Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_028585708.1 G494_RS0118460 mercuric reductase
Query= CharProtDB::CH_123536 (491 letters) >NCBI__GCF_000429965.1:WP_028585708.1 Length = 489 Score = 243 bits (619), Expect = 1e-68 Identities = 166/464 (35%), Positives = 243/464 (52%), Gaps = 16/464 (3%) Query: 22 STKKYDVVVIGGGPGGYVAAIKAAQLGLNTACIEKRGALGGTCLNVGCIPSKSLLNNSHL 81 ST YD+ +IGGG G AAQLG T IEK LGG CL+ GC+PSK+L+ ++H+ Sbjct: 2 STFDYDIGIIGGGAAGLTITAGAAQLGARTLLIEKEPLLGGDCLHYGCVPSKTLIKSAHV 61 Query: 82 LHQIQHEAKERGISIQGEVGVDFPKLMAAKEKAVK--QLTGGIEMLFKKNKVDYLKGAGS 139 HQI+ EA+ G+ V+F + A ++ + Q+ +E F + G Sbjct: 62 YHQIK-EAERYGLPTAAIGPVNFRSIAARIQEVISTIQVHDSVER-FCRLGAQVGFGQAE 119 Query: 140 FVNEKTVKVTPIDGSEAQEVEADHIIVATGSEPTPFPGIE-IDEERIVTSTGILSLKEVP 198 FV+E TV +DGS A + ++ATGSEP P P ++ + E ++T+ I SL E+P Sbjct: 120 FVDEHTVL---LDGSRR---SAKYWVIATGSEPAP-PRVKCLTEIEMITNRDIFSLDELP 172 Query: 199 ERLAIIGGGIIGLEMASVYARLGSKVTVIEFQNAIGAGMDAEVAKQSQKLLAKQGLDFKL 258 + ++G G I +EMA + RLG++V+VI+ I + D ++A + ++G+ F L Sbjct: 173 GSMIVLGAGPIAMEMAQAFNRLGTQVSVIQRSAQILSKEDRDMADTVMAAMEEEGVRFFL 232 Query: 259 GTKVVKGERDGEVVKIEVEDVKSGKKSDLEADVLLVAIGRRPFTEGLNFEAIGLEKDNKG 318 G V+ + G +IE G + LEAD +L+A GR P T L E I L D +G Sbjct: 233 GATVLAASQKGGRRRIEF-STGDGSRHQLEADQVLLAQGRTPNTRDLGLERIELAHDLRG 291 Query: 319 RLIIDDQFKTKHDHIRVIGDVTFGPMLAHKA-EEEGIAAAEYIKKGHGHVNYANIPSVMY 377 + +D + +T H HI GD+T H A E GI + I + NY +P Y Sbjct: 292 -VTVDRRLRTSHRHIFAAGDITGSYQFTHAAGYEGGIVVSNAIFRLPRKTNYTWLPWCTY 350 Query: 378 THPEVAWVGLNEEQLKEQGIKYKVGKFPFIANSRAKTNMDTDGFVKFIADAETQRVLGVH 437 T PE+A VGLNE + + GI Y V F AN RA T G +K + D E ++ +GV Sbjct: 351 TDPELASVGLNERRARALGIDYTVWSEEFAANDRALAEGATRGKLKLLLD-EREKPIGVQ 409 Query: 438 IIGPNAGEMIAEAGLALEYGASTEDISRTCHAHPTLSEAFKEAA 481 I GP AG+++ E L G ++ T H +PTL E K A Sbjct: 410 IAGPRAGDLLGEWIAILGGGVKLSTLAGTVHPYPTLGEINKRVA 453 Lambda K H 0.316 0.135 0.381 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: 458 Number of extensions: 24 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: 491 Length of database: 489 Length adjustment: 34 Effective length of query: 457 Effective length of database: 455 Effective search space: 207935 Effective search space used: 207935 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