GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Pseudomonas fluorescens FW300-N2E3

Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7) (characterized)
to candidate AO353_26890 AO353_26890 aspartate aminotransferase

Query= BRENDA::Q16773
         (422 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_26890
          Length = 395

 Score =  170 bits (430), Expect = 8e-47
 Identities = 110/319 (34%), Positives = 172/319 (53%), Gaps = 26/319 (8%)

Query: 29  DVVNLGQGFPDFPPPDFAVEA-FQHAVSGDFMLNQYTKTFGYPPLTKILASFFGELLGQE 87
           DV+ L  G PDF  P   V+A     ++GD     Y++  G   L   +A       GQ 
Sbjct: 33  DVLLLSVGDPDFDTPKPIVQAAIDSLLAGD---THYSEVRGTRSLRTSIARRHTRRSGQV 89

Query: 88  IDPLRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCYEPMTMMAGGRPVFVSLKPG 147
           +D   +VLV  G   A+++  Q L+D GDEV++ EP +  YE +    G + V ++++P 
Sbjct: 90  VDA-DHVLVLPGAQCAVYSVVQCLLDPGDEVLVAEPMYVTYEGVFGACGAKVVPIAVRP- 147

Query: 148 PIQNGELGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELELVASLCQQHD 207
             +NG       +++DP ++A + T RT+A++LN+PNNP G   S    + +A LC +HD
Sbjct: 148 --ENG-------FRVDPTDIAARITPRTRAILLNSPNNPSGASLSLAIWQALARLCVKHD 198

Query: 208 VVCITDEVYQWMVYDGHQHISIASLPGMWERTLTIGSAGKTFSATGWKVGWVLGPDHIMK 267
           +  I+DEVY  ++Y+G +HIS ASLPGM ERT T+ S  K+ + TGW+VGWV+GP  + +
Sbjct: 199 LWLISDEVYSELLYEG-EHISPASLPGMAERTATVNSLSKSHAMTGWRVGWVIGPKRLTE 257

Query: 268 HLRTVHQNSVFHCP--TQSQAAVAESFEREQLLFRQPSSYFVQFPQAMQRCRDHMIRSLQ 325
           HL  +    +F  P   Q+ A VA   +  +L   + + Y  +      R  D       
Sbjct: 258 HLENLSLCMLFGIPDFVQNAARVALEADLPELALMR-NEYRARRDLVCARLGD------- 309

Query: 326 SVGLKPIIPQGSYFLITDI 344
             G+ P+IP G  F++ D+
Sbjct: 310 CPGISPVIPDGGMFVMVDV 328


Lambda     K      H
   0.323    0.139    0.435 

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: 398
Number of extensions: 20
Number of successful extensions: 4
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: 422
Length of database: 395
Length adjustment: 31
Effective length of query: 391
Effective length of database: 364
Effective search space:   142324
Effective search space used:   142324
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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