Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_010936475.1 DET_RS03860 diaminopimelate aminotransferase
Query= curated2:O67781 (394 letters) >NCBI__GCF_000011905.1:WP_010936475.1 Length = 388 Score = 177 bits (450), Expect = 4e-49 Identities = 125/390 (32%), Positives = 189/390 (48%), Gaps = 18/390 (4%) Query: 5 LASRVSHLKPSPTLTITAKAKELRAKGVDVIGFGAGEPDFDTPDFI-KEACIRALREGKT 63 L+ R+ +L P + I+ K E RAKG +VI F G+PD TP I E C A Sbjct: 3 LSKRIENLPPYLFVQISKKIAEKRAKGEEVISFAIGDPDLPTPKHILAELCKAAEDPANH 62 Query: 64 KYAPSAGIPELREAIAEKLLKENKVEYKP-SEIVVSAGAKMVLFLIFMAILDEGDEVLLP 122 +Y + G+P LR+A+AE K V+ P +E++ G+K + LD GD L+P Sbjct: 63 RYPETEGLPVLRKAMAEWYEKRFGVKLNPDTEVLPLIGSKEGIGHAAWCFLDPGDVALVP 122 Query: 123 SPYWVTYPEQIRFFGGVPVEVPLKKEKGFQLSLEDVKEKVTERTKAIVINSPNNPTGAVY 182 P + Y + G +PL KE F + + V + K + IN PNNPTGAV Sbjct: 123 DPAYPVYAISSQLAGAEVFYMPLNKENNFLPDFNAIPQDVLSKAKILWINYPNNPTGAVA 182 Query: 183 EEEELKKIAEFCVERGIFIISDECYEYFVYGDAKFVSPASF--SDEVKNITFTVNAFSKS 240 + K+ AEF + + + D Y + + P SF +D K + ++ SKS Sbjct: 183 GLDFFKEAAEFAAKHNLAVCHDGPYSEIAFDGYR---PVSFLEADGAKEVGIEFHSLSKS 239 Query: 241 YSMTGWRIGYVACPEEYAKVIASLNSQSVSNVTTFAQYGALEALKNPKSKDFVNEMRNAF 300 Y+MTGWRIG + + S S + Q A+ AL S+D +++ + Sbjct: 240 YNMTGWRIGMAVGNAKMIDALRRFKSNLDSGIPQAIQLMAIAALNG--SQDVISQNCAVY 297 Query: 301 ERRRDTAVEELSKIPGMDVVKPEGAFYIF-PDFSAYAEKLGGDVKLSEFLLEKAKVAVVP 359 +RRRD VE L I GM+V P+ + YI+ P Y + LL+K V V P Sbjct: 298 QRRRDRLVEALRNI-GMEVTAPKASLYIWAPVPEGYT-----SASFATELLDKTGVVVTP 351 Query: 360 GSAFG--APGFLRLSYALSEERLVEGIRRI 387 G+ +G G++RLS + +E+L +GI ++ Sbjct: 352 GTGYGTSGEGYIRLSLTVPDEQLEKGIAKL 381 Lambda K H 0.317 0.135 0.383 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: 377 Number of extensions: 23 Number of successful extensions: 8 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: 394 Length of database: 388 Length adjustment: 31 Effective length of query: 363 Effective length of database: 357 Effective search space: 129591 Effective search space used: 129591 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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