Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7) (characterized)
to candidate PfGW456L13_2943 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::Q16773 (422 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2943 Length = 395 Score = 158 bits (400), Expect = 2e-43 Identities = 106/318 (33%), Positives = 167/318 (52%), Gaps = 24/318 (7%) Query: 29 DVVNLGQGFPDFPPPDFAVEA-FQHAVSGDFMLNQYTKTFGYPPLTKILASFFGELLGQE 87 DV+ L G PDF P V+A ++GD Y G L +A GQ Sbjct: 33 DVLLLSIGDPDFDTPQPIVQAAIGSLLAGD---THYPAVRGSQGLRDSIARHHRRRSGQA 89 Query: 88 IDPLRNVLVTVGGYGALFTAFQALVDEGDEVIIIEPFFDCYEPMTMMAGGRPVFVSLKPG 147 +D ++V+V G A+++ Q L+D GDEV++ EP + YE + G + V P Sbjct: 90 VDA-QHVIVFPGAQCAVYSVAQCLLDPGDEVLVAEPMYVTYEGVFGACGAKVV-----PV 143 Query: 148 PIQNGELGSSSNWQLDPMELAGKFTSRTKALVLNTPNNPLGKVFSREELELVASLCQQHD 207 P++ S + +++DP ++A T T+A++LN+PNNP G + +A+LC +HD Sbjct: 144 PVR-----SQNGFRVDPADVAALITPNTRAMLLNSPNNPSGASLPLTAWKALAALCIRHD 198 Query: 208 VVCITDEVYQWMVYDGHQHISIASLPGMWERTLTIGSAGKTFSATGWKVGWVLGPDHIMK 267 + I+DEVY ++++G +HIS ASLPGM ERT TI S K+ + +GW+VGWV+GP + + Sbjct: 199 LWLISDEVYSELLFEG-EHISPASLPGMAERTATINSLSKSHAMSGWRVGWVIGPQSLCE 257 Query: 268 HLRTVHQNSVFHCPTQSQAAVAESFEREQLLFRQPSSYFVQFPQAMQRCRDHMIRSLQ-S 326 HL + +F P Q A QL + + Q + ++ RD + SL Sbjct: 258 HLVNLSLCMLFGIPDFIQNAA-------QLALDENLPHVAQMREEYRQRRDLVCASLNLC 310 Query: 327 VGLKPIIPQGSYFLITDI 344 G++ I P G F++ D+ Sbjct: 311 PGIQAIRPDGGMFVMVDV 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: 442 Number of extensions: 18 Number of successful extensions: 3 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