Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate BWI76_RS20205 BWI76_RS20205 aminotransferase AlaT
Query= curated2:O67781 (394 letters) >FitnessBrowser__Koxy:BWI76_RS20205 Length = 405 Score = 153 bits (386), Expect = 1e-41 Identities = 111/360 (30%), Positives = 183/360 (50%), Gaps = 21/360 (5%) Query: 20 ITAKAKELRAKGVDVIGFGAGEP---DFDTPDFIKEACIRALREGKTKYAPSAGIPELRE 76 + +AK L +G V+ G P FD PD I IR L + Y+ S G+ R+ Sbjct: 21 VLKEAKRLEEEGNKVLKLNIGNPAPFGFDAPDEILVDVIRNLPTSQG-YSDSKGLYSARK 79 Query: 77 AIAEKLLKENKVEYKPSEIVVSAGAKMVLFLIFMAILDEGDEVLLPSPYWVTYPEQIRFF 136 AI + + +I + G ++ A+L+ GDE+L+P+P + + + Sbjct: 80 AIMQHYQARGMRDVTVEDIYIGNGVSELIVQAMQALLNSGDEMLVPAPDYPLWTAAVSLS 139 Query: 137 GGVPVEVPLKKEKGFQLSLEDVKEKVTERTKAIVINSPNNPTGAVYEEEELKKIAEFCVE 196 G V + + L+D++ K+T RT+ IVI +PNNPTGAVY +E L +I E + Sbjct: 140 SGKAVHYLCDESSDWFPDLDDIRAKITPRTRGIVIINPNNPTGAVYSKELLMEIVEIARQ 199 Query: 197 RGIFIISDECYEYFVYGDAKFVSPASFSDEVKNITFTVNAFSKSYSMTGWRIGYVAC--P 254 + I +DE Y+ +Y +A+ S A + ++ ITF N SK+Y + G+R G++ P Sbjct: 200 HNLIIFADEIYDKILYDEAQHHSIAPLAPDLLTITF--NGLSKTYRVAGFRQGWMVLNGP 257 Query: 255 EEYAK-------VIASLNSQSVSNVTTFAQYGALEALKNPKS-KDFVNEMRNAFERRRDT 306 +++AK ++AS+ + +NV AQ+ AL +S +F+ +E +R+ Sbjct: 258 KKHAKGYIEGLEMLASM--RLCANVP--AQHAIQTALGGYQSISEFIVPGGRLYE-QRNR 312 Query: 307 AVEELSKIPGMDVVKPEGAFYIFPDFSAYAEKLGGDVKLSEFLLEKAKVAVVPGSAFGAP 366 A E ++ IPG+ KP+GA Y+FP A + D K+ L + KV +V G+AF P Sbjct: 313 AWELINDIPGVSCTKPKGALYMFPKIDAKRFNIHDDQKMVLDFLLQEKVLLVQGTAFNWP 372 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: 392 Number of extensions: 23 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: 394 Length of database: 405 Length adjustment: 31 Effective length of query: 363 Effective length of database: 374 Effective search space: 135762 Effective search space used: 135762 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 Jul 25 2024. The underlying query database was built on Jul 25 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