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 HSERO_RS15115 HSERO_RS15115 aminotransferase
Query= SwissProt::Q08415 (423 letters) >FitnessBrowser__HerbieS:HSERO_RS15115 Length = 385 Score = 229 bits (584), Expect = 1e-64 Identities = 142/409 (34%), Positives = 203/409 (49%), Gaps = 33/409 (8%) Query: 9 RLDGIDQNLWVEFGKLTKEYDVVNLGQGFPDFSPPDFATQAFQQATSGNFMLNQYTRAFG 68 +L + ++ L E VNLGQGFPDF A QA LNQY G Sbjct: 9 KLPKVGTTIFTVMSALASEKGAVNLGQGFPDFHCDPALVAAVTQAMQEG--LNQYPPMAG 66 Query: 69 YPPLTNVLASFFGKLLGQEMDPLTNVLVTVGAYGALFTRFQALVDEGDEVIIMEPAFDCY 128 P L +A KL G DP++ + VT GA + T V GDEVI++EP +DCY Sbjct: 67 VPVLREAIAEKVEKLYGHRYDPVSEITVTAGATQGILTSVLCAVHPGDEVIVIEPVYDCY 126 Query: 129 EPMTMMAGGCPVFVTLKPSPAPKGKLGASNDWQLDPAELASKFTPRTKILVLNTPNNPLG 188 P +AGG PVFV ++ G G S W ++ + TP+T+++++NTP+NP G Sbjct: 127 VPAIELAGGVPVFVQMEV-----GAQGYSIPWD----KVKAAVTPKTRMIMVNTPHNPTG 177 Query: 189 KVFSRMELELVANLCQQHDVVCISDEVYQWLVYDGHQHVSIASLPGMWDRTLTIGSAGKS 248 V ++ +A++ + D++ +SDEVY+ +VYDG H S+A P + +R+ S GK+ Sbjct: 178 SVMRAADVAALADIVRGTDILILSDEVYEHMVYDGQPHESLARHPELAERSFINSSFGKT 237 Query: 249 FSATGWKVGWVMGPDNIMKHLRTVHQNSIFHCPTQAQAAVAQCFEREQQHFGQPSSYFLQ 308 + TGWKVG+V P + R VHQ ++F T Q +A + P+ Y L Sbjct: 238 YHVTGWKVGYVAAPAALTAEFRKVHQFNVFTVNTPVQYGLA-------AYMKDPAPY-LD 289 Query: 309 LPQAMELNRDHMIRSLQSVGLKLWISQGSYFLIADISDFKSKMPDLPGAEDEPYDRRFAK 368 LP + RD L + +L SQG+YF + LP AE F K Sbjct: 290 LPAFYQHKRDLFRTGLANTRFELLPSQGTYFQCVKYGAISA----LPEAE-------FCK 338 Query: 369 WMIKNMGLVGIPVSTFFSRPHQKDFDHYIRFCFVKDKATLQAMDERLRK 417 W+ +G+ IPVS F++ P + +RFCF K TLQ ERL K Sbjct: 339 WLTSEIGVAAIPVSAFYNTPRESGI---VRFCFAKKDETLQLALERLAK 384 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: 441 Number of extensions: 15 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: 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 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