Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_041305954.1 MVAN_RS08155 NAD(P)H-quinone dehydrogenase
Query= BRENDA::P50970 (466 letters) >NCBI__GCF_000015305.1:WP_041305954.1 Length = 471 Score = 226 bits (575), Expect = 2e-63 Identities = 140/461 (30%), Positives = 247/461 (53%), Gaps = 17/461 (3%) Query: 7 LIVLGGGPGGYVAAIRAAQLN---LKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEM 63 ++++GGGP GY AA+ AA L +V +++ LGG C+ + C+P+K+ + S V E+ Sbjct: 5 IVIIGGGPAGYEAALVAAGLGRDLTQVTVIDSDGLGGACVLYDCVPSKTFIASTGVRTEL 64 Query: 64 QNAEAYGLTSFKPD--FDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLT---- 117 + A+ G D L KI R + +A ++ + + L V +I G G+L Sbjct: 65 RRAQGMGFDIGIDDAPISLPKINNRVKTLAASQSADIGSQLLNQGVTIIGGRGELVDDIA 124 Query: 118 --GNQQMLVETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKK 175 + ++ V T++G+ +L+A ++IATGA R LPN DG+ I T+ H +P+ Sbjct: 125 GMAHHRVKVTTSDGKVGVLKADVVLIATGASPRVLPNAVPDGERILTWRHVYDLDELPEH 184 Query: 176 LLVIGSGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQS 235 L+++GSG G EF + Y + G V++V QILP ED++ +A + + F +RG+ ++ + Sbjct: 185 LVIVGSGVTGAEFCNAYTELGVTVTVVASRDQILPHEDSDAAAVLEEVFAERGVTLVKNA 244 Query: 236 ALQNLTPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLD-RGFIA 294 ++T + GV +++ ADG+ + SHA++ +G V N +N+GL+++GI L+ G+I Sbjct: 245 RADSVTRTETGV--KVSMADGRTVEG--SHALMTVGSVPNTKNLGLERVGITLNPGGYIP 300 Query: 295 VDGFGRTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYAR 354 VD RT V+A GD G LA A+ QG IA G + V P+ + + T+ R Sbjct: 301 VDRVSRTPAPGVYAAGDCTGLLPLASVAAMQGRIAMYHALG-EGVSPIRLRTVASATFTR 359 Query: 355 PQVASVGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMV 414 P++A+VG+ + + P N +A GFVK +G ++G +V Sbjct: 360 PEIAAVGIPQSAIDDGSVPARTLMLPLSTNARAKMSLLRHGFVKIFCRPATGVVIGGVVV 419 Query: 415 GAEVTEMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHES 455 +E+I +A + +++ +T+ +P+LS ++ E+ Sbjct: 420 APIASELILPIALAVQNRISVSDLAQTLSVYPSLSGSIVEA 460 Lambda K H 0.319 0.135 0.393 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: 532 Number of extensions: 28 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: 466 Length of database: 471 Length adjustment: 33 Effective length of query: 433 Effective length of database: 438 Effective search space: 189654 Effective search space used: 189654 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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