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_043743334.1 AMB_RS03565 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q08415 (423 letters) >NCBI__GCF_000009985.1:WP_043743334.1 Length = 386 Score = 264 bits (675), Expect = 3e-75 Identities = 151/397 (38%), Positives = 216/397 (54%), Gaps = 35/397 (8%) Query: 23 KLTKEYDVVNLGQGFPD-FSPPDFATQAFQQATSGNFMLNQYTRAFGYPPLTNVLASFFG 81 +L + + VNLGQGFP+ P D +A + +G NQY G P L +A Sbjct: 21 RLAQAHGAVNLGQGFPEGLEPADVVARAAEALVAGP---NQYPSMMGTPDLRQAIARHER 77 Query: 82 KLLGQEMDPLTNVLVTVGAYGALFTRFQALVDEGDEVIIMEPAFDCYEPMTMMAGGCPVF 141 + G E+DP+ V+VT GA AL L++ GDEV+++EP +D Y P+ AGG P Sbjct: 78 RFYGTELDPMAEVMVTSGATEALADCLFGLIEPGDEVVLIEPLYDSYLPIIRRAGGIPKL 137 Query: 142 VTLKPSPAPKGKLGASNDWQLDPAELASKFTPRTKILVLNTPNNPLGKVFSRMELELVAN 201 V ++P W L LA+ F+PRTK+++LNTP NP GKV+SR E+ VA Sbjct: 138 VRVEPP-----------HWDLPRETLAAAFSPRTKLMILNTPMNPSGKVWSRDEMAFVAG 186 Query: 202 LCQQHDVVCISDEVYQWLVYDGHQHVSIASLPGMWDRTLTIGSAGKSFSATGWKVGWVMG 261 L ++ D C+ DEVY+ LVYDG +H+ + +LPGM +R L IGSAGK FS TGWKVGWV+ Sbjct: 187 LLERFDAYCVCDEVYEHLVYDGRRHLPLMTLPGMRERCLKIGSAGKIFSLTGWKVGWVVA 246 Query: 262 PDNIMKHLRTVHQNSIFHCPTQAQAAVAQCFEREQQHFGQPSSYFLQLPQAMELNRDHMI 321 +++ L VHQ F P Q+AVA ++E SY+ L + RD + Sbjct: 247 APDLLAPLAKVHQYLTFATPPNLQSAVAWGLDKE-------DSYYDGLAAMLAERRDRLA 299 Query: 322 RSLQSVGLKLWISQGSYFLIADISDFKSKMPDLPGAEDEPYDRRFAKWMIKNMGLVGIPV 381 L+ VG ++ + GSYFL AD G +D+ F + + + G+ IP+ Sbjct: 300 EGLRGVGFEVMAAGGSYFLTADFRPL-----GFAGDDDD-----FCRHITEKAGVAAIPI 349 Query: 382 STFFSRPHQKDFDHYIRFCFVKDKATLQAMDERLRKW 418 STF+ D DH+ RFCF K ++ + RLR++ Sbjct: 350 STFY---QGGDVDHFARFCFAKTESAIDEAVMRLRRY 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: 478 Number of extensions: 22 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: 386 Length adjustment: 31 Effective length of query: 392 Effective length of database: 355 Effective search space: 139160 Effective search space used: 139160 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