Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate WP_092483105.1 BM299_RS08755 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q9HUI9 (393 letters) >NCBI__GCF_900115975.1:WP_092483105.1 Length = 397 Score = 204 bits (520), Expect = 3e-57 Identities = 131/374 (35%), Positives = 195/374 (52%), Gaps = 13/374 (3%) Query: 20 IHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIA 79 I +A + +G +++ G+PDF TP I QA + ++ T Y V G LR+ I Sbjct: 18 IDAQAKKMIAEGIKVINFGAGEPDFGTPENIKQAGVKAIENDMTRYTPVAGIEPLRRAIV 77 Query: 80 ERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGAR 139 ++ +G + Q+VV AGA+ +LY Q L GDEVI+ P +V+Y GAR Sbjct: 78 KKLAEDNGLDYEPGQIVVSAGAKHSLYNAFQVLCQEGDEVILPAPYWVSYLEQIKLTGAR 137 Query: 140 VVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDL 199 V V R EN F++ +E+ ITP TR + LNSP NP+GA AL E+ + + Sbjct: 138 PVIVSTRVENNFKLTPDELRRAITPNTRLIVLNSPSNPTGAVYTGDELVALGEILEQNKI 197 Query: 200 WMISDEVYSELLFDG-EHVSPASL-PGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCA 257 +ISDE+Y +L++DG EHVS A+L PG+ + T +N +SKS+AMTGWR+G+ PA + Sbjct: 198 AVISDEIYEKLIYDGLEHVSIAALSPGLKELTVVINGVSKSYAMTGWRIGYAAAPAPVAK 257 Query: 258 HLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLR 317 + +L Q A+ ALE + M + +RRD ++E L PG+ R Sbjct: 258 AMADLQSHSTSNPTSIAQAASVEALEGTQEPVRQMVAEFVKRRDYMVERLNAMPGVNCNR 317 Query: 318 PDGGMFVMVDIRP------TGL---SAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGL 368 P G +V +I+P G+ SA A LL++ V+++ G AFG RL Sbjct: 318 PGGAFYVFPEIKPLLGKSYEGVKIDSASDLAKVLLEKAHVAIVPGIAFGDDTC--FRLSY 375 Query: 369 VLGAEPLREACRRI 382 + +RE RI Sbjct: 376 ATSMDNIREGLDRI 389 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: 404 Number of extensions: 17 Number of successful extensions: 2 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: 397 Length adjustment: 31 Effective length of query: 362 Effective length of database: 366 Effective search space: 132492 Effective search space used: 132492 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