Align valine-pyruvate transaminase (EC 2.6.1.66) (characterized)
to candidate GFF1326 HP15_1296 valine-pyruvate transaminase
Query= BRENDA::P09053 (417 letters) >FitnessBrowser__Marino:GFF1326 Length = 425 Score = 438 bits (1126), Expect = e-127 Identities = 208/421 (49%), Positives = 291/421 (69%), Gaps = 5/421 (1%) Query: 1 MTFSLFGDKFTRHSGITLLMEDLNDGLRT-PGAIMLGGGNPAQIPEMQDYFQTLLTDMLE 59 M S FG KFT +GIT LM+DL + + + IM+GGGNP IPE+Q Q +L DM Sbjct: 1 MKLSAFGRKFTADAGITSLMDDLGNAMASGDDMIMMGGGNPGHIPEIQQRVQEILADMSR 60 Query: 60 S-GKATDALCNYDGPQGKTELLTLLAGMLREKLGWDIEPQNIALTNGSQSAFFYLFNLFA 118 + G + YD PQG+ + + LA +L + GW ++P+NIALTNGSQ+AFF LFN+F Sbjct: 61 NEGDVRRLVGIYDPPQGEKQFIASLAELLNREYGWGLKPENIALTNGSQAAFFMLFNMFG 120 Query: 119 GRRADGRVKKVLFPLAPEYIGYADAGLEEDLFVSARPNIELLPEGQFKYHVDFEHLHIGE 178 G DG K +L PLAPEYIGYADAG+E LF + +P+I +FKY VDF+ + + Sbjct: 121 GDYGDGNRKHILLPLAPEYIGYADAGIEPGLFHAVQPDISFTDAHEFKYRVDFDAVEVTG 180 Query: 179 ETGMICVSRPTNPTGNVITDEELLKLDALANQHGIPLVIDNAYGVPFPGIIFSEARPLWN 238 ETG ICVSRPTNPTGNV+TDEEL +L+ LA QH IPL++D AYG PFP ++F +A P WN Sbjct: 181 ETGAICVSRPTNPTGNVVTDEELARLEELARQHDIPLIVDGAYGTPFPSLLFVDAAPTWN 240 Query: 239 PNIVLCMSLSKLGLPGSRCGIIIANEKIITAITNMNGIISLAPGGIGPAMMCEMIKRNDL 298 I+LC+SLSKLGLP +R GI+IA E +I A++ +N I++LA G G + +++ ++ Sbjct: 241 DQIILCLSLSKLGLPAARTGIVIAAEPVIKALSGINAIMNLATGSFGAMLAEPLVRSGEI 300 Query: 299 LRLSETVIKPFYYQRVQETIAIIRRYLPENRC--LIHKPEGAIFLWLWFKDLPITTKQLY 356 L LS V+ PFY +++ ++ R + E+ C +HKPEGA+FLWLWF DLPI++ +LY Sbjct: 301 LSLSRDVVCPFYKAKMERAVSAFREAMGEDSCRWYVHKPEGAMFLWLWFPDLPISSLELY 360 Query: 357 QRLKARGVLMVPGHNFFPGL-DKPWPHTHQCMRMNYVPEPEKIEAGVKILAEEIERAWAE 415 QRLK+RGVL+V GH FFPGL + W H H+C+R+ Y + +++ G++I+A+E++ W E Sbjct: 361 QRLKSRGVLVVSGHYFFPGLPEDGWRHRHECLRVTYSQDDDRVAEGLRIIADEVKAVWRE 420 Query: 416 S 416 + Sbjct: 421 A 421 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: 529 Number of extensions: 22 Number of successful extensions: 5 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: 425 Length adjustment: 32 Effective length of query: 385 Effective length of database: 393 Effective search space: 151305 Effective search space used: 151305 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