Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate H281DRAFT_04024 H281DRAFT_04024 Aspartate/methionine/tyrosine aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >FitnessBrowser__Burk376:H281DRAFT_04024 Length = 399 Score = 183 bits (464), Expect = 9e-51 Identities = 120/359 (33%), Positives = 172/359 (47%), Gaps = 9/359 (2%) Query: 31 GEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAV 90 G +I+ + +G+PDF P P+++AA ++L G T Y G ALR+ I+ + G V Sbjct: 37 GRDIIHMGIGEPDFTAPEPVIEAAANALRRGVTQYTSALGLHALREAISAHYAEVYGVNV 96 Query: 91 DAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENG 150 D ++VV AGA AL L++ DEV++ +P Y A + V VP Sbjct: 97 DPARIVVTAGASAALLLACAALVDRDDEVLMPDPCYPCNRHFVIAAEGKPVMVPSGPAER 156 Query: 151 FRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSEL 210 F++ A +V L RTR + L SP NP+G S+ A E + + A + I DE+Y L Sbjct: 157 FQLTAADVERLWNERTRGVLLASPSNPTGTSIEPAELERIVKAVRARGGFTIVDEIYQGL 216 Query: 211 LFDGEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGS 270 +D + VS S D T+NS SK MTGWR+GW+V P + + E LA + + Sbjct: 217 SYDAKPVSALS---YGDDVITVNSFSKYFNMTGWRLGWLVVPPGMVSAFEKLAQNLFICA 273 Query: 271 PEFIQDAACTALE-APLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVDIR 329 Q AA E + EA R ++RRRD + L P+ PDG +V D R Sbjct: 274 SALAQHAALACFEPQTIATYEARRLEFKRRRDFIAPALESLGFTVPVMPDGAFYVYADCR 333 Query: 330 ----PTGLSAQAFADRLLDRHGVSVLAGEAFGPSA-AGHIRLGLVLGAEPLREACRRIA 383 P + A +L GV ++ G FG A +IRL E L EA R+A Sbjct: 334 SVAHPAAGDSSALTKAMLHEAGVVLVPGMDFGSHAPKQYIRLSYATAYEKLEEAVERLA 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: 418 Number of extensions: 27 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: 399 Length adjustment: 31 Effective length of query: 362 Effective length of database: 368 Effective search space: 133216 Effective search space used: 133216 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