Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate GFF2657 PS417_13545 arginine aminotransferase
Query= BRENDA::Q6YP21 (454 letters) >FitnessBrowser__WCS417:GFF2657 Length = 664 Score = 158 bits (399), Expect = 6e-43 Identities = 108/344 (31%), Positives = 169/344 (49%), Gaps = 32/344 (9%) Query: 43 KRIEGLDSNVW----IEFTKLAADPSVVNLGQGFPDISPPTYVKEELSKIAAIDSLNQ-- 96 +RI G W F + ++ L G PD + P+++ + AA+ +L + Sbjct: 8 ERIAGQGVAAWDIHHAAFQAASQGEDIIILSVGDPDFATPSFITD-----AAVSALREGD 62 Query: 97 --YTRGFGHPSLVKALSYLYEKLYQKQIDSNKEILVTVGAYGSLFNTIQALIDEGDEVIL 154 YT G P+L +A++ Y K + + S + ++ GA +LF T L+ GDEV++ Sbjct: 63 THYTEIPGRPALREAIAARYSKTLARAL-SAENVITVAGAQNALFVTSLCLLQAGDEVLV 121 Query: 155 IVPFYDCYEPMVRMAGATPVFIPLRSKPVYGKRWSSSDWTLDPQELESKFNSKTKAIILN 214 + P Y YE ++ +GAT V +P + S + LD Q L + +T+AI + Sbjct: 122 LDPMYVTYEATLKASGATLVRVPCSPE---------SGFRLDAQLLGAAITPRTRAIFFS 172 Query: 215 TPHNPLGKVYNREELQVIADLCIKYDTLCISDEVYEWLVYSGNKHLKIATFPGMWERTIT 274 P+NP G V N +ELQ IADL I D + DEVYE LV+ G H +A PGM ER + Sbjct: 173 NPNNPTGVVLNLQELQAIADLAIARDLWVVVDEVYESLVFDGEYH-SLAALPGMAERCVV 231 Query: 275 IGSAGKTFSVTGWKLGWSIGPNHLIKHLQTVQQNTIYTCATPLQEALAQAFWIDIKRMDD 334 IGS K+ ++TGW++GW I ++ H +T+ + +Y + EA A + DD Sbjct: 232 IGSLSKSHAMTGWRIGWIIATPQMVAHAETLVLSMLYGLPGFVMEAATAA----VLAHDD 287 Query: 335 PECYFNSLPKELEVKRDR-MVRLLESVGLKPIVPDGGYFIIADV 377 + + +RD M L G+K P G F++ DV Sbjct: 288 VTQGMREIYRR---RRDLVMAGLSACPGIKVQAPQAGMFVLVDV 328 Lambda K H 0.319 0.135 0.407 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: 532 Number of extensions: 29 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: 454 Length of database: 664 Length adjustment: 36 Effective length of query: 418 Effective length of database: 628 Effective search space: 262504 Effective search space used: 262504 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 (21.8 bits) S2: 53 (25.0 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