Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate Dsui_2909 Dsui_2909 aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::Q2RK33 (390 letters) >FitnessBrowser__PS:Dsui_2909 Length = 395 Score = 340 bits (872), Expect = 4e-98 Identities = 160/390 (41%), Positives = 246/390 (63%), Gaps = 3/390 (0%) Query: 1 MQEARRIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPE 60 M++ RI+ LPPY+F + AR RG DII + +G+PD TP H++DK+V + Sbjct: 1 MKDFPRIKRLPPYVFNITGELKMAARRRGEDIIDMSMGNPDGATPKHIVDKMVDATQRGD 60 Query: 61 NHRYPTSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINL 120 H Y S+G+ R+A+ DWY R Y V+ DP E V IGSKEG+AH+ L +D GD L Sbjct: 61 THGYSVSKGIPRLRKAICDWYLRRYNVEFDPDSEAVVTIGSKEGLAHLMLATLDRGDTVL 120 Query: 121 VPDPGYPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGA 180 VP+P YP++ G ++AG + + +T F +L + + K+M + +P+NPT Sbjct: 121 VPNPSYPIHIYGAIIAGANTRSVRMTDDVDFFEELQRAIRECTPKPKMMILGFPSNPTAR 180 Query: 181 VADLKFFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPY 240 +L FF+ VV A+ +D++V HD AY++I +DGYRAPS ++ PGA++V +EF ++SK Y Sbjct: 181 CVELDFFERVVALAKEHDILVVHDLAYADIVFDGYRAPSIMEVPGARDVAVEFFTMSKSY 240 Query: 241 NMTGWRLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQER 300 NM GWR+G+ G ++ ALARIKS D G F +Q A + AL GPQ+ + EVR+ Y+ R Sbjct: 241 NMAGWRVGYMVGNKELCAALARIKSYHDYGTFTPIQVASVIALDGPQDCVEEVRQTYELR 300 Query: 301 RDIIVEGFNSLGWHLEKPKATFYVWAPVPRGYT---SASFAEMVLEKAGVIITPGNGYGN 357 R+++ +G + GW +E PKA+ Y+WA +P Y S FA+ +L +A V ++PG G+G+ Sbjct: 301 RNVLAKGLHEAGWMVEVPKASMYIWAKIPEPYAHLGSLEFAKKLLAEAKVAVSPGIGFGD 360 Query: 358 YGEGYFRIALTISKERMQEAIERLRRVLGK 387 YG+ + R AL ++ R ++AI ++ + K Sbjct: 361 YGDDHVRFALIENEARTRQAIRGIKDMFRK 390 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: 451 Number of extensions: 17 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: 395 Length adjustment: 31 Effective length of query: 359 Effective length of database: 364 Effective search space: 130676 Effective search space used: 130676 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