Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate GFF2657 PS417_13545 arginine aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__WCS417:GFF2657 Length = 664 Score = 398 bits (1022), Expect = e-115 Identities = 202/392 (51%), Positives = 265/392 (67%) Query: 1 MRYSDFTQRIAGDGAAAWDIHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLA 60 MR+S F +RIAG G AAWDIH+ A QGE+I++LSVGDPDF TP+ I AA+ +L Sbjct: 1 MRFSPFVERIAGQGVAAWDIHHAAFQAASQGEDIIILSVGDPDFATPSFITDAAVSALRE 60 Query: 61 GNTHYADVRGKRALRQRIAERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVI 120 G+THY ++ G+ ALR+ IA R+ + +A+ AE V+ +AGAQ AL+ CLL GDEV+ Sbjct: 61 GDTHYTEIPGRPALREAIAARYSKTLARALSAENVITVAGAQNALFVTSLCLLQAGDEVL 120 Query: 121 VAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGA 180 V +PMYVTYEA A GA +V VP E+GFR+ A+ + A ITPRTRA+ ++P+NP+G Sbjct: 121 VLDPMYVTYEATLKASGATLVRVPCSPESGFRLDAQLLGAAITPRTRAIFFSNPNNPTGV 180 Query: 181 SLPRATWEALAELCMAHDLWMISDEVYSELLFDGEHVSPASLPGMADRTATLNSLSKSHA 240 L +A+A+L +A DLW++ DEVY L+FDGE+ S A+LPGMA+R + SLSKSHA Sbjct: 181 VLNLQELQAIADLAIARDLWVVVDEVYESLVFDGEYHSLAALPGMAERCVVIGSLSKSHA 240 Query: 241 MTGWRVGWVVGPAALCAHLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRR 300 MTGWR+GW++ + AH E L L MLYG P F+ +AA A+ A + MRE YRRRR Sbjct: 241 MTGWRIGWIIATPQMVAHAETLVLSMLYGLPGFVMEAATAAVLAHDDVTQGMREIYRRRR 300 Query: 301 DLVIECLADSPGLRPLRPDGGMFVMVDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSA 360 DLV+ L+ PG++ P GMFV+VD+R TGL + FA RL GVSVL AFG A Sbjct: 301 DLVMAGLSACPGIKVQAPQAGMFVLVDVRGTGLGSLDFAWRLFREAGVSVLDAAAFGAPA 360 Query: 361 AGHIRLGLVLGAEPLREACRRIALCAAELLGQ 392 G +RL LG E L EAC+RIA A+L G+ Sbjct: 361 QGFVRLSFTLGEERLSEACQRIAHFVAKLAGE 392 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: 710 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: 664 Length adjustment: 34 Effective length of query: 359 Effective length of database: 630 Effective search space: 226170 Effective search space used: 226170 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