Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate 8501126 DvMF_1862 FAD linked oxidase domain protein (RefSeq)
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__Miya:8501126 Length = 461 Score = 283 bits (723), Expect = 1e-80 Identities = 158/458 (34%), Positives = 269/458 (58%), Gaps = 10/458 (2%) Query: 12 AAIKE---LIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHN 68 A IKE ++ + VF + +S+D P ++++ T+TE++ K+++ E+ Sbjct: 5 ALIKEFEAVVGKDNVFTSEADRQSYSYDSAVLEAVVPALVVRPTTTEQLGKVVRLCNENG 64 Query: 69 IPVVVRGSGTGLVGACVP-LFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVE 127 P+ VRG+GT L G +P GI++ T +N I+E++ E+L VEPGV+ + + V Sbjct: 65 NPITVRGAGTNLSGGTIPDPREGIVILTNSLNRIIEINEEDLYAVVEPGVVTAKFAAEVA 124 Query: 128 ENDLFYPPDPGEKS-ATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKI 186 + LFYPPDPG ++ +T+ GN++ NAGG+R +KYGVT+DYV G+ NG +++ G + Sbjct: 125 KRGLFYPPDPGSQAVSTLGGNVAENAGGLRGLKYGVTKDYVMGIEFFDVNGGLVKTGSRT 184 Query: 187 VKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKS 246 VK +GY+L L++ SEGTL V + +LKL+P P+ + +++ F++++ A+ V II + Sbjct: 185 VKCVTGYNLAGLMVASEGTLGVFSNIVLKLVPPPQASKAMMAVFDDVNKASEAVAGIIAA 244 Query: 247 KAIPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLA 306 +P +EFM++ TI + +DF P + A +L+ DG+ QV + E V + Sbjct: 245 HVVPCTLEFMDQATIRYVDDFTKAGLP-RDAQAILLIEVDGHA-GQVAEDAEKVEKVLNK 302 Query: 307 EGAKDVYIVDTVERKDSVWSARGAFLEAI-KASTTEMDECDVVVPRNRIAEFIEFTHDLA 365 GA ++ + K +W AR L A+ +A T + E D VPR++I ++ +D+A Sbjct: 303 VGATEIKVAKDAAEKFKLWEARRNALPALARAKPTTVLE-DATVPRSKIPAMVKAINDIA 361 Query: 366 KEMDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGLVSGEHGI 425 + ++ I +FGHAGDGNLH + D + ++E ++ A+D ++ AL+ G +SGEHGI Sbjct: 362 AKYNISIGTFGHAGDGNLHPTILCDRRDKHEFE-RVEHAVDEIFDVALSLHGTLSGEHGI 420 Query: 426 GYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 G AK K++ + + +K+ DPK +LNP K+ Sbjct: 421 GMAKSKWMEKETSKATIEFSRNMKRAIDPKYILNPGKI 458 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: 525 Number of extensions: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 466 Length of database: 461 Length adjustment: 33 Effective length of query: 433 Effective length of database: 428 Effective search space: 185324 Effective search space used: 185324 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