Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate 3608683 Dshi_2076 FAD linked oxidase domain protein (RefSeq)
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__Dino:3608683 Length = 472 Score = 159 bits (403), Expect = 1e-43 Identities = 143/469 (30%), Positives = 214/469 (45%), Gaps = 17/469 (3%) Query: 6 VEASDIAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAY 65 V A A++ +P E F E+ + + G +L+ +TEEV+ +++ A Sbjct: 5 VPADFETAVRAALP-EAAF--PELSAAYLEEPRGRYAGSGGLLVAPGATEEVATLVRLAQ 61 Query: 66 EHNIPVVVRGSGTGLVGACVPLFGGI--MLETTLMNNILELDTENLTVTVEPGVLLMELS 123 H +P++ G GTGLVG + G + +L M +I + E + + G +L E+ Sbjct: 62 AHKVPIIPYGGGTGLVGGQIAPAGPVPVILSLRRMRSIRAVYPEENVLVADAGAVLAEVQ 121 Query: 124 KFVEENDLFYPPD-PGEKSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIEL 182 + + +P E SATI G ++TNAGG+ ++YG RD GL V+ +G I Sbjct: 122 QAARDVGRLFPLSLASEGSATIGGVLATNAGGVNVLRYGNARDLCLGLEAVMPDGAIWHG 181 Query: 183 GGKIVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPK 242 ++ KN+ GY L+ L+IG+EGTL +IT A L+L PLP+ L+ + S AA + Sbjct: 182 LTRLRKNNMGYDLRHLLIGAEGTLGIITGAALRLSPLPQRHGVGLLVVD--SPAAALDLL 239 Query: 243 IIKSKAIPTAIEFME----RQTILFAEDFLGKKFPDSSSNAY-ILLTFDGNTKEQVEAEY 297 + + I E R FAE + P A+ +L+ G + E Sbjct: 240 ALAGEVAGDTISAFELISGRGFEFFAETMPEMRAPLDPVPAWSVLIDLAGASGFDPEGAL 299 Query: 298 ETV-ANLCLAEGAKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAE 356 ET+ A A D I + + D++W+ R EA + D+ VP + I Sbjct: 300 ETLFARAAEAGLVSDGVIAQSEAQADALWALRENIPEA-NRRIGSVSSHDISVPLSEIPN 358 Query: 357 FIE-FTHDLAKEMDVRIPSFGHAGDGNLHIYVC-RDELCQADWEAKLAEAMDRMYAKALT 414 FIE T LA D RI FGH GDGNLH V + +AD E + ++ Sbjct: 359 FIETATARLAGIGDYRINCFGHVGDGNLHYNVFPQPGRSRADHEDERPAIKTCVHDLVHE 418 Query: 415 FEGLVSGEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 G VS EHG+G K + L A M IK DP L+NP V Sbjct: 419 LGGSVSAEHGVGRLKVEDLERYGDPVKQAAMRAIKDALDPHGLMNPGAV 467 Lambda K H 0.318 0.136 0.388 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: 495 Number of extensions: 20 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: 472 Length adjustment: 33 Effective length of query: 433 Effective length of database: 439 Effective search space: 190087 Effective search space used: 190087 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: 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