Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate GFF2781 PGA1_c28240 putative D-lactate dehydrogenase
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__Phaeo:GFF2781 Length = 467 Score = 226 bits (576), Expect = 1e-63 Identities = 147/453 (32%), Positives = 234/453 (51%), Gaps = 19/453 (4%) Query: 21 ERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPVVVRGSGTGL 80 E++ G I E H + P+ ++ TST+EV+ I++ ++ +PV+ G+GT L Sbjct: 27 EQLQTGQAIREQHGHTTTWITNQPPDAVVFPTSTDEVADIVRTCADYGVPVIPYGTGTSL 86 Query: 81 VGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEENDLFYPPDPGEK 140 G GGI ++ M+ IL + E+L V V+PGV +L+ ++ + LF+P DPG Sbjct: 87 EGHVNAPAGGICVDMMRMDKILAVHAEDLDVVVQPGVTREQLNTYLRDQGLFFPIDPGA- 145 Query: 141 SATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNSSGYSLKDLVI 200 +A++ G +T A G AV+YG +D V L V+A+G +I + K+S+GY + L++ Sbjct: 146 NASLGGMAATRASGTNAVRYGTMKDNVLALEAVMADGGVIRTAQRAKKSSAGYDMTRLLV 205 Query: 201 GSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAIPTAIEFMERQT 260 GSEGTL +IT+ L+L +P+ S F ++ DA V I+ + IE ++ + Sbjct: 206 GSEGTLGLITELTLRLQGIPEAIRSARCAFRSVDDACRAVMMTIQYGIPVSRIELLDEMS 265 Query: 261 ILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGAKDVYIVDTVER 320 + A + G P+ +LL F G+ VE + +T A + G D+ T E Sbjct: 266 VRAANAYSGLDLPEM---PLLLLEFHGSDAGVVE-QADTFAQIAEEFGGFDIAATSTAEE 321 Query: 321 KDSVWSARGAFLEA---IKASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMDVRIPSFGH 377 + +W AR A ++ + DV VP +++AE + A+EM++ P GH Sbjct: 322 RSKLWQARHDMYWASLQLRPGAKGI-STDVCVPISKLAECVSAARSKAEEMNLLAPMVGH 380 Query: 378 AGDGNLHIYVCRDELCQADWEAKLAEAMDR----MYAKALTFEGLVSGEHGIGYAKRKYL 433 GDGN H + L D A+ EA D + A++ EG +GEHGIG KR YL Sbjct: 381 VGDGNFHALL----LINMD-SAEEREAADAYVGWLNELAISIEGTCTGEHGIGQGKRPYL 435 Query: 434 LNDFGTEHLALMAGIKQTFDPKNLLNPKKVCQM 466 + G E MA IK DP+N+LNP K+ ++ Sbjct: 436 QQELG-ETTRYMAAIKAALDPENILNPGKILEI 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: 474 Number of extensions: 19 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: 467 Length adjustment: 33 Effective length of query: 433 Effective length of database: 434 Effective search space: 187922 Effective search space used: 187922 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