Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate WP_086510442.1 BZY95_RS13490 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::Q9HUI9 (393 letters) >NCBI__GCF_002151265.1:WP_086510442.1 Length = 386 Score = 195 bits (495), Expect = 2e-54 Identities = 131/365 (35%), Positives = 185/365 (50%), Gaps = 13/365 (3%) Query: 24 ALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHR 83 A AR G +++ L VG+PDF TP P+V A +L AG T Y+ G ALR+ IA + Sbjct: 22 AQAREAAGHDVIHLEVGEPDFATPEPVVAAGQAALAAGLTRYSPAAGLPALREAIAGHYG 81 Query: 84 RRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPV 143 G VD +V+V GA AL Q L+ PGD V++A+P Y GA V V Sbjct: 82 EHFGADVDPRRVLVTPGASGALLLASQLLVGPGDRVLMADPNYPCNRHFMALAGAEVDTV 141 Query: 144 PVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMIS 203 P+ ++G+++ A VA TR L +P NP+G L A +A+A+ A ++ Sbjct: 142 PIGPQSGWQLDANLVARHWQDATRLAMLATPSNPTGHMLDAAQLKAVADTVAARGGHLLV 201 Query: 204 DEVYSELLFDGEHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLA 263 DE+Y L +D ++P S+ + +NS SK MTGWR+GW++ P A L LA Sbjct: 202 DEIYQGLSYD---IAPLSVASLTADAFVVNSFSKYFGMTGWRLGWLLAPQAAVEPLTRLA 258 Query: 264 LCMLYGSPEFIQDAACTALEAPLPELEAMREAYR----RRRDLVIECLADSPGLRP-LRP 318 + +P Q A AL A PE A+ EA R RRRD ++ LA GL P L P Sbjct: 259 QNVFLAAPTPAQHA---ALAAFTPECRALLEARRSELGRRRDALLAGLA-RLGLAPSLPP 314 Query: 319 DGGMFVMVDIRPTGLSAQAFADRLLDRHGVSVLAGEAFGPSAAG-HIRLGLVLGAEPLRE 377 G ++ +DI +QAF RLL+ V++ G F + H+R+ G E L E Sbjct: 315 QGAFYLWLDISRYSRDSQAFCQRLLEEENVAITPGIDFAVTGGEYHVRIAFTTGIERLEE 374 Query: 378 ACRRI 382 A R+ Sbjct: 375 AVSRL 379 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: 446 Number of extensions: 24 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: 386 Length adjustment: 30 Effective length of query: 363 Effective length of database: 356 Effective search space: 129228 Effective search space used: 129228 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 Apr 09 2024. 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