GapMind for Amino acid biosynthesis

 

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

Align Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase; PhPPA-AT; EC 2.6.1.1; EC 2.6.1.78; EC 2.6.1.79 (characterized)
to candidate Pf1N1B4_2863 Valine--pyruvate aminotransferase (EC 2.6.1.66)

Query= SwissProt::E9L7A5
         (479 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2863
          Length = 390

 Score =  198 bits (504), Expect = 2e-55
 Identities = 137/401 (34%), Positives = 199/401 (49%), Gaps = 22/401 (5%)

Query: 74  ISLSPRVNSVKPSKTVAITDQATALVQAGVPVIRLAAGEPDFDTPAPIVEAGINAIREGH 133
           +S S R  +++P   +A+  +A  L  AG  VI L  GEPDF T  PI++AG  A+  G 
Sbjct: 3   LSYSARSRAIEPFHVMALLARANELQAAGHDVIHLEIGEPDFTTAEPIIQAGQAALTAGK 62

Query: 134 TRYTPNAGTMELRSAISHKLKEENGLSYTPDQILVSNGAKQSIIQAVLAVCSPGDEVLIP 193
           TRYT   G  ELR AIS   ++  GL+  P +IL++ G   +++ A   +  PG   L+ 
Sbjct: 63  TRYTAARGIPELREAISGFYQQRYGLNIDPQRILITPGGSGALLLASALLVDPGKHWLLA 122

Query: 194 APYWVSYPEMARLADATPVILPTSISEDFLLDPKLLESKLTEKSRLLILCSPSNPTGSVY 253
            P +       RL +    ++P      + L P L+       S   ++ SP+NPTG++ 
Sbjct: 123 DPGYPCNRHFLRLVEGAAQLVPVGPDVRYQLTPDLVARHWDHDSVGALVASPANPTGTIL 182

Query: 254 PRKLLEQI-AEIVARHPRLLVISDEIYEHIIYAPATHTSFASLPGMWDRTLTVNGFSKAF 312
            R  L  + A I ARH  L+V  DEIY  + Y     T  AS+  + D    +N FSK F
Sbjct: 183 TRDELAGLSAAIKARHGHLVV--DEIYHGLTYG----TEAASVLEVDDSAFVLNSFSKYF 236

Query: 313 AMTGWRLGYIAGPKHFIAACNKIQSQFTSGASSISQKAAVAALGLGYAGGELVATMVKSF 372
            MTGWRLG++  P+  +    K+       A S++Q AA+A      A  ++       F
Sbjct: 237 GMTGWRLGWLVAPEAAVGELEKLAQNLYISAPSMAQHAALAC--FEPATIQIFEERRAEF 294

Query: 373 RERRDYLVKSFGEIEGVKISEPRGAFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKA 432
             RRD+L+ +  E+      EP GAFYL+ D+S + G   D F       + CR+ L+  
Sbjct: 295 GRRRDFLLPALRELGFGIAVEPEGAFYLYADISKFGG---DAF-------AFCRHFLETE 344

Query: 433 QVALVPGDAFGDDTC---IRISYAASLSTLQAAVERIKKAL 470
            VA+ PG  FG       +R +Y  SL  LQ AVERI + L
Sbjct: 345 HVAITPGLDFGRYQAGHHVRFAYTQSLPRLQEAVERIARGL 385


Lambda     K      H
   0.317    0.132    0.375 

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: 427
Number of extensions: 14
Number of successful extensions: 4
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: 479
Length of database: 390
Length adjustment: 32
Effective length of query: 447
Effective length of database: 358
Effective search space:   160026
Effective search space used:   160026
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: 51 (24.3 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