Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate CCNA_01799 CCNA_01799 pyruvate dehydrogenase E1 component alpha subunit
Query= metacyc::MONOMER-11683 (330 letters) >FitnessBrowser__Caulo:CCNA_01799 Length = 343 Score = 145 bits (365), Expect = 2e-39 Identities = 101/318 (31%), Positives = 158/318 (49%), Gaps = 10/318 (3%) Query: 15 EAVDMYRTMLLARKIDERMWLLNRSGKIP-FVISCQGQEAAQVGAAFALDREMDYVLPYY 73 E + Y+ MLL R+ +ER L G I F GQEA VG ++ ++ D ++ Y Sbjct: 27 ELLKFYQDMLLIRRFEERAGQLYGMGLIGGFCHLYIGQEAIAVGMQ-SISQKGDQIITGY 85 Query: 74 RDMGVVLAFGMTAKDLM--MSGFAKAADPNSGGRQMPGHFGQKKNRIVTGSSPVTTQVPH 131 RD G +LA GM +++M ++G A + GG H G V QV Sbjct: 86 RDHGHMLAAGMDPREVMAELTGRAGGSSKGKGGSM---HMFDIATGFYGGHGIVGAQVAL 142 Query: 132 AVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNKYAISVPY 191 G+ALA ++ G+G++NQG +E N A + KLPV+++ ENN+YA+ Sbjct: 143 GTGLALANSYRNNGNVSYAYMGDGAANQGQVYESFNMAQLWKLPVVYVIENNQYAMGTAV 202 Query: 192 DKQVACENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIETISYRLTP 251 ++ + R + + +PG V+G D + V +A A E AR G+GP ++E +YR Sbjct: 203 ERAASETAFHKRGVSFRIPGEEVDGMDVIAVREAGARATEHARSGQGPYILEMKTYRYRG 262 Query: 252 HSSDDDDSSYRGREEVEEAKKS-DPLLTYQAYLKETGLLSDEIEQTMLDEIMAIVNEATD 310 HS D + YR +EEV+E K + DP+ + L + G+ D+++ E+ IV EA + Sbjct: 263 HSM-SDPAKYRTKEEVDEVKTTRDPIDHIKERLAKAGVTEDDLKGVDA-EVKRIVAEAAE 320 Query: 311 EAENAPYAAPESALDYVY 328 A +P P VY Sbjct: 321 FARTSPEPDPSELYTDVY 338 Lambda K H 0.316 0.132 0.377 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: 278 Number of extensions: 19 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: 330 Length of database: 343 Length adjustment: 28 Effective length of query: 302 Effective length of database: 315 Effective search space: 95130 Effective search space used: 95130 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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