Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate WP_011385361.1 AMB_RS15030 FAD-binding protein
Query= BRENDA::H6LBS1 (466 letters) >NCBI__GCF_000009985.1:WP_011385361.1 Length = 457 Score = 218 bits (556), Expect = 3e-61 Identities = 146/451 (32%), Positives = 229/451 (50%), Gaps = 21/451 (4%) Query: 21 ERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPVVVRGSGTGL 80 ER + E DE PE ++ STEEV++ +K H PV+ G+GT L Sbjct: 17 ERFSTAQAVREQHGKDESHFPACPPEAVVFAQSTEEVAETVKACAAHGTPVIAFGTGTSL 76 Query: 81 VGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEENDLFYPPDPGEK 140 G L GG+ ++ + MN +LE+ E+L VTV+PGV +L++++ + LF+P DPG Sbjct: 77 EGHVAALKGGVCIDVSGMNRVLEVRAEDLDVTVQPGVTRKQLNEYLRDTGLFFPIDPG-A 135 Query: 141 SATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNSSGYSLKDLVI 200 A++ G +T A G AV+YG R+ V L VVL +G +I G+ K+S+GY L L + Sbjct: 136 DASLGGMAATRASGTNAVRYGTMRENVLSLQVVLPDGRVIRTAGRARKSSAGYDLTRLFV 195 Query: 201 GSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAIPTAIEFMERQT 260 GSEGTL +IT+ L+L +P+ + + PF +I A V I+S IEF+++ Sbjct: 196 GSEGTLGIITELTLRLQGIPEAISAAVCPFPSIEAAVNTVILTIQSGVPVARIEFLDKVM 255 Query: 261 ILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGAKDVYIVDTVER 320 I + D + F G + V+ + E V + GA+ E Sbjct: 256 IGAVNRY---SKTDHREAPTLFFEFHG-SPASVQEQAEKVEAIATEFGAEGFQWATGAEE 311 Query: 321 KDSVWSAR-GAFLEAI------KASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMDVRIP 373 + +W+AR A+ + +A TT D VP +R+AE + T + K + Sbjct: 312 RTKLWAARHNAYYAGVGLRPGCRAWTT-----DACVPISRLAECLLETEEDLKTTPLISA 366 Query: 374 SFGHAGDGNLHIYVCRDELCQADWEAKLAEAMD-RMYAKALTFEGLVSGEHGIGYAKRKY 432 GH GDGN H+ + D EA AE ++ R+ +AL +G +GEHG+G+ K + Sbjct: 367 IVGHVGDGNFHVMLLVDP--GKPEEAAEAERINHRIVRRALAMDGTCTGEHGVGHGKMAF 424 Query: 433 LLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 L ++G E L +M +K+ DP ++NP K+ Sbjct: 425 LEEEYG-EALDVMRAVKRAIDPAGIMNPGKI 454 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: 469 Number of extensions: 21 Number of successful extensions: 5 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: 457 Length adjustment: 33 Effective length of query: 433 Effective length of database: 424 Effective search space: 183592 Effective search space used: 183592 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