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 GFF1235 Psest_1268 Aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::Q08415 (423 letters) >FitnessBrowser__psRCH2:GFF1235 Length = 382 Score = 220 bits (561), Expect = 5e-62 Identities = 134/409 (32%), Positives = 204/409 (49%), Gaps = 36/409 (8%) Query: 9 RLDGIDQNLWVEFGKLTKEYDVVNLGQGFPDFSPPDFATQAFQQATSGNFML--NQYTRA 66 +L + ++ +L + +NL QGFPDF P+ A ++A +G+ M NQY Sbjct: 5 KLPNVGTTIFTTMSQLAADTGALNLSQGFPDFDGPE----ALREAVAGHVMAGHNQYAPM 60 Query: 67 FGYPPLTNVLASFFGKLLGQEMDPLTNVLVTVGAYGALFTRFQALVDEGDEVIIMEPAFD 126 G P L +A+ L G+++D V +T GA A+F QA++ GDEVI+ +P +D Sbjct: 61 TGLPALREQVAAKVAGLYGRDVDAAAEVTITPGATQAIFCAIQAVIRPGDEVIVFDPCYD 120 Query: 127 CYEPMTMMAGGCPVFVTLKPSPAPKGKLGASNDWQLDPAELASKFTPRTKILVLNTPNNP 186 YEP +AGG + L + D+++D LA TPRT+++VLNTP+NP Sbjct: 121 SYEPSVQLAGGVCIHQQL-----------SLPDFRIDWQRLADAITPRTRMIVLNTPHNP 169 Query: 187 LGKVFSRMELELVANLCQQHDVVCISDEVYQWLVYDGHQHVSIASLPGMWDRTLTIGSAG 246 G + +L+ +A L ++ D+ +SDEVY+ LV+DG +H S+ ++ R I S G Sbjct: 170 SGALIDADDLDRLAALIRERDIYLLSDEVYEHLVFDGREHASVLRHDELYQRAFVISSFG 229 Query: 247 KSFSATGWKVGWVMGPDNIMKHLRTVHQNSIFHCPTQAQAAVAQCFEREQQHFGQPSSYF 306 K++ TGWK G+V+ P + LR VHQ F T Q A+A +H Sbjct: 230 KTYHVTGWKTGYVVAPPMLSVELRKVHQYVSFTGVTPLQWALADFMAAHPEHLA------ 283 Query: 307 LQLPQAMELNRDHMIRSLQSVGLKLWISQGSYFLIADISDFKSKMPDLPGAEDEPYDRRF 366 +LP + RD L + G+YF +AD S + PDL D Sbjct: 284 -ELPAFYQAKRDLFCDLLAGSRFSFTRAAGTYFQLADYSAIR---PDLD-------DVAM 332 Query: 367 AKWMIKNMGLVGIPVSTFFSRPHQKDFDHYIRFCFVKDKATLQAMDERL 415 A+W+ + G+ IP+S F+ P +RFCF K + TL+ ERL Sbjct: 333 AEWLTREHGVACIPISVFYQHPPAN--LRLVRFCFAKREETLRQAAERL 379 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: 463 Number of extensions: 20 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: 382 Length adjustment: 31 Effective length of query: 392 Effective length of database: 351 Effective search space: 137592 Effective search space used: 137592 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 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