  R  +SA+
Sbjct: 48  WHDAKVVARGPLSLDPATAVLHYAQEIFEGLKAYRTG-DEGTAL-FRPLENARRFRESAQ 105

Query: 69  FLHY-DISAEKIKEVIVDFVKKNQP------DKSFYIRPLVYSSG--LGIAPRLHNLEKD 119
            +   ++  +     I   VK ++         S Y+RP +++S   LG+ P    L   
Sbjct: 106 RMAMPELPDDLFLGSIEALVKADREWIPQIEGGSLYLRPFMFASEVFLGVKPASEYL--- 162

Query: 120 FLVYGLEMGDYL--AADGVSCRISSWYRQEDRSFPLRGKISAAYITSALAKTEAVESGFD 177
           +LV     G Y    A  V+  +S  Y +         K    Y +S +A+ EA+  G D
Sbjct: 163 YLVIASPAGAYFKGGAPAVTIWVSDHYTRAAPGGTGAAKCGGNYASSLVAQAEAIREGCD 222

Query: 178 EAILMNSQGK--VCEATGMNVFMV-RNGQIVTPGNEQDILEGITRDSILTIAADLGIPTC 234
           + + +++  +  V E  GMN+F V  +G +VTP     IL GITR+SILT+A + GI   
Sbjct: 223 QVVFLDAVERRWVEELGGMNLFFVFDDGSMVTPPLGGTILPGITRESILTLAREQGITVR 282

Query: 235 QRP--IDKSELMIAD----EVFLSGTAAKITPVKRIEN----FTLGGDRP--ITEKLRSV 282
           + P  ID+ +         E F  GTAA +TPV ++++    FT+G   P  +TE L++ 
Sbjct: 283 EEPYAIDQWKADAGSGKLVETFACGTAAVVTPVGKVKSRDGEFTIGSGGPGQVTEALKAR 342

Query: 283 LTAVTENREPKYQDWVFK 300
           LTA+   + P    WV +
Sbjct: 343 LTAIQRGQAPDIHGWVHR 360


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: 253
Number of extensions: 17
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: 305
Length of database: 362
Length adjustment: 28
Effective length of query: 277
Effective length of database: 334
Effective search space:    92518
Effective search space used:    92518
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