Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of branched-chain alpha-keto acid dehydrogenase complex; LPD-Val (uncharacterized)
to candidate Echvi_0722 Echvi_0722 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes
Query= curated2:P54533 (474 letters) >FitnessBrowser__Cola:Echvi_0722 Length = 458 Score = 238 bits (608), Expect = 2e-67 Identities = 146/459 (31%), Positives = 238/459 (51%), Gaps = 15/459 (3%) Query: 5 YDVVILGGGTGGYVAAIRAAQLGLKTAVVEKEKLGGTCLHKGCIPSKALLRSAEVYRTAR 64 YD ++LG G G A + ++LGL A++EK +GGTC++ GC P+K ++ SA V Sbjct: 4 YDAIVLGAGQSGMPLAKKISKLGLSVALIEKRVIGGTCINDGCSPTKTMVSSARVAHIVS 63 Query: 65 EADQFGVETAGVSLNFEKVQQRKQAVVDKLAAGVNHLMKKGK-IDVYTGYGRILGPSIFS 123 A FG ++ V++RK +V+ G ++K + ID+ ++G + F Sbjct: 64 RAADFGTILPHYRIDQRIVKKRKDHIVELFRGGAEKSLRKNESIDI------LMGSAAFK 117 Query: 124 PLPGTISVERGNGEENDMLIPKQVIIATGSRPRMLPGLE-VDGKSVLTSDEALQMEELPQ 182 TI + GE + + ++ I TGS PR +P +E + LTS +++EE P+ Sbjct: 118 D-SRTIQITSDTGEIS-FISGTKIFINTGSEPR-IPEIEGLADTPYLTSTTIMELEETPE 174 Query: 183 SIIIVGGGVIGIEWASMLHDFGVKVTVIEYADRILPTEDLEISKEMESLLKKKGIQFITG 242 ++I+GGG IG+E+A M FG KVT+I+ A+R++ ED ++ KE+ + ++GI + Sbjct: 175 HLLIMGGGYIGLEFAQMFSRFGSKVTIIDRAERLVHKEDEDVCKEISQIFSEEGIDTLFN 234 Query: 243 AKVLPDTMTKTSDDISIQAEKDGETVTYSAEKMLVSIGRQANIEGIGLENTDI-VTENGM 301 A+V D + E + +LV+ GR + +GLENT + +T+ G Sbjct: 235 AEV---RKVSYQDGFKLTTETPKGLLDIKGSHLLVATGRIPSSAHLGLENTRVKLTDKGF 291 Query: 302 ISVNESCQTKESHIYAIGDVIGGLQLAHVASHEGIIAVEHFAGLNPHPLDPTLVPKCIYS 361 I ++ QT E HIYA+GDV G H+A H+ IA +H N LVP C++ Sbjct: 292 IQTDDFLQTSEKHIYALGDVAGSAPFTHIAYHDAHIAFQHAFKENAVSKHERLVPYCVFI 351 Query: 362 SPEAASVGLTEDEAKANGHNVKIGKFPFMAIGKALVYGESDGFVKIVADRDTDDILGVHM 421 P+ +GL E EA+A G K GKF G+ L E+ GF K+ D ++ ILG + Sbjct: 352 DPQLGRIGLNEQEAQAKGIPYKTGKFLMKHAGRTLEVDETRGFFKVQVDPESKKILGATI 411 Query: 422 IGPHVTDMISEAGLAKVLDATPWEVGQTIHPHPTLSEAI 460 + ++++ +A V T + HPTL+E++ Sbjct: 412 LSLDGGEILATLQMAMVGGVTYDTIATLPIAHPTLAESL 450 Lambda K H 0.315 0.135 0.382 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: 482 Number of extensions: 20 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: 474 Length of database: 458 Length adjustment: 33 Effective length of query: 441 Effective length of database: 425 Effective search space: 187425 Effective search space used: 187425 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: 42 (22.0 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