Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate Ga0059261_1691 Ga0059261_1691 FAD/FMN-containing dehydrogenases
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__Korea:Ga0059261_1691 Length = 484 Score = 172 bits (437), Expect = 2e-47 Identities = 134/466 (28%), Positives = 223/466 (47%), Gaps = 11/466 (2%) Query: 11 IAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIP 70 ++A+ E + A+ + D G+ S + + + ST EV+++++ A I Sbjct: 20 LSALSETLGADLFVRDEDARAACLRDMTGNWPSGAQAVARPRSTAEVARLVQAAAAQGIA 79 Query: 71 VVVRGSGTGLVGAC-VPL-FGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEE 128 +V +G TGLVG C VP ++L T + +I +D V E G +L E+ + V Sbjct: 80 IVPQGGNTGLVGGCAVPAETPALLLSTRRLRSIRAIDLHAPAVIAEAGCILAEVQEAVAA 139 Query: 129 NDLFYPPDPG-EKSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIV 187 + P G E SATI G +STNAGG+RA+++GV R+ V GL VVL +G + + Sbjct: 140 HGFTIPLGLGSEGSATIGGLVSTNAGGIRALRHGVMRNQVLGLEVVLPDGRVWNGLRTLA 199 Query: 188 KNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSK 247 KN+ GY LK L IG EGTL V+T A L+L+P + +L + E+ + A ++ + + Sbjct: 200 KNNMGYDLKQLFIGGEGTLGVVTAAALRLVPASRQIETLWLAVEDPAAALALLGALRTAL 259 Query: 248 A-IPTAIEFMERQTILFAEDFL-GKKFPDSSSNAYILL--TFDGNTKEQVEAEYETVANL 303 + T+ E ++R+ + + + G + PDS ++ + +L T + A E Sbjct: 260 GDLVTSFELIQRRGVEWGMAAVPGLRVPDSGAHGWFVLAEVATAATGLPLRAAVEAALAD 319 Query: 304 CLAEG-AKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTH 362 +G A D + ++ ++ +W R A + KA+ DV VP ++ F+ T Sbjct: 320 VFEQGLALDGMLAESEAQRRELWRIREAVVVG-KAAGKPSISVDVAVPLGQVPAFLVETE 378 Query: 363 DLAKEM--DVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGLVS 420 A + FGH GDGN+H V R + ++ A AL G + Sbjct: 379 AAAAGLLPGCETLGFGHLGDGNIHFSVHRGANDTERFAGTAEAIAAKVEAIALRLGGTIC 438 Query: 421 GEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKVCQM 466 EHG+G R + + L L+ +K+ DP N +NP V ++ Sbjct: 439 AEHGVGRRMRAAVADALDAAELDLIRAVKRALDPHNRMNPGAVIEL 484 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: 439 Number of extensions: 19 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: 484 Length adjustment: 33 Effective length of query: 433 Effective length of database: 451 Effective search space: 195283 Effective search space used: 195283 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