Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate AO356_06055 AO356_06055 succinyldiaminopimelate transaminase
Query= BRENDA::Q82IK5 (364 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_06055 Length = 399 Score = 153 bits (386), Expect = 9e-42 Identities = 128/401 (31%), Positives = 187/401 (46%), Gaps = 43/401 (10%) Query: 1 MSAVSDRLPTFPWDKLEPYKARAAAHPDGI-VDLSVGTPVDPVPELIQKALVAAADSPG- 58 M+ ++L +P++KL +PD + LS+G P P + +AL + + Sbjct: 1 MNNALNQLQPYPFEKLRALLGSVTPNPDKRPIALSIGEPKHRSPSFVAEALASNLEKMAV 60 Query: 59 YPTVWGTPELRDALTGWVERRLGARGV---THHHVLPIVGSKE-LVAWLPTQLGLGPGDK 114 YPT G PELR+A+TGW ERR HVLP+ G++E L A+ T + G Sbjct: 61 YPTTLGIPELREAITGWCERRFNVPTGWLDPARHVLPVNGTREALFAFTQTVVNRGDDAL 120 Query: 115 VAHPRLAYPTYEVGARLARAD--HVVYDDPTELDPT----------GLKLLWLNSPSNPT 162 V P Y YE A LA A ++ D +P ++L+L SP NPT Sbjct: 121 VVSPNPFYQIYEGAAFLAGAKPHYLPCLDANGFNPDFDAVSPDIWKRCQILFLCSPGNPT 180 Query: 163 GKVLSKAELTRIVAWAREHGILVFSDECYLELGWEAD--PVSVLHPDVCGG--SYEGIVS 218 G ++ L +++A A EH ++ +DECY EL ++ P +L V G ++ V Sbjct: 181 GALIPVDVLKKLIALADEHDFVIAADECYSELYFDEQTPPPGLLSACVELGRKDFKRCVV 240 Query: 219 VHSLSKRSNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVREQ 278 HSLSKRSNL G R+ F+AGD +L L R + G TQ A +AA D+ HVR Sbjct: 241 FHSLSKRSNLPGLRSGFVAGDADILKGFLLYRTYHGCAMPVQTQLASIAAWNDEVHVRAN 300 Query: 279 RERYAARRTALRDALLSHGFRIEHSEASLYLWATRGESCWDTVAHLADL----GILVAPG 334 R Y + A+ + +LS ++ + S YLW D A DL + V PG Sbjct: 301 RALYREKFDAVLE-ILSPVLDVQRPDGSFYLWP---NVAGDDAAFCRDLFEQEHVTVVPG 356 Query: 335 DFYG------SAGEQFVRVALTA-------TDERVAAAVRR 362 + + G VR+AL A ER+ A ++R Sbjct: 357 SYLSRDVDGVNPGAGRVRMALVAPLAECVEAAERIRAFIQR 397 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: 446 Number of extensions: 33 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: 399 Length adjustment: 30 Effective length of query: 334 Effective length of database: 369 Effective search space: 123246 Effective search space used: 123246 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