Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate WP_026329593.1 F612_RS0102765 alanine transaminase
Query= SwissProt::Q2RK33 (390 letters) >NCBI__GCF_000381085.1:WP_026329593.1 Length = 398 Score = 342 bits (877), Expect = 1e-98 Identities = 160/386 (41%), Positives = 247/386 (63%), Gaps = 3/386 (0%) Query: 5 RRIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHRY 64 +RI LPPY+F + + AEAR RG DII G+G+PD TP H++DKL+ HRY Sbjct: 6 QRINRLPPYVFNIVGELKAEARRRGEDIIDFGMGNPDQDTPKHIVDKLIEVVQREGTHRY 65 Query: 65 PTSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDP 124 S+G+ R+A+ +WY+ + V+LD E V IGSKEG+AH+++ VD GD LVP+P Sbjct: 66 SVSQGIPRLRKAICNWYKTKFDVELDYATEAVVTIGSKEGLAHLAMATVDKGDTVLVPNP 125 Query: 125 GYPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAVADL 184 YP++ G ++AG + + +T F +L + + K++ +N+P NPT +L Sbjct: 126 AYPIHPFGFVIAGADVRHVKMTPDVDFFEELEKAIKESWPKPKMLILNFPGNPTTQTVEL 185 Query: 185 KFFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYNMTG 244 +FF+ V+ A+ +++ V HD AY++I +DGY APS LQ GAK++ +EF ++SK YNM G Sbjct: 186 EFFERVIAIAKEHNIWVIHDLAYADIVFDGYIAPSILQVEGAKDIAVEFYTLSKSYNMPG 245 Query: 245 WRLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQERRDII 304 WR+G+ G ++ AL RIKS +D G F +Q A IAAL GPQE + E+ +Y+ RRD++ Sbjct: 246 WRVGFMVGNPTLVNALKRIKSYLDYGTFTPIQVAAIAALEGPQECVQEICDMYKLRRDVL 305 Query: 305 VEGFNSLGWHLEKPKATFYVWAPVPRGYT---SASFAEMVLEKAGVIITPGNGYGNYGEG 361 EG N++GW + PKAT ++WAP+P+ Y S F++ +L +A V ++PG G+G+YG+ Sbjct: 306 CEGLNTIGWPVVPPKATMFIWAPIPKEYKAMGSIEFSKKLLTEAKVAVSPGIGFGDYGDD 365 Query: 362 YFRIALTISKERMQEAIERLRRVLGK 387 + R L ++ R ++AI +R + K Sbjct: 366 HVRFGLIENEHRTRQAIRGIRDMFRK 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: 440 Number of extensions: 19 Number of successful extensions: 1 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: 398 Length adjustment: 31 Effective length of query: 359 Effective length of database: 367 Effective search space: 131753 Effective search space used: 131753 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 10 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