Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate AZOBR_RS22250 AZOBR_RS22250 pyruvate dehydrogenase E1 component beta subunit
Query= metacyc::MONOMER-11684 (327 letters) >FitnessBrowser__azobra:AZOBR_RS22250 Length = 465 Score = 267 bits (683), Expect = 3e-76 Identities = 136/317 (42%), Positives = 204/317 (64%), Gaps = 3/317 (0%) Query: 8 DAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIAGVG 67 +A+ AM EEM RD VF++GE+V + G +K + GL ++FG +RV+DTP+ E AG+G Sbjct: 146 EALRDAMAEEMRRDPTVFLMGEEVAQYQGAYKVSQGLLQEFGADRVIDTPITEIGFAGLG 205 Query: 68 IGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVHGAL 127 +GAA G+RPI E +F + A++ I++ AAK Y S CPIV R P G A Sbjct: 206 VGAAFRGLRPIVEFMTFNFALQAIDHIVNSAAKTLYMSGGQMGCPIVFRGPNGAAARVAA 265 Query: 128 YHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLIKGEVP-A 186 HSQ +A+ PGLK+V P + D KGL+K+A+RD +PV+F E++ Y EVP + Sbjct: 266 QHSQDFTPWYASIPGLKVVAPYSASDFKGLMKSAIRDPNPVIFLENEILYGQ-SFEVPES 324 Query: 187 DDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYPLDKEA 246 +D+++PIG+A ++R G D+T+ + L V +AL AA+ LEKDGISA V+DLRT+ PLD E Sbjct: 325 EDFIVPIGRAKIRRAGTDVTITAHSLMVSYALAAADLLEKDGISAEVIDLRTIRPLDTET 384 Query: 247 IIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMPYAPTM 306 I+ + KT +++ V E I +E++A++ E LDAP+ R+ G D+P MPYA + Sbjct: 385 IVNSVKKTNRLVTVEEAWPTCGIGAELSALMMEQAFDYLDAPVIRVTGLDVP-MPYAANL 443 Query: 307 EKYFMVNPDKVEAAMRE 323 EK + +PD++ A ++ Sbjct: 444 EKLVLPSPDRIAEAAKK 460 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: 412 Number of extensions: 24 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: 465 Length adjustment: 30 Effective length of query: 297 Effective length of database: 435 Effective search space: 129195 Effective search space used: 129195 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: 50 (23.9 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