Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate AO353_28150 AO353_28150 arginine aminotransferase
Query= curated2:O67781 (394 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28150 Length = 667 Score = 220 bits (560), Expect = 1e-61 Identities = 131/374 (35%), Positives = 206/374 (55%), Gaps = 15/374 (4%) Query: 24 AKELRAKGVDVIGFGAGEPDFDTPDFIKEACIRALREGKTKYAPSAGIPELREAIAEKLL 83 A + + +G DVI G+PDF TPDFI +A + ALREG T Y AG LREAIA + Sbjct: 24 AFDAQRRGEDVIILSVGDPDFPTPDFITDAAVDALREGDTHYTEIAGRLALREAIAARYS 83 Query: 84 KENKVEYKPSEIVVSAGAKMVLFLIFMAILDEGDEVLLPSPYWVTYPEQIRFFGGVPVEV 143 + E + S ++ AGA+ LF+ + +L GDEVL P +VTY ++ G V V Sbjct: 84 QLFGRELQASNVINVAGAQNALFITSLCLLTAGDEVLALDPMYVTYEATLKASGATLVRV 143 Query: 144 PLKKEKGFQLSLEDVKEKVTERTKAIVINSPNNPTGAVYEEEELKKIAEFCVERGIFIIS 203 P + GF+L + + +T RT+AI +++PNNPTG V EEL+ IA+ + ++++ Sbjct: 144 PCAADSGFRLDAAVLAKAITPRTRAIFLSNPNNPTGVVLNREELQAIADLAITHDLWVVV 203 Query: 204 DECYEYFVYGDAKFVSPASFSDEVKNITFTVNAFSKSYSMTGWRIGYVACPEEYAKVIAS 263 DE YE + + + +S A+ + + + SKS++MTGWRIG++ E + Sbjct: 204 DEVYESLAF-EREHLSLAALPGMAERCV-VIGSLSKSHAMTGWRIGWIVADETLVAHAET 261 Query: 264 LNSQSVSNVTTFAQYGALEALKNPKSKDFVNEMRNAFERRRDTAVEELSKIPGMDVVKPE 323 L + + F AL+A++ ++ + MR + RRRD V+ LS PG+ V+ P+ Sbjct: 262 LMLSMLYGLPGFVMEAALKAVQ--AHEEVTHGMREIYRRRRDLVVKGLSDCPGISVLTPD 319 Query: 324 GAFYIFPDFSAYAEKLGGDVKLSEF---LLEKAKVAVVPGSAFGAP--GFLRLSYALSEE 378 ++ D G + EF LL +A+V+V+ +AFG P GF+RLS+ L EE Sbjct: 320 AGMFVLVDVR------GTGLSSLEFAWRLLREARVSVLDAAAFGEPAQGFVRLSFTLGEE 373 Query: 379 RLVEGIRRIKKALE 392 RL + +RI+ ++ Sbjct: 374 RLAQACQRIRDFIQ 387 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: 531 Number of extensions: 19 Number of successful extensions: 5 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: 667 Length adjustment: 35 Effective length of query: 359 Effective length of database: 632 Effective search space: 226888 Effective search space used: 226888 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: 52 (24.6 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