GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Acidovorax sp. GW101-3H11

Align Aromatic-amino-acid aminotransferase 2; ARAT-II; AROAT; EC 2.6.1.57 (characterized)
to candidate Ac3H11_1602 Aspartate aminotransferase (EC 2.6.1.1)

Query= SwissProt::H3ZPU1
         (389 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1602
          Length = 408

 Score =  242 bits (618), Expect = 1e-68
 Identities = 149/395 (37%), Positives = 225/395 (56%), Gaps = 22/395 (5%)

Query: 4   SDRLEMVNPSEIRKLFDLAQGI----EGIISLGIGEPDFDTPEHIKEYAKEALDKGLTHY 59
           +DRL  +  SEI +L   A  +    + +I LG+GEPDFDTP HI E A++A+ +G THY
Sbjct: 13  ADRLGAIGVSEIVRLTQEANQLKRQGQPVIVLGLGEPDFDTPAHILEAAQQAMARGETHY 72

Query: 60  SPNIGILELREAVAEKFKKHNGIDADPKTQIMITVGTNQQILMGLATFLKDNEEVLIPSP 119
           +   G  EL+ A+  KFK +NG+D     +I    G  Q +   L   +   +EV++P+P
Sbjct: 73  TVLDGTAELKAAIQHKFKHYNGLDFQ-LNEITAGAGAKQILYNALMASVNPGDEVILPAP 131

Query: 120 MFVSYAPAVILAGGKPVEVPTYEENEFRLSVDELEKYVTPKTRALIINTPNNPTGAVLTK 179
            + SYA  V++AGG PV VP  E N FR++ ++LE  +TP+TR + IN+P+NP+GA  + 
Sbjct: 132 YWTSYADMVLIAGGVPVVVPCTEANGFRITPEQLEAAITPRTRWVFINSPSNPSGAAYSA 191

Query: 180 KDLEEIADFAVEH-DLMILSDEVYEYFVYDGVKNYSIAS-LDGMFERTITMNGFSKTFAM 237
           + L  + +    H  + +L+D++YE+ +YDG    + A+ L  + +RT+T+NG SK +AM
Sbjct: 192 EQLRPVLEVVERHPQVWLLADDIYEHILYDGRAFATPAAVLPSLRDRTLTVNGVSKAYAM 251

Query: 238 TGWRLGFLAAPEWVVEKMVRFQMYNATCPVTFIQYAAAKALRDERSWQAVEEMRREYERR 297
           TGWRLG+ A P+ ++  M   Q    +CP +  Q AA  AL   +    V E  + ++ R
Sbjct: 252 TGWRLGYGAGPKALIAAMAVVQSQATSCPSSISQAAAVAALTGPQ--DVVRERCQAFQDR 309

Query: 298 RNLVWKRLN-EMGLPTVKPKGAFYIFP-------RIKDTGL---SSKEFSELMIKEAKVV 346
           R+LV   LN   GL    P+GAFY F        R    GL   +  +F   +++E  V 
Sbjct: 310 RDLVVAALNVSPGLRCRVPEGAFYTFASCEGALGRTTPGGLLLRTDADFCAYLLREHHVA 369

Query: 347 VVPGSAFGQAGEGYVRISYATAYEKLEEAMDRMEK 381
           VVPG   G A   Y RISYA +   L+EA  R+++
Sbjct: 370 VVPGGVLGLA--PYFRISYAASTADLQEACARIQR 402


Lambda     K      H
   0.318    0.135    0.387 

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: 350
Number of extensions: 16
Number of successful extensions: 5
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: 389
Length of database: 408
Length adjustment: 31
Effective length of query: 358
Effective length of database: 377
Effective search space:   134966
Effective search space used:   134966
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: 50 (23.9 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