Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate N515DRAFT_3724 N515DRAFT_3724 NADPH-glutathione reductase
Query= SwissProt::P85207 (461 letters) >FitnessBrowser__Dyella79:N515DRAFT_3724 Length = 448 Score = 199 bits (505), Expect = 2e-55 Identities = 154/455 (33%), Positives = 232/455 (50%), Gaps = 25/455 (5%) Query: 3 TYDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHHL 62 TYDLIV+G G GG A R A+ G +V ++ +GG C+NVGC+P K+L AA+ H L Sbjct: 4 TYDLIVLGAGSGGLAMAFRAARHGARVALLDPGALGGTCVNVGCVPKKSLWFAAQIAHSL 63 Query: 63 K-----GAEGFGLKAKPELDLKKLGAWRDGVVKKLTGGVAGLLKGNKVELLRGFARFKGP 117 + G EG + E ++ A+ DG+ ++ +A V+ LR RF Sbjct: 64 QLAGPYGFEGVAGRLDWEHFRQRRLAYIDGIKQRYEERLAAA----GVQWLREAGRFVAA 119 Query: 118 REIEV-NGETYGAQSFIIATGSEPM--PLKGFPFGEDVWDSTRALRVEEGIPKRLLVIGG 174 + +G A +IATG+ P PL GF G V D ALR +P+ + ++GG Sbjct: 120 DTVATESGAELRAPQIVIATGARPQRPPLPGFELGL-VSDDMFALR---ELPRHVGIVGG 175 Query: 175 GAVGLELGQIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGYE 234 G + +E + LGSEVTL +L DRE L + + +G+ + TG + Sbjct: 176 GYIAVEFAGLLRALGSEVTL-HVRERMLRTFDRELVDSLEEHMRTQGITLATGARISAAR 234 Query: 235 KKQDGLHVLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARM 294 ++ D + VL + + G E D +L A+GR P TE L L+ AGV+ D G + + Sbjct: 235 REGDAI-VLDDDSCG---ERGPYDAVLWALGRVPNTERLDLDAAGVQCDVLGHVVTDPWQ 290 Query: 295 ETSAPGVYAIGDVARPPLLAHKAMKEGLVAAENAAG--KNALFDF-QVPSVVYTGPEWAG 351 T+ PG+ A+GDV L A+ G A+ G A D+ VPSVV++ P Sbjct: 291 NTNVPGIAALGDVTGRLALTPVAVAAGRRLADRWFGGRNEARLDYDDVPSVVFSEPPLGA 350 Query: 352 VGLTEEEAR-KAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQA 410 VGLTE +AR K G +V+V + F+ AL + L+K+V + + + GV V+GP A Sbjct: 351 VGLTEAQARAKFGDSVRVYRSRFTPMQWALAGQHGQTLMKLVCVGDDERVAGVHVLGPGA 410 Query: 411 GELIAEATLALEMGATVSDLGLTIHPHPTLSEGLM 445 E++ +A++MGA DL T+ HP+ E L+ Sbjct: 411 DEMLQGFAVAVKMGACKRDLDATVAIHPSSGEELV 445 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: 550 Number of extensions: 29 Number of successful extensions: 6 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: 461 Length of database: 448 Length adjustment: 33 Effective length of query: 428 Effective length of database: 415 Effective search space: 177620 Effective search space used: 177620 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