GapMind for Amino acid biosynthesis

 

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

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Ac3H11_1602 Aspartate aminotransferase (EC 2.6.1.1)

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1602
          Length = 408

 Score =  434 bits (1117), Expect = e-126
 Identities = 215/394 (54%), Positives = 271/394 (68%)

Query: 5   ADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKY 64
           AD L  +  S  + ++Q+A +LK +G+ VI LG GEPDFDTP +I +AA  A+ RGET Y
Sbjct: 13  ADRLGAIGVSEIVRLTQEANQLKRQGQPVIVLGLGEPDFDTPAHILEAAQQAMARGETHY 72

Query: 65  TPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPY 124
           T + G  EL+ AI  KFK  N LD+   +   G G KQIL+NA MA++NPGDEV++PAPY
Sbjct: 73  TVLDGTAELKAAIQHKFKHYNGLDFQLNEITAGAGAKQILYNALMASVNPGDEVILPAPY 132

Query: 125 WVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHE 184
           W SY +MV + GG PV VP  + N F++  E L+ AITP+T+W   NSPSNPSGAAYS E
Sbjct: 133 WTSYADMVLIAGGVPVVVPCTEANGFRITPEQLEAAITPRTRWVFINSPSNPSGAAYSAE 192

Query: 185 ELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMT 244
           +L+ + +V+ +HP VW+L DD+YEH+ Y    FATP  V P L +RTLT+NGVSKAYAMT
Sbjct: 193 QLRPVLEVVERHPQVWLLADDIYEHILYDGRAFATPAAVLPSLRDRTLTVNGVSKAYAMT 252

Query: 245 GWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDL 304
           GWR+GY AGP  LI AM ++Q Q TS  +SI+Q AAV AL GPQD +    + FQ RRDL
Sbjct: 253 GWRLGYGAGPKALIAAMAVVQSQATSCPSSISQAAAVAALTGPQDVVRERCQAFQDRRDL 312

Query: 305 VVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVH 364
           VV+ LN + G+ C  PEGAFY + SC G +G+T P G ++ TD DF + LL    VAVV 
Sbjct: 313 VVAALNVSPGLRCRVPEGAFYTFASCEGALGRTTPGGLLLRTDADFCAYLLREHHVAVVP 372

Query: 365 GSAFGLGPNFRISYATSEALLEEACRRIQRFCAA 398
           G   GL P FRISYA S A L+EAC RIQR C A
Sbjct: 373 GGVLGLAPYFRISYAASTADLQEACARIQRACQA 406


Lambda     K      H
   0.318    0.134    0.402 

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: 502
Number of extensions: 15
Number of successful extensions: 1
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: 400
Length of database: 408
Length adjustment: 31
Effective length of query: 369
Effective length of database: 377
Effective search space:   139113
Effective search space used:   139113
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