Align valine-pyruvate transaminase (EC 2.6.1.66) (characterized)
to candidate WP_011317937.1 AVA_RS05535 valine--pyruvate transaminase
Query= BRENDA::P09053 (417 letters) >NCBI__GCF_000204075.1:WP_011317937.1 Length = 427 Score = 296 bits (757), Expect = 1e-84 Identities = 149/412 (36%), Positives = 240/412 (58%), Gaps = 5/412 (1%) Query: 7 GDKFTRHSGITLLMEDLNDGLRTPGA---IMLGGGNPAQIPEMQDYFQTLLTDMLESGKA 63 GD+ + +G+ +M+D+ + L++ G I L GNP +PE++ ++ ++L S + Sbjct: 9 GDQMSNLTGVRAIMKDIIETLKSGGGQDLINLSAGNPLILPEVEQLWRDCTAELLASQEY 68 Query: 64 TDALCNYDGPQGKTELLTLLAGMLREKLGWDIEPQNIALTNGSQSAFFYLFNLFAGRRAD 123 + +C Y QG L+ + + G ++ +N+ +T GSQ+ +FY N+F G + Sbjct: 69 GEVVCRYGSSQGYAPLIEAVVKDFNRRYGLNLTDRNVLITPGSQTLYFYAANVFGGYTGN 128 Query: 124 GRVKKVLFPLAPEYIGYADAGLEEDLFVSARPNIEL-LPEGQFKYHVDFEHLHIGEETGM 182 G +K+++ PL+P+Y GY L + V+ +P++++ FKY DF + I E TG Sbjct: 129 GDLKQIVLPLSPDYTGYGGICLVPEALVAYKPSLDIDAAAHSFKYRPDFSQVSISESTGC 188 Query: 183 ICVSRPTNPTGNVITDEELLKLDALANQHGIPLVIDNAYGVPFPGIIFSEARPLWNPNIV 242 + SRP NPTGNV+TD+E+ K+ ALA + +P++ID+AY PFP + F++ ++ NI+ Sbjct: 189 VIFSRPCNPTGNVLTDDEVRKIAALAAPYNVPVLIDSAYAPPFPALNFTDMSLIFGENIL 248 Query: 243 LCMSLSKLGLPGSRCGIIIANEKIITAITNMNGIISLAPGGIGPAMMCEMIKRNDLLRLS 302 C SLSK GLPG R GI I NE++I + + SL G A+ I L +++ Sbjct: 249 HCTSLSKAGLPGERIGIAIGNERLIQVLESFQTNASLHSSRYGQAIAARAINSGALAQIA 308 Query: 303 ETVIKPFYYQRVQETIAIIRRYLP-ENRCLIHKPEGAIFLWLWFKDLPITTKQLYQRLKA 361 E VI+PFY + + +P E +H+ EGAIF WLW +DLPIT +LYQ LK Sbjct: 309 EQVIRPFYQNKFAIVENALEAAMPKELPWFLHRGEGAIFSWLWLQDLPITDWELYQELKK 368 Query: 362 RGVLMVPGHNFFPGLDKPWPHTHQCMRMNYVPEPEKIEAGVKILAEEIERAW 413 GV++VPG FFPGL + W H HQC+R++ +I G++ LA+ +E+ + Sbjct: 369 VGVIVVPGSTFFPGLKEEWAHKHQCVRISLTGSDTEIALGMQRLAKAVEQVY 420 Lambda K H 0.322 0.141 0.437 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: 479 Number of extensions: 18 Number of successful extensions: 4 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: 417 Length of database: 427 Length adjustment: 32 Effective length of query: 385 Effective length of database: 395 Effective search space: 152075 Effective search space used: 152075 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 10 2024. The underlying query database was built on Apr 09 2024.
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