GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Pseudomonas simiae WCS417

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate GFF2657 PS417_13545 arginine aminotransferase

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__WCS417:GFF2657
          Length = 664

 Score =  202 bits (513), Expect = 3e-56
 Identities = 124/383 (32%), Positives = 195/383 (50%), Gaps = 19/383 (4%)

Query: 19  VSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPVSGIPELREAIA 78
           +   A +  ++G D+I L  G+PDF TP  I  AA+ A+  G+T YT + G P LREAIA
Sbjct: 20  IHHAAFQAASQGEDIIILSVGDPDFATPSFITDAAVSALREGDTHYTEIPGRPALREAIA 79

Query: 79  KKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVALCGGT 138
            ++ +      +A   I   G +  LF   +  L  GDEV++  P +V+Y   +   G T
Sbjct: 80  ARYSKTLARALSAENVITVAGAQNALFVTSLCLLQAGDEVLVLDPMYVTYEATLKASGAT 139

Query: 139 PVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVLMKHPH 198
            V VP   E+ F+L A+ L  AITP+T+   F++P+NP+G   + +EL+A+ D+ +    
Sbjct: 140 LVRVPCSPESGFRLDAQLLGAAITPRTRAIFFSNPNNPTGVVLNLQELQAIADLAIAR-D 198

Query: 199 VWVLTDDMYEHLTY-GDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGYAAGPLHL 257
           +WV+ D++YE L + G++     +   PG+ ER + +  +SK++AMTGWRIG+      +
Sbjct: 199 LWVVVDEVYESLVFDGEYHSLAAL---PGMAERCVVIGSLSKSHAMTGWRIGWIIATPQM 255

Query: 258 IKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVVSMLNQAKGISC 317
           +   + +      G       AA  A+    D     +EI++ RRDLV++ L+   GI  
Sbjct: 256 VAHAETLVLSMLYGLPGFVMEAATAAVLAHDDVTQGMREIYRRRRDLVMAGLSACPGIKV 315

Query: 318 PTPEGAFYVYPSCAGL-IGKTAPSGKVIETDEDFVSELLETEGVAVVHGSAFGLGPN--F 374
             P+   +V     G  +G             DF   L    GV+V+  +AFG       
Sbjct: 316 QAPQAGMFVLVDVRGTGLGSL-----------DFAWRLFREAGVSVLDAAAFGAPAQGFV 364

Query: 375 RISYATSEALLEEACRRIQRFCA 397
           R+S+   E  L EAC+RI  F A
Sbjct: 365 RLSFTLGEERLSEACQRIAHFVA 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: 570
Number of extensions: 27
Number of successful extensions: 5
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: 664
Length adjustment: 35
Effective length of query: 365
Effective length of database: 629
Effective search space:   229585
Effective search space used:   229585
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: 52 (24.6 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