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_085218250.1 B9N75_RS07610 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q08415 (423 letters) >NCBI__GCF_900177405.1:WP_085218250.1 Length = 389 Score = 145 bits (366), Expect = 2e-39 Identities = 89/254 (35%), Positives = 140/254 (55%), Gaps = 22/254 (8%) Query: 94 VLVTVGAYGALFTRFQALVDEGDEVIIMEPAFDCYEPMTMMAGGCPVFVTLKPSPAPKGK 153 +LVT G A F F A +D GDEVI++EP + + +AGG V AP Sbjct: 93 ILVTNGLTHASFAAFMAAIDPGDEVILLEPYYPQHVAKVELAGGTVV-------TAP--- 142 Query: 154 LGASNDWQLDPAELASKFTPRTKILVLNTPNNPLGKVFSRMELELVANLCQQHDVVCISD 213 L A+N++ + A +A+K TP+T+++VL P NP G+V++R ELE+VA L HD++ + D Sbjct: 143 LDAANNFAISHAAIAAKITPKTRMIVLVNPANPTGRVYTRAELEIVAELAIAHDLIVLCD 202 Query: 214 EVYQWLVYDGHQHVSIASLPGMWDRTLTIGSAGKSFSATGWKVGWVMGPDNIMKHLRTVH 273 EVY+++ YDG +HVSIASLPGM +RT+T + K++S GW+VG++ ++ + + Sbjct: 203 EVYEYITYDGAEHVSIASLPGMRERTITCFAFTKAYSMDGWRVGYLTADARLIPAILRII 262 Query: 274 QNSIFHCP--TQAQAAVAQCFEREQQHFGQPSSYFLQLPQAMELNRDHMIRSL-QSVGLK 330 + H Q A A +E H + +A R+ ++R+L Q G+ Sbjct: 263 TTDVTHVNVFVQEGARAAVTGPQEPMH---------AMVEADRRKREIVVRALNQMPGVT 313 Query: 331 LWISQGSYFLIADI 344 QG+ + DI Sbjct: 314 CAEPQGTIYAFPDI 327 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: 384 Number of extensions: 12 Number of successful extensions: 2 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: 389 Length adjustment: 31 Effective length of query: 392 Effective length of database: 358 Effective search space: 140336 Effective search space used: 140336 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 26 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