Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate Ac3H11_4615 Mercuric ion reductase (EC 1.16.1.1)
Query= SwissProt::P11959 (470 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4615 Length = 561 Score = 228 bits (580), Expect = 5e-64 Identities = 153/456 (33%), Positives = 241/456 (52%), Gaps = 12/456 (2%) Query: 9 ETETLVVGAGPGGYVAAIRAAQLGQKVTIVEKGNLGGVCLNVGCIPSKALISASHRYEQA 68 + + V+G+G AA++A + G VT++E+G +GG C+N+GC+PSK +I A+H Sbjct: 98 QLQIAVIGSGGAAMAAALKAVEQGAHVTLIERGTIGGTCVNIGCVPSKIMIRAAHIAHLR 157 Query: 69 KHSE-EMGIKAENVTIDFAKVQEWKASVVKKLTGG-VEGLLKGNK-VEIVKGEAYFVDAN 125 + S + GI A ID +K+ + ++V +L EG+L N + ++ GEA F D Sbjct: 158 RESPFDGGITATVPAIDRSKLLAQQQALVDELRHAKYEGILDSNSAITVLHGEARFKDDQ 217 Query: 126 TVRV-VNGDSAQTYTFKNAIIATGSRPI--ELPNFKFSNRILDSTGALNLGEVPKSLVVI 182 +V V +N + F ++ATG+ P +P K S ST AL VP+ L VI Sbjct: 218 SVVVRLNEGGERVVMFDRCLVATGASPAVPPIPGLKESP-YWTSTEALVSETVPERLAVI 276 Query: 183 GGGYIGIELGTAYANFGTKVTILEGAGEILSGFEKQMAAIIKKRLKKKGVEVVTNALAKG 242 G + +EL A+A G++VTIL + + + + + +G+ V+ + A Sbjct: 277 GSSVVALELAQAFARLGSQVTIL-ARRTLFFREDPAIGEAVTDAFRAEGITVLEHTQASQ 335 Query: 243 AEEREDGVTVTYEANGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNRGLIEVDQQC 302 +T +GE I AD +LV GR PNT L L+ G+ + +G I +D+ Sbjct: 336 VAHVNREFVLT-TGHGE---IRADKLLVATGRTPNTRSLALDAAGVTVNAQGAIVIDKGM 391 Query: 303 RTSVPNIFAIGDIVPGPALAHKASYEGKVAAEAIAGHPSAVDYVAIPAVVFSDPECASVG 362 RTS P+I+A GD P + A+ G AA + G +A+D A+PAVVF+DP+ A+VG Sbjct: 392 RTSTPHIYAAGDCADQPQFVYVAAAAGTRAAINMTGGDAALDLTAMPAVVFTDPQVATVG 451 Query: 363 YFEQQAKDEGIDVIAAKFPFAANGRALALNDTDGFLKLVVRKEDGVIIGAQIIGPNASDM 422 Y E +A +GI+ + RALA DT GF+KLV+ + G +IG Q + P A ++ Sbjct: 452 YSEAEAHHDGIETDSRTLTLDNVPRALANFDTRGFIKLVIEEGSGRLIGVQAVAPEAGEL 511 Query: 423 IAELGLAIEAGMTAEDIALTIHAHPTLGEIAMEAAE 458 I LAI MT +++A + + T+ E AA+ Sbjct: 512 IQTAVLAIRNRMTVQELADQLFPYLTMVEGLKLAAQ 547 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: 569 Number of extensions: 30 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: 470 Length of database: 561 Length adjustment: 35 Effective length of query: 435 Effective length of database: 526 Effective search space: 228810 Effective search space used: 228810 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: 52 (24.6 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