Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate GFF1433 Psest_1470 succinyldiaminopimelate transaminase
Query= BRENDA::Q82IK5 (364 letters) >FitnessBrowser__psRCH2:GFF1433 Length = 398 Score = 142 bits (357), Expect = 2e-38 Identities = 122/392 (31%), Positives = 180/392 (45%), Gaps = 30/392 (7%) Query: 1 MSAVSDRLPTFPWDKLEPYKARAAAHPDGI-VDLSVGTPVDPVPELIQKALVAAADSPG- 58 M+ + L +P++KL A A A D + LS+G P P+ + +AL D Sbjct: 1 MNNALNLLHPYPFEKLRGLLAGAEAPTDKRHIALSIGEPKHRSPDFVAQALADNLDQLAV 60 Query: 59 YPTVWGTPELRDALTGWVERRLGARGVT---HHHVLPIVGSKE-LVAWLPTQLGLGPGDK 114 YPT G P LR+ + W ERR G HVLP+ G++E L A+ + Sbjct: 61 YPTTLGIPALRETIARWCERRFGLAADALDPARHVLPVNGTREALFAFTQAVVDRETDGL 120 Query: 115 VAHPRLAYPTYEVGARLARAD--HVVYDDPTELDPT----------GLKLLWLNSPSNPT 162 V P Y YE A LA A ++ + +P ++L+L SP NPT Sbjct: 121 VVSPNPFYQIYEGAALLAGATPHYLPCLEQNGFNPDFAAVPAEVWQRCQILFLCSPGNPT 180 Query: 163 GKVLSKAELTRIVAWAREHGILVFSDECYLELGW-EADPVSVLHPDVCG---GSYEGIVS 218 G ++ L +++A A ++ ++ +DECY EL + EA+P + L Y+ V Sbjct: 181 GALVPLETLKKLIALADQYDFVIAADECYSELYFDEANPPAGLLTACAALGRNDYKRCVV 240 Query: 219 VHSLSKRSNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVREQ 278 HSLSKRSNL G R+ F+AGD +L L R + G TQ A +AA D+ HVR Sbjct: 241 FHSLSKRSNLPGLRSGFVAGDAEILKAFLLYRTYHGCAMPVQTQLASIAAWNDEIHVRAN 300 Query: 279 RERYAARRTALRDALLSHGFRIEHSEASLYLW-ATRGESCWDTVAHLADLGILVAPGDFY 337 RE Y A+ A+ + +L+ ++ + YLW T + T A + V PG + Sbjct: 301 RELYRAKFDAVLE-ILAPVMDVQRPDGGFYLWPKTPMDDQQFTCELFAREHVTVVPGSYL 359 Query: 338 ------GSAGEQFVRVALTATDERVAAAVRRL 363 S G VR+AL A A +R+ Sbjct: 360 SREVDGASPGAGRVRMALVAPLAECIEAAQRI 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: 404 Number of extensions: 26 Number of successful extensions: 3 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 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