Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate RR42_RS35305 RR42_RS35305 aspartate aminotransferase
Query= SwissProt::Q2RK33 (390 letters) >FitnessBrowser__Cup4G11:RR42_RS35305 Length = 401 Score = 178 bits (451), Expect = 3e-49 Identities = 126/392 (32%), Positives = 190/392 (48%), Gaps = 22/392 (5%) Query: 6 RIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHRYP 65 R+ + P + +++ E R G D+I L G+PD TP+H I + A RY Sbjct: 7 RLNRIKPSPSSMAGQRVRELRAAGRDVIGLTAGEPDFETPAH-IREAAWRAMQAGKTRYT 65 Query: 66 TSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDPG 125 G R A A ++R G+D E++ G+K+ I + +C V GD +VP P Sbjct: 66 DVGGTAELRHAAAQKFKRENGLDY-AASEIIVSTGAKQVIFNALMCTVQQGDEVIVPAPY 124 Query: 126 YPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAV---A 182 + Y TL AGG F+ A NGF + ++ R + + +N PNNP+GA Sbjct: 125 WVSYPDITLFAGGVPVFVACQAENGFKLTPEELERAISARTRWLILNSPNNPSGAAYTRT 184 Query: 183 DLKFFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQA-PGAKEVGIEFNSVSKPYN 241 +L EV+E R + V D Y +TYDG + QA P K + N VSK Y Sbjct: 185 ELVAIAEVLE--RHPHVWVMTDDIYEHLTYDGAAFVTLAQAAPSLKARTLTINGVSKAYA 242 Query: 242 MTGWRLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQERR 301 MTGWR+G+A A +I+A+ +++S SGA Q A IAAL GPQ+ +A + V+Q RR Sbjct: 243 MTGWRIGYAGAPAPLIKAMVKLQSQSTSGANAVAQAAAIAALDGPQDFIAANKAVFQARR 302 Query: 302 DIIVEGFNSL-GWHLEKPKATFYVWAP--------VPRG---YTSASFAEMVLEKAGVII 349 D +V + G H + P FYV+A P G +S + VL+ + + Sbjct: 303 DRVVAALGQVDGIHCQAPAGAFYVFASCEALIGARTPHGSVIRSSDDWVNWVLDSQDLAV 362 Query: 350 TPGNGYGNYGEGYFRIALTISKERMQEAIERL 381 G+ YG + +FR++ S ++ E R+ Sbjct: 363 LQGSAYG--VDTHFRLSFAASMAQLDEGCRRI 392 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: 348 Number of extensions: 15 Number of successful extensions: 3 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: 401 Length adjustment: 31 Effective length of query: 359 Effective length of database: 370 Effective search space: 132830 Effective search space used: 132830 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