Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate Synpcc7942_0276 Synpcc7942_0276 glycolate oxidase subunit GlcD
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__SynE:Synpcc7942_0276 Length = 490 Score = 231 bits (588), Expect = 5e-65 Identities = 147/453 (32%), Positives = 230/453 (50%), Gaps = 6/453 (1%) Query: 13 AIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPVV 72 A +E++ E+V E + D L + P +++ STEEV+ ++ + ++ V Sbjct: 19 AFREVLGREQVVERREELLVYECDGLTNHRQIPPLVVLPRSTEEVAAAVRLCNQFDLSFV 78 Query: 73 VRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEENDLF 132 RG+GTGL G +P+ +++ T M ILE+D +NL V V+PGV+ +++ F Sbjct: 79 ARGAGTGLSGGALPVEDSVLIVTARMRQILEIDYDNLRVRVQPGVINSWVTQATTGAGFF 138 Query: 133 YPPDPGEKS-ATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNSS 191 Y PDP +S +I GN++ N+GG+ +K+GVT ++V GLT+VL + +I++GG I + Sbjct: 139 YAPDPSSQSVCSIGGNVAENSGGVHCLKHGVTNNHVLGLTLVLPDASVIQVGGAIA-DLP 197 Query: 192 GYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAIPT 251 GY L + +GSEGTL + T+ L+L PLP+ LL F +I A V II + +P Sbjct: 198 GYDLCGIFVGSEGTLGIATEVTLRLQPLPQSVQVLLADFSSIEAAGAAVSGIIAAGILPA 257 Query: 252 AIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGAKD 311 +E M+ +I ED + + A +L DG E V + V +C GA+ Sbjct: 258 GLELMDNFSINAVEDVVKSDCYPRDAAAILLAELDGRASE-VAQQIRDVEAVCRQHGARS 316 Query: 312 VYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMDVR 371 + I E + +W R A A+ + D V+PR+ + + L ++ R Sbjct: 317 IAIATDAEDRLRLWKGRKAAFAAVGRISPSYYVQDGVIPRSTLPFVLHEIEQLGQKHGYR 376 Query: 372 IPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAK-ALTFEGLVSGEHGIGYAKR 430 + + HAGDGNLH + D E EA+ K + G +SGEHGIG KR Sbjct: 377 VANVFHAGDGNLHPLILYDRNDPGALER--VEALGGEILKLCVNVGGSISGEHGIGADKR 434 Query: 431 KYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 Y+ F +E L M ++ FDP NP KV Sbjct: 435 CYMPAMFSSEDLETMQWLRHAFDPLERANPTKV 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: 494 Number of extensions: 28 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: 490 Length adjustment: 34 Effective length of query: 432 Effective length of database: 456 Effective search space: 196992 Effective search space used: 196992 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