Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate 3607347 Dshi_0762 aminotransferase class I and II (RefSeq)
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Dino:3607347 Length = 400 Score = 221 bits (562), Expect = 4e-62 Identities = 139/375 (37%), Positives = 208/375 (55%), Gaps = 20/375 (5%) Query: 21 SNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKK 80 + L A DVI L G+PDF TP ++K A K AID T YT G EL++A+ K+ Sbjct: 24 NELKAAGRDVIGLGAGEPDFDTPQNIKDAGKAAIDAGKTKYTAVDGIPELKKAIVAKFKR 83 Query: 81 KADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIV 140 +YD +++ + G Q + A ++PGDEVI+P P + Y ++ L G +PVI Sbjct: 84 DNGLDYDT-TQVTVANGGKQILINALMATMNPGDEVIIPAPYWVSYPDMVLLAGGEPVIA 142 Query: 141 DTTSH-GFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIA-ALLKGRNVFVL 198 + + GFKLTA +E A+TP TK + PSNPTG + ELK + LL+ +V+V+ Sbjct: 143 EASIQTGFKLTADQLEAAITPRTKWFIFNSPSNPTGAGYTAAELKELTDVLLRHPHVWVM 202 Query: 199 SDEIYSELTYDRPHYS----IATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHIL 254 +D++Y L YD ++ + L ++T+ NG+SK+++MTGWRIG+ PK++ + Sbjct: 203 TDDMYEHLVYDDFEFATPAQVEPKLYNRTLTCNGVSKAYAMTGWRIGYAAGPKELIGAMR 262 Query: 255 KVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRL-VSMGLDVVKPSG 313 K+ + S SISQ AA+EA+ D + +K+R D V L + G+ KP G Sbjct: 263 KIQSQSTSNPCSISQWAAVEALDGTQDYIPENNKTFKRRRDLVVGMLNDAQGISCPKPEG 322 Query: 314 AFYIFPSIKS-FGMTSFD---------FSMALLEDAGVALVPGSSFSTYGEGYVRLSFAC 363 AFY++PSI G TS F+ ALLE+ GVA+V G++F R+S+A Sbjct: 323 AFYVYPSIAGCIGKTSAGGTKITDDEAFAKALLEEKGVAVVFGAAFGL--SPNFRVSYAT 380 Query: 364 SMDTLREGLDRLELF 378 S D L E R++ F Sbjct: 381 SDDALTEACTRIQDF 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: 334 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: 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