Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate AO353_28150 AO353_28150 arginine aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28150 Length = 667 Score = 396 bits (1018), Expect = e-115 Identities = 202/393 (51%), Positives = 265/393 (67%) Query: 1 MRYSDFTQRIAGDGAAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLA 60 MR+S F +RI+G G AAWDIH A +GE++++LSVGDPDF TP I AA+D+L Sbjct: 1 MRFSPFVERISGQGVAAWDIHNAAFDAQRRGEDVIILSVGDPDFPTPDFITDAAVDALRE 60 Query: 61 GNTHYADVRGKRALRQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVI 120 G+THY ++ G+ ALR+ IA R+ + G+ + A V+ +AGAQ AL+ CLL GDEV+ Sbjct: 61 GDTHYTEIAGRLALREAIAARYSQLFGRELQASNVINVAGAQNALFITSLCLLTAGDEVL 120 Query: 121 VAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGA 180 +PMYVTYEA A GA +V VP +++GFR+ A +A ITPRTRA+ L++P+NP+G Sbjct: 121 ALDPMYVTYEATLKASGATLVRVPCAADSGFRLDAAVLAKAITPRTRAIFLSNPNNPTGV 180 Query: 181 SLPRATWEALAELCMAHDLWMISDEVYSELLFDGEHVSPASLPGMADRTATLNSLSKSHA 240 L R +A+A+L + HDLW++ DEVY L F+ EH+S A+LPGMA+R + SLSKSHA Sbjct: 181 VLNREELQAIADLAITHDLWVVVDEVYESLAFEREHLSLAALPGMAERCVVIGSLSKSHA 240 Query: 241 MTGWRVGWVVGPAALCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRR 300 MTGWR+GW+V L AH E L L MLYG P F+ +AA A++A MRE YRRRR Sbjct: 241 MTGWRIGWIVADETLVAHAETLMLSMLYGLPGFVMEAALKAVQAHEEVTHGMREIYRRRR 300 Query: 301 DLVIECLADSPGLRPLRPDGGMFVMVDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSA 360 DLV++ L+D PG+ L PD GMFV+VD+R TGLS+ FA RLL VSVL AFG A Sbjct: 301 DLVVKGLSDCPGISVLTPDAGMFVLVDVRGTGLSSLEFAWRLLREARVSVLDAAAFGEPA 360 Query: 361 AGHIRLGLVLGAEPLREACRRIALCAAELLGQA 393 G +RL LG E L +AC+RI L G+A Sbjct: 361 QGFVRLSFTLGEERLAQACQRIRDFIQVLKGEA 393 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: 724 Number of extensions: 25 Number of successful extensions: 1 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: 667 Length adjustment: 35 Effective length of query: 358 Effective length of database: 632 Effective search space: 226256 Effective search space used: 226256 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: 52 (24.6 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