Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate GFF1405 HP15_1371 aspartate aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Marino:GFF1405 Length = 394 Score = 219 bits (559), Expect = 8e-62 Identities = 134/371 (36%), Positives = 217/371 (58%), Gaps = 16/371 (4%) Query: 19 KFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYM 78 K + L A +D+I L G+PDF TP H+K AA +AI+ T YT G L++A+ Sbjct: 23 KAAELRAAGQDIIGLGAGEPDFDTPDHIKQAAIEAINNGQTKYTAVDGTPALKKAIIAKF 82 Query: 79 KKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPV 138 K+ +Y+A ++I++++G Q+ L+PGDE I+P P + Y ++ + KPV Sbjct: 83 KRDNGLDYEA-NQILVSSGGKQSFFNLALATLNPGDEAIIPAPYWVSYPDMVLVAEGKPV 141 Query: 139 IVDTTSH-GFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGR-NVF 196 I++T + FK+T +E+A+T T+ V+ PSNP+G+ + EEL++I +LK N+ Sbjct: 142 IIETGAETRFKITPEQLENAITERTRLFVINSPSNPSGMAYTLEELQAIGEVLKKHPNIM 201 Query: 197 VLSDEIYSELTY-DRPHYSI---ATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKH 252 + +D++Y + + +P +I L D+T V+NG+SK++SMTGWRIG+ P I Sbjct: 202 IATDDMYEPILWTGKPFCNILNATPELYDRTFVLNGVSKAYSMTGWRIGYAAGPAKIIGA 261 Query: 253 ILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKP 311 + K+ + S +SISQ AA A+ M + +K+R D++ + L + G++ + Sbjct: 262 MKKIQSQSTSNPASISQAAAQAALDGDQGCVGEMVKAFKERHDWLVEALNKLPGVECLNG 321 Query: 312 SGAFYIFPSIK------SFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSM 365 G FY+FPS + S T +F+ LL DAGVALVPGS+F G++RLSFA SM Sbjct: 322 DGTFYVFPSFQGAIDADSSVSTDVEFAEKLLTDAGVALVPGSAFGC--PGHMRLSFATSM 379 Query: 366 DTLREGLDRLE 376 + L + ++RL+ Sbjct: 380 ENLEKAVERLQ 390 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: 324 Number of extensions: 18 Number of successful extensions: 7 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: 394 Length adjustment: 31 Effective length of query: 362 Effective length of database: 363 Effective search space: 131406 Effective search space used: 131406 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: 50 (23.9 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