GapMind for Amino acid biosynthesis

 

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

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate Pf6N2E2_3073 N-succinyl-L,L-diaminopimelate aminotransferase alternative (EC 2.6.1.17)

Query= BRENDA::A0LEA5
         (388 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3073
          Length = 399

 Score =  185 bits (470), Expect = 2e-51
 Identities = 132/397 (33%), Positives = 195/397 (49%), Gaps = 30/397 (7%)

Query: 9   LKLLPPYLFQEIDRLKAELTAK-GVDVINLGVGDPDLPTPDHIIARLKTAAEDPSTHQYP 67
           L  L PY F+++  L   +T       I L +G+P   +P  +   L +  E  +   YP
Sbjct: 5   LNQLQPYPFEKLRALLGSVTPNPDKRPIALSIGEPKHRSPSFVAEALASNLEKMAV--YP 62

Query: 68  SYSGMNDFKVSVAGWYKRRFGVE---LDPLSEVLTLIGSKEGLAHFPLAVINPGDLALV- 123
           +  G+ + + ++ GW +RRF V    LDP   VL + G++E L  F   V+N GD ALV 
Sbjct: 63  TTLGIPELREAITGWCERRFNVPNGWLDPARHVLPVNGTREALFAFTQTVVNRGDDALVV 122

Query: 124 -PTPAYPVYHVATMFAGGESYFMPLVRENGFLPDLDSIPADVARRAKVMFINYPNNPTGA 182
            P P Y +Y  A   AG + +++P + ENGF PD D++  D+ +R +++F+  P NPTGA
Sbjct: 123 SPNPFYQIYEGAAFLAGAKPHYLPCLDENGFNPDFDAVSPDIWKRCQILFLCSPGNPTGA 182

Query: 183 TAERDFFEKVIAFAREYDVIVCHDAAYTEMAFGGYRPLSFLELPGAGEVG-------VEF 235
               D  +K+IA A E+D ++  D  Y+E+ F    P   L L    E+G       V F
Sbjct: 183 LIPVDVLKKLIALADEHDFVIAADECYSELYFDEQTPPPGL-LSACVELGRKDFKRCVVF 241

Query: 236 HSLSKTYNMTGWRLGFAVGNADILAGLGQVKSNIDSGAFNAVQWAGITALEGDQGCVVEM 295
           HSLSK  N+ G R GF  G+ADIL G    ++          Q A I A   D+  V   
Sbjct: 242 HSLSKRSNLPGLRSGFVAGDADILKGFLLYRTYHGCAMPVQTQLASIAAW-NDEVHVRAN 300

Query: 296 QRIYKERLDILIEGLKRIGLHPEVPRATFYVWCPTPPGYSSKD--FSSLLLREAGIVATP 353
           + +Y+E+ D ++E L  + L  + P  +FY+W    P  +  D  F   L  +  +   P
Sbjct: 301 RALYREKFDAVLEILSPV-LDVQRPDGSFYLW----PNVAGDDAAFCRDLFEQEHVTVVP 355

Query: 354 GSGFGA------PGEGYIRMALTVDKERVREAVERMR 384
           GS          PG G +RMAL        EA ER+R
Sbjct: 356 GSYLSREVDGVNPGAGRVRMALVAPLAECVEAAERIR 392


Lambda     K      H
   0.321    0.140    0.423 

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: 470
Number of extensions: 26
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: 388
Length of database: 399
Length adjustment: 31
Effective length of query: 357
Effective length of database: 368
Effective search space:   131376
Effective search space used:   131376
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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