Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate BPHYT_RS03515 BPHYT_RS03515 D-lactate dehydrogenase
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__BFirm:BPHYT_RS03515 Length = 471 Score = 222 bits (565), Expect = 2e-62 Identities = 144/456 (31%), Positives = 234/456 (51%), Gaps = 28/456 (6%) Query: 20 AERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPVVVRGSGTG 79 A+RV V + DE P+ ++ +TE+V I+K ++N+P++ G+G+ Sbjct: 27 ADRVSVSEVVRTHHGRDESPFDPQLPDAVVFARTTEDVQTIVKLCGQYNVPIIPYGNGSS 86 Query: 80 LVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEENDLFYPPDPGE 139 L G + + GG+ ++ + MN +L ++ E+LTVTVEPG+ +L++ + + LF+P DPG Sbjct: 87 LEGHLLAVQGGVSIDLSEMNRVLSINAEDLTVTVEPGISRKQLNEALRDTGLFFPIDPG- 145 Query: 140 KSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNSSGYSLKDLV 199 A+I G +T A G AV+YG R+ V GLTVVLA+G +I+ G + K+S+GY L + Sbjct: 146 ADASIGGMSATRASGTNAVRYGTMRENVLGLTVVLADGRVIKTGTRARKSSAGYDLTRMF 205 Query: 200 IGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAIPTAIEFMERQ 259 +GSEGTL VIT+ ++L P P+ + + F ++ A V + I+ +EF++ Sbjct: 206 VGSEGTLGVITEITVRLYPQPEAVSAAVCAFPSMGAAVRAVIETIQMGVPIARVEFVDSL 265 Query: 260 TILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGAKDVYIVDTVE 319 I ++ + + F G T+ V+ + E V + + E Sbjct: 266 AIRSINRHSNLTLREAPT---LFFEFHG-TEAGVKEQAELVQEIAAQNAGEGFEWATRPE 321 Query: 320 RKDSVWSARG----AFLE---AIKASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMDVRI 372 + +W+AR A L+ +A TT DV VP +R+AE +E T + + Sbjct: 322 DRSRLWNARHNAYFAMLQLKPGCRAVTT-----DVCVPISRLAECVEETEQDLQASPLPC 376 Query: 373 PSFGHAGDGNLHIYVCRD-----ELCQADWEAKLAEAMDRMYAKALTFEGLVSGEHGIGY 427 P GH GDGN H+ + D EL +A+ R+ +AL +G +GEHG+G Sbjct: 377 PIVGHVGDGNFHVAILIDPNKPEELVEAE------RLNHRIVQRALRMDGTCTGEHGVGL 430 Query: 428 AKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 K +LL + G + M IK DP NL+NP K+ Sbjct: 431 HKMGFLLEEHGEVAVDTMRSIKHALDPHNLMNPGKI 466 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: 468 Number of extensions: 12 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: 471 Length adjustment: 33 Effective length of query: 433 Effective length of database: 438 Effective search space: 189654 Effective search space used: 189654 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