Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate WP_073036213.1 BUB04_RS01305 mercuric reductase
Query= SwissProt::P11959 (470 letters) >NCBI__GCF_900129305.1:WP_073036213.1 Length = 514 Score = 234 bits (596), Expect = 7e-66 Identities = 156/456 (34%), Positives = 242/456 (53%), Gaps = 18/456 (3%) Query: 13 LVVGAGPGGYVAAIRAAQLGQKVTIVEKGNLGGVCLNVGCIPSKALISASHRYEQAKHSE 72 +V+GAG G V A AA LG KV +VE+ LGG CLNVGC+PSKAL++AS + + Sbjct: 42 VVIGAGTAGLVTAAGAAGLGAKVALVERHLLGGDCLNVGCVPSKALLAASRAAAAVRDAH 101 Query: 73 EMGIKA-ENVTIDFAKVQE----WKASVVKKLTGGVEGLLKGNKVEIVKGEAYFVDANTV 127 GI E +DF +V E +ASV + L V++ G A FVD+ TV Sbjct: 102 RFGIHVPEGARVDFPRVMERMRRLRASVAPNDSAR---RLTELGVDVFFGNARFVDSETV 158 Query: 128 RVVNGDSAQTYTFKNAIIATGSRPIELPNFKFSNRI--LDSTGALNLGEVPKSLVVIGGG 185 V F+ A+IATG+R P +R+ L + +L E+P+ ++G G Sbjct: 159 DV----DGTRLRFQKAVIATGARAAA-PAIPGLDRVPYLTNETLFSLTELPRRFGIVGAG 213 Query: 186 YIGIELGTAYANFGTKVTILEGAGEILSGFEKQMAAIIKKRLKKKGVEVVTNALAKGAEE 245 IG E+ A+A FG+KV ++E IL + ++I+ K +++ GVE++ E Sbjct: 214 PIGCEMSQAFARFGSKVFLVEAMHGILPREDPDASSIVWKVMEEDGVELLCCGRDLVLEP 273 Query: 246 REDG-VTVTYEANGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNRGLIEVDQQCRT 304 E G V + ++G T + D VLV VGR PN + L L+++G+ T +G++ VD RT Sbjct: 274 GESGSVLMELHSHGGTTRVQVDRVLVAVGRAPNLEGLDLDRVGVAATPKGVV-VDDHLRT 332 Query: 305 SVPNIFAIGDIVPGPALAHKASYEGKVAAE-AIAGHPSAVDYVAIPAVVFSDPECASVGY 363 + P I+A GD+ H A + ++ + A+ + + IP ++DPE A VG Sbjct: 333 TNPRIYAAGDVCSPYQFTHAADFMARIVIQNALFWGRAKASGLTIPWCTYTDPEIAHVGL 392 Query: 364 FEQQAKDEGIDVIAAKFPFAANGRALALNDTDGFLKLVVRKEDGVIIGAQIIGPNASDMI 423 +E+ A+ G +V A P + RA+ +G +++ VRK I+GA I+ PNA DMI Sbjct: 393 YERDARARGWEVQAFTLPLSHVDRAVLEGRAEGLVRVHVRKGTDRIVGATIVAPNAGDMI 452 Query: 424 AELGLAIEAGMTAEDIALTIHAHPTLGEIAMEAAEV 459 EL LA+ + + +A IH +PT+GE + ++ Sbjct: 453 GELSLAMTHRIGLKGLASAIHPYPTVGEALRKVGDL 488 Score = 26.2 bits (56), Expect = 0.003 Identities = 12/29 (41%), Positives = 16/29 (55%) Query: 178 SLVVIGGGYIGIELGTAYANFGTKVTILE 206 +LVVIG G G+ A G KV ++E Sbjct: 40 NLVVIGAGTAGLVTAAGAAGLGAKVALVE 68 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: 541 Number of extensions: 33 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: 2 Length of query: 470 Length of database: 514 Length adjustment: 34 Effective length of query: 436 Effective length of database: 480 Effective search space: 209280 Effective search space used: 209280 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 24 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