Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate GFF2657 PS417_13545 arginine aminotransferase
Query= SwissProt::Q2RK33 (390 letters) >FitnessBrowser__WCS417:GFF2657 Length = 664 Score = 174 bits (440), Expect = 9e-48 Identities = 109/367 (29%), Positives = 179/367 (48%), Gaps = 5/367 (1%) Query: 24 EARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHRYPTSEGLLAFRQAVADWYQR 83 +A +G DII L +GDPD TPS + D V+ + H Y G A R+A+A Y + Sbjct: 26 QAASQGEDIIILSVGDPDFATPSFITDAAVSALREGDTH-YTEIPGRPALREAIAARYSK 84 Query: 84 LYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDPGYPVYNIGTLLAGGESYFM 143 L V+T+ G++ + SLC + GD LV DP Y Y +G + Sbjct: 85 TLARALSAEN-VITVAGAQNALFVTSLCLLQAGDEVLVLDPMYVTYEATLKASGATLVRV 143 Query: 144 PLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAVADLKFFQEVVEFARSYDLIVCH 203 P + +GF D + + + R + +F + PNNPTG V +L+ Q + + A + DL V Sbjct: 144 PCSPESGFRLDAQLLGAAITPRTRAIFFSNPNNPTGVVLNLQELQAIADLAIARDLWVVV 203 Query: 204 DAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYNMTGWRLGWACGRADVIEALARI 263 D Y + +DG S PG E + S+SK + MTGWR+GW ++ + Sbjct: 204 DEVYESLVFDG-EYHSLAALPGMAERCVVIGSLSKSHAMTGWRIGWIIATPQMVAHAETL 262 Query: 264 KSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQERRDIIVEGFNSL-GWHLEKPKATF 322 ++ G V A AA+ + +R +Y+ RRD+++ G ++ G ++ P+A Sbjct: 263 VLSMLYGLPGFVMEAATAAVLAHDDVTQGMREIYRRRRDLVMAGLSACPGIKVQAPQAGM 322 Query: 323 YVWAPV-PRGYTSASFAEMVLEKAGVIITPGNGYGNYGEGYFRIALTISKERMQEAIERL 381 +V V G S FA + +AGV + +G +G+ R++ T+ +ER+ EA +R+ Sbjct: 323 FVLVDVRGTGLGSLDFAWRLFREAGVSVLDAAAFGAPAQGFVRLSFTLGEERLSEACQRI 382 Query: 382 RRVLGKV 388 + K+ Sbjct: 383 AHFVAKL 389 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: 592 Number of extensions: 35 Number of successful extensions: 4 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: 664 Length adjustment: 34 Effective length of query: 356 Effective length of database: 630 Effective search space: 224280 Effective search space used: 224280 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: 52 (24.6 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