Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate Echvi_1750 Echvi_1750 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit
Query= metacyc::MONOMER-11684 (327 letters) >FitnessBrowser__Cola:Echvi_1750 Length = 661 Score = 271 bits (694), Expect = 3e-77 Identities = 140/305 (45%), Positives = 198/305 (64%), Gaps = 6/305 (1%) Query: 7 IDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIAGV 66 +DAI+ ++ M + S + ++G+D+G GG FK TAG +FG ERV +TPL ESAI G Sbjct: 348 VDAISDGLRLSMRQFSNLVLMGQDIGEYGGAFKVTAGFLSEFGAERVRNTPLCESAIIGA 407 Query: 67 GIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVHGA 126 +G ++ G + + EMQFADF+ NQI++ AK+ YR +V+R P G GV Sbjct: 408 ALGLSVKGFKSVVEMQFADFVSCGFNQIVNNLAKVHYRWGQH--ADVVIRMPTGAGVGAG 465 Query: 127 LYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLIKGEVPA 186 +HSQS EA F + PGLKI+ PS+P DAKGLL AA+ D +P LFFEHK YR + G+VP Sbjct: 466 PFHSQSNEAWFFHTPGLKILYPSSPQDAKGLLAAAIEDPNPCLFFEHKALYRSVIGQVPD 525 Query: 187 DDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYPLDKEA 246 + Y + IGKA + +EGD TV+TYG+ VH+A + E L+ + ++DLRT+ P DKEA Sbjct: 526 EYYTVEIGKAHLVKEGDQATVVTYGMGVHWAKRVMESLD---VRVDLLDLRTLLPWDKEA 582 Query: 247 IIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMPYAPTM 306 + ++ KT KV+++ ED G I +E+AA ISEHC LDAP+ R D P +P+A + Sbjct: 583 VEKSVKKTNKVMILHEDCLTGGIGAEIAAWISEHCFECLDAPVMREGSLDTP-VPFAANL 641 Query: 307 EKYFM 311 E+ F+ Sbjct: 642 EENFL 646 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: 518 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 327 Length of database: 661 Length adjustment: 33 Effective length of query: 294 Effective length of database: 628 Effective search space: 184632 Effective search space used: 184632 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: 51 (24.3 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