Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate 8500823 DvMF_1564 aminotransferase class I and II (RefSeq)
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Miya:8500823 Length = 400 Score = 186 bits (471), Expect = 1e-51 Identities = 118/382 (30%), Positives = 188/382 (49%), Gaps = 10/382 (2%) Query: 8 KAREIEISGIRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTS--YTPNA 65 + R I IS + L A+ +SL G P F TP H+ A +A+ ++ T+ Y+ Sbjct: 16 RVRNIRISATKLMPMLAAKVGGCVSLGQGVPSFRTPDHIVEAVCRALRDDPTAGRYSLQP 75 Query: 66 GYLELRQAVQLYMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPG 125 G LR+A+ + + +D E+EI +T GA +A+ T++ GDEVI+P P Y Sbjct: 76 GMPALREAIAADILARKGARFDPETEIGVTVGAMEALVMIMLTVVERGDEVIIPSPGYAS 135 Query: 126 YEPIINLCGAKPVIVDTTSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKS 185 + + + PV V + + L + A+TP T+ +++ P NPTG + ++++ Sbjct: 136 HAEQVLMAEGVPVHVPLRAADWGLDVEAVRFAVTPRTRAIIVCSPGNPTGGVYDDADVRA 195 Query: 186 IAALLKGRNVFVLSDEIYSELTYDR----PHYSIATY--LRDQTIVINGLSKSHSMTGWR 239 + L R++ ++ D+ Y + Y P +S + LR I +N SK +++TGWR Sbjct: 196 LCDLALERDLVLIVDDTYDYMVYGEQPGTPRFSPVSQPELRRHVITVNSFSKKYALTGWR 255 Query: 240 IGFLFAPKDIAKHILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYD 299 +G++ A +LKVH CA ++SQ AAL A+T D +MR R D Sbjct: 256 VGYVAADAAWMAELLKVHDATAVCAPTVSQHAALAALTGPQDCVDVMRAALTARRDLTCR 315 Query: 300 RLVSMG--LDVVKPSGAFYIFPSIKSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYV 357 RL ++ V P GAFY S + +LE+A V VPG SF GE ++ Sbjct: 316 RLDALAPHFAYVPPRGAFYAMARYTFTDADSMTVARRMLEEARVITVPGGSFGPTGERHL 375 Query: 358 RLSFACSMDTLREGLDRLELFV 379 RLSF L E DR++ +V Sbjct: 376 RLSFGMDEAELTEAFDRIQHWV 397 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: 355 Number of extensions: 11 Number of successful extensions: 4 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