Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate 208541 DVU3027 glycolate oxidase, subunit GlcD
Query= BRENDA::H6LBS1 (466 letters) >MicrobesOnline__882:208541 Length = 461 Score = 295 bits (755), Expect = 2e-84 Identities = 164/459 (35%), Positives = 273/459 (59%), Gaps = 7/459 (1%) Query: 8 ASDIAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEH 67 AS I + +I E VF + +++D P ++++ T TE++ K++K YE+ Sbjct: 4 ASLIKEFEAIIGKENVFTSEPDRQSYAYDSAVLDQVVPALVLRPTETEQLGKLVKLCYEN 63 Query: 68 NIPVVVRGSGTGLVGACVP-LFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFV 126 + P+ VRG+GT L G +P GI++ T +N I+E++ ++L VEPGV+ + + V Sbjct: 64 DHPITVRGAGTNLSGGTIPDKREGIVILTNSLNKIIEINEQDLYAVVEPGVVTAKFAAEV 123 Query: 127 EENDLFYPPDPGEKS-ATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGK 185 + LFYPPDPG ++ +T+ GN++ NAGG+R +KYGVT+DYV G+ NG +++ G + Sbjct: 124 AKRGLFYPPDPGSQAVSTLGGNVAENAGGLRGLKYGVTKDYVMGIEFFDVNGGLVKTGSR 183 Query: 186 IVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIK 245 VK +GY+L L+ SEGTL V ++ LKL+P PK + +++ F++++ A+ V II Sbjct: 184 TVKCVTGYNLAGLMAASEGTLGVFSQITLKLVPPPKASKAMMAVFDDVNKASEAVAAIIA 243 Query: 246 SKAIPTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCL 305 + +P +EFM++ +I + EDF P ++ A +L+ DG+ QVE + TV Sbjct: 244 AHVVPCTLEFMDKSSINYVEDFTKAGLPREAA-AILLIEVDGH-PAQVEDDAATVVKALN 301 Query: 306 AEGAKDVYIVDTVERKDSVWSARGAFLEAI-KASTTEMDECDVVVPRNRIAEFIEFTHDL 364 A GA +V++ K +W AR L A+ +A T + E D VPR++I ++ +D+ Sbjct: 302 ASGATEVHVAKDAAEKFKLWEARRNALPALARARATTVLE-DATVPRSQIPAMVKAINDI 360 Query: 365 AKEMDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRMYAKALTFEGLVSGEHG 424 AK+ ++ I +FGHAGDGNLH + D + ++E ++ A+D ++ AL+ G +SGEHG Sbjct: 361 AKKHNIAIGTFGHAGDGNLHPTILCDRRDKHEFE-RVESAVDEIFDVALSLHGTLSGEHG 419 Query: 425 IGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 IG AK K++ + + +K+ DPK +LNP K+ Sbjct: 420 IGLAKSKWMEKETSKATIEYSRNMKRAIDPKYILNPGKI 458 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: 512 Number of extensions: 32 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: 461 Length adjustment: 33 Effective length of query: 433 Effective length of database: 428 Effective search space: 185324 Effective search space used: 185324 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