Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate GFF1405 HP15_1371 aspartate aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Marino:GFF1405 Length = 394 Score = 194 bits (494), Expect = 3e-54 Identities = 115/361 (31%), Positives = 192/361 (53%), Gaps = 11/361 (3%) Query: 31 GEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAV 90 G++I+ L G+PDFDTP I QAAI+++ G T Y V G AL++ I + +R +G Sbjct: 31 GQDIIGLGAGEPDFDTPDHIKQAAIEAINNGQTKYTAVDGTPALKKAIIAKFKRDNGLDY 90 Query: 91 DAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENG 150 +A Q++V +G + + + + LNPGDE I+ P +V+Y + + V + +E Sbjct: 91 EANQILVSSGGKQSFFNLALATLNPGDEAIIPAPYWVSYPDMVLVAEGKPVIIETGAETR 150 Query: 151 FRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAH-DLWMISDEVYSE 209 F++ E++ IT RTR +NSP NPSG + +A+ E+ H ++ + +D++Y Sbjct: 151 FKITPEQLENAITERTRLFVINSPSNPSGMAYTLEELQAIGEVLKKHPNIMIATDDMYEP 210 Query: 210 LLFDGEHVSPA--SLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCML 267 +L+ G+ + P + DRT LN +SK+++MTGWR+G+ GPA + ++ + Sbjct: 211 ILWTGKPFCNILNATPELYDRTFVLNGVSKAYSMTGWRIGYAAGPAKIIGAMKKIQSQST 270 Query: 268 YGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVM-- 325 Q AA AL+ + M +A++ R D ++E L PG+ L DG +V Sbjct: 271 SNPASISQAAAQAALDGDQGCVGEMVKAFKERHDWLVEALNKLPGVECLNGDGTFYVFPS 330 Query: 326 ----VDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLREACRR 381 +D + + FA++LL GV+++ G AFG GH+RL E L +A R Sbjct: 331 FQGAIDADSSVSTDVEFAEKLLTDAGVALVPGSAFG--CPGHMRLSFATSMENLEKAVER 388 Query: 382 I 382 + Sbjct: 389 L 389 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: 360 Number of extensions: 15 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: 393 Length of database: 394 Length adjustment: 31 Effective length of query: 362 Effective length of database: 363 Effective search space: 131406 Effective search space used: 131406 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