Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate AO356_25355 AO356_25355 aspartate aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25355 Length = 404 Score = 204 bits (520), Expect = 3e-57 Identities = 137/372 (36%), Positives = 208/372 (55%), Gaps = 22/372 (5%) Query: 25 AQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADF 84 AQ +ISL G+PDF TP H++ AA +AI + T YT AG LR+AV +++ Sbjct: 32 AQGAKIISLCAGEPDFDTPKHIREAAIEAIGQGHTRYTQVAGVRSLREAVAAKFRQENGL 91 Query: 85 NYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTTS 144 + + + ++ G Q I A L GD+VI+P P + Y ++ LCG + IV + Sbjct: 92 DVTWQ-DTLVCNGGKQVIYNALAATLDEGDQVIVPAPYWVSYPEMVQLCGGESRIVTCDA 150 Query: 145 H-GFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIA-ALLKGRNVFVLSDEI 202 GFKLT ++ A+TP T+ ++L PSNPTG S EEL+++A LL +V +L+D+I Sbjct: 151 DSGFKLTPAALDAAITPQTRWLILNSPSNPTGAVYSREELQALADVLLAHPHVLILADDI 210 Query: 203 YSELTYD-RPHYSIATY---LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQ 258 Y L +D + Y++A L +T+ +NG+SK+++MTGWRIGF P+ + + + K+ Sbjct: 211 YEHLIFDDQVFYTLAQVEPRLASRTLTMNGVSKAYAMTGWRIGFATGPRWLLEAMEKLQG 270 Query: 259 YNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRL-VSMGLDVVKPSGAFYI 317 S ASSISQ+AAL A+ D R +++R D + L + GL P GAFY Sbjct: 271 QQTSGASSISQQAALAALDGPKDFIRESRAVFQRRRDLMVALLNATPGLACASPGGAFYA 330 Query: 318 FPSIKS-FGMTSF---------DFSMALLEDAGVALVPGSSFSTYGEG-YVRLSFACSMD 366 F S G TS D + ALL++A VA+V GS+F G G Y+R+++A Sbjct: 331 FASCAGLIGRTSSGGRVLHTDEDVAHALLDEADVAVVHGSAF---GLGPYIRIAYALDDA 387 Query: 367 TLREGLDRLELF 378 +LR+ + + F Sbjct: 388 SLRQACEAIRGF 399 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: 352 Number of extensions: 25 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: 404 Length adjustment: 31 Effective length of query: 362 Effective length of database: 373 Effective search space: 135026 Effective search space used: 135026 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