Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate Synpcc7942_0143 Synpcc7942_0143 pyruvate/2-oxoglutarate dehydrogenase complex dehydrogenase (E1) component
Query= metacyc::MONOMER-11684 (327 letters) >FitnessBrowser__SynE:Synpcc7942_0143 Length = 326 Score = 279 bits (713), Expect = 8e-80 Identities = 148/317 (46%), Positives = 208/317 (65%), Gaps = 3/317 (0%) Query: 8 DAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIAGVG 67 +A+ A+ EEM RD VFVLGEDVG GG +K T LY+++G+ R++DTP+AE+ G+ Sbjct: 8 NALRAAIDEEMARDPNVFVLGEDVGHYGGSYKVTKDLYQKYGDFRLLDTPIAENGFTGMA 67 Query: 68 IGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVHGAL 127 +GAAM G+RPI E F++ A NQI + A +RY S +++ PIV R P G G Sbjct: 68 VGAAMTGLRPIVEGMNMGFLLLAFNQIANNAM-LRYTSGGNFTIPIVFRGPGGVGRQLGA 126 Query: 128 YHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLIKGEVPAD 187 HSQ +EA F PGLKIV STPY+AKGLLKAA+RD +PVLFFEH Y L K ++P + Sbjct: 127 EHSQRLEAYFHAVPGLKIVACSTPYNAKGLLKAAIRDNNPVLFFEHVLLYNL-KEDLPDE 185 Query: 188 DYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYPLDKEAI 247 +Y+ P+ KA++ R G D+TV+TY + LQA + LEK+G V+DL ++ P D EAI Sbjct: 186 EYICPLDKAEIVRPGKDVTVLTYSRMRYHCLQAVKTLEKEGFDPEVIDLISLKPFDFEAI 245 Query: 248 IEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMPYAPTME 307 + KT +V++V E K G I +E++A I E C +LDAP+ RL+ DIP PY +E Sbjct: 246 EASVRKTHRVVIVEECMKTGGIAAELSAAIMERCFDELDAPVVRLSSQDIPT-PYNGKLE 304 Query: 308 KYFMVNPDKVEAAMREL 324 +V P+++ AA+++L Sbjct: 305 NLTIVQPEQIVAAVKDL 321 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: 303 Number of extensions: 16 Number of successful extensions: 4 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: 326 Length adjustment: 28 Effective length of query: 299 Effective length of database: 298 Effective search space: 89102 Effective search space used: 89102 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