Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate 3607759 Dshi_1168 aminotransferase class I and II (RefSeq)
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Dino:3607759 Length = 391 Score = 157 bits (396), Expect = 6e-43 Identities = 120/355 (33%), Positives = 161/355 (45%), Gaps = 10/355 (2%) Query: 31 GEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAV 90 G I+ + VG P P P +A L Y G LR+ IA + R G + Sbjct: 28 GRHIIHMEVGQPGTAAPLPARRAVAAQLDQDAMGYTVALGLPELRRAIAGLYARWYGVDL 87 Query: 91 DAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENG 150 D +VVV +G+ A + G V VAEP Y +Y + A V +P + E G Sbjct: 88 DPARVVVTSGSSAAFLLAFTTYFDAGARVGVAEPGYPSYRQILKALSLAPVGLPTQPETG 147 Query: 151 FRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSEL 210 R+ AE AL + SP+NP+G L R AL C D ISDE+Y L Sbjct: 148 HRMTAE---ALAQADIAGAIIASPNNPTGTMLDRDGLGALIAACRDRDRVFISDEIYHGL 204 Query: 211 LFDGEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGS 270 + VS + +D +NS SK +MTGWR+GW+V P A +E LA M + Sbjct: 205 HYGDRAVSALEI---SDDVCVINSFSKYFSMTGWRIGWLVVPEAQVRVVERLAQNMFICA 261 Query: 271 PEFIQDAACTAL-EAPLPELEAMREAYRRRRDLVIECLADSPGLRPLR-PDGGMFVMVDI 328 P Q AA AL +A PELEA R Y R LVI+ L + GL PDG +V VD Sbjct: 262 PHVAQIAALGALGDAARPELEANRAVYAANRQLVIDGLR-AAGLDAFAPPDGAFYVYVDT 320 Query: 329 RPTGLSAQAFADRLLDRHGVSVLAGEAFGP-SAAGHIRLGLVLGAEPLREACRRI 382 ++ A +L++ GV+V G F P G +RL E + E R+ Sbjct: 321 GALSSDSRTLAADILEKAGVAVTPGLDFDPVRGHGTLRLSYARATEDIAEGMTRL 375 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: 375 Number of extensions: 32 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: 391 Length adjustment: 31 Effective length of query: 362 Effective length of database: 360 Effective search space: 130320 Effective search space used: 130320 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