Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_018123199.1 B149_RS0100510 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_000375485.1:WP_018123199.1 Length = 388 Score = 214 bits (544), Expect = 4e-60 Identities = 128/370 (34%), Positives = 197/370 (53%), Gaps = 10/370 (2%) Query: 17 IRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQL 76 + K + + V+ L IG+PDF TP +K AA A+D+ T YT + G ELR+A+ Sbjct: 19 LEKAQRMEREGASVVHLEIGEPDFDTPASIKRAACAALDDGHTHYTHSLGIRELREAISD 78 Query: 77 YMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAK 136 +++ D IIIT G S A+ F IL G EVI P Y Y I G + Sbjct: 79 DYRQRYGVEVDP-GRIIITQGTSPAMFVLFSAILRQGQEVIASNPCYACYHNFIRFAGGE 137 Query: 137 --PVIVDTTSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRN 194 PV V T G++ + +A++ T+ +++ P+NPTG LS E +K++A L + Sbjct: 138 VNPVPV-TEQDGWQYRVSAVREAVSDRTRALLINSPANPTGTLLSSERMKALAELADEKG 196 Query: 195 VFVLSDEIYSELTYDRPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHIL 254 + ++SDEIY L Y+ +S+ + D V NG SK ++MTGWR+G+L AP+ + + Sbjct: 197 LHLVSDEIYHGLVYEGREHSVLEF-SDDAFVFNGFSKLYAMTGWRLGYLIAPESFVRPLQ 255 Query: 255 KVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLDVVK-PSG 313 Q A+S++Q A + A+ +D M+ Y R Y+ RL MGL + P+G Sbjct: 256 IACQNFFISANSMAQWAGVAALREAGEDVEHMKAVYDDRRRYMLSRLEGMGLSIPNPPTG 315 Query: 314 AFYIFPSIKS----FGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLR 369 AFYI + F +S + +LE A + + PG F EGY+R S+A S++ +R Sbjct: 316 AFYILVDFRKYAERFDGSSLKLAYDILEKAAIGVTPGVDFGPGAEGYIRFSYANSLENIR 375 Query: 370 EGLDRLELFV 379 EG+DRLE ++ Sbjct: 376 EGMDRLERYL 385 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: 352 Number of extensions: 16 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: 388 Length adjustment: 31 Effective length of query: 362 Effective length of database: 357 Effective search space: 129234 Effective search space used: 129234 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