Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate 206471 DVU1037 mercuric reductase, putative
Query= SwissProt::P11959 (470 letters) >MicrobesOnline__882:206471 Length = 480 Score = 238 bits (606), Expect = 4e-67 Identities = 156/456 (34%), Positives = 241/456 (52%), Gaps = 14/456 (3%) Query: 9 ETETLVVGAGPGGYVAAIRAAQLGQKVTIVEKG-NLGGVCLNVGCIPSKALISASHRYEQ 67 + + LV+G G G A AA+LG +V + ++G LGG CL+ GC+PSK LI+++ Sbjct: 4 DADLLVIGGGAAGLTVAAGAARLGARVVLADRGPTLGGDCLHHGCVPSKTLIASARARRT 63 Query: 68 AKHSEEMGIKAENVT-IDFAKVQEWKASV--VKKLTGGVEGLLKGNKVEIVKGEAYFVDA 124 + + G+ + +DF V A V V + VE G VE+ G+A FVD Sbjct: 64 MRDAPRFGLPEVALPPVDFKAVAAHIAGVQSVIQKHDSVERF-SGLGVEVRFGDAVFVDE 122 Query: 125 NTVRVVNGDSAQTYTFKNAIIATGSRPIELPNFK--FSNRILDSTGALNLGEVPKSLVVI 182 +TV V + + + ++ATGS P ++P F L + L +P SL+V+ Sbjct: 123 HTVAV----EGRRISARRIVVATGSSP-QIPAFPGLADTPYLTNRDIFTLETLPASLIVL 177 Query: 183 GGGYIGIELGTAYANFGTKVTILEGAGEILSGFEKQMAAIIKKRLKKKGVEVVTNALAKG 242 GGG I +E+ A+A G++V +++ G ILS + MAA++ + L++ GV ++T A + Sbjct: 178 GGGPIAVEMAQAFARLGSRVVLVQRGGHILSREDADMAAVVHEALEQDGVRIMTGATVEV 237 Query: 243 AEEREDGVTVTYEANGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNRGLIEVDQQC 302 A ++ GV VT E + + +LV +GR PN + L L G+ + RG + VD + Sbjct: 238 ARRQDAGVVVTVRVGDEHVDVHGERLLVALGRTPNVEGLHLGNAGVVFSERG-VPVDARM 296 Query: 303 RTSVPNIFAIGDIVPGPALAHKASYEGK-VAAEAIAGHPSAVDYVAIPAVVFSDPECASV 361 RTS +I A GD+ H A YEG V A A+ P Y +P F+DPE ASV Sbjct: 297 RTSQSHILAAGDVTGAWQFTHAAGYEGSVVVANAVLRLPRKAKYDRMPWCTFTDPELASV 356 Query: 362 GYFEQQAKDEGIDVIAAKFPFAANGRALALNDTDGFLKLVVRKEDGVIIGAQIIGPNASD 421 G E++A +GI V F++N RALA G LKLV+ + ++G QI GP+A + Sbjct: 357 GLNEREAHRQGIGVDVHTESFSSNDRALAEGTACGLLKLVLARGTQRVLGVQIAGPHAGE 416 Query: 422 MIAELGLAIEAGMTAEDIALTIHAHPTLGEIAMEAA 457 +I +A+ G+ +A + +PTLGEI+ A Sbjct: 417 LINGWCMALGGGVRLTTLAGGVMPYPTLGEISRRVA 452 Lambda K H 0.316 0.135 0.376 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: 499 Number of extensions: 23 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: 470 Length of database: 480 Length adjustment: 33 Effective length of query: 437 Effective length of database: 447 Effective search space: 195339 Effective search space used: 195339 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 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