Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_013074746.1 BTUS_RS03510 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_000092905.1:WP_013074746.1 Length = 408 Score = 313 bits (803), Expect = 4e-90 Identities = 166/383 (43%), Positives = 241/383 (62%), Gaps = 3/383 (0%) Query: 2 EHLLNPKAREIEISGIRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSY 61 E L+P R I SGIR+F +L A + VISL +G+PDF TP V+ A A++ TSY Sbjct: 5 EDRLSPTVRAIPPSGIRRFFDLAATTQGVISLGVGEPDFVTPWRVRDACVDALERGYTSY 64 Query: 62 TPNAGYLELRQAVQLYMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGP 121 T N G LR+AV Y++ + +Y+ ++E+++T GAS+ IDAA R ILSPGDEV++P P Sbjct: 65 TSNRGLPALRRAVARYLEDRFRVSYNPDTEVLVTVGASEGIDAALRAILSPGDEVLIPEP 124 Query: 122 IYPGYEPIINLCGAKPVIVDTTSHG-FKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSE 180 Y Y P + L G PV V T + FKL A IE +TP TK ++L YP+NPTG TL E Sbjct: 125 SYVSYGPCVQLAGGAPVYVPTRAEDQFKLKASTIERFITPRTKALLLGYPNNPTGATLGE 184 Query: 181 EELKSIAALLKGRNVFVLSDEIYSELTYDRPHYSIATY--LRDQTIVINGLSKSHSMTGW 238 ++L+ I A++ ++ V+SDEIY+EL+Y PH S + +R++T+++ G+SK+++MTGW Sbjct: 185 KDLEQIRAIVLKHDLLVISDEIYAELSYVLPHTSFPSLPGMRERTMLLTGMSKAYAMTGW 244 Query: 239 RIGFLFAPKDIAKHILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVY 298 R+GF P+ ++K+HQY + CA +SQ AA+EA+T + M QY++R V Sbjct: 245 RVGFATGPRAWIDAMVKIHQYTILCAPIMSQMAAVEALTKASRERDEMVAQYEERRRLVV 304 Query: 299 DRLVSMGLDVVKPSGAFYIFPSIKSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVR 358 MGL +P GAFY FPS+K G+ F+ LL+ VA+VPG F G G++R Sbjct: 305 SAFRRMGLSCHEPEGAFYAFPSVKETGLDDEVFAEELLKREKVAVVPGRVFGPGGVGHIR 364 Query: 359 LSFACSMDTLREGLDRLELFVLK 381 S+A +D L E +R+E F+ K Sbjct: 365 CSYATGVDQLLEAFERMERFLEK 387 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: 369 Number of extensions: 18 Number of successful extensions: 3 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: 408 Length adjustment: 31 Effective length of query: 362 Effective length of database: 377 Effective search space: 136474 Effective search space used: 136474 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 10 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