Align valine-pyruvate transaminase (EC 2.6.1.66) (characterized)
to candidate Synpcc7942_2258 Synpcc7942_2258 valine--pyruvate transaminase
Query= BRENDA::P09053 (417 letters) >FitnessBrowser__SynE:Synpcc7942_2258 Length = 427 Score = 310 bits (794), Expect = 5e-89 Identities = 157/419 (37%), Positives = 242/419 (57%), Gaps = 4/419 (0%) Query: 2 TFSLFGDKFTRHSGITLLMEDLNDGLRTPGA---IMLGGGNPAQIPEMQDYFQTLLTDML 58 + S +G + ++ +G+ +M+D+ + LR+ I L GNP +PE++ ++ D+L Sbjct: 5 SLSRYGRQMSQLTGVRAIMKDIIETLRSGQGQTFINLSAGNPVVLPEVEQLWRDCTADLL 64 Query: 59 ESGKATDALCNYDGPQGKTELLTLLAGMLREKLGWDIEPQNIALTNGSQSAFFYLFNLFA 118 S + + Y QG L+ + ++ GW I +NI +T GSQS +F N F Sbjct: 65 GSAEYGQVVGRYGTSQGYEPLIAAIIQEFNQRYGWSISDRNILITPGSQSLYFLAANAFG 124 Query: 119 GRRADGRVKKVLFPLAPEYIGYADAGLEEDLFVSARPNIELLPEGQFKYHVDFEHLHIGE 178 G DG ++K+L PL+P+Y GY LE V+ARP IE + + +FKY DFE L IG Sbjct: 125 GWAEDGSLRKILLPLSPDYTGYGGVCLEPQAVVAARPQIERIGDHRFKYRPDFEQLQIGA 184 Query: 179 ETGMICVSRPTNPTGNVITDEELLKLDALANQHGIPLVIDNAYGVPFPGIIFSEARPLWN 238 +TGM+ SRP NPTGNVI+D EL +L LA +P+ +D+AY PFPG+ F+E P + Sbjct: 185 DTGMLLFSRPCNPTGNVISDAELERLATLAAAQNVPVFVDSAYAPPFPGLNFTEMTPFFG 244 Query: 239 PNIVLCMSLSKLGLPGSRCGIIIANEKIITAITNMNGIISLAPGGIGPAMMCEMIKRNDL 298 NIV C+SLSK GLPG R GI I E +I + + + G A+ I L Sbjct: 245 DNIVHCLSLSKAGLPGERLGIAIGPEPVIQVLEAFQTNLCIHSSRYGQAIAARAIASGQL 304 Query: 299 LRLSETVIKPFYYQRVQETIAIIRRYLPEN-RCLIHKPEGAIFLWLWFKDLPITTKQLYQ 357 ++ETVI+P+Y + + LP++ +H+ EG IF WLW ++ P+ Q+YQ Sbjct: 305 TAIAETVIRPYYAAKFARVERQLDALLPDSLPWRLHQGEGGIFAWLWLEEAPLDDWQIYQ 364 Query: 358 RLKARGVLMVPGHNFFPGLDKPWPHTHQCMRMNYVPEPEKIEAGVKILAEEIERAWAES 416 +LK GV++VPG +FFPGL + W HT QC+R++ E ++E G++ LA +++ + ++ Sbjct: 365 QLKQAGVIVVPGSSFFPGLREDWVHTRQCLRISLAAEDHELETGMERLATTVQQIYRQA 423 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: 489 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: 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 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