Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate AZOBR_RS12970 AZOBR_RS12970 aspartate aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__azobra:AZOBR_RS12970 Length = 401 Score = 208 bits (530), Expect = 2e-58 Identities = 137/381 (35%), Positives = 207/381 (54%), Gaps = 22/381 (5%) Query: 14 ISGIRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQA 73 I+ +K L A DVI L G+PDF TP ++K AA KAI T YT G L++A Sbjct: 17 IAVTQKARELAAAGRDVIGLGAGEPDFDTPDNIKDAAIKAIQAGDTKYTAVDGTPALKKA 76 Query: 74 VQLYMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLC 133 + +++ Y A +I + G Q + A L+PGDEVI+P P + Y ++ L Sbjct: 77 ICAKFERENGLKY-APDQITVGVGGKQVLYNALMATLTPGDEVIIPAPYWVSYPDMVELA 135 Query: 134 GAKPVIVDTTSH-GFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIA-ALLK 191 PV V + GFKL +E A+TP TK ++L PSNP+G + +E+K++ L+K Sbjct: 136 EGTPVFVSCPAEQGFKLQPADLEKAITPKTKWLILNSPSNPSGAAYTRDEMKALTDVLVK 195 Query: 192 GRNVFVLSDEIYSELTYDRPHY----SIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPK 247 V+V++D++Y L YD + + L D+T+ +NG+SKS++MTGWRIG+ PK Sbjct: 196 HPQVWVMTDDMYEHLLYDGIEFVTPAQVEPALYDRTLTVNGVSKSYAMTGWRIGYAGGPK 255 Query: 248 DIAKHILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQ-YKKRLDYVYDRL-VSMG 305 + K + + + S +SI+Q AA+EA+ NG D + R + +R D V L + G Sbjct: 256 ALIKAMGVIQSQSTSNPTSIAQAAAVEAL-NGPQDFIAERAAVFAQRRDLVVSMLNQAKG 314 Query: 306 LDVVKPSGAFYIFPSIK-SFGMTS---------FDFSMALLEDAGVALVPGSSFSTYGEG 355 + KP GAFY++PS + G T+ DF LLE GVA+V GS+F Sbjct: 315 ISCPKPEGAFYVYPSCAGTIGKTTPDGKVIETDEDFVTYLLESEGVAVVQGSAFGL--AP 372 Query: 356 YVRLSFACSMDTLREGLDRLE 376 + R+S+A S + L E R++ Sbjct: 373 HFRISYATSTEALEEACKRIQ 393 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: 20 Number of successful extensions: 6 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: 401 Length adjustment: 31 Effective length of query: 362 Effective length of database: 370 Effective search space: 133940 Effective search space used: 133940 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