Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate GFF1390 Psest_1427 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit
Query= metacyc::MONOMER-11684 (327 letters) >FitnessBrowser__psRCH2:GFF1390 Length = 340 Score = 265 bits (676), Expect = 2e-75 Identities = 139/316 (43%), Positives = 204/316 (64%), Gaps = 9/316 (2%) Query: 13 AMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIAGVGIGAAM 72 A+ +EM D +VFV+GED+G+ GGVF T GLYE+FG+ R+ DTP++E+A G +GAA Sbjct: 19 AVAQEMRLDPKVFVMGEDIGQLGGVFGNTRGLYEEFGKTRIRDTPISETAFIGAAVGAAS 78 Query: 73 YGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVHGALYHSQS 132 GMRPI E+ F DF ++ I + AK Y S P+V+ A G G A HSQ Sbjct: 79 DGMRPIVELMFVDFFGVCMDAIYNLMAKNTYFSGGKVPVPMVLMASTGAGYSDAGQHSQC 138 Query: 133 VEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRL-----IKG---EV 184 + FA+ PG+K+V+PS YDAKGL+ AA+RD++PV++ HK + KG V Sbjct: 139 LYGTFAHLPGMKVVVPSNAYDAKGLMTAAIRDDNPVVYLFHKALQGMGWLGTEKGATVPV 198 Query: 185 PADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYPLDK 244 P + Y++ IGKA REG D+++++ G VH AL+AA +LEKDG+SA V+DLR++ PLD+ Sbjct: 199 PEEPYIVEIGKAKTVREGRDVSLVSLGAGVHHALRAAAQLEKDGVSAEVIDLRSLVPLDR 258 Query: 245 EAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMPYAP 304 E +I + KTG+++++ ED + E+ A + EH + L A +R+A PDIP +P+ P Sbjct: 259 EHVIASVRKTGRLIVIDEDYHSFGVSGEIIASVVEHDIGMLKARPQRVAFPDIP-IPFTP 317 Query: 305 TMEKYFMVNPDKVEAA 320 ME++ + N DK+ AA Sbjct: 318 VMEQWALPNADKIVAA 333 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: 297 Number of extensions: 16 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: 340 Length adjustment: 28 Effective length of query: 299 Effective length of database: 312 Effective search space: 93288 Effective search space used: 93288 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: 49 (23.5 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