GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Pseudomonas fluorescens GW456-L13

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate PfGW456L13_2943 Aspartate aminotransferase (EC 2.6.1.1)

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2943
          Length = 395

 Score =  194 bits (494), Expect = 3e-54
 Identities = 111/363 (30%), Positives = 198/363 (54%), Gaps = 5/363 (1%)

Query: 26  QHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFN 85
           Q  DV+ L+IG PDF TP  +  AA  ++    T Y    G   LR ++  + ++++   
Sbjct: 30  QGVDVLLLSIGDPDFDTPQPIVQAAIGSLLAGDTHYPAVRGSQGLRDSIARHHRRRSGQA 89

Query: 86  YDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTTS- 144
            DA+  +I+  GA  A+ +  + +L PGDEV++  P+Y  YE +   CGAK V V   S 
Sbjct: 90  VDAQ-HVIVFPGAQCAVYSVAQCLLDPGDEVLVAEPMYVTYEGVFGACGAKVVPVPVRSQ 148

Query: 145 HGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYS 204
           +GF++    +   +TPNT+ ++L  P+NP+G +L     K++AAL    +++++SDE+YS
Sbjct: 149 NGFRVDPADVAALITPNTRAMLLNSPNNPSGASLPLTAWKALAALCIRHDLWLISDEVYS 208

Query: 205 ELTYDRPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVS 262
           EL ++  H S A+   + ++T  IN LSKSH+M+GWR+G++  P+ + +H++ +    + 
Sbjct: 209 ELLFEGEHISPASLPGMAERTATINSLSKSHAMSGWRVGWVIGPQSLCEHLVNLSLCMLF 268

Query: 263 CASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRL-VSMGLDVVKPSGAFYIFPSI 321
                 Q AA  A+         MRE+Y++R D V   L +  G+  ++P G  ++   +
Sbjct: 269 GIPDFIQNAAQLALDENLPHVAQMREEYRQRRDLVCASLNLCPGIQAIRPDGGMFVMVDV 328

Query: 322 KSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRLELFVLK 381
           +  G+++  F+  LL+  GV+++ G +F     G++R+        L +   R+ + V  
Sbjct: 329 RQTGLSAQHFAERLLDGYGVSVLAGEAFGPSAAGHIRIGLVVDRPKLADACRRIVMCVTN 388

Query: 382 KRE 384
             E
Sbjct: 389 MLE 391


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: 347
Number of extensions: 16
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: 395
Length adjustment: 31
Effective length of query: 362
Effective length of database: 364
Effective search space:   131768
Effective search space used:   131768
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.

Links

Downloads

Related tools

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