Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate CCNA_01603 CCNA_01603 aspartate aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Caulo:CCNA_01603 Length = 400 Score = 212 bits (539), Expect = 2e-59 Identities = 139/373 (37%), Positives = 205/373 (54%), Gaps = 20/373 (5%) Query: 23 LVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKA 82 L A DVI+L+ G+PDF TP ++K AA +AI T YT G EL+ A+ K++ Sbjct: 26 LKAAGRDVIALSAGEPDFDTPDNIKNAAIEAIKAGKTKYTDPDGMPELKAAICAKFKREN 85 Query: 83 DFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT 142 Y S+I + G I A L+PGDEVI+P P + Y + L G PV V+T Sbjct: 86 GLEYKP-SQIHVAPGGKPVIYNALVATLNPGDEVIIPAPYWVSYPDMTLLAGGTPVSVET 144 Query: 143 TSH-GFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIA-ALLKGRNVFVLSD 200 T+ GFK+T +E A+TP TK +++ PSNP+G S EL++IA LL+ V+VL+D Sbjct: 145 TAESGFKITPEALEAAITPKTKWLIINSPSNPSGGAYSRAELQAIADVLLRHPQVWVLTD 204 Query: 201 EIYSELTYDRPHYS----IATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKV 256 ++Y L +D ++ + L D+T+ +NG+SK +SMTGWRIG+ P+ + K + K+ Sbjct: 205 DMYEHLVFDDFEFTTIAQVEPKLYDRTLTMNGVSKGYSMTGWRIGYAAGPEPLIKAMGKM 264 Query: 257 HQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRL-VSMGLDVVKPSGAF 315 S SISQ AALEA+ D + +++R D V L + GL P GAF Sbjct: 265 ISQTTSNPCSISQWAALEALNGTQDFIKPNAKLFQERRDLVVSMLNQATGLHCPTPEGAF 324 Query: 316 YIFPSIKS-FGMTS---------FDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSM 365 Y++PS G T+ DF+ LLE GVA+V G++F + R+S+A S Sbjct: 325 YVYPSCAGLIGKTAPSGKVIESDEDFATELLESEGVAVVHGAAFGL--SPFFRISYATSN 382 Query: 366 DTLREGLDRLELF 378 + L + R++ F Sbjct: 383 EVLEDACSRIQRF 395 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: 346 Number of extensions: 18 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: 400 Length adjustment: 31 Effective length of query: 362 Effective length of database: 369 Effective search space: 133578 Effective search space used: 133578 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