Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate GFF2092 PGA1_c21250 aspartate aminotransferase AatA
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Phaeo:GFF2092 Length = 400 Score = 209 bits (531), Expect = 1e-58 Identities = 134/373 (35%), Positives = 204/373 (54%), Gaps = 20/373 (5%) Query: 23 LVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKA 82 L A DVI L+ G+PDF TP ++K AA +AI T YT G EL+QAV + Sbjct: 26 LRAAGRDVIGLSAGEPDFDTPDNIKEAAIRAIQAGKTKYTAPDGIAELKQAVCDKFARDN 85 Query: 83 DFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT 142 Y +++ + TG Q + A L+PGDEV++P P + Y ++ L G P+ V++ Sbjct: 86 GLEY-TPAQVSVGTGGKQILYNALMATLNPGDEVVIPAPYWVSYPDMVRLAGGTPICVES 144 Query: 143 TSH-GFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIA-ALLKGRNVFVLSD 200 + GFK+T +E A+TP TK V PSNPTG ELK++ LL+ +V+V++D Sbjct: 145 SLETGFKITPDQLEAAITPKTKWFVFNSPSNPTGAGYHPNELKALTDVLLRHPHVWVMTD 204 Query: 201 EIYSELTYDRPHY----SIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKV 256 ++Y L +D + I L D+T+ NG+SK+++MTGWRIG+ PK + + K+ Sbjct: 205 DMYEHLVFDDFTFCTPAQIEPKLYDRTLTCNGVSKAYAMTGWRIGYAAGPKPLIDAMRKI 264 Query: 257 HQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAF 315 + S +ISQ AA+EA+ D L +++R D V L + G+ P GAF Sbjct: 265 QSQSTSNPCTISQWAAVEALNGTQDYILPNTAVFRRRRDLVISMLSQIEGVACPVPDGAF 324 Query: 316 YIFPSIKS-FGMTSFD---------FSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSM 365 Y++PSI G TS F+ ALLE+A VA+V G+++ R+S+A + Sbjct: 325 YVYPSIAGLIGRTSAGGVAITDDEAFAKALLEEADVAVVHGAAYGL--SPNFRISYAAAD 382 Query: 366 DTLREGLDRLELF 378 +TL E R+++F Sbjct: 383 ETLTEACRRIQVF 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: 353 Number of extensions: 23 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: 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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