Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7) (characterized)
to candidate Pf1N1B4_4996 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::Q16773 (422 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4996 Length = 395 Score = 161 bits (407), Expect = 4e-44 Identities = 111/321 (34%), Positives = 173/321 (53%), Gaps = 30/321 (9%) Query: 29 DVVNLGQGFPDFPPPDFAVEA-FQHAVSGDFMLNQYTKTFGYPPLTKILASFFGELLGQE 87 DV+ L G PDF P + A ++GD Y+ G L +AS GQ Sbjct: 33 DVLLLSIGDPDFDTPLPIIHAAIDSLLAGD---THYSDVRGTRTLRSSIASRHQRRSGQL 89 Query: 88 IDPLRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCYEPMTMMAGGRPVFVSLKPG 147 +D +V+V G A+++ Q L+D GDEVI+ EP + YE + G V V+++P Sbjct: 90 VDA-DHVIVLPGAQCAVYSVAQCLLDPGDEVIVAEPMYVTYEGVFGACGASVVPVAVRP- 147 Query: 148 PIQNGELGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELELVASLCQQHD 207 +NG ++++P ++A TS+T+ ++LN+PNNP G S + + +A+LC QHD Sbjct: 148 --ENG-------FRVEPADVAALITSKTRVILLNSPNNPSGASLSLKSWKALAALCVQHD 198 Query: 208 VVCITDEVYQWMVYDGHQHISIASLPGMWERTLTIGSAGKTFSATGWKVGWVLGPDHIMK 267 + I+DEVY ++++G +HIS ASLPGM ERT TI S K+ + TGW+VGW++GP + + Sbjct: 199 LWLISDEVYSDLLFEG-EHISPASLPGMAERTATINSLSKSHAMTGWRVGWMIGPKPLAE 257 Query: 268 HLRTVHQNSVFHCPTQSQAAVAESFER---EQLLFRQPSSYFVQFPQAMQRCRDHMIRSL 324 HL + +F P Q A + ++ E L R+ + QR RD + L Sbjct: 258 HLMHLSLCMLFGLPDFVQNAAQVALDKDLPEVALMRE---------EYRQR-RDLVCARL 307 Query: 325 QSV-GLKPIIPQGSYFLITDI 344 G++PI P G F++ D+ Sbjct: 308 SGCPGIRPIKPDGGMFVMVDV 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: 427 Number of extensions: 17 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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