Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate 351943 BT2415 aspartate aminotransferase (NCBI ptt file)
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Btheta:351943 Length = 397 Score = 245 bits (625), Expect = 2e-69 Identities = 148/386 (38%), Positives = 224/386 (58%), Gaps = 17/386 (4%) Query: 5 LNPKAREIEISGIRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPN 64 LN + ++ +K + L AQ DVI+L++G+PDF TP H+K AAKKAID+N + Y+P Sbjct: 8 LNSLSPSATLAMSQKSNELKAQGIDVINLSVGEPDFNTPDHIKEAAKKAIDDNFSRYSPV 67 Query: 65 AGYLELRQAVQLYMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYP 124 GY LR A+ +KK+ Y A ++I GA Q++ A +++PGDEVI+P P + Sbjct: 68 PGYPALRNAIVEKLKKENGLEYTA-AQISCANGAKQSVCNAILVLVNPGDEVIVPAPYWV 126 Query: 125 GYEPIINLCGAKPVIVDT-TSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEEL 183 Y ++ + PVIV FK+T + +E A+TP TK ++L PSNPTG S+EEL Sbjct: 127 SYPEMVKMAEGTPVIVSAGIEQDFKITPKQLEAAITPKTKALILCSPSNPTGSVYSKEEL 186 Query: 184 KSIAALL-KGRNVFVLSDEIYSELTYDRPHYSIATY--LRDQTIVINGLSKSHSMTGWRI 240 +AA+L K V V++DEIY + Y H SIA + ++++T+++NG+SK+++MTGWRI Sbjct: 187 AGLAAVLAKYPQVVVIADEIYEHINYIGAHQSIAQFPEMKERTVIVNGVSKAYAMTGWRI 246 Query: 241 GFLFAPKDIAKHILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDR 300 GF+ P+ I K K+ S S+SQKAA A + M++ +++R D + Sbjct: 247 GFIAGPEWIVKACNKLQGQYTSGPCSVSQKAAEAAYVGTQEPVKEMQKAFERRRDLIVKL 306 Query: 301 LVSM-GLDVVKPSGAFYIFPSIKSFG---------MTSFDFSMALLEDAGVALVPGSSFS 350 + G +V P GAFY+FP F S D +M LLEDA VA V G+SF Sbjct: 307 AKEVPGFEVNVPQGAFYLFPKCSYFFGKSNGERKIENSDDLAMYLLEDAHVACVGGTSFG 366 Query: 351 TYGEGYVRLSFACSMDTLREGLDRLE 376 +R+S+A S + + E + R++ Sbjct: 367 --APECIRMSYATSDENIVEAIRRIK 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: 350 Number of extensions: 15 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: 397 Length adjustment: 31 Effective length of query: 362 Effective length of database: 366 Effective search space: 132492 Effective search space used: 132492 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