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_013518998.1 ALIDE2_RS11740 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q08415 (423 letters) >NCBI__GCF_000204645.1:WP_013518998.1 Length = 383 Score = 221 bits (563), Expect = 3e-62 Identities = 142/418 (33%), Positives = 205/418 (49%), Gaps = 37/418 (8%) Query: 1 MTKRLQARRLDGIDQNLWVEFGKLTKEYDVVNLGQGFPDFSPPDFATQAFQQATSGNFML 60 MT RL + ++ L E+ VNLGQGFPDF+ A +A Sbjct: 1 MTTPTFPSRLPNVGTTIFTVMSALAAEHKAVNLGQGFPDFACDPALVDAVTRAMQTGH-- 58 Query: 61 NQYTRAFGYPPLTNVLASFFGKLLGQEMDPLTNVLVTVGAYGALFTRFQALVDEGDEVII 120 NQY G P L +AS L + P + + +T GA A+ T A V GDEVI+ Sbjct: 59 NQYPPMVGVPALREAVASKIETLHARRYCPNSEITITAGATQAILTAILACVQPGDEVIV 118 Query: 121 MEPAFDCYEPMTMMAGGCPVFVTLKPSPAPKGKLGASNDWQLDPAELASKFTPRTKILVL 180 +EP +D Y P +AGG V V L P ++ D A +++ TPRT++++ Sbjct: 119 LEPCYDSYVPNIELAGGVVVRVPLTPG-----------SFRPDFARISAAITPRTRLIIA 167 Query: 181 NTPNNPLGKVFSRMELELVANLCQQHDVVCISDEVYQWLVYDGHQHVSIASLPGMWDRTL 240 NTP+NP V++ ++ + L ++ ISDEVY+ +V+DG +H S A PG+ DR Sbjct: 168 NTPHNPSATVWTAEDMRALEELLAPTGILLISDEVYEHMVFDGAEHQSAARFPGLADRAF 227 Query: 241 TIGSAGKSFSATGWKVGWVMGPDNIMKHLRTVHQNSIFHCPTQAQAAVAQCFEREQQHFG 300 + S GK+F TGWK+G V P + R VHQ ++F T Q +A + G Sbjct: 228 IVSSFGKTFHVTGWKIGTVAAPAPLTAEFRKVHQFNVFTVNTPMQYGLA-------DYLG 280 Query: 301 QPSSYFLQLPQAMELNRDHMIRSLQSVGLKLWISQGSYFLIADISDFKSKMPDLPGAEDE 360 P+ Y LQLP + RD + L+ L+L S GSYF DI S + DL A+ Sbjct: 281 NPAPY-LQLPAFYQAKRDLFRQGLEGSRLRLLPSTGSYFQCVDI----SAVSDLGEAD-- 333 Query: 361 PYDRRFAKWMIKNMGLVGIPVSTFFSRPHQKDFD-HYIRFCFVKDKATLQAMDERLRK 417 F +W+ + +G+ IP+S F+ FD +RFCF K TL+ RLR+ Sbjct: 334 -----FCQWLTREIGVAAIPLSAFYG----DGFDQRVVRFCFAKKDETLREALTRLRR 382 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: 469 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: 383 Length adjustment: 31 Effective length of query: 392 Effective length of database: 352 Effective search space: 137984 Effective search space used: 137984 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