Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_058930071.1 AU252_RS06805 NAD(P)/FAD-dependent oxidoreductase
Query= BRENDA::A0A0H2ZB32 (464 letters) >NCBI__GCF_001484605.1:WP_058930071.1 Length = 501 Score = 155 bits (393), Expect = 2e-42 Identities = 137/487 (28%), Positives = 222/487 (45%), Gaps = 55/487 (11%) Query: 9 LLIVGGGPGGYVAAIRAGQLGIPTVLVEGAALGGTCLNVGCIPSKALIHAAEEYLKARHY 68 ++++G G G A R Q G+ VLVE +GG C C+PSKAL+ A+ Sbjct: 12 VIVIGAGAVGENVADRVVQGGLTAVLVEAELVGGECSYWACMPSKALLRPGTALHGAQTV 71 Query: 69 AGRS-ALGIQVQAPSIDIAR---TVEWKDAIVDRLTSGVAALLKKHGVDVVQGWARILDG 124 G + A+ + + A ++ R T W+D L+ G+++++G I + Sbjct: 72 PGAAEAVTLTLDAVAVLKRRDYFTANWQD-------DSQVKWLEDTGIELIRGHGWITEP 124 Query: 125 KSVAVELAGGGSQRIECEH-LLLAAGSQSVELPILPLGG-KVISSTEALAPGSLPKRLVV 182 ++V V G + ++ H ++LA GS PI L +V + EA + +P+RL V Sbjct: 125 RTVEVVGLDGNTYELKARHAVVLATGSTPTTPPIDGLADLQVWGTREATSAKEVPERLAV 184 Query: 183 VGGGYIGLELGTAYRKLGVEVAVVEAQPRILPGYDEELTKPVAQALRKLGVELYLGHSLL 242 +GGG G EL A+ +LG +V +V A+ +L + E +K V LR GV + L S Sbjct: 185 IGGGVAGSELAQAFARLGSDVTLV-ARSGLLGTFPAEASKLVVAGLRADGVAVRLYTSTE 243 Query: 243 GPSENG-----VRVRDGAGEERE-IAADQVLVAVGRKPRSEGWNLESLGLD-MNGRAVKV 295 EN + ++D + R + AD+VLV+ GR P EG LESLG + +G+ +K+ Sbjct: 244 SVRENDDGTFTLTLQDQTPDGRTTVIADKVLVSTGRHPALEGLGLESLGFEAQDGQPLKL 303 Query: 296 DDQCRTSMR-----------------NVW--AIGDLAGEPMLAHRAMAQGEMVAELIAGK 336 ++ N W A+GD AG H+ + + IA + Sbjct: 304 TTDSTGLVQGLPDVPGTPGTPGEDGENPWLYAVGDAAGRNFFTHQGKYEARATGDAIAAR 363 Query: 337 RR-----------QFAPVA----IPAVCFTDPEVVVAGLSPEQAKDAGLDCLVASFPFAA 381 + ++A A +P V FTDPE+ G S EQAK G + P Sbjct: 364 AKGELSGAPEAWSRYAQTANQHAVPNVVFTDPELAAVGRSVEQAKRDGYNVSSVELPIQV 423 Query: 382 NGRAMTLEANEGFVRVVARRDNHLVVGWQAVGKAVSELSTAFAQSLEMGARLEDIAGTIH 441 +G ++ E EG+ ++V D +++G G V EL A ++ LE + + Sbjct: 424 SGSSLHSEHYEGWAQLVVDEDRRVLLGATFAGPEVGELLHAATIAVVGEVPLERLWHAVP 483 Query: 442 AHPTLGE 448 + PT+ E Sbjct: 484 SFPTVSE 490 Lambda K H 0.318 0.136 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: 645 Number of extensions: 44 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: 464 Length of database: 501 Length adjustment: 34 Effective length of query: 430 Effective length of database: 467 Effective search space: 200810 Effective search space used: 200810 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 (21.7 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