Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate AZOBR_RS07830 AZOBR_RS07830 aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__azobra:AZOBR_RS07830 Length = 424 Score = 175 bits (444), Expect = 2e-48 Identities = 121/364 (33%), Positives = 179/364 (49%), Gaps = 13/364 (3%) Query: 31 GEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTH-YADVRGKRALRQRIAERHRRRSGQA 89 GE+I+ L +G+PD TP IV I+++ TH Y++ RG LR+ A ++RR Sbjct: 31 GEDIIDLGMGNPDQPTPQHIVDKLIEAVRDPKTHRYSNSRGIPGLRKAHAAYYKRRFNVD 90 Query: 90 VDAE-QVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSE 148 VD E + +V G++ L + Q + +PGD ++V P Y + F GA V +PV Sbjct: 91 VDPESECIVTIGSKEGLANLAQAITSPGDIILVPNPSYPIHPFGFILAGASVRHLPVGQA 150 Query: 149 NG-------FRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWM 201 NG F + E P+ A+ LN P NP+ + + + E C H +++ Sbjct: 151 NGTSTDIDSFMIMLERAVRHSVPKPLALVLNYPSNPTAEVVGLDFYRPIVEFCRKHGIYI 210 Query: 202 ISDEVYSELLFDGEHV-SPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLE 260 +SD Y+E+ FDGE S +P + S+SK+++M GWR+G+ G L L Sbjct: 211 LSDLAYAEVFFDGEPPPSILEIPEAREVAVEFTSMSKTYSMAGWRIGFATGNKKLITALA 270 Query: 261 NLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDG 320 + + YG+ IQ AA AL P +E +R YR+RRD++IE LA S G P Sbjct: 271 RIKSYLDYGAFTPIQVAATAALNGPQECVEQVRTMYRQRRDVMIEGLA-SAGWTVPSPSA 329 Query: 321 GMFVMVDIRP--TGLSAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGLVLGAEPLREA 378 MF I L + F+ LL V+V G FG GH+RL LV +R+A Sbjct: 330 SMFAWAPIPEPFAHLGSLEFSKLLLQEAKVAVAPGIGFGEYGDGHVRLALVENVHRIRQA 389 Query: 379 CRRI 382 R I Sbjct: 390 TRNI 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: 391 Number of extensions: 19 Number of successful extensions: 5 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: 424 Length adjustment: 31 Effective length of query: 362 Effective length of database: 393 Effective search space: 142266 Effective search space used: 142266 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