Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_004326337.1 C665_RS18455 hypothetical protein
Query= SwissProt::P85207 (461 letters) >NCBI__GCF_000310185.1:WP_004326337.1 Length = 722 Score = 246 bits (627), Expect = 2e-69 Identities = 167/461 (36%), Positives = 244/461 (52%), Gaps = 29/461 (6%) Query: 5 DLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHHLKG 64 +L+VIG G G + A + KV VEA +GG CLN GC+P+KAL+ +A H ++ Sbjct: 237 NLVVIGAGAAGLVTSYIAAAVKAKVTLVEAGRMGGDCLNTGCVPSKALIRSARLAHQIRH 296 Query: 65 AEGFGLK-AKPELDLKKLGAWRDGVVKKLTG-GVAGLLKGNKVELLRGFARFKGPREIEV 122 A+ +GL+ +PE+D ++L A V++K+ VE+L+G AR P +EV Sbjct: 297 ADRYGLEPGEPEIDFRRLMARVRAVIRKIEPHDSVERYSALGVEVLQGRARIVDPWTVEV 356 Query: 123 ---NGET--YGAQSFIIATGSEP-------MPLKGFPFGEDVWDSTRALRVEEGIPKRLL 170 G T +S +IATG+ P + G+ + VWD+ AL + P+RLL Sbjct: 357 ALNEGGTRRLSTRSIVIATGARPTVPDLPGLEAVGYLTSDTVWDAFAAL---DAPPRRLL 413 Query: 171 VIGGGAVGLELGQIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKA 230 V+GGG +G EL Q RLGS+V L+ P++LP D + A R ALE +G++V TG A Sbjct: 414 VLGGGPIGCELAQACARLGSQVVLVGRAPQLLPREDADVGAFARAALEADGVEVLTGVAA 473 Query: 231 VGYEKKQ-----DGLHVLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDER 285 + E++ D V+ + A GG + I D +L AVGR R EG GLE G+ Sbjct: 474 LRCEQETAAGGTDKFLVVADPASGG-ERRIAFDTLLCAVGRSARLEGFGLEALGIPTGAT 532 Query: 286 GFIQVNARMETSAPGVYAIGDVARPPLLAHKAMKEGLVAAENAAG---KNALFDFQ-VPS 341 + + ++T P + A GDVA P H A + AA NA + D++ VP Sbjct: 533 --VATDDFLQTRYPNILAAGDVAGPLQFTHVAAHQAWHAAVNALFGHLRRFRVDYRCVPH 590 Query: 342 VVYTGPEWAGVGLTEEEARKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLL 401 +T PE A VGL E EAR G + ++ + RA+T G G +KV+ D +L Sbjct: 591 TTFTDPEVARVGLNETEARARGIAFEFTRYDLAELDRAITDGADRGFVKVLTVPGKDRIL 650 Query: 402 GVFVVGPQAGELIAEATLALEMGATVSDLGLTIHPHPTLSE 442 G +VG AGEL+AE LA++ G ++ L TIH +PT +E Sbjct: 651 GATIVGEHAGELLAEFVLAMKHGLGLNKLLGTIHAYPTFAE 691 Score = 27.3 bits (59), Expect = 0.002 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 3/53 (5%) Query: 167 KRLLVIGGGAVGLELGQIYHRLGSEVTLIE---YMPEILPAGDRETAALLRKA 216 + L+VIG GA GL I + ++VTL+E + L G + AL+R A Sbjct: 236 RNLVVIGAGAAGLVTSYIAAAVKAKVTLVEAGRMGGDCLNTGCVPSKALIRSA 288 Lambda K H 0.316 0.138 0.395 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: 868 Number of extensions: 49 Number of successful extensions: 6 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: 461 Length of database: 722 Length adjustment: 36 Effective length of query: 425 Effective length of database: 686 Effective search space: 291550 Effective search space used: 291550 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: 53 (25.0 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