Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate RR42_RS17285 RR42_RS17285 2-hydroxy-acid oxidase
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__Cup4G11:RR42_RS17285 Length = 472 Score = 223 bits (567), Expect = 1e-62 Identities = 145/464 (31%), Positives = 239/464 (51%), Gaps = 27/464 (5%) Query: 13 AIKELIPA---ERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNI 69 A+++ + A ER + + DE + P+ ++ +TEEV+++ + EH + Sbjct: 18 AVRDALQARFGERFSTSPGVCDHHGRDESPFPPAAPDGVVFAHTTEEVAEVARLCNEHRV 77 Query: 70 PVVVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEEN 129 P++ G+G+ L G + + GGI L+ + MN +L + E+L VTV+PGV +L++ ++++ Sbjct: 78 PLIAYGAGSSLEGHLLAVAGGISLDLSEMNKVLSVQPEDLNVTVQPGVTRKQLNQEIKDS 137 Query: 130 DLFYPPDPGEKSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKN 189 LF+P DPG A++ G +T A G AV+YG R+ V LTVV A+G II+ G K+ Sbjct: 138 GLFFPIDPG-ADASLGGMCATRASGTNAVRYGTMRENVLALTVVTADGRIIKTGTHARKS 196 Query: 190 SSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAI 249 S+GY L L+IGSEGTL +IT+ ++L P P+ + + F ++ A + I+ Sbjct: 197 SAGYDLTRLMIGSEGTLGIITEVTVRLYPQPEAISAAICSFPSMGSAVRATIETIQLGVP 256 Query: 250 PTAIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGA 309 +EF++ I P++ ++ F G T+ V+ + ETV + G Sbjct: 257 VARVEFVDALAIRAINRHDNLSMPEA---PHLFFEFHG-TEAGVKEQAETVQQIAADNGG 312 Query: 310 KDVYIVDTVERKDSVWSARGAFLEAI-------KASTTEMDECDVVVPRNRIAEFIEFTH 362 + E + +W+AR A+ KA TT DV VP +R+A+ + T Sbjct: 313 QGFEWATRPEDRSRLWNARHTAYFAMLQLKPGCKAVTT-----DVCVPISRLADCVTETE 367 Query: 363 DLAKEMDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMD---RMYAKALTFEGLV 419 + P GH GDGN H+ + D + +LAEA R+ +AL G Sbjct: 368 RDLNASSLPCPIVGHVGDGNFHVAILTD----PEKPEELAEAETINRRIVERALAMGGTC 423 Query: 420 SGEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 +GEHG+G K +L+++ G + L LM IK DP ++LNP K+ Sbjct: 424 TGEHGVGLHKMDFLVSEHGEDALDLMRAIKNALDPNHILNPGKI 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: 472 Number of extensions: 20 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: 472 Length adjustment: 33 Effective length of query: 433 Effective length of database: 439 Effective search space: 190087 Effective search space used: 190087 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