Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate AO356_25355 AO356_25355 aspartate aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25355 Length = 404 Score = 217 bits (552), Expect = 5e-61 Identities = 132/381 (34%), Positives = 203/381 (53%), Gaps = 15/381 (3%) Query: 15 AAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRAL 74 +A + I R R QG +I+ L G+PDFDTP I +AAI+++ G+T Y V G R+L Sbjct: 18 SATYRIMDRVAERRAQGAKIISLCAGEPDFDTPKHIREAAIEAIGQGHTRYTQVAGVRSL 77 Query: 75 RQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFG 134 R+ +A + R+ +G V + +V G + +Y + L+ GD+VIV P +V+Y + Sbjct: 78 REAVAAKFRQENGLDVTWQDTLVCNGGKQVIYNALAATLDEGDQVIVPAPYWVSYPEMVQ 137 Query: 135 ACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELC 194 CG V +++GF++ + A ITP+TR + LNSP NP+GA R +ALA++ Sbjct: 138 LCGGESRIVTCDADSGFKLTPAALDAAITPQTRWLILNSPSNPTGAVYSREELQALADVL 197 Query: 195 MAH-DLWMISDEVYSELLFDGE--HVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVG 251 +AH + +++D++Y L+FD + + P +A RT T+N +SK++AMTGWR+G+ G Sbjct: 198 LAHPHVLILADDIYEHLIFDDQVFYTLAQVEPRLASRTLTMNGVSKAYAMTGWRIGFATG 257 Query: 252 PAALCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSP 311 P L +E L G+ Q AA AL+ P + R ++RRRDL++ L +P Sbjct: 258 PRWLLEAMEKLQGQQTSGASSISQQAALAALDGPKDFIRESRAVFQRRRDLMVALLNATP 317 Query: 312 GLRPLRPDGGMFVMVD----IRPTGLSAQAF------ADRLLDRHGVSVLAGEAFGPSAA 361 GL P G + I T + A LLD V+V+ G AFG Sbjct: 318 GLACASPGGAFYAFASCAGLIGRTSSGGRVLHTDEDVAHALLDEADVAVVHGSAFG--LG 375 Query: 362 GHIRLGLVLGAEPLREACRRI 382 +IR+ L LR+AC I Sbjct: 376 PYIRIAYALDDASLRQACEAI 396 Lambda K H 0.322 0.136 0.411 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: 484 Number of extensions: 30 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: 393 Length of database: 404 Length adjustment: 31 Effective length of query: 362 Effective length of database: 373 Effective search space: 135026 Effective search space used: 135026 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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