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_085217296.1 B9N75_RS02070 aminotransferase
Query= SwissProt::Q08415 (423 letters) >NCBI__GCF_900177405.1:WP_085217296.1 Length = 384 Score = 219 bits (559), Expect = 9e-62 Identities = 133/393 (33%), Positives = 199/393 (50%), Gaps = 39/393 (9%) Query: 26 KEYDVVNLGQGFPDFS-PPDFATQAFQQATSGNFMLNQYTRAFGYPPLTNVLASFFGKLL 84 +E VNLGQGFPDF P D +A + T +QY G P L +A + + Sbjct: 21 RELGAVNLGQGFPDFGWPEDVVAKAAELLTGA---ASQYPPMRGLPELRAAVADHYSQHQ 77 Query: 85 GQEMDPLTNVLVTVGAYGALFTRFQALVDEGDEVIIMEPAFDCYEPMTMMAGGCPVFVTL 144 G P + VT GA AL + AL++ GDEV++ +P +D Y PM GG P +V L Sbjct: 78 GIAYAP-DEITVTSGATEALASALLALIEPGDEVLLFQPLYDAYVPMVRRGGGVPRYVAL 136 Query: 145 KPSPAPKGKLGASNDWQLDPAELASKFTPRTKILVLNTPNNPLGKVFSRMELELVANLCQ 204 +P +W++ + + TPRT+++V N P+NP G+ FS+ EL +A +C Sbjct: 137 RPP-----------EWRITREAIEAALTPRTRLVVFNNPHNPTGRAFSQDELTALAEVCV 185 Query: 205 QHDVVCISDEVYQWLVYDGHQHVSIASLPGMWDRTLTIGSAGKSFSATGWKVGWVMGPDN 264 D++ +SDEV++ ++ G H+ +ASLPGM DRT+ +GSAGK FS TGWKVGW+ P Sbjct: 186 ARDLIVLSDEVWEHVMPGGAAHLPLASLPGMSDRTVKVGSAGKIFSLTGWKVGWIAAPAA 245 Query: 265 IMKHLRTVHQNSIFHCPTQAQAAVAQCFEREQQHFGQPSSYFLQLPQAMELNRDHMIRSL 324 + + HQ F P QAAVA G+ +Y+ + A + RD + L Sbjct: 246 LGDPITKAHQFVTFTTPPNLQAAVA-------YGLGKDEAYYRDMRAAFAVARDRLADGL 298 Query: 325 QSVGLKLWISQGSYFLIADISDFKSKMPDLPGAEDEPYDRRFAKWMIKNMGLVGIPVSTF 384 G + +GSYFL D++ DL F + ++ G+ IP++ F Sbjct: 299 ADAGYVVLPGEGSYFLCVDLTASGIAADDL----------TFCERAVREAGIAAIPLTAF 348 Query: 385 FSRPHQKDFDHYIRFCFVKDKATLQAMDERLRK 417 F + + IR CF K + T+ DE L++ Sbjct: 349 F---EETPVTNVIRLCFAKKQETI---DEGLKR 375 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: 455 Number of extensions: 19 Number of successful extensions: 5 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 Jul 26 2024. The underlying query database was built on Jul 25 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