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 H281DRAFT_02737 H281DRAFT_02737 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component
Query= curated2:P54533 (474 letters) >FitnessBrowser__Burk376:H281DRAFT_02737 Length = 465 Score = 225 bits (573), Expect = 3e-63 Identities = 145/460 (31%), Positives = 236/460 (51%), Gaps = 15/460 (3%) Query: 5 YDVVILGGGTGGYVAAIRAAQLGLKTAVVEKEKLGGTCLHKGCIPSKALLRSAEVYRTAR 64 +D +ILG G GG + A + G + AVVE++ +GG+C C+PSK + SA V AR Sbjct: 7 FDTLILGSGQGGKLLAWHLGRSGQRVAVVERQWVGGSCPAVACLPSKNEIWSARVAHLAR 66 Query: 65 EADQFGVETAGVSLNFEKVQQRKQAVVDKLAAGVNHLMKKGKIDVYTGYGRILGPSIFSP 124 A FG T ++++ KV++RK+ ++++ AA ++ G GR +GP Sbjct: 67 HAGDFGTTTGPIAVDMAKVRERKRGMIEREAAFHVQAYASSGAELIMGSGRFIGPK---- 122 Query: 125 LPGTISVERGNGEENDMLIPKQVIIATGSRPRM--LPGLEVDGKSVLTSDEALQMEELPQ 182 TI+V+ +G L QV++ G+ + +PGL G LT AL ++ P Sbjct: 123 ---TIAVQLNDGGTR-TLAGDQVVVNVGTHAAIPDVPGLLAAGP--LTHIGALDLDYAPA 176 Query: 183 SIIIVGGGVIGIEWASMLHDFGVKVTVIEYADRILPTEDLEISKEMESLLKKKGIQFITG 242 ++++GGG IGIE A FG +VT++E R++ ED++IS+EM +L +GI +TG Sbjct: 177 HLVVLGGGYIGIEMAQAYRRFGSRVTIVERGARLMAREDVDISEEMRGILSNEGIDIVTG 236 Query: 243 AKVLPDTMTKTSDDISIQAEKDGETVTYSAEKMLVSIGRQANIEGIGLENTDI-VTENGM 301 A+ + + + GE V ++ +LV+ GR N GIGLE I + E G Sbjct: 237 AETVRVEGRSGTQVRVVLRTASGERVIEGSD-ILVAAGRVPNTAGIGLEQAGIELDERGY 295 Query: 302 ISVNESCQTKESHIYAIGDVIGGLQLAHVASHEGIIAVEHFAGLNPHPLDPTLVPKCIYS 361 I VN+ Q ++AIG+V G Q HV+ + I ++ AG + LVP +++ Sbjct: 296 IRVNDRLQASAPGVWAIGEVAGSPQFTHVSVDDFRIVRDNLAGTD-RTTTGRLVPYTLFT 354 Query: 362 SPEAASVGLTEDEAKANGHNVKIGKFPFMAIGKALVYGESDGFVKIVADRDTDDILGVHM 421 P A VGL E +A G V++ P + + E+ GF+K++ D D ILG M Sbjct: 355 DPPLARVGLNERDALRYGIAVRVATLPMSNVLRTEATDETQGFMKVLVDAKDDRILGFSM 414 Query: 422 IGPHVTDMISEAGLAKVLDATPWEVGQTIHPHPTLSEAIG 461 IGP ++++ A + + ++ + H T +E +G Sbjct: 415 IGPEAGEVMASVQTAMIAELPYPKLRDAVISHLTFAEGLG 454 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: 484 Number of extensions: 31 Number of successful extensions: 5 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: 465 Length adjustment: 33 Effective length of query: 441 Effective length of database: 432 Effective search space: 190512 Effective search space used: 190512 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