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_041643952.1 AZO_RS16855 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q08415 (423 letters) >NCBI__GCF_000061505.1:WP_041643952.1 Length = 385 Score = 214 bits (545), Expect = 4e-60 Identities = 138/410 (33%), Positives = 205/410 (50%), Gaps = 39/410 (9%) Query: 9 RLDGIDQNLWVEFGKLTKEYDVVNLGQGFPDFSPPD--FATQAFQQATSGNFMLNQYTRA 66 RL + ++ +L +E +NL QGFPDF+ D F A T N QY Sbjct: 11 RLPQVGTTIFTVMSRLAQECGAINLSQGFPDFNADDALFERVAHWMRTGHN----QYAPM 66 Query: 67 FGYPPLTNVLASFFGKLLGQEMDPLTNVLVTVGAYGALFTRFQALVDEGDEVIIMEPAFD 126 G P L +A L G D V +T GA ALFT ALV GDEVI+ EP +D Sbjct: 67 AGVPALREAVAGKVAALYGSTYDVEHEVTITAGATQALFTAVAALVHPGDEVIVFEPVYD 126 Query: 127 CYEPMTMMAGGCPVFVTLKPSPAPKGKLGASNDWQLDPAELASKFTPRTKILVLNTPNNP 186 Y P +AGG V + L A+ D++ D A +A+ TPRT+++++N+P+NP Sbjct: 127 SYGPAVELAGGRVVRMQL-----------AAPDYRPDWAAVAAAITPRTRMIMINSPHNP 175 Query: 187 LGKVFSRMELELVANLCQQHDVVCISDEVYQWLVYDGHQHVSIASLPGMWDRTLTIGSAG 246 V++ + + +A L + ++ +SDEVY+ +V+DG QH S A+ P + R++ + S G Sbjct: 176 TATVWTAADYDRLAALLRDTGIIVVSDEVYEHIVFDGLQHRSCAAHPELAARSIVVSSFG 235 Query: 247 KSFSATGWKVGWVMGPDNIMKHLRTVHQNSIFHCPTQAQAAVAQCFEREQQHFGQPSSYF 306 K++ TGWKVG+V+ P +M R VHQ ++F T Q A+A +H G + Y Sbjct: 236 KTYHITGWKVGYVVAPRELMAEFRKVHQFNVFTVNTPVQYALADYMAEASRHLGLAAFY- 294 Query: 307 LQLPQAMELNRDHMIRSLQSVGLKLWISQGSYFLIADISDFKSKMPDLPGAEDEPYDRRF 366 + R+ +L +L S+G+YF +A S A + D F Sbjct: 295 -------QAKRNLFRDALAGSRFELLPSRGTYFQLARYS-----------AISDEGDVAF 336 Query: 367 AKWMIKNMGLVGIPVSTFFSRPHQKDFDHYIRFCFVKDKATLQAMDERLR 416 + + +G+ IPVS FF+ + IRFCF K+ TL A ERLR Sbjct: 337 CNRLARQVGVAAIPVSAFFADGRD---ERVIRFCFAKNDTTLNAACERLR 383 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: 388 Number of extensions: 17 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: 423 Length of database: 385 Length adjustment: 31 Effective length of query: 392 Effective length of database: 354 Effective search space: 138768 Effective search space used: 138768 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 Apr 10 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