GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysN in Dyella japonica UNC79MFTsu3.2

Align 2-aminoadipate:2-oxoglutarate aminotransferase (EC 2.6.1.39) (characterized)
to candidate N515DRAFT_1410 N515DRAFT_1410 methionine aminotransferase

Query= reanno::Smeli:SMc04386
         (410 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1410 N515DRAFT_1410
           methionine aminotransferase
          Length = 381

 Score =  161 bits (407), Expect = 3e-44
 Identities = 114/367 (31%), Positives = 175/367 (47%), Gaps = 28/367 (7%)

Query: 46  LGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKKAIREKFQRENGLAYEL-DEI 104
           LG G PDF+ P+ +++A + A+  G  +Y    G P L++ I  K +R  G   +   E+
Sbjct: 30  LGQGFPDFEPPQALREAIARAMAEGRNQYAPGIGLPTLREQIALKTERMYGRRIDAAGEV 89

Query: 105 TVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEGKPVLIACDASSGFRLTA 164
           TV +GA + LF A+ A +  GDEVI+  P + SY  ++ +   K V I     S F +  
Sbjct: 90  TVTSGATEALFAAIAAVVRAGDEVIVFDPAYDSYEPVIELQGAKAVHIPLTVPS-FGVDW 148

Query: 165 EKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLRHPHVWLLVDDMYEHIVYDG 224
           +++  A+TPRTR +L+NSP NPSGA  SAAD    L  ++R   + +L D++YEHIV+DG
Sbjct: 149 QRVRDAVTPRTRMILINSPHNPSGAVLSAADL-DQLAAIVRDTEIVVLSDEVYEHIVFDG 207

Query: 225 FRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPRELIKAMAVVQSQATSCPSS 284
               +  +    L  R++ V+   K Y  TGW++GYA  P  L      V    T C   
Sbjct: 208 ALHQSVLR-HAELAARSIVVSSFGKTYHCTGWKLGYAVAPAALSAEFRKVHQYLTFCTFH 266

Query: 285 ISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVL 344
            +Q A    +    +   E    +Q +R          D     +    F       G  
Sbjct: 267 PAQVAFAEFMASTPEHYLELPAFYQAKR----------DRFRALIAPSRFKLLDVPGGYF 316

Query: 345 GKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAFGLSPFF---------RISYATSEAEL 395
             V  S  R + D  FC +L++   VA +P     L+PF+         R+ +A S+A +
Sbjct: 317 QLVDYSAIRDEPDVTFCEWLVKQGGVAAIP-----LAPFYETAPDTRLVRLCFAKSDATM 371

Query: 396 KEALERI 402
             A ER+
Sbjct: 372 DAAAERL 378


Lambda     K      H
   0.318    0.134    0.393 

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: 352
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: 410
Length of database: 381
Length adjustment: 31
Effective length of query: 379
Effective length of database: 350
Effective search space:   132650
Effective search space used:   132650
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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