Align (S)-2-hydroxyglutarate oxidase (characterized)
to candidate WP_090274570.1 BLU11_RS14525 NAD(P)/FAD-dependent oxidoreductase
Query= metacyc::G1G01-3089-MONOMER (416 letters) >NCBI__GCF_900105005.1:WP_090274570.1 Length = 370 Score = 143 bits (360), Expect = 1e-38 Identities = 110/394 (27%), Positives = 178/394 (45%), Gaps = 51/394 (12%) Query: 3 DFIIIGGGIVGMSTAMHLIKVYPDAKMLLLEKESGPARHQTGHNSGVIHAGVYYTPGSLK 62 + I++G G+VG++ A L D +++LE+E+ H + NS VIHAG+YY GSLK Sbjct: 5 EVIVVGAGVVGLAIAQRLASGGRD--VMILEREASIGEHASSRNSEVIHAGIYYPSGSLK 62 Query: 63 ARFCLEGNKATKAFCTQHGIRFDECGKLLVATNDLEMQRMKALWERTAANGLERYWLSAD 122 AR CL+G A+C H + GKLLVAT D E+ ++ L A G++ L+A Sbjct: 63 ARLCLDGRDRLYAWCEAHRVPHRRIGKLLVATADDELPALEQLRFNAQACGVQLQSLNAA 122 Query: 123 ELREREPNIVGMGGIFVPSSGIVNYAQVTAAMAAEFQRAGGEIRYGAEVVGLQEQANEVI 182 ++ E EP + +GG+F P +GIV+ + + GG++ V ++ Q + Sbjct: 123 QVHELEPAVTAVGGLFSPLTGIVDSHALMQSFETVLLGQGGQLCLRTRVDRVERQGERWL 182 Query: 183 VRTQRD----ELHSRFLVTCSGLMADRVVGMLGLRTEFVICPF---RGEYYLLPKQHNQI 235 V+ Q + R+L+ GL A ++ + +I P +G Y+ + Sbjct: 183 VQGQSSGQPFAVSCRWLINAGGLFAQQLAHSIDCYPAALIPPLHYCQGRYF--SYSGSSP 240 Query: 236 VNHLIYPIPDPSMPFLGVHLTRMIDGTVTVGPNAVLAMKREGYRKTDVSPSDLFQTLTTP 295 HL+YP+P+P+ LGVH T + G + GP DV +D Sbjct: 241 FRHLVYPMPEPNAVGLGVHATLDLGGQLRFGP--------------DVRYTDSIDYQVDA 286 Query: 296 GILKVLAKNFRPGLIEMKNSLFKGGYLKQVQKYCPSIIKADLTPYPAGVRAQAVSRDGKL 355 G + A++ +Q+Y P L P AGVRA+ +S G Sbjct: 287 GSGESFARS--------------------IQRYWPECRAERLQPGYAGVRAK-LSGPGAA 325 Query: 356 IDDFLFVNTA-----RSVNVCNAPSPAATSAIPI 384 DF+ A V++ SP T+++ + Sbjct: 326 AADFMIQGPAIHGLQGVVSLFGIESPGLTASLAL 359 Lambda K H 0.321 0.137 0.409 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: 394 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 416 Length of database: 370 Length adjustment: 31 Effective length of query: 385 Effective length of database: 339 Effective search space: 130515 Effective search space used: 130515 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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