Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate Ac3H11_4909 D-Lactate dehydrogenase, cytochrome c-dependent (EC 1.1.2.4)
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4909 Length = 474 Score = 219 bits (557), Expect = 2e-61 Identities = 139/439 (31%), Positives = 235/439 (53%), Gaps = 12/439 (2%) Query: 29 IGEDFSHDELGSIHSYP-EVLIKVTSTEEVSKIMKYAYEHNIPVVVRGSGTGLVGACVPL 87 + E DE GS+ + P ++ ST++V+ +K A ++ +PV+ G+G+ L G + + Sbjct: 41 VREQHGRDE-GSLQAPPPSAVVFAESTQDVADAVKLASQYEVPVIPYGAGSSLEGHLLAV 99 Query: 88 FGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEENDLFYPPDPGEKSATIAGN 147 GGI ++ + MN +L ++ E+LTVTV+PG+ L++ +++ LF+P DPG A+I G Sbjct: 100 QGGISIDVSRMNQVLSINAEDLTVTVQPGITRKALNEAIKDTGLFFPIDPGA-DASIGGM 158 Query: 148 ISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNSSGYSLKDLVIGSEGTLC 207 +T A G AV+YG R+ V L VV A+GE+I G + K+S+GY L L++GSEGTL Sbjct: 159 CATRASGTNAVRYGTMRENVLALEVVTASGEVIHTGTRAKKSSAGYDLTRLMVGSEGTLG 218 Query: 208 VITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAIPTAIEFMERQTILFAEDF 267 ++T+ ++L PLP+ + + F +I A + I+ +E ++ T+ Sbjct: 219 IMTEITVRLYPLPEAVSAAICSFPSIEAAVRTTIQTIQIGVPIARVELIDHHTVRMVNAH 278 Query: 268 LGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGAKDVYIVDTVERKDSVWSA 327 + +L+ F G + V+ + E V ++ G + T E + +W+A Sbjct: 279 SKLTLRE---EPMLLMEFHG-SPASVKEQAEMVQDIASEFGGQAFEWASTPEERTRLWTA 334 Query: 328 R-GAFLEAIKAST-TEMDECDVVVPRNRIAEFIEFTHDLAKEMDVRIPSFGHAGDGNLHI 385 R A+ A+++ D VP +R+A+ + + D + + GH GDGN H Sbjct: 335 RHNAYFAAVQSRPGCRAISTDTCVPISRLADCLLESVDEVEASGIPYFLVGHVGDGNFHF 394 Query: 386 YVCRDELCQADWEAKLAEAMDR-MYAKALTFEGLVSGEHGIGYAKRKYLLNDFGTEHLAL 444 D + E AEAM+ + A+AL+ G +GEHG+G K +LL++ GT + + Sbjct: 395 GYLIDP--NSAEERTKAEAMNHTLVARALSMGGTCTGEHGVGVHKMGFLLDETGTGAVDM 452 Query: 445 MAGIKQTFDPKNLLNPKKV 463 M IK+ DPKN+LNP K+ Sbjct: 453 MRAIKRALDPKNILNPGKI 471 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: 456 Number of extensions: 9 Number of successful extensions: 4 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: 474 Length adjustment: 33 Effective length of query: 433 Effective length of database: 441 Effective search space: 190953 Effective search space used: 190953 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