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_089322761.1 CHB58_RS03675 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q08415 (423 letters) >NCBI__GCF_900188395.1:WP_089322761.1 Length = 396 Score = 163 bits (413), Expect = 8e-45 Identities = 115/378 (30%), Positives = 182/378 (48%), Gaps = 36/378 (9%) Query: 26 KEYDVVNLGQGFPDFSPPDFATQAFQQATSGNFMLNQYTRAFGYPPLTNVLASFFGKLLG 85 K DV+ G G PDF P +A +A F +YT A G P L V+A + G Sbjct: 29 KGIDVIGFGAGEPDFDTPSHVKEAAIKAIEEGF--TKYTPAAGIPELREVIAQKLLRENG 86 Query: 86 QEMDPLTNVLVTVGAYGALFTRFQALVDEGDEVIIMEPAFDCYEPMTMMAGGCPVFVTLK 145 E + ++VT GA ALF+ +++DEGDEVII P + Y AGG PVFV Sbjct: 87 IEYSS-SQIVVTDGAKFALFSLMLSVIDEGDEVIIPAPYWVTYPEQVKFAGGKPVFVNTS 145 Query: 146 PSPAPKGKLGASNDWQLDPAELASKFTPRTKILVLNTPNNPLGKVFSRMELELVANLCQQ 205 N + L T RTK+L+L +P+NP G V EL+ + C + Sbjct: 146 EE----------NGFIFTLELLEKVVTERTKLLILCSPSNPTGAVIPEDELKRIGEFCAE 195 Query: 206 HDVVCISDEVYQWLVYDGHQHVSIASLPG-MWDRTLTIGSAGKSFSATGWKVGWVMGPDN 264 ++ SDE Y+ LVY+G +HVSIAS+ + + T+TI + K++S TGW+VG+ GP Sbjct: 196 KGILIASDECYEKLVYEGEKHVSIASISDELKEITITINALSKAYSMTGWRVGYAAGPSE 255 Query: 265 IMKHLRTVHQNSIFHCPTQAQAAVAQCFEREQQHFGQPSSYFLQLPQAMELNRDHMIRSL 324 I+ + ++ S+ + + AQ A P + +A + R +M+ Sbjct: 256 IISSMIKINSQSVSNVNSIAQKAAVAALT-------GPQEFLKDWLKAFDERRRYMVERF 308 Query: 325 QSV-GLKLWISQGSYFLIADISDFKSKMPDLPGAEDEPYDRRFAKWMIKNMGLVGIPVST 383 S+ G+ + +G+++ +I K+ + G +D D FA ++I+N + +P S Sbjct: 309 NSIPGVSCTVPKGAFYAFPNI----KKVLERGGFKD---DFEFADFLIENAKVAAVPGSA 361 Query: 384 FFSRPHQKDFDHYIRFCF 401 F + Y+RF + Sbjct: 362 F-------GYPGYMRFSY 372 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: 375 Number of extensions: 23 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: 396 Length adjustment: 31 Effective length of query: 392 Effective length of database: 365 Effective search space: 143080 Effective search space used: 143080 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