Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate Dsui_0132 Dsui_0132 aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__PS:Dsui_0132 Length = 385 Score = 176 bits (447), Expect = 8e-49 Identities = 119/359 (33%), Positives = 180/359 (50%), Gaps = 10/359 (2%) Query: 23 LVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKA 82 L AQ D+I + +G+PDF TP + AAA++ + + YTP G ELR+A+ + +++ Sbjct: 26 LEAQGRDIIHMEVGEPDFPTPEPILAAAREFLQDGRVFYTPALGLPELREAISGFYRQRY 85 Query: 83 DFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT 142 A S I IT GAS A+ A + +PG E ++ P YP + PV + Sbjct: 86 GIAVPA-SRIAITAGASGALTLALACLAAPGSEWLLTDPGYPCNRHFVRAFEGVPVSIPV 144 Query: 143 -TSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDE 201 + F+ T +E T + P+NPTG L EL IA ++ R ++ DE Sbjct: 145 GAASNFQPTRLDLEQHWNERTAGALFASPANPTGTMLDAAELADIADFVRQRQGQLIIDE 204 Query: 202 IYSELTY--DRPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQY 259 IY LTY D P A D V+ SK MTGWR+G+L P+ + + K+ Q Sbjct: 205 IYHGLTYNGDAP---TALAAGDNIFVVQSFSKYFQMTGWRLGWLVIPEPFVRDVEKLAQN 261 Query: 260 NVSCASSISQKAALEAVTNGFDDALIMRE-QYKKRLDYVYDRLVSMGLDV-VKPSGAFYI 317 AS+ +Q AAL A L R ++K R DY+ L ++G + +P GAFY+ Sbjct: 262 LFISASTPAQHAALAAFQPETIALLEQRRAEFKARRDYLAPALEAIGFRITAQPEGAFYL 321 Query: 318 FPSIKSFGMTSFDFSMALLEDAGVALVPGSSFSTYG-EGYVRLSFACSMDTLREGLDRL 375 + + SF F+ LLE+AGVA+ PG F +G +VR ++ + L EG++R+ Sbjct: 322 YADCSTLTDDSFGFARRLLEEAGVAITPGIDFGNHGASSHVRFAYTNAQARLAEGVERI 380 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: 312 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: 385 Length adjustment: 30 Effective length of query: 363 Effective length of database: 355 Effective search space: 128865 Effective search space used: 128865 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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