GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Pseudomonas fluorescens FW300-N1B4

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Pf1N1B4_4996 Aspartate aminotransferase (EC 2.6.1.1)

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4996
          Length = 395

 Score =  213 bits (541), Expect = 1e-59
 Identities = 135/387 (34%), Positives = 211/387 (54%), Gaps = 16/387 (4%)

Query: 14  SATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPVSGIPEL 73
           +A   +  +A EL+ +G DV+ L  G+PDFDTP  I  AAID++  G+T Y+ V G   L
Sbjct: 15  AAAWKIHDRALELREQGVDVLLLSIGDPDFDTPLPIIHAAIDSLLAGDTHYSDVRGTRTL 74

Query: 74  REAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVA 133
           R +IA + +R +     A   IV  G +  +++     L+PGDEV++  P +V+Y  +  
Sbjct: 75  RSSIASRHQRRSGQLVDADHVIVLPGAQCAVYSVAQCLLDPGDEVIVAEPMYVTYEGVFG 134

Query: 134 LCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVL 193
            CG + V V  R EN F+++  D+   IT KT+  + NSP+NPSGA+ S +  KAL  + 
Sbjct: 135 ACGASVVPVAVRPENGFRVEPADVAALITSKTRVILLNSPNNPSGASLSLKSWKALAALC 194

Query: 194 MKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGYAAG 253
           ++H  +W+++D++Y  L + +    +P  + PG+ ERT T+N +SK++AMTGWR+G+  G
Sbjct: 195 VQH-DLWLISDEVYSDLLF-EGEHISPASL-PGMAERTATINSLSKSHAMTGWRVGWMIG 251

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

Query: 314 GISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVHGSAFG--LG 371
           GI    P+G  +V       + +T          +DF   LLE  GV+V+ G AFG    
Sbjct: 312 GIRPIKPDGGMFVMVD----VRQTGLGA------QDFAERLLEGYGVSVLAGEAFGPSAA 361

Query: 372 PNFRISYATSEALLEEACRRIQRFCAA 398
            + RI     +A L +AC+RI   CAA
Sbjct: 362 GHIRIGLVVDQARLADACQRIAS-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: 386
Number of extensions: 21
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: 395
Length adjustment: 31
Effective length of query: 369
Effective length of database: 364
Effective search space:   134316
Effective search space used:   134316
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