Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7) (characterized)
to candidate AZOBR_RS12970 AZOBR_RS12970 aspartate aminotransferase
Query= BRENDA::Q16773 (422 letters) >FitnessBrowser__azobra:AZOBR_RS12970 Length = 401 Score = 169 bits (429), Expect = 1e-46 Identities = 120/393 (30%), Positives = 203/393 (51%), Gaps = 34/393 (8%) Query: 7 ARRLDGIDYNPWVEFVKLASE-----HDVVNLGQGFPDFPPPDFAVEAFQHAV-SGDFML 60 A RL I +P + + A E DV+ LG G PDF PD +A A+ +GD Sbjct: 5 ASRLSRIKPSPTIAVTQKARELAAAGRDVIGLGAGEPDFDTPDNIKDAAIKAIQAGD--- 61 Query: 61 NQYTKTFGYPPLTKILASFFGELLGQEIDPLRNVLVTVGGYGALFTAFQALVDEGDEVII 120 +YT G P L K + + F G + P + V VGG L+ A A + GDEVII Sbjct: 62 TKYTAVDGTPALKKAICAKFERENGLKYAP-DQITVGVGGKQVLYNALMATLTPGDEVII 120 Query: 121 IEPFFDCYEPMTMMAGGRPVFVSLKPGPIQNGELGSSSNWQLDPMELAGKFTSRTKALVL 180 P++ Y M +A G PVFVS P + G ++L P +L T +TK L+L Sbjct: 121 PAPYWVSYPDMVELAEGTPVFVSC---PAEQG-------FKLQPADLEKAITPKTKWLIL 170 Query: 181 NTPNNPLGKVFSREELELVASLCQQHDVVCI-TDEVYQWMVYDGHQHISIASL-PGMWER 238 N+P+NP G ++R+E++ + + +H V + TD++Y+ ++YDG + ++ A + P +++R Sbjct: 171 NSPSNPSGAAYTRDEMKALTDVLVKHPQVWVMTDDMYEHLLYDGIEFVTPAQVEPALYDR 230 Query: 239 TLTIGSAGKTFSATGWKVGWVLGPDHIMKHLRTVHQNSVFHCPTQSQAAVAESFEREQLL 298 TLT+ K+++ TGW++G+ GP ++K + + S + + +QAA E+ Q Sbjct: 231 TLTVNGVSKSYAMTGWRIGYAGGPKALIKAMGVIQSQSTSNPTSIAQAAAVEALNGPQDF 290 Query: 299 FRQPSSYFVQFPQAMQRCRDHMIRSL-QSVGLKPIIPQGSYFLITDIS-DFKRKMPDLPG 356 + ++ F Q RD ++ L Q+ G+ P+G++++ + + PD G Sbjct: 291 IAERAAVFAQ-------RRDLVVSMLNQAKGISCPKPEGAFYVYPSCAGTIGKTTPD--G 341 Query: 357 AVDEPYDRRFVKWMIKNKGLVAIPVSIFYSVPH 389 V E D FV ++++++G+ + S F PH Sbjct: 342 KVIET-DEDFVTYLLESEGVAVVQGSAFGLAPH 373 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: 397 Number of extensions: 20 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: 422 Length of database: 401 Length adjustment: 31 Effective length of query: 391 Effective length of database: 370 Effective search space: 144670 Effective search space used: 144670 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.
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