Align valine-pyruvate transaminase (EC 2.6.1.66) (characterized)
to candidate WP_028585523.1 G494_RS0117340 valine--pyruvate transaminase
Query= BRENDA::P09053 (417 letters) >NCBI__GCF_000429965.1:WP_028585523.1 Length = 418 Score = 447 bits (1151), Expect = e-130 Identities = 211/416 (50%), Positives = 292/416 (70%), Gaps = 1/416 (0%) Query: 1 MTFSLFGDKFTRHSGITLLMEDLNDGLRTPGAIMLGGGNPAQIPEMQDYFQTLLTDMLES 60 M S FG+K + +GI LM+DL + + IM+GGGNP QIP +Q+ + L+++L Sbjct: 1 MKISRFGEKISGDAGILSLMDDLGNAMAEGNMIMMGGGNPGQIPAIQEVIREQLSELLHD 60 Query: 61 GKATDALCN-YDGPQGKTELLTLLAGMLREKLGWDIEPQNIALTNGSQSAFFYLFNLFAG 119 +A + L YD P G+ E + LA +LR + WDI P NI LTNGSQ+AFF LFNLF G Sbjct: 61 EEALNRLVGVYDPPGGEKEFIAALAELLRREYDWDISPANICLTNGSQTAFFLLFNLFGG 120 Query: 120 RRADGRVKKVLFPLAPEYIGYADAGLEEDLFVSARPNIELLPEGQFKYHVDFEHLHIGEE 179 R ADG KK+L P+APEYIGYAD G+++DLFV+ RP IE + E FKY VDF ++ I +E Sbjct: 121 RYADGSQKKILLPMAPEYIGYADLGIDDDLFVAVRPRIECVGENLFKYRVDFSNITITDE 180 Query: 180 TGMICVSRPTNPTGNVITDEELLKLDALANQHGIPLVIDNAYGVPFPGIIFSEARPLWNP 239 G ICVSRPTNPTGNV+TD+E+ L ALA +H IPL++D+AYGVPFP +IF+EARP+WN Sbjct: 181 IGAICVSRPTNPTGNVLTDDEIQGLAALAREHQIPLIVDSAYGVPFPNMIFTEARPIWNQ 240 Query: 240 NIVLCMSLSKLGLPGSRCGIIIANEKIITAITNMNGIISLAPGGIGPAMMCEMIKRNDLL 299 ++VL MSLSK GLP R GI+IA E +I+ ++ MN ++SLAPG G + +++ ++L Sbjct: 241 DLVLTMSLSKFGLPAVRTGIVIAAEPVISMLSGMNAVVSLAPGSFGAMLTTPLLRSGEIL 300 Query: 300 RLSETVIKPFYYQRVQETIAIIRRYLPENRCLIHKPEGAIFLWLWFKDLPITTKQLYQRL 359 RLS VIKP+Y ++++ +A+I +H PEGA+FLW WF DLPIT+++LY+RL Sbjct: 301 RLSREVIKPYYQEKMERVMAVINEAFSGCPYKVHIPEGAMFLWFWFPDLPITSRELYERL 360 Query: 360 KARGVLMVPGHNFFPGLDKPWPHTHQCMRMNYVPEPEKIEAGVKILAEEIERAWAE 415 K R VL+V G FFPGL+ W H +C+R+NY + ++ G++++AEEI +AE Sbjct: 361 KGRKVLVVAGDYFFPGLEPGWRHIDECIRVNYSQDEAEVHQGIRLIAEEIRTIYAE 416 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: 540 Number of extensions: 18 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: 417 Length of database: 418 Length adjustment: 32 Effective length of query: 385 Effective length of database: 386 Effective search space: 148610 Effective search space used: 148610 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