Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate Synpcc7942_1794 Synpcc7942_1794 succinyldiaminopimelate transaminase
Query= SwissProt::Q2RK33 (390 letters) >FitnessBrowser__SynE:Synpcc7942_1794 Length = 392 Score = 335 bits (859), Expect = 1e-96 Identities = 160/386 (41%), Positives = 244/386 (63%), Gaps = 2/386 (0%) Query: 4 ARRIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHR 63 ++R+ L +FA +++ A A G ++I L +G D+P P HV+ + A +P H Sbjct: 7 SQRLAPLQRNVFADMDRAKAVAIAAGREVIDLSLGSSDLPAPDHVVAVIAASLQDPSTHG 66 Query: 64 YPTSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPD 123 Y +G L FRQ A WY+R +G+ +DP EV+ LIGS+EG AH+ L ++PG+I L+ D Sbjct: 67 YLLHQGTLPFRQVAAAWYERKFGLGVDPETEVLLLIGSQEGTAHLPLAVMEPGEIALLQD 126 Query: 124 PGYPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAVAD 183 PGYP + G LAGGE Y +P TA GFLPD IP+++ R++L+ ++YP+NPT A+A Sbjct: 127 PGYPSHAGGVYLAGGEIYRLPTTADRGFLPDFSTIPTEILSRSRLLVLSYPHNPTTAIAP 186 Query: 184 LKFFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYNMT 243 L FF+E V F R + L++ HD Y ++ +DG PS QA K+ IEF S+SK YNM Sbjct: 187 LAFFEEAVAFCRHHQLVLAHDFPYPDLGFDGVEVPSIFQADRQKQQAIEFFSLSKSYNMG 246 Query: 244 GWRLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQERRDI 303 G+R+G+A G A++I AL R+K+ +D +Q + IAALTGPQ + R+ +++RRDI Sbjct: 247 GFRVGFAIGNAELIGALRRLKAVVDFNQYQGILAGAIAALTGPQACVEATRQRFRDRRDI 306 Query: 304 IVEGFNSLGWHLEKPKATFYVWAPVPRGYTSAS--FAEMVLEKAGVIITPGNGYGNYGEG 361 + + GW + KP +T Y+WAP+P + + S F E ++ + GV +PG G+G+ GEG Sbjct: 307 FINALAATGWTIPKPVSTMYLWAPLPEPWQTRSLEFCEKLVAETGVAASPGIGFGDCGEG 366 Query: 362 YFRIALTISKERMQEAIERLRRVLGK 387 + R AL ++R++EA R+ + L + Sbjct: 367 FVRFALVHDRDRLEEAARRITQFLAR 392 Lambda K H 0.320 0.139 0.421 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: 443 Number of extensions: 17 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: 390 Length of database: 392 Length adjustment: 31 Effective length of query: 359 Effective length of database: 361 Effective search space: 129599 Effective search space used: 129599 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 (21.8 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