Align Kynurenine--oxoglutarate transaminase 1; Kynurenine--oxoglutarate transaminase I; Cysteine-S-conjugate beta-lyase; Glutamine transaminase K; GTK; Glutamine--phenylpyruvate transaminase; Kynurenine aminotransferase 1; Kynurenine aminotransferase I; KATI; EC 2.6.1.7; EC 4.4.1.13; EC 2.6.1.64 (characterized)
to candidate WP_038217041.1 Q392_RS28935 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q08415 (423 letters) >NCBI__GCF_000745855.1:WP_038217041.1 Length = 386 Score = 234 bits (597), Expect = 3e-66 Identities = 147/410 (35%), Positives = 206/410 (50%), Gaps = 37/410 (9%) Query: 9 RLDGIDQNLWVEFGKLTKEYDVVNLGQGFPDFSPPDFATQAFQQATSGNFMLNQYTRAFG 68 RL + ++ L E + VNLGQGFPDF TQA A + NQY G Sbjct: 12 RLPSVGTTIFTVMSALAAEKNAVNLGQGFPDFGCDPKLTQAVTDAMAAGH--NQYPPMPG 69 Query: 69 YPPLTNVLASFFGKLLGQEMDPLTNVLVTVGAYGALFTRFQALVDEGDEVIIMEPAFDCY 128 P L +A+ L G+ DP T + VT GA A+ T ALV GDEVI++EP +D Y Sbjct: 70 VPALREAIAAKIEALYGRRYDPATEITVTAGATQAIITTVLALVRPGDEVIVLEPCYDSY 129 Query: 129 EPMTMMAGGCPVFVTLKPSPAPKGKLGASNDWQLDPAELASKFTPRTKILVLNTPNNPLG 188 P +AG V V L P ++ D +A+ TPRT+++++NTP+NP Sbjct: 130 VPNIELAGAAVVRVPLTPG-----------SFRPDFDRIAAALTPRTRMILINTPHNPSA 178 Query: 189 KVFSRMELELVANLCQQHDVVCISDEVYQWLVYDGHQHVSIASLPGMWDRTLTIGSAGKS 248 V++ E+ + L DV ISDEVY+ +VYDG +H S+A PG+ R++ + S GK+ Sbjct: 179 TVWTEGEMRRLEELLAPTDVFVISDEVYEHMVYDGARHESVARFPGLAARSVIVSSFGKT 238 Query: 249 FSATGWKVGWVMGPDNIMKHLRTVHQNSIFHCPTQAQAAVAQCFEREQQHFGQPSSYFLQ 308 + TGWKVG+V P + R VHQ ++F T Q A+A + P+ Y L+ Sbjct: 239 YHVTGWKVGYVAAPAPLTAEFRKVHQFNVFTVNTPMQHALA-------AYMADPAPY-LE 290 Query: 309 LPQAMELNRDHMIRSLQSVGLKLWISQGSYFLIADISDFKSKMPDLPGAEDEPYDRRFAK 368 LP RD L LKL SQGSYF DIS A + ++ F + Sbjct: 291 LPAFYSAKRDLFAEGLARTRLKLLPSQGSYFQCVDIS-----------AVSDLHEAEFCQ 339 Query: 369 WMIKNMGLVGIPVSTFFSRPHQKDFD-HYIRFCFVKDKATLQAMDERLRK 417 W+ +G+ IP+S F+ FD +RFC+ K TL+A ERL + Sbjct: 340 WLTAEIGVAAIPLSAFYG----DGFDQRVVRFCYAKKDETLRAALERLAR 385 Lambda K H 0.322 0.137 0.431 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: 478 Number of extensions: 22 Number of successful extensions: 6 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: 423 Length of database: 386 Length adjustment: 31 Effective length of query: 392 Effective length of database: 355 Effective search space: 139160 Effective search space used: 139160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 Jul 25 2024. The underlying query database was built on Jul 25 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