Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate GFF1405 HP15_1371 aspartate aminotransferase
Query= SwissProt::Q2RK33 (390 letters) >FitnessBrowser__Marino:GFF1405 Length = 394 Score = 183 bits (464), Expect = 8e-51 Identities = 125/397 (31%), Positives = 202/397 (50%), Gaps = 16/397 (4%) Query: 1 MQEARRIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPE 60 +Q + R++ + P + K AE R G DII LG G+PD TP H I + EA N Sbjct: 3 LQLSSRVQAIKPSPTLAVTNKAAELRAAGQDIIGLGAGEPDFDTPDH-IKQAAIEAINNG 61 Query: 61 NHRYPTSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINL 120 +Y +G A ++A+ ++R G+D + + +V+ G K+ +++L ++PGD + Sbjct: 62 QTKYTAVDGTPALKKAIIAKFKRDNGLDYEANQILVSS-GGKQSFFNLALATLNPGDEAI 120 Query: 121 VPDPGYPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGA 180 +P P + Y L+A G+ + A F + + + R +L IN P+NP+G Sbjct: 121 IPAPYWVSYPDMVLVAEGKPVIIETGAETRFKITPEQLENAITERTRLFVINSPSNPSGM 180 Query: 181 VADLKFFQEVVEFARSY-DLIVCHDAAYSEITYDGYRAPSFLQA-PGAKEVGIEFNSVSK 238 L+ Q + E + + ++++ D Y I + G + L A P + N VSK Sbjct: 181 AYTLEELQAIGEVLKKHPNIMIATDDMYEPILWTGKPFCNILNATPELYDRTFVLNGVSK 240 Query: 239 PYNMTGWRLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQ 298 Y+MTGWR+G+A G A +I A+ +I+S S Q A AAL G Q + E+ + ++ Sbjct: 241 AYSMTGWRIGYAAGPAKIIGAMKKIQSQSTSNPASISQAAAQAALDGDQGCVGEMVKAFK 300 Query: 299 ERRDIIVEGFNSL-GWHLEKPKATFYVWAPVPRG--------YTSASFAEMVLEKAGVII 349 ER D +VE N L G TFYV+ P +G T FAE +L AGV + Sbjct: 301 ERHDWLVEALNKLPGVECLNGDGTFYVF-PSFQGAIDADSSVSTDVEFAEKLLTDAGVAL 359 Query: 350 TPGNGYGNYGEGYFRIALTISKERMQEAIERLRRVLG 386 PG+ +G G+ R++ S E +++A+ERL++ LG Sbjct: 360 VPGSAFG--CPGHMRLSFATSMENLEKAVERLQKALG 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: 332 Number of extensions: 17 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: 394 Length adjustment: 31 Effective length of query: 359 Effective length of database: 363 Effective search space: 130317 Effective search space used: 130317 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