Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate GFF3277 PGA1_c33280 putative LL-diaminopimelate aminotransferase
Query= SwissProt::Q2RK33 (390 letters) >FitnessBrowser__Phaeo:GFF3277 Length = 392 Score = 184 bits (466), Expect = 5e-51 Identities = 129/404 (31%), Positives = 207/404 (51%), Gaps = 32/404 (7%) Query: 1 MQEARRIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPE 60 M R LPPY F R+ + + + G D++ + IG+P P+ V D +V A + Sbjct: 1 MNFPERFSNLPPYAFPRL-RALLDHHTPGGDVVHMTIGEPKHDFPAWVTDVIVDNAAGFQ 59 Query: 61 NHRYPTSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGI--AHISLCYVDPGD- 117 + YP +EG R A++DW +R Y V +DP +V+ L G++EG+ A ++LC Sbjct: 60 S--YPPNEGSAELRGAISDWIKRRYDVSVDPMTQVMALNGTREGLYNAAMALCPEQKNGA 117 Query: 118 --INLVPDPGYPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPN 175 + L+P+P Y VY + ++ E F+P TA LPD +P +V R + +I P Sbjct: 118 KPVVLIPNPFYQVYMVASISVAAEPVFVPATADTDHLPDYVGLPPEVLNRTAVAYICSPA 177 Query: 176 NPTGAVADLKFFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPG-AKEVGIE-- 232 NP GAVA ++ ++++ A YD + D YSEI YRA + + A A+E+G + Sbjct: 178 NPQGAVASRAYWTQLIQLAEQYDFRIFADECYSEI----YRASAPVGALSVAQELGADPE 233 Query: 233 ----FNSVSKPYNMTGWRLGWACGRADVIEALARIKSNIDSGA-FQAVQYAGIAALTGPQ 287 FNS+SK N+ G R G G D ++ + ++++ SGA A A A + + Sbjct: 234 RVVLFNSLSKRSNLAGLRSGLIAGGPDTMKRVHQLRAY--SGAPLPAPLQAAAARVWADE 291 Query: 288 EGLAEVRRVYQERRDIIVEGFNSLGWHLEKPKATFYVWAPVPRGYTSASFAEMVLEKAGV 347 + E R +YQE+ I + F+ L ++ P+A F++W PV G +A + + GV Sbjct: 292 AHVTENRALYQEKYRIADQVFDGLDGYM-APEAGFFLWLPVEDGEAAAL---KLWQDTGV 347 Query: 348 IITP------GNGYGNYGEGYFRIALTISKERMQEAIERLRRVL 385 + P G+G N G+GY R+AL E+ + A+ LR L Sbjct: 348 RVLPGAYLAQGDGTANPGKGYIRVALVAPAEQTEVALRTLRSCL 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: 385 Number of extensions: 28 Number of successful extensions: 5 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