Align Dihydrolipoyl dehydrogenase, mitochondrial; Dihydrolipoamide dehydrogenase; Glycine decarboxylase complex subunit L; Lipoamide dehydrogenase component of pyruvate dehydrogenase complex; Pyruvate dehydrogenase complex E3 component; EC 1.8.1.4 (characterized)
to candidate Echvi_4146 Echvi_4146 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes
Query= SwissProt::P09624 (499 letters) >FitnessBrowser__Cola:Echvi_4146 Length = 447 Score = 192 bits (487), Expect = 3e-53 Identities = 136/463 (29%), Positives = 235/463 (50%), Gaps = 31/463 (6%) Query: 25 KSHDVVIIGGGPAGYVAAIKAAQLGFNTACVEKRGKLGGTCLNVGCIPSKALLNNSHLFH 84 K +DV++IG G AG A K A+ G TA + R GGTC GC P K L+ + + Sbjct: 2 KKYDVIVIGSGMAGMTIANKCAKKGLKTAITDSR-PYGGTCALRGCDPKKILVGAAEIIG 60 Query: 85 QMHTEAQKRGIDVNGDIKINVANFQKAKDDAVKQLTGGIELLFKKNKVTYYKGNGSFEDE 144 ++ + GI ++GDI IN + K+D V ++ G+E ++K V Y G SFE E Sbjct: 61 RVD---KMSGIGISGDISINWEDLMAYKNDFVSKMPKGVEKGYEKAGVKKYHGVASFESE 117 Query: 145 TKIRVTPVDGLEGTVKEDHILDVKNIIVATGSEVTPFPGIEIDEEKI-VSSTGALSLKEI 203 +R+ + +L+ I++ATG+ ++I + + ST L+L+++ Sbjct: 118 NTVRIG-----------NDLLEGGKIVIATGARPVT---LDITGGDLPIDSTDFLNLEKL 163 Query: 204 PKRLTIIGGGIIGLEMGSVYSRLGSKVTVVEFQPQIGASMDGEVAKATQKFLKKQGLDFK 263 P+ +T +GGG I +E + +R GSK+T+ + + D + K K K G+ Sbjct: 164 PEHITFVGGGYIAMEFAHLAARAGSKITIFHRGERPLENFDEHIVKHLVKATKDLGILLH 223 Query: 264 LSTKVISAKRNDDKNVVEIVVEDTKTNKQENLEAEVLLVAVGRRPYIAGLGAEKIGLEVD 323 + T+VI +++ D + +V +N ++ ++L+ A GR P + G+ EK + + Sbjct: 224 VETEVIGIEKDGD----QFIVFTKSSNGEQTHHTDLLVNAAGRVPELDGMNLEKASIAYN 279 Query: 324 KRGRLVIDDQFNSKFPHIKVVGDV--TFGPMLAHKAEEEGIAAVEMLKTGHGHV-NYNNI 380 K+G V + + P + GD + G L A EG A + G+ V +Y + Sbjct: 280 KKGIEVNEYLQSESNPTVYAAGDAANSNGLNLTPVAVMEGHAVAANIIRGNSKVPDYTEM 339 Query: 381 PSVMYSHPEVAWVGKTEEQLKEAGIDYKIGKFPFAAN--SRAKTNQDTEGFVKILIDSKT 438 PS +++ P +A VG TE+Q KE ++Y++ K A+N + + N+ T + +I K Sbjct: 340 PSAVFTLPTLAAVGMTEKQAKELDVEYQV-KSASASNWYNAKRINESTYAYK--VISHKD 396 Query: 439 ERILGAHIIGPNAGEMIAEAGLALEYGASAEDVARVCHAHPTL 481 ILGAHIIGP+A EMI +A+ D+ + +++P++ Sbjct: 397 GHILGAHIIGPHAEEMINLFAMAIRGKLKVADIRNMVYSYPSM 439 Lambda K H 0.316 0.134 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: 541 Number of extensions: 38 Number of successful extensions: 7 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: 499 Length of database: 447 Length adjustment: 33 Effective length of query: 466 Effective length of database: 414 Effective search space: 192924 Effective search space used: 192924 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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