Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate 16484 b2379 hypothetical protein (NCBI)
Query= BRENDA::Q2RK33 (390 letters) >FitnessBrowser__Keio:16484 Length = 412 Score = 342 bits (878), Expect = 9e-99 Identities = 161/380 (42%), Positives = 244/380 (64%), Gaps = 3/380 (0%) Query: 6 RIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHRYP 65 RI LPPY+F + AR RG DII +G+PD TP H+++KL A P+ H Y Sbjct: 12 RIDRLPPYVFNITAELKMAARRRGEDIIDFSMGNPDGATPPHIVEKLCTVAQRPDTHGYS 71 Query: 66 TSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDPG 125 TS G+ R+A++ WYQ Y V++DP E + IGSKEG+AH+ L +D GD LVP+P Sbjct: 72 TSRGIPRLRRAISRWYQDRYDVEIDPESEAIVTIGSKEGLAHLMLATLDHGDTVLVPNPS 131 Query: 126 YPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAVADLK 185 YP++ G ++AG + +PL F +L + + K+M + +P+NPT +L+ Sbjct: 132 YPIHIYGAVIAGAQVRSVPLVEGVDFFNELERAIRESYPKPKMMILGFPSNPTAQCVELE 191 Query: 186 FFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYNMTGW 245 FF++VV A+ YD++V HD AY++I YDG++APS +Q PGA++V +EF ++SK YNM GW Sbjct: 192 FFEKVVALAKRYDVLVVHDLAYADIVYDGWKAPSIMQVPGARDVAVEFFTLSKSYNMAGW 251 Query: 246 RLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQERRDIIV 305 R+G+ G ++ ALARIKS D G F +Q A IAAL G Q+ + ++ Y+ RRD++V Sbjct: 252 RIGFMVGNKTLVSALARIKSYHDYGTFTPLQVAAIAALEGDQQCVRDIAEQYKRRRDVLV 311 Query: 306 EGFNSLGWHLEKPKATFYVWAPVPRGYT---SASFAEMVLEKAGVIITPGNGYGNYGEGY 362 +G + GW +E PKA+ YVWA +P Y S FA+ +L +A V ++PG G+G+YG+ + Sbjct: 312 KGLHEAGWMVEMPKASMYVWAKIPEPYAAMGSLEFAKKLLNEAKVCVSPGIGFGDYGDTH 371 Query: 363 FRIALTISKERMQEAIERLR 382 R AL +++R+++AI ++ Sbjct: 372 VRFALIENRDRIRQAIRGIK 391 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: 500 Number of extensions: 15 Number of successful extensions: 2 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: 412 Length adjustment: 31 Effective length of query: 359 Effective length of database: 381 Effective search space: 136779 Effective search space used: 136779 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 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