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 H281DRAFT_02293 H281DRAFT_02293 2-keto-4-methylthiobutyrate aminotransferase apoenzyme
Query= SwissProt::Q08415 (423 letters) >FitnessBrowser__Burk376:H281DRAFT_02293 Length = 384 Score = 199 bits (505), Expect = 2e-55 Identities = 125/409 (30%), Positives = 198/409 (48%), Gaps = 36/409 (8%) Query: 1 MTKRLQAR-RLDGIDQNLWVEFGKLTKEYDVVNLGQGFPDFSPPDFATQAFQQATSGNFM 59 M QAR +L + ++ G+L ++D +NL QG P+F+P QA Sbjct: 1 MQSATQARSKLPDVGTTIFTVIGQLAAQHDALNLSQGAPNFAPDAKLVDGVAQAMRDGH- 59 Query: 60 LNQYTRAFGYPPLTNVLASFFGKLLGQEMDPLTNVLVTVGAYGALFTRFQALVDEGDEVI 119 NQY G L LA L G DP + V V A L++ ALV GDEVI Sbjct: 60 -NQYAPMAGIAALREALADKVQTLYGVRYDPTSEVTVIASASEGLYSTISALVHPGDEVI 118 Query: 120 IMEPAFDCYEPMTMMAGGCPVFVTLKPSPAPKGKLGASNDWQLDPAELASKFTPRTKILV 179 EP+FD Y P+ + G PV + L S D++++ E+A+ TP+T++++ Sbjct: 119 YFEPSFDSYGPIVRLQGATPVPIKLSLS-----------DFRVNWDEVAAAITPKTRMII 167 Query: 180 LNTPNNPLGKVFSRMELELVANLCQQHDVVCISDEVYQWLVYDGHQHVSIASLPGMWDRT 239 +NTP+NP VFS ++ + + + D+V ++DEVY+ +V+DG +H S+A + +R+ Sbjct: 168 INTPHNPTATVFSEADVARLKAITRNTDIVILADEVYEHVVFDGAKHQSMACHSELAERS 227 Query: 240 LTIGSAGKSFSATGWKVGWVMGPDNIMKHLRTVHQNSIFHCPTQAQAAVAQCFEREQQHF 299 + + S GKS+ TGW+VG+ + P +M +R VHQ +F T Q A + + Sbjct: 228 VIVSSFGKSYHVTGWRVGYCLAPAELMNEIRKVHQFMVFSADTPMQYAFVDALSNRESYL 287 Query: 300 GQPSSYFLQLPQAMELNRDHMIRSLQSVGLKLWISQGSYFLIADISDFKSKMPDLPGAED 359 G + Y + RD + +L +L S+GS+F++A F + Sbjct: 288 GLSAFY--------QQKRDLLAHALSESRFELLPSEGSFFMLARFRGFSDES-------- 331 Query: 360 EPYDRRFAKWMIKNMGLVGIPVSTFFSRPHQKDFDHYIRFCFVKDKATL 408 D F +I++ + IP+S F+S IR F KD ATL Sbjct: 332 ---DSDFVLRLIRDARVATIPLSAFYSDGTDSGL---IRLSFSKDDATL 374 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: 380 Number of extensions: 22 Number of successful extensions: 4 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: 384 Length adjustment: 31 Effective length of query: 392 Effective length of database: 353 Effective search space: 138376 Effective search space used: 138376 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