Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate 3609512 Dshi_2896 FAD linked oxidase domain protein (RefSeq)
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__Dino:3609512 Length = 480 Score = 223 bits (569), Expect = 8e-63 Identities = 139/455 (30%), Positives = 235/455 (51%), Gaps = 9/455 (1%) Query: 11 IAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIP 70 +A ++E++P + V + D L + P + +STEEV+ ++K + +P Sbjct: 18 VALLQEVLPRDAVIHEPHETRAYECDALTAYKCPPLAAVLPSSTEEVAAVLKICHAEGVP 77 Query: 71 VVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEEND 130 VV RGSGT L G +P ++L +N +LE D +N + V+ G + +S VEE D Sbjct: 78 VVPRGSGTSLAGGALPTADCVILGVARLNKVLETDYDNRIIRVQSGRTNLSVSGAVEEED 137 Query: 131 LFYPPDPGEKSA-TIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKN 189 FY PDP + A IAGNI+ N+GG +KYGVT + + G+T+V+ +G ++ +GG + + Sbjct: 138 FFYAPDPSSQLACAIAGNIAMNSGGAHCLKYGVTTNNLLGVTMVMMDGTVVTIGGAHL-D 196 Query: 190 SSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAI 249 + G L ++ GSEG L V+T+A L++L P+ +LI F+ A V IIK+ + Sbjct: 197 AGGLDLLGVICGSEGQLGVVTEATLRILRKPEGARPVLIAFDENEVAGACVADIIKAGVL 256 Query: 250 PTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGA 309 P AIEFM++ I E+F +P+ A +++ +G+ E ++A+ + ++ Sbjct: 257 PVAIEFMDKLCIETCENFAKAGYPE--CEALLIVEVEGSEAE-IDAQLGVILDIARKHNP 313 Query: 310 KDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMD 369 ++ + E +W R + AI M D +P + + + +++KE Sbjct: 314 VELRQSQSAEESAKIWLGRKSAFGAIGQLNDYMC-LDGTIPVSELPYVLRRIGEMSKEYG 372 Query: 370 VRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAK-ALTFEGLVSGEHGIGYA 428 +++ + HAGDGN+H + D D + +L EA K + G ++GEHG+G Sbjct: 373 LQVGNVFHAGDGNMHPLILFD--ANKDGDLELCEAFGAEILKLCVEVGGCLTGEHGVGIE 430 Query: 429 KRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 KR + F + + +K FDP LLNP KV Sbjct: 431 KRDLMGAQFTGADMEMQLRVKDVFDPAWLLNPAKV 465 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: 520 Number of extensions: 29 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: 480 Length adjustment: 33 Effective length of query: 433 Effective length of database: 447 Effective search space: 193551 Effective search space used: 193551 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