GapMind for Amino acid biosynthesis

 

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

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 Pf6N2E2_5161 Valine--pyruvate aminotransferase (EC 2.6.1.66) ## AvtA

Query= SwissProt::E9L7A5
         (479 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5161
          Length = 390

 Score =  190 bits (483), Expect = 6e-53
 Identities = 129/397 (32%), Positives = 195/397 (49%), Gaps = 20/397 (5%)

Query: 77  SPRVNSVKPSKTVAITDQATALVQAGVPVIRLAAGEPDFDTPAPIVEAGINAIREGHTRY 136
           S R  +++P   +A+  +A  L  AG  VI L  GEPDF T  PI++AG  A+  G TRY
Sbjct: 6   SARSRAIEPFHVMALLARANELQAAGHDVIHLEIGEPDFTTAEPIIQAGQAALAAGKTRY 65

Query: 137 TPNAGTMELRSAISHKLKEENGLSYTPDQILVSNGAKQSIIQAVLAVCSPGDEVLIPAPY 196
           T   G  ELR AI+    +  G+   P +ILV+ G   +++ A   +  PG   L+  P 
Sbjct: 66  TAARGIPELREAIAGFYGQRYGVEIDPRRILVTPGGSGALLLASALLVDPGKHWLLADPG 125

Query: 197 WVSYPEMARLADATPVILPTSISEDFLLDPKLLESKLTEKSRLLILCSPSNPTGSVYPRK 256
           +       RL +    ++P      + L P L+     + S   ++ SP+NPTG++  R 
Sbjct: 126 YPCNRHFLRLVEGAAQLVPVGPEVRYQLTPDLVNRHWDQDSVGALVASPANPTGTILTRD 185

Query: 257 LLEQIAEIVARHPRLLVISDEIYEHIIYAPATHTSFASLPGMWDRTLTVNGFSKAFAMTG 316
            L  +++++  H   LV+ DEIY  + Y     T  AS+  + D    +N FSK F MTG
Sbjct: 186 ELAGLSKVIKGHNGHLVV-DEIYHGLTYG----TDAASVLEVDDDAFVLNSFSKYFGMTG 240

Query: 317 WRLGYIAGPKHFIAACNKIQSQFTSGASSISQKAAVAALGLGYAGGELVATMVKSFRERR 376
           WRLG++  P   +    K+       A S++Q AA+A      A  E+       F  RR
Sbjct: 241 WRLGWLVAPSAAVGELEKLAQNLYISAPSMAQYAALAC--FEPATIEIFEQRRAEFARRR 298

Query: 377 DYLVKSFGEIEGVKISEPRGAFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKAQVAL 436
           D+L+ +  E+      EP GAFYL+ D+S++ G   D F       + C++ L+   VA 
Sbjct: 299 DFLLPALRELGFGIAVEPEGAFYLYADISAFGG---DAF-------AFCQHFLETEHVAF 348

Query: 437 VPGDAFGDDTC---IRISYAASLSTLQAAVERIKKAL 470
            PG  FG       +R +Y  SL  L+ AV RI++ L
Sbjct: 349 TPGLDFGRHQAGHHVRFAYTQSLPRLEEAVARIERGL 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: 420
Number of extensions: 17
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