Align valine-pyruvate transaminase (EC 2.6.1.66) (characterized)
to candidate BWI76_RS27065 BWI76_RS27065 valine--pyruvate transaminase
Query= BRENDA::P09053 (417 letters) >FitnessBrowser__Koxy:BWI76_RS27065 Length = 419 Score = 784 bits (2025), Expect = 0.0 Identities = 376/415 (90%), Positives = 397/415 (95%) Query: 1 MTFSLFGDKFTRHSGITLLMEDLNDGLRTPGAIMLGGGNPAQIPEMQDYFQTLLTDMLES 60 MTFSLFGDKFTRHSGIT LMEDLNDGLRTPGAIMLGGGNPAQIPEM DYF +LL DML S Sbjct: 1 MTFSLFGDKFTRHSGITRLMEDLNDGLRTPGAIMLGGGNPAQIPEMNDYFHSLLADMLNS 60 Query: 61 GKATDALCNYDGPQGKTELLTLLAGMLREKLGWDIEPQNIALTNGSQSAFFYLFNLFAGR 120 GKA DALCNYDGPQGK+ELLTLLA MLR++LGW+IEPQNIALTNGSQSAFFYLFNLFAGR Sbjct: 61 GKALDALCNYDGPQGKSELLTLLAQMLRDELGWEIEPQNIALTNGSQSAFFYLFNLFAGR 120 Query: 121 RADGRVKKVLFPLAPEYIGYADAGLEEDLFVSARPNIELLPEGQFKYHVDFEHLHIGEET 180 RADG +KVLFPL PEYIGYAD+GLEEDLFV+ RPNIELLPEGQFKYHVDFEHL + +ET Sbjct: 121 RADGTTRKVLFPLTPEYIGYADSGLEEDLFVATRPNIELLPEGQFKYHVDFEHLQVTDET 180 Query: 181 GMICVSRPTNPTGNVITDEELLKLDALANQHGIPLVIDNAYGVPFPGIIFSEARPLWNPN 240 GMICVSRPTNPTGNVITD+EL+KLDALANQHGIPLVIDNAYGVPFPGIIFS+ARPLWNPN Sbjct: 181 GMICVSRPTNPTGNVITDDELIKLDALANQHGIPLVIDNAYGVPFPGIIFSDARPLWNPN 240 Query: 241 IVLCMSLSKLGLPGSRCGIIIANEKIITAITNMNGIISLAPGGIGPAMMCEMIKRNDLLR 300 IVLCMSLSKLGLPGSRCGIIIANEKIITAI+NMNGIISLAPGG+GPAMMCEMIKRNDLLR Sbjct: 241 IVLCMSLSKLGLPGSRCGIIIANEKIITAISNMNGIISLAPGGMGPAMMCEMIKRNDLLR 300 Query: 301 LSETVIKPFYYQRVQETIAIIRRYLPENRCLIHKPEGAIFLWLWFKDLPITTKQLYQRLK 360 LSETVIKPFYYQRVQETIAIIRRYLPE+RCLIHKPEGAIFLWLWFKDLPI+T+ LYQRLK Sbjct: 301 LSETVIKPFYYQRVQETIAIIRRYLPEDRCLIHKPEGAIFLWLWFKDLPISTELLYQRLK 360 Query: 361 ARGVLMVPGHNFFPGLDKPWPHTHQCMRMNYVPEPEKIEAGVKILAEEIERAWAE 415 RGVLMVPG FFPGLDKPWPHTHQCMRMNYVP+PEKIEAGV+ILAEE+ERAW E Sbjct: 361 KRGVLMVPGDYFFPGLDKPWPHTHQCMRMNYVPDPEKIEAGVRILAEEVERAWRE 415 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: 758 Number of extensions: 18 Number of successful extensions: 1 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: 419 Length adjustment: 32 Effective length of query: 385 Effective length of database: 387 Effective search space: 148995 Effective search space used: 148995 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 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