Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7) (characterized)
to candidate WP_011382998.1 AMB_RS02875 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q16773 (422 letters) >NCBI__GCF_000009985.1:WP_011382998.1 Length = 400 Score = 169 bits (427), Expect = 2e-46 Identities = 128/421 (30%), Positives = 212/421 (50%), Gaps = 39/421 (9%) Query: 7 ARRLDGIDYNPWVEFVKLASE-----HDVVNLGQGFPDFPPPDFAVEAFQHAVSGDFMLN 61 A RL I +P + + A+E DV+ LG G PDF PD A + A+ D L Sbjct: 5 ADRLSAIKPSPTIAVTQKAAELKAAGRDVIGLGAGEPDFDTPDNIKAAAKAAI--DKGLT 62 Query: 62 QYTKTFGYPPLTKILASFFGELLGQEIDPLRNVLVTVGGYGALFTAFQALVDEGDEVIII 121 +Y G L + +A+ F G + V V VGG G +F AF A ++ GDEVI+ Sbjct: 63 KYGPPAGTVDLRQAIAAKFKRENGLDYTA-DQVTVGVGGKGVIFNAFMATINPGDEVIVP 121 Query: 122 EPFFDCYEPMTMMAGGRPVFVSLKPGPIQNGELGSSSNWQLDPMELAGKFTSRTKALVLN 181 P++ Y + +M GG+PVFV P P ++ ++L P +L T RTK LVLN Sbjct: 122 APYWVSYPDIALMFGGKPVFV---PCP-------ETAGFKLQPADLEKAITPRTKWLVLN 171 Query: 182 TPNNPLGKVFSREELELVASLCQQHDVVCI-TDEVYQWMVYDGHQHISIASL-PGMWERT 239 +P+NP G +S +E++ + + +H V I +D++Y+ +VYD + + A + P +++RT Sbjct: 172 SPSNPTGAAYSWDEMKALTDVLLRHPHVWIMSDDMYEHLVYDDFKFCTPAQVEPKLYDRT 231 Query: 240 LTIGSAGKTFSATGWKVGWVLGPDHIMKHLRTVHQNSVFHCPTQSQAAVAESFEREQLLF 299 LT+ K ++ TGW+VG+ GP I+K + + SV H + SQAA E+ Q Sbjct: 232 LTMNGVSKAYAMTGWRVGYAAGPAAIIKAINMIQSQSVTHTSSISQAASVEALNGTQDFI 291 Query: 300 RQPSSYFVQFPQAMQRCRDHMIRSL-QSVGLKPIIPQGSYFLITDISD-FKRKMPDLPGA 357 + ++ F +R RD ++ L Q G+ P+G++++ + +K PD G Sbjct: 292 PKNAAVF-------KRRRDLIVGLLNQCPGITCRTPEGAFYVYPSCAGVIGKKTPD--GK 342 Query: 358 VDEPYDRRFVKWMIKNKGLVAIPVSIFYSVPHQKHFDHYIRFCFVKDEATLQAMDEKLRK 417 V D FV +++ +G+ + + F P Y R + +A L E++++ Sbjct: 343 V-IANDTDFVGALLEAEGVAVVQGAAFGLEP-------YFRISYATSDAALTKAAERIKR 394 Query: 418 W 418 + Sbjct: 395 F 395 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: 392 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: 400 Length adjustment: 31 Effective length of query: 391 Effective length of database: 369 Effective search space: 144279 Effective search space used: 144279 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