Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate RR42_RS02275 RR42_RS02275 aspartate aminotransferase
Query= curated2:O67781 (394 letters) >FitnessBrowser__Cup4G11:RR42_RS02275 Length = 397 Score = 182 bits (463), Expect = 1e-50 Identities = 126/388 (32%), Positives = 189/388 (48%), Gaps = 22/388 (5%) Query: 9 VSHLKPSPTLTITAKAKELRAKGV---DVIGFGAGEPDFDTPDFIKEACIRALREGKTKY 65 V HL+ S + +E+ G+ DV+ F GE D TP FI++A RAL G T Y Sbjct: 19 VHHLRAS-------RIREVANAGIGLPDVLPFWFGESDQVTPAFIRDAASRALAGGATFY 71 Query: 66 APSAGIPELREAIAEKLLKENKVEYKPSEIVVSAGAKMVLFLIFMAILDEGDEVLLPSPY 125 + GI LR A+A+ + + + +V SAG L L + GD + +P Sbjct: 72 THNLGIAPLRSALADYVSALHGATALDNVVVTSAGVN-ALMLAAQLVAGPGDRAVAVTPL 130 Query: 126 WVTYPEQIRFFGGVPVEVPLKK-EKGFQLSLEDVKEKVTERTKAIVINSPNNPTGAVYEE 184 W E + G V L G+ L L+ + +T T+ ++INSPNNPTG V Sbjct: 131 WPNLVEIPKILGAEVETVSLDYGAHGWTLDLDKLLAALTPDTRLLMINSPNNPTGWVMSR 190 Query: 185 EELKKIAEFCVERGIFIISDECYEYFVYGDAKFVSPASFSDEVK--NITFTVNAFSKSYS 242 + + + C GI+II+DE YE YG SF D VN+FSK++ Sbjct: 191 ADQQAVLAHCRRHGIWIIADEVYERLYYGKGDGAIAPSFLDIASRDERVICVNSFSKAWL 250 Query: 243 MTGWRIGYVACPEEYAKVIASLNSQSVSNVTTFAQYGALEALKNPKSKDFVNEMRNAFER 302 MTGWR+G++ P + L + S +F Q + A++ + + F E+ Sbjct: 251 MTGWRLGWMVLPAALTDDLGKLVEYNTSCAPSFVQEAGIVAVR--EGEAFTRELVGRLRA 308 Query: 303 RRDTAVEELSKIPGMDVVKPEGAFYIFPDFSAYAEKLGGDVKLSEFLLEKAKVAVVPGSA 362 RD V L+ +PG+DV PEGA Y+F + ++ L L + L+ +A++ + PGSA Sbjct: 309 ARDHLVSALAVVPGVDVHAPEGAMYVFFRLAGASDSLA----LCKQLVREARLGLAPGSA 364 Query: 363 FG--APGFLRLSYALSEERLVEGIRRIK 388 FG GF+R YA RL EG+RR++ Sbjct: 365 FGDEGEGFVRWCYACDPARLDEGVRRLR 392 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: 370 Number of extensions: 27 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: 397 Length adjustment: 31 Effective length of query: 363 Effective length of database: 366 Effective search space: 132858 Effective search space used: 132858 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 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