Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate Pf1N1B4_4425 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4425 Length = 403 Score = 187 bits (475), Expect = 5e-52 Identities = 133/404 (32%), Positives = 197/404 (48%), Gaps = 16/404 (3%) Query: 1 MRYSDFTQRIAGDGAAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLA 60 +R S QR++ AA +A A E G +IL L++G+PDFDTP I QAA ++ Sbjct: 3 VRLSKRVQRVSLSANAA--AKSQATALREAGRDILDLTIGEPDFDTPEHIKQAAYAAIAG 60 Query: 61 GNTHYADVRGKRALRQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVI 120 G T Y G +ALR + + R+ + E +V+ GA+ ++ L+ GD+V+ Sbjct: 61 GATKYTPTPGVKALRIAVQRKLRQENHLDYPLESIVIANGAKQIIFNAFAATLDDGDQVL 120 Query: 121 VAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGA 180 V P + ++ G V + G ++ AE++ I RTR + LN P NPSGA Sbjct: 121 VPTPYWPSFPDSVRFNGGEPVFIECGLAQGCKLTAEQLEQYIGERTRWLILNGPGNPSGA 180 Query: 181 SLPRATWEALAELCMAH-DLWMISDEVYSELLFDGEHVSP--ASLPGMADRTATLNSLSK 237 A +ALAE+ H + ++ DE+Y + FDG + P + R + +SK Sbjct: 181 VYSAAELQALAEVLRRHPQVLILLDELYEHIRFDGRPAQSLLSVAPDLQSRCLLVGGVSK 240 Query: 238 SHAMTGWRVGWVVGPAALCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYR 297 ++AMTGWR+G+ GP AL + + G+ Q AA A + L L + AY+ Sbjct: 241 TYAMTGWRIGFGAGPQALANAMTVVQSQSTSGASSVGQAAALAAFDGGLDFLRSQVAAYQ 300 Query: 298 RRRDLVIECLADSPGLRPLRPDGGMFVMV-------DIRPTGLSAQAFAD--RLLDRHGV 348 +RRDL++ L GL L P GG FV + RP G Q AD L GV Sbjct: 301 QRRDLLVSALRKVDGLEVLEPQGGFFVFIRCAGLLGRYRPDGQRLQTDADVVAYLLEEGV 360 Query: 349 SVLAGEAFGPSAAGHIRLGLVLGAEPLREACRRIALCAAELLGQ 392 + +AG A+G S RL + E + EA RRIA +L G+ Sbjct: 361 AGVAGSAYGLSP--WFRLSIATATETVAEAGRRIAQACGQLRGE 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: 424 Number of extensions: 20 Number of successful extensions: 2 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