GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Pseudomonas putida KT2440

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate PP_3721 PP_3721 Arginine--pyruvate transaminase AruH

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__Putida:PP_3721
          Length = 396

 Score =  194 bits (493), Expect = 4e-54
 Identities = 112/357 (31%), Positives = 194/357 (54%), Gaps = 5/357 (1%)

Query: 23  LVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKA 82
           L A+ +D++ L++G PDF TP  +  AA  ++    T Y    G L LRQA+    ++++
Sbjct: 27  LQAEDKDILLLSVGDPDFDTPAPIVEAAIDSLRAGHTHYADVRGKLALRQAIANRHRQRS 86

Query: 83  DFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT 142
                A+ ++ +  GA  A+    + IL PGDEVI+  P+Y  YE +   CGAK V V  
Sbjct: 87  GQAVSAD-QVTVLAGAQCALYCVAQCILDPGDEVIVAEPMYVTYEAVFGACGAKVVPVPV 145

Query: 143 T-SHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDE 201
              +GF++  R + + +TP T+ + L  P NP+G +L     +++A L    +++++SDE
Sbjct: 146 KPENGFRVCPRDVAERITPRTRALALNSPHNPSGASLPRATWEALAELCVAHDLWLISDE 205

Query: 202 IYSELTYDRPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQY 259
           +YSEL Y+  H S  +   + ++T  +N LSKSH+MTGWR+G++     +A H+  +   
Sbjct: 206 VYSELLYEGEHVSPGSLPGMAERTATLNSLSKSHAMTGWRMGWVVGSTALATHLENLALC 265

Query: 260 NVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAFYIF 318
            +       Q AA+ A+ +   +   MRE Y++R D V ++L    GL  +KP G  ++ 
Sbjct: 266 MLYGLPDFVQDAAVVALEHPLPELDAMREAYRQRRDLVCEQLAGCPGLKALKPDGGMFVM 325

Query: 319 PSIKSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRL 375
             I+  G+++  F+  LL+  GV+++ G +F     G++RL      + L +   R+
Sbjct: 326 LDIRETGVSAQAFADYLLDSQGVSVLAGEAFGPSAAGHIRLGLVLGNEALVDACQRI 382


Lambda     K      H
   0.319    0.135    0.388 

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: 296
Number of extensions: 12
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: 393
Length of database: 396
Length adjustment: 31
Effective length of query: 362
Effective length of database: 365
Effective search space:   132130
Effective search space used:   132130
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 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