Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate 8500823 DvMF_1564 aminotransferase class I and II (RefSeq)
Query= SwissProt::Q2RK33 (390 letters) >FitnessBrowser__Miya:8500823 Length = 400 Score = 157 bits (397), Expect = 5e-43 Identities = 109/357 (30%), Positives = 170/357 (47%), Gaps = 8/357 (2%) Query: 33 ISLGIGDPDMPTPSHVIDKLV-AEAHNPENHRYPTSEGLLAFRQAVADWYQRLYGVDLDP 91 +SLG G P TP H+++ + A +P RY G+ A R+A+A G DP Sbjct: 39 VSLGQGVPSFRTPDHIVEAVCRALRDDPTAGRYSLQPGMPALREAIAADILARKGARFDP 98 Query: 92 RREVVTLIGSKEGIAHISLCYVDPGDINLVPDPGYPVYNIGTLLAGGESYFMPLTAANGF 151 E+ +G+ E + I L V+ GD ++P PGY + L+A G +PL AA+ Sbjct: 99 ETEIGVTVGAMEALVMIMLTVVERGDEVIIPSPGYASHAEQVLMAEGVPVHVPLRAADWG 158 Query: 152 LPDLGAIPSDVARRAKLMFINYPNNPTGAVADLKFFQEVVEFARSYDLIVCHDAAYSEIT 211 L D+ A+ V R + + + P NPTG V D + + + A DL++ D Y + Sbjct: 159 L-DVEAVRFAVTPRTRAIIVCSPGNPTGGVYDDADVRALCDLALERDLVLIVDDTYDYMV 217 Query: 212 Y---DGYRAPSFLQAPGAKEVGIEFNSVSKPYNMTGWRLGWACGRADVIEALARIKSNID 268 Y G S + P + I NS SK Y +TGWR+G+ A + L ++ Sbjct: 218 YGEQPGTPRFSPVSQPELRRHVITVNSFSKKYALTGWRVGYVAADAAWMAELLKVHDATA 277 Query: 269 SGAFQAVQYAGIAALTGPQEGLAEVRRVYQERRDIIVEGFNSLGWHLE--KPKATFYVWA 326 A Q+A +AALTGPQ+ + +R RRD+ ++L H P+ FY A Sbjct: 278 VCAPTVSQHAALAALTGPQDCVDVMRAALTARRDLTCRRLDALAPHFAYVPPRGAFYAMA 337 Query: 327 PVP-RGYTSASFAEMVLEKAGVIITPGNGYGNYGEGYFRIALTISKERMQEAIERLR 382 S + A +LE+A VI PG +G GE + R++ + + + EA +R++ Sbjct: 338 RYTFTDADSMTVARRMLEEARVITVPGGSFGPTGERHLRLSFGMDEAELTEAFDRIQ 394 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: 388 Number of extensions: 19 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: 400 Length adjustment: 31 Effective length of query: 359 Effective length of database: 369 Effective search space: 132471 Effective search space used: 132471 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