GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Pseudomonas fluorescens FW300-N2E2

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Pf6N2E2_462 Aspartate aminotransferase (EC 2.6.1.1)

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_462
          Length = 394

 Score =  213 bits (541), Expect = 1e-59
 Identities = 128/387 (33%), Positives = 206/387 (53%), Gaps = 16/387 (4%)

Query: 14  SATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPVSGIPEL 73
           +A   +  +A  ++ +G DV+ L  G+PDFDTP  I  AA+ ++  GET Y+ + G+  L
Sbjct: 15  AAAWQIHDRALAMREQGMDVLLLSVGDPDFDTPRAIVDAAVGSLRAGETHYSDIRGLHTL 74

Query: 74  REAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVA 133
           R +IA++ +        A Q +V  G +  ++      LNPGDEV++  P +V+Y  +  
Sbjct: 75  RTSIARRHRLRCGQPAGAEQVVVLPGAQCAVYAVAQCLLNPGDEVIVAEPMYVTYEAVFG 134

Query: 134 LCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVL 193
            CG T V V  R EN F+++  D+ R +TP+T+  + NSP+NPSGA+      +AL  + 
Sbjct: 135 ACGATVVPVAVRPENGFRVEPADVARLVTPRTRAMLLNSPNNPSGASLPMPTWQALARLC 194

Query: 194 MKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGYAAG 253
           ++H  +W+++D++Y  L Y D    +P  + PG+ ERT T+N +SK++AMTGWRIG+  G
Sbjct: 195 IEH-DLWLISDEVYSDLLY-DGEHISPASL-PGMAERTATINSLSKSHAMTGWRIGWVIG 251

Query: 254 PLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVVSMLNQAK 313
           P  L   +  +      G     Q AA  AL      + +  + ++ RRDLV +ML+   
Sbjct: 252 PESLADHLANLSLCMLFGLPDFVQRAAQVALEQALPEVAQMHDEYRQRRDLVCAMLDDCP 311

Query: 314 GISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVHGSAFG--LG 371
           G+    P+G  +V       + +T    +       F   LL+  GV+V+ G AFG    
Sbjct: 312 GLKPVRPDGGMFVMVD----VRRTGLDAQA------FAERLLDDYGVSVLAGEAFGPSAA 361

Query: 372 PNFRISYATSEALLEEACRRIQRFCAA 398
            + R+     +  L +AC+RI   CAA
Sbjct: 362 GHIRLGLVVDQVKLADACQRITS-CAA 387


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: 371
Number of extensions: 16
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: 400
Length of database: 394
Length adjustment: 31
Effective length of query: 369
Effective length of database: 363
Effective search space:   133947
Effective search space used:   133947
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