Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate GFF194 HP15_194 mercuric ion reductase
Query= SwissProt::P11959 (470 letters) >FitnessBrowser__Marino:GFF194 Length = 468 Score = 244 bits (623), Expect = 4e-69 Identities = 150/443 (33%), Positives = 243/443 (54%), Gaps = 11/443 (2%) Query: 14 VVGAGPGGYVAAIRAAQLGQKVTIVEKGNLGGVCLNVGCIPSKALISASHRYEQAKHSE- 72 V+G+G AA++A + G +VT++E+G +GG C+NVGC+PSK +I A+H K S Sbjct: 11 VIGSGGAAMAAALKATERGARVTLIERGTVGGTCVNVGCVPSKIMIRAAHIAHLRKESPF 70 Query: 73 EMGIKAENVTIDFAKVQEWKASVVKKLTGG-VEGLLKGNK-VEIVKGEAYFVDANTVRVV 130 + GI A +D AK+ + + + V++L E +L+ +K + ++ GEA F+D N++ V Sbjct: 71 DAGISAAAPEVDRAKLLQQQLARVEELRDTKYEKILREHKDITVLNGEARFLDTNSLLVT 130 Query: 131 NGDSAQTYT-FKNAIIATGSRPIELPNFKFSNR-ILDSTGALNLGEVPKSLVVIGGGYIG 188 + + F A I TG+RP E P ++ L ST AL L PK L+VIG G++ Sbjct: 131 LAEGGEKPVHFDRAFIGTGARPAEPPITGLADTPYLTSTSALTLDTGPKRLIVIGAGFVA 190 Query: 189 IELGTAYANFGTKVTILEGAGEILSGFEKQMAAIIKKRLKKKGVEVVTNALAKGAEERED 248 +EL A+A G+KVT+L +LS + + I ++G+EV++ L + ++ Sbjct: 191 LELAQAFARLGSKVTVL-ARSRVLSSEDPAIGEAIAGAFNREGIEVLSQTLPSNVDYSDN 249 Query: 249 GVTVTYEANGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNRGLIEVDQQCRTSVPN 308 V A T+ AD +LV GR PNT+ L L IG++ T+R I+VD+ +T+VP Sbjct: 250 EFIVETPAG----TLRADQLLVATGRTPNTEALNLASIGVE-TSRDAIQVDEHLQTTVPG 304 Query: 309 IFAIGDIVPGPALAHKASYEGKVAAEAIAGHPSAVDYVAIPAVVFSDPECASVGYFEQQA 368 I+A GD P + A+ G AA + + +D+ A+P V+F+DP+ A+VG E +A Sbjct: 305 IYAAGDCTNQPQFVYVAAAGGSRAAINMTEGEAKLDFSAMPGVMFTDPQVATVGLSEAEA 364 Query: 369 KDEGIDVIAAKFPFAANGRALALNDTDGFLKLVVRKEDGVIIGAQIIGPNASDMIAELGL 428 G V RAL DT GF+K+V + G ++G QI+ ++I + Sbjct: 365 VARGYSVDTRLLDLENVPRALVNFDTQGFIKMVAERNSGRLLGVQIVAAEGGEIIQTAVM 424 Query: 429 AIEAGMTAEDIALTIHAHPTLGE 451 A+ AG+T ++I + + T+ E Sbjct: 425 ALRAGLTVQEIGDDLFPYLTMVE 447 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: 492 Number of extensions: 30 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 470 Length of database: 468 Length adjustment: 33 Effective length of query: 437 Effective length of database: 435 Effective search space: 190095 Effective search space used: 190095 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