Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate 3607113 Dshi_0535 Transketolase central region (RefSeq)
Query= metacyc::MONOMER-11684 (327 letters) >FitnessBrowser__Dino:3607113 Length = 327 Score = 244 bits (622), Expect = 3e-69 Identities = 131/321 (40%), Positives = 197/321 (61%), Gaps = 3/321 (0%) Query: 5 SYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIA 64 +Y DA+ LA+ E M +D V V+GE+VGR GG + T L ++FG ERV+DTP++E+AI Sbjct: 7 TYRDALRLALSEAMTKDENVIVMGEEVGRYGGAYGVTKDLIKEFGPERVIDTPISEAAIV 66 Query: 65 GVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVH 124 G +GAAM G+RP+AE+ + DFI ++Q+ ++AAKIRY P+V+R G G Sbjct: 67 GAAVGAAMTGLRPVAELMYVDFIGMTMDQLANQAAKIRYMFGGQIGVPMVLRTQGGTGRS 126 Query: 125 GALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLIKGEV 184 HSQS+E + PGL++ MP+T DA LL+ +++ DPV+F EHK Y + KG + Sbjct: 127 AGAQHSQSLEGYIMHTPGLRLAMPATVEDAYHLLRQSLQQPDPVVFIEHKGLYTM-KGAL 185 Query: 185 PADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLE-KDGISAHVVDLRTVYPLD 243 D G+A V REGDD+ ++TY VH AL+AAE L GI+ VVDLRT+ PLD Sbjct: 186 DPDAAPAGWGEATVLREGDDLVIVTYSRQVHHALEAAETLAGAHGINVTVVDLRTLNPLD 245 Query: 244 KEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMPYA 303 + I G+ ++V+E + +E++A I+E C L+ P+ R+AG DIP + + Sbjct: 246 FDTIRPLVEAAGRAMVVSEGVMTCGVAAELSARITEECFDFLEEPVVRVAGEDIP-ISVS 304 Query: 304 PTMEKYFMVNPDKVEAAMREL 324 P +E+ + P+ + R++ Sbjct: 305 PLLEQNSVPTPELIVDIARKM 325 Lambda K H 0.319 0.136 0.392 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: 316 Number of extensions: 11 Number of successful extensions: 3 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: 327 Length of database: 327 Length adjustment: 28 Effective length of query: 299 Effective length of database: 299 Effective search space: 89401 Effective search space used: 89401 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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