Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate WP_027721528.1 H589_RS0107920 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P16524 (393 letters) >NCBI__GCF_000425265.1:WP_027721528.1 Length = 386 Score = 236 bits (603), Expect = 6e-67 Identities = 136/369 (36%), Positives = 208/369 (56%), Gaps = 12/369 (3%) Query: 17 IRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQL 76 + K + + +I + IG+PDF TP +K A +A+D+ T YT + G ELR+A+ Sbjct: 20 LEKAQQMEREGRSIIHMEIGEPDFDTPDCIKKACCEAMDKGETHYTHSLGIPELREAISK 79 Query: 77 YMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAK 136 Y K + + + D + +IIT G S A+ F IL GD VI+ P Y Y I+ GA+ Sbjct: 80 YHKDRYNVDVDPD-RVIITQGTSPAMLLLFTFILDKGDNVIVSDPCYACYSNFISFAGAE 138 Query: 137 PVIVDTTSH-GFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNV 195 + T GF+ I+ A+ TK +++ PSNPTG LS E +K IA G Sbjct: 139 ANRITTFEEDGFQYRPEAIKKAINTKTKAILINSPSNPTGTLLSPERMKEIA----GMGP 194 Query: 196 FVLSDEIYSELTYDRPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILK 255 +++SDEIY L Y +SI Y D V+NG SK +MTGWR+G++ +P+ + + K Sbjct: 195 WIISDEIYHGLVYGEKEHSILEYT-DHAFVLNGFSKLFAMTGWRLGYIISPEKYVRPLQK 253 Query: 256 VHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLDV-VKPSGA 314 + Q A+S++Q+A + A+T +DD ++ Y +R Y+ RL MG D+ V+P+GA Sbjct: 254 LCQNFFISANSMAQRAGVAALTESWDDVNRIKNTYDERRKYMLKRLREMGFDIKVEPTGA 313 Query: 315 FYIFPSIK----SFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLRE 370 FY+ ++K F +S + +LE AG+ + PG F EGY+RLS+A S++ L E Sbjct: 314 FYVLVNMKHLAAKFDGSSLKLAFDILEQAGIGVTPGIDFGDGAEGYIRLSYANSIENLAE 373 Query: 371 GLDRLELFV 379 G+DRLE +V Sbjct: 374 GMDRLENYV 382 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: 379 Number of extensions: 18 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: 386 Length adjustment: 30 Effective length of query: 363 Effective length of database: 356 Effective search space: 129228 Effective search space used: 129228 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