Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate BPHYT_RS15405 BPHYT_RS15405 aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__BFirm:BPHYT_RS15405 Length = 398 Score = 179 bits (453), Expect = 2e-49 Identities = 123/369 (33%), Positives = 175/369 (47%), Gaps = 13/369 (3%) Query: 31 GEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAV 90 G +I+ + +G+PDF P P+++AA +L G T Y G ALR+ I+ + G V Sbjct: 37 GRDIIHMGIGEPDFTAPEPVIEAAASALRRGVTQYTSALGLHALREAISAHYADFYGVDV 96 Query: 91 DAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENG 150 D ++VV AGA AL L++ DEV++ +P Y A R V VP Sbjct: 97 DPARIVVTAGASAALLLACAALVDRDDEVLMPDPCYPCNRHFVIAAEGRPVMVPSGPAER 156 Query: 151 FRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSEL 210 F++ A +V L TR + L SP NP+G S+ A E + + A + I DE+Y L Sbjct: 157 FQLTAADVERLWNEHTRGVLLASPSNPTGTSIEPAELERIVKAVRARGGFTIVDEIYQGL 216 Query: 211 LFDGEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGS 270 +D + VS S D T+NS SK MTGWR+GW+V P + + E LA + + Sbjct: 217 SYDAKPVSALS---FGDDVITVNSFSKYFNMTGWRLGWLVVPPGMVSAFEKLAQNLFICA 273 Query: 271 PEFIQDAACTALE-APLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVDIR 329 Q AA E + EA R+ ++RRRD + L P+ PDG +V D R Sbjct: 274 SALAQHAALACFEPETIAIYEARRQEFKRRRDFIAPALESLGFSVPVMPDGAFYVYADCR 333 Query: 330 PTGLSA----QAFADRLLDRHGVSVLAGEAFGPSA-AGHIRLGLVLGAEPLREACRRIAL 384 SA A +L GV ++ G FG A +IRL L EA R+ Sbjct: 334 TVAHSAAGDSAALTKAMLHDAGVVLVPGMDFGTHAPKDYIRLSYATAYPKLEEAVDRL-- 391 Query: 385 CAAELLGQA 393 A+L G+A Sbjct: 392 --AKLFGKA 398 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: 430 Number of extensions: 28 Number of successful extensions: 3 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: 398 Length adjustment: 31 Effective length of query: 362 Effective length of database: 367 Effective search space: 132854 Effective search space used: 132854 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