Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate GFF973 Psest_1004 Aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__psRCH2:GFF973 Length = 390 Score = 171 bits (432), Expect = 4e-47 Identities = 113/363 (31%), Positives = 184/363 (50%), Gaps = 6/363 (1%) Query: 17 IRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQL 76 + + + L Q DVI L IG+PDF T + AA + A+ T YTP G +LR+A+ Sbjct: 21 LERANQLQVQGHDVIHLEIGEPDFTTAAPIVAAGQAALAAGHTRYTPARGLPQLREAIAA 80 Query: 77 YMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLC-GA 135 + ++ + D I+IT G S A+ A ++ PG ++ P YP + L GA Sbjct: 81 FYAQRYGLSID-PGRILITPGGSGALLLAASLLVDPGKHWLLADPGYPCNRHFLRLVEGA 139 Query: 136 KPVIVDTTSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNV 195 ++ ++LT L+E ++ ++ P+NPTG L +EL ++A LK R Sbjct: 140 AQLVPVGPDVRYQLTPELVERYWDRDSVGALVASPANPTGTLLERDELARLSAALKERGG 199 Query: 196 FVLSDEIYSELTYDRPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILK 255 ++ DEIY LTY S+ + D V+N SK MTGWR+G+L AP + K Sbjct: 200 HLVVDEIYHGLTYGVDAASVLE-VDDDAFVLNSFSKYFGMTGWRLGWLVAPPTAVPELEK 258 Query: 256 VHQYNVSCASSISQKAALEAVTNGFDDAL-IMREQYKKRLDYVYDRLVSMGLDV-VKPSG 313 + Q A S++Q AAL + L R ++ +R D++ L +G + V+P G Sbjct: 259 LAQNLYISAPSMAQHAALACFEPATLEILEARRAEFARRRDFLLPALRELGFGIAVEPQG 318 Query: 314 AFYIFPSIKSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEG-YVRLSFACSMDTLREGL 372 AFY++ I +FG ++ F +LE VA+ PG F + G +VR ++ + L++ + Sbjct: 319 AFYLYADISAFGGDAYAFCQHMLETEFVAITPGLDFGRFQAGHHVRFAYTQDLPRLQQAV 378 Query: 373 DRL 375 +R+ Sbjct: 379 ERI 381 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: 324 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: 390 Length adjustment: 31 Effective length of query: 362 Effective length of database: 359 Effective search space: 129958 Effective search space used: 129958 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