Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate Pf6N2E2_1496 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1496 Length = 403 Score = 176 bits (447), Expect = 8e-49 Identities = 130/383 (33%), Positives = 185/383 (48%), Gaps = 16/383 (4%) Query: 23 RALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERH 82 RA A E G +IL L+ G+PDFDTP I QAA ++ AG T Y G +ALR + + Sbjct: 23 RATALREAGRDILDLTTGEPDFDTPTHIKQAAYAAIAAGATKYTPTPGVKALRVAVQRKL 82 Query: 83 RRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVP 142 + E +V+ GA+ ++ L+ GDEV+V P + ++ G V Sbjct: 83 CTENQLDYPLESIVIANGAKQIIFNAFAATLDDGDEVLVPTPYWPSFPDSVRFNGGEPVF 142 Query: 143 VPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAH-DLWM 201 + E G ++ +++ I RTR + LNSP NPSGA A + LA++ H + + Sbjct: 143 IECGLEQGCKLTPQQLEQHIGERTRWLILNSPGNPSGAVYSEAELQGLAQVLRRHAHVLI 202 Query: 202 ISDEVYSELLFDGEHVSPA--SLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHL 259 + DE+Y + FDG P + R + +SK++AMTGWR+G+ GP AL + Sbjct: 203 LLDELYEHIRFDGRAAQNLLNVAPDLQARCLLVGGVSKTYAMTGWRIGFGAGPQALSDAM 262 Query: 260 ENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPD 319 + G+ Q AA A E L L AYR+RRD ++ L GL L P Sbjct: 263 TVVQSQSTSGASSVGQAAALAAFEGGLEFLPEQVAAYRQRRDGLVSTLRTVEGLEVLEPH 322 Query: 320 GGMFVMV-------DIRPTGLSAQAFAD---RLLDRHGVSVLAGEAFGPSAAGHIRLGLV 369 GG FV V RP G + AD LLD GV+ +AG A+G S RL + Sbjct: 323 GGFFVFVRCAGLLGRYRPDGQRLEHDADVVAYLLD-EGVAGVAGSAYGLSP--WFRLSIA 379 Query: 370 LGAEPLREACRRIALCAAELLGQ 392 E + EA RRIA +L G+ Sbjct: 380 TATETVAEAGRRIAHACRQLRGE 402 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: 455 Number of extensions: 24 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: 403 Length adjustment: 31 Effective length of query: 362 Effective length of database: 372 Effective search space: 134664 Effective search space used: 134664 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