Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_057508832.1 ABB28_RS11865 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_001431535.1:WP_057508832.1 Length = 425 Score = 152 bits (384), Expect = 2e-41 Identities = 116/395 (29%), Positives = 190/395 (48%), Gaps = 31/395 (7%) Query: 18 RKFSNLVAQHEDVISLTIGQPDFF---TPHHVKAAAKKAIDENVTSYTPNAGYLELRQAV 74 R+ L AQ +I L IG P F P H++ A + YT G E R+A+ Sbjct: 28 RRARELEAQGRTLIKLNIGNPGNFGFRAPEHLQRAIADDMGRT-DPYTHQQGLPEAREAI 86 Query: 75 QL-YMKKKADFNYDAESE-IIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINL 132 Y ++ A DA + + I G S+ ID + R +L+PGDEV++P P YP + L Sbjct: 87 AAAYARRGAP---DAHPDRVFIGNGVSELIDLSLRALLNPGDEVLVPSPDYPLWSAATIL 143 Query: 133 CGAKPVIVDTT-SHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLK 191 +PV +GF+ IE ++ T+ +VL P+NP+G + S E L+ I A+ + Sbjct: 144 NDGRPVYYRCAPENGFQPDPSEIEALVSSRTRAIVLINPNNPSGASYSRELLERIVAIAR 203 Query: 192 GRNVFVLSDEIYSELTYDRPHYS-IATYLRDQ-TIVINGLSKSHSMTGWRIGFLFAPKD- 248 N+ ++ DEIY ++ YD + +A DQ I +GLSK H GWR+G+ D Sbjct: 204 KHNLLLMVDEIYDQILYDDAVFQPVAPLAGDQPCITFSGLSKVHRACGWRVGWAMLSGDA 263 Query: 249 -------IAKHILKVHQYNVSCASSISQKAALEAVTNGFDDALIM----REQYKKRLDYV 297 A +L + +++ + A++A NG D + Y+ R + Sbjct: 264 GRLGEFRAAMDLLSA----LRLCANVPGQYAIDAAVNGPDTITPLCTPGGRLYETRRAVI 319 Query: 298 YDRLVSMGLDVVKPSGAFYIFPSI---KSFGMTSFDFSMALLEDAGVALVPGSSFSTYGE 354 S L +V P+GA Y FP++ + G+ DF++ L+ D GV +VPGSSF+ Sbjct: 320 DACAASEHLSLVAPAGALYAFPAVVGDAAKGLDDHDFALDLMTDEGVLVVPGSSFNVPYR 379 Query: 355 GYVRLSFACSMDTLREGLDRLELFVLKKREAMQTI 389 + R++ +RE R++ + ++ EA + + Sbjct: 380 HHFRVTLLPEATVMREVFSRIDRALARRAEANRKV 414 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: 400 Number of extensions: 21 Number of successful extensions: 5 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: 425 Length adjustment: 31 Effective length of query: 362 Effective length of database: 394 Effective search space: 142628 Effective search space used: 142628 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