Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate GFF2657 PS417_13545 arginine aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__WCS417:GFF2657 Length = 664 Score = 204 bits (518), Expect = 8e-57 Identities = 125/361 (34%), Positives = 193/361 (53%), Gaps = 5/361 (1%) Query: 25 AQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADF 84 +Q ED+I L++G PDF TP + AA A+ E T YT G LR+A+ K Sbjct: 29 SQGEDIIILSVGDPDFATPSFITDAAVSALREGDTHYTEIPGRPALREAIAARYSKTLAR 88 Query: 85 NYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTTS 144 AE+ +I GA A+ +L GDEV++ P+Y YE + GA V V + Sbjct: 89 ALSAEN-VITVAGAQNALFVTSLCLLQAGDEVLVLDPMYVTYEATLKASGATLVRVPCSP 147 Query: 145 H-GFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIY 203 GF+L A+L+ A+TP T+ + P+NPTGV L+ +EL++IA L R+++V+ DE+Y Sbjct: 148 ESGFRLDAQLLGAAITPRTRAIFFSNPNNPTGVVLNLQELQAIADLAIARDLWVVVDEVY 207 Query: 204 SELTYDRPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNV 261 L +D ++S+A + ++ +VI LSKSH+MTGWRIG++ A + H + + Sbjct: 208 ESLVFDGEYHSLAALPGMAERCVVIGSLSKSHAMTGWRIGWIIATPQMVAHAETLVLSML 267 Query: 262 SCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAFYIFPS 320 +AA AV D MRE Y++R D V L + G+ V P ++ Sbjct: 268 YGLPGFVMEAATAAVLAHDDVTQGMREIYRRRRDLVMAGLSACPGIKVQAPQAGMFVLVD 327 Query: 321 IKSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRLELFVL 380 ++ G+ S DF+ L +AGV+++ ++F +G+VRLSF + L E R+ FV Sbjct: 328 VRGTGLGSLDFAWRLFREAGVSVLDAAAFGAPAQGFVRLSFTLGEERLSEACQRIAHFVA 387 Query: 381 K 381 K Sbjct: 388 K 388 Lambda K H 0.319 0.135 0.388 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: 451 Number of extensions: 16 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: 393 Length of database: 664 Length adjustment: 34 Effective length of query: 359 Effective length of database: 630 Effective search space: 226170 Effective search space used: 226170 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: 52 (24.6 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