Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate RR42_RS35305 RR42_RS35305 aspartate aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Cup4G11:RR42_RS35305 Length = 401 Score = 207 bits (528), Expect = 3e-58 Identities = 135/376 (35%), Positives = 209/376 (55%), Gaps = 20/376 (5%) Query: 18 RKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLY 77 ++ L A DVI LT G+PDF TP H++ AA +A+ T YT G ELR A Sbjct: 21 QRVRELRAAGRDVIGLTAGEPDFETPAHIREAAWRAMQAGKTRYTDVGGTAELRHAAAQK 80 Query: 78 MKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKP 137 K++ +Y A SEII++TGA Q I A + GDEVI+P P + Y I G P Sbjct: 81 FKRENGLDY-AASEIIVSTGAKQVIFNALMCTVQQGDEVIVPAPYWVSYPDITLFAGGVP 139 Query: 138 VIVDTTS-HGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGR-NV 195 V V + +GFKLT +E A++ T+ ++L P+NP+G + EL +IA +L+ +V Sbjct: 140 VFVACQAENGFKLTPEELERAISARTRWLILNSPNNPSGAAYTRTELVAIAEVLERHPHV 199 Query: 196 FVLSDEIYSELTYDRPHY----SIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAK 251 +V++D+IY LTYD + A L+ +T+ ING+SK+++MTGWRIG+ AP + K Sbjct: 200 WVMTDDIYEHLTYDGAAFVTLAQAAPSLKARTLTINGVSKAYAMTGWRIGYAGAPAPLIK 259 Query: 252 HILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVK 310 ++K+ + S A++++Q AA+ A+ D + ++ R D V L + G+ Sbjct: 260 AMVKLQSQSTSGANAVAQAAAIAALDGPQDFIAANKAVFQARRDRVVAALGQVDGIHCQA 319 Query: 311 PSGAFYIFPSIK----------SFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLS 360 P+GAFY+F S + S +S D+ +L+ +A++ GS++ + + RLS Sbjct: 320 PAGAFYVFASCEALIGARTPHGSVIRSSDDWVNWVLDSQDLAVLQGSAYGV--DTHFRLS 377 Query: 361 FACSMDTLREGLDRLE 376 FA SM L EG R+E Sbjct: 378 FAASMAQLDEGCRRIE 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: 316 Number of extensions: 13 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: 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 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