Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate PP_1588 PP_1588 N-succinyl-L,L-diaminopimelate aminotransferase alternative
Query= BRENDA::Q82IK5 (364 letters) >FitnessBrowser__Putida:PP_1588 Length = 398 Score = 149 bits (377), Expect = 1e-40 Identities = 119/392 (30%), Positives = 181/392 (46%), Gaps = 30/392 (7%) Query: 1 MSAVSDRLPTFPWDKLEPYKARAAAHPDG-IVDLSVGTPVDPVPELIQKALVAAADSPG- 58 M+ +L +P++KL D + LS+G P P + +A+ D Sbjct: 1 MNHALTQLQPYPFEKLRALLGSVKPAADKRAIALSIGEPKHESPAFVAQAMADNLDKLAV 60 Query: 59 YPTVWGTPELRDALTGWVERRLGARGV---THHHVLPIVGSKE-LVAWLPTQLGLGPGDK 114 YP+ G P LR A+ W ERR G H+LP+ G++E L A+ + Sbjct: 61 YPSTLGLPALRQAIGQWCERRFGVPAGWLDADRHILPVNGTREALFAFTQAVVNRADDGL 120 Query: 115 VAHPRLAYPTYEVGARLARA--------DHVVYDDPTELDPTGL----KLLWLNSPSNPT 162 V P Y YE A LA A ++ ++ + P + ++L+L SP NPT Sbjct: 121 VISPNPFYQIYEGAALLAGATPHYLPCLENNGFNPDFDAVPAEVWKRCQILFLCSPGNPT 180 Query: 163 GKVLSKAELTRIVAWAREHGILVFSDECYLELGWEAD--PVSVLHP--DVCGGSYEGIVS 218 G ++ L +++A A EH ++ +DECY EL ++ D P +L ++ + V Sbjct: 181 GALVPMNTLKKLIALADEHDFVIAADECYSELYFDEDAPPPGLLSACAELGRSDFARCVV 240 Query: 219 VHSLSKRSNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVREQ 278 HSLSKRSNL G R+ F+AGD ++ P L R + G TQ A +AA D+AHVRE Sbjct: 241 FHSLSKRSNLPGLRSGFVAGDAQIIKPFLLYRTYHGCAMPVQTQLASIAAWQDEAHVREN 300 Query: 279 RERYAARRTALRDALLSHGFRIEHSEASLYLWA-TRGESCWDTVAHLADLGILVAPGDFY 337 R++Y A+ A+ D +L ++ + S YLWA G+ T + V PG + Sbjct: 301 RDQYRAKYDAVLD-ILQPVLDVQRPDGSFYLWAKVPGDDAEFTRDLFEAQHVTVVPGSYL 359 Query: 338 G------SAGEQFVRVALTATDERVAAAVRRL 363 + G VR+AL A A R+ Sbjct: 360 SREVDGVNPGAGRVRMALVAPLAECIEAAERI 391 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: 409 Number of extensions: 33 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: 398 Length adjustment: 30 Effective length of query: 334 Effective length of database: 368 Effective search space: 122912 Effective search space used: 122912 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 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