Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate AZOBR_RS02295 AZOBR_RS02295 aspartate aminotransferase
Query= BRENDA::Q82IK5 (364 letters) >FitnessBrowser__azobra:AZOBR_RS02295 Length = 410 Score = 151 bits (381), Expect = 3e-41 Identities = 129/396 (32%), Positives = 180/396 (45%), Gaps = 43/396 (10%) Query: 6 DRLPTFPWDKLEPYKA----RAAAHPDGIVDLSVGTPVDPVPELIQKALVAAADSPG-YP 60 DRL +P+ +L + RA A P + +SVG P P +I + L A A G YP Sbjct: 17 DRLSDYPFTRLAALLSGVTPRANAEP---IMMSVGEPQHQPPAIIDETLRANAHLWGKYP 73 Query: 61 TVWGTPELRDALTGWVERRLGARGV---THHHVLPIVGSKE------LVAWLPTQLGLGP 111 V GTPE R+A+ W+ RR VLP+ G++E L+A P++ G P Sbjct: 74 PVGGTPEFREAVGAWLARRYALPDGLFDAEKSVLPVSGTREALFLLALLAVPPSKAGRQP 133 Query: 112 GDKVAHPRLAYPTYEVGARLARADHVVYDDPTE---------LDPTGLK---LLWLNSPS 159 V P Y YE A LA A+ V E L P L+ L +L +P+ Sbjct: 134 A--VLMPNPFYAPYEGAALLAGAEPVFLPSTRETGFLPDLDALTPELLERTALFYLCTPA 191 Query: 160 NPTGKVLSKAELTRIVAWAREHGILVFSDECYLELGWEADPVSVLHP----DVCGGSYEG 215 NP G A L R + AR +G ++ DECY E+ + PV L D G + Sbjct: 192 NPQGAAADAAYLERAIGLARRYGFILAVDECYAEIYLDKPPVGALQVASGLDHGGKPWAN 251 Query: 216 IVSVHSLSKRSNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHV 275 I+ HSLSKRS+ AG R+ F+AGDP ++ ++R + P AA A D+AHV Sbjct: 252 ILVFHSLSKRSSAAGLRSGFVAGDPELMSRFTRLRSYSNAGMPLPVLAASAALWRDEAHV 311 Query: 276 REQRERYAARRTALRDALLSHGFRIEHSEASLYLWATRGESCWDTVAHLADLGILVAPGD 335 E R Y A+ A +A L + + +LW G+ T A+ GI V PG Sbjct: 312 EENRALYRAKFDA-AEASLKGRYGYYRPDGGFFLWLEVGDGEEATRRLWAEGGIRVLPGA 370 Query: 336 FY-------GSAGEQFVRVALTATDERVAAAVRRLA 364 + + G F+R+AL E VA A +A Sbjct: 371 YLTRCNPGEANPGAPFIRIALVNDAETVAHACSTIA 406 Lambda K H 0.319 0.135 0.420 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: 438 Number of extensions: 33 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: 364 Length of database: 410 Length adjustment: 30 Effective length of query: 334 Effective length of database: 380 Effective search space: 126920 Effective search space used: 126920 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 (21.7 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