Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate N515DRAFT_3582 N515DRAFT_3582 FAD/FMN-containing dehydrogenase
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__Dyella79:N515DRAFT_3582 Length = 467 Score = 205 bits (521), Expect = 3e-57 Identities = 141/471 (29%), Positives = 223/471 (47%), Gaps = 24/471 (5%) Query: 7 EASDIAAIKEL---IPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKY 63 ++ +AA+ EL +P R+ E + D P + + EE ++++ Sbjct: 6 QSPKVAALAELAARLPGLRLLTAPADLEHYGRDWTRRWTPAPLAIALPATVEEAQAVLRW 65 Query: 64 AYEHNIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELS 123 A EH + VV G TGL G V G ++L MN +L D + T+TV+ G+ L + Sbjct: 66 ANEHGVAVVPSGGRTGLSGGAVAAQGELVLSLERMNRVLGFDPIDRTLTVQAGIALQAVH 125 Query: 124 KFVEENDLFYPPDPGEK-SATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIEL 182 + L YP D + S +I GNI+TNAGG+R ++YG TR+++ GL V+ NGE++EL Sbjct: 126 DAARSHGLIYPVDFAARGSCSIGGNIATNAGGIRVIRYGNTREWIAGLKVIAGNGELLEL 185 Query: 183 GGKIVKNSSGYSLKDLVIGSEGTLCVITKAILKLL--PLPKMTLSLLIPFENISDAAGI- 239 ++KNSSGY L+ L IGSEGTL ++ +A L+L P P + L +P D A + Sbjct: 186 NRGLIKNSSGYDLRHLTIGSEGTLGIVVEATLRLAEPPPPSQVMLLALP-----DMAALM 240 Query: 240 -VPKIIKSKAIPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYE 298 V + +++ A EF + ++ D Y++ FD + +A Sbjct: 241 QVFALFRARLKLQAFEFFTDIALRHVLAHGAQRALDGEHPFYVVTEFDAADEAAQDAALA 300 Query: 299 TVANLCLAEGAKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFI 358 + D I + + ++W R E++ ++ + RI Sbjct: 301 AFEHGVNEGWIADGAIAQSEAQAAALWRLREGITESLAPHKPYKNDISL-----RIGALP 355 Query: 359 EFTHDLAKEMDVRIPS-----FGHAGDGNLHIYVCRDE-LCQADWEAKLAEAMDRMYAKA 412 F ++ + P FGH GDGNLHI V + E L A++ A+ + + A Sbjct: 356 AFLDEIQALLGDAYPHFEVVWFGHIGDGNLHINVLKPEGLADAEFIAQCEQVTKLLAAAL 415 Query: 413 LTFEGLVSGEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 G +S EHGIG K+ YL + +ALM G+KQ FDP +LNP K+ Sbjct: 416 QRHGGSISAEHGIGLVKKPYLESTRSAAEIALMRGVKQVFDPNGILNPGKL 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: 458 Number of extensions: 23 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: 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