Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate BPHYT_RS12185 BPHYT_RS12185 succinyldiaminopimelate aminotransferase
Query= BRENDA::Q82IK5 (364 letters) >FitnessBrowser__BFirm:BPHYT_RS12185 Length = 405 Score = 152 bits (383), Expect = 2e-41 Identities = 128/400 (32%), Positives = 191/400 (47%), Gaps = 41/400 (10%) Query: 1 MSAVSDRLPTFPWDKLEPYKARAAAHPDGIVDLS--VGTPVDPVPELIQKALVAAADS-P 57 M+ + D L +P++KL A G+ +S +G P P PELI+ A+VA+ Sbjct: 1 MNPLLDSLQPYPFEKLRALFADVTPSA-GLAHISFGIGEPKHPTPELIRDAVVASLGGLS 59 Query: 58 GYPTVWGTPELRDALTGWVERRLGARGVTHH-HVLPIVGSKELVAWL------PTQLGLG 110 YP G+P LR+++ WV RR V VLP+ GS+E + L P + G Sbjct: 60 SYPATIGSPALRESIAKWVTRRYNLPPVDPATQVLPVSGSREALFALAQTVLDPKKNADG 119 Query: 111 PGDKVAHPRLAYPTYEVGARLARAD-HVVYDDPTE-------LDPTGL----KLLWLNSP 158 V P Y YE A LA A + V DP P + +LL++ SP Sbjct: 120 EPAIVLCPNPFYQIYEGAAILAGAQPYFVNSDPARNFACDYSAVPADIWARTQLLYVCSP 179 Query: 159 SNPTGKVLSKAELTRIVAWAREHGILVFSDECYLELGW-EADP----VSVLHPDVCGGSY 213 NPTG VL+ + + A + +G ++ SDECY E+ + EA+P + H G + Sbjct: 180 GNPTGAVLTLDDWRELFALSDRYGFVIASDECYSEIYFDEANPPLGGLEAAHK--LGRGF 237 Query: 214 EGIVSVHSLSKRSNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDA 273 E +V + SLSKRSN+ G R+ F+AGD A+L L R + G S Q+A + A D+ Sbjct: 238 ERLVMLSSLSKRSNVPGMRSGFVAGDAAILKDFLLYRTYHGAALSTVFQSASIVAWNDET 297 Query: 274 HVREQRERYAARRTALRDALLSHGFRIEHSEASLYLWA---TRGESCWDTVAHL-ADLGI 329 HVRE R +Y + + + +L+ + +A+ YLWA G + + L AD + Sbjct: 298 HVRENRAKYVQKFSTV-TPMLAEVLDVRLPDAAFYLWADVSRTGLTDTEFAQRLYADYNV 356 Query: 330 LVAPGDFYG------SAGEQFVRVALTATDERVAAAVRRL 363 V PG F + G FVR+AL A + +R+ Sbjct: 357 TVLPGSFLARTAHGVNPGRNFVRMALVAGVDECTQGAQRI 396 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: 421 Number of extensions: 23 Number of successful extensions: 4 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: 405 Length adjustment: 30 Effective length of query: 334 Effective length of database: 375 Effective search space: 125250 Effective search space used: 125250 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