Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate PP_5154 PP_5154 putative Oxidoreductase, FAD-binding
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__Putida:PP_5154 Length = 455 Score = 199 bits (507), Expect = 1e-55 Identities = 131/428 (30%), Positives = 216/428 (50%), Gaps = 16/428 (3%) Query: 45 PEVLIKVTSTEEVSKIMKYAYEHNIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNILEL 104 P ++ + E+V I+ +A H + +V G TGL V G +++ MN IL Sbjct: 31 PSAIVFPKTIEQVQAIVHWANAHKVALVPSGGRTGLSAGAVAANGEVVVAFDYMNQILGF 90 Query: 105 DTENLTVTVEPGVLLMELSKFVEENDLFYPPD-PGEKSATIAGNISTNAGGMRAVKYGVT 163 + + TV +PGV+ +L + EE L+YP D S+ I GNI TNAGG++ ++YG+T Sbjct: 91 NAFDRTVVCQPGVVTRQLQTYAEEQGLYYPVDFASSGSSQIGGNIGTNAGGIKVIRYGMT 150 Query: 164 RDYVRGLTVVLANGEIIELGGKIVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMT 223 R++V GL VV GE++EL ++KN++GY L+ L IG+EGTL + +A ++L P+ Sbjct: 151 RNWVAGLKVVTGKGELLELNKDLIKNATGYDLRQLFIGAEGTLGFVVEATMRLDRAPRNL 210 Query: 224 LSLLIPFENISDAAGIVPKI--IKSKAIPTAIEFMERQTI--LFAEDFLGKKFPDSSSNA 279 ++++ D I+P + + K TA EF + + + A + F + Sbjct: 211 TAMVL---GTPDFDSIMPVLHAFQGKLDLTAFEFFSDKGLAKILARGDVPAPFA-TDCPF 266 Query: 280 YILLTFDGNTKEQVEAEYETVANLCLAEG-AKDVYIVDTVERKDSVWSARGAFLEAIKAS 338 Y LL F+ +T E V E C+ +G D + + + ++W R E I Sbjct: 267 YALLEFEAST-EDVANEALATFEHCVEQGWVLDGVMSQSESQLKNLWKLREYLSETISHW 325 Query: 339 TTEMDECDVVVPRNRIAEFIEFTHDLAKE--MDVRIPSFGHAGDGNLHIYVCRDE-LCQA 395 T ++ V V +++ F+ + E D + +GH GDGNLH+ + + E + + Sbjct: 326 TPYKNDISVTV--SKVPAFLRDIDAIVSEHYPDYEVVWYGHIGDGNLHLNILKPEHMSKD 383 Query: 396 DWEAKLAEAMDRMYAKALTFEGLVSGEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPK 455 D+ A A+ ++ + G +S EHG+G KR YL E +A M IK FDP Sbjct: 384 DFFASCAKVNKWVFEIVERYNGSISAEHGVGMTKRDYLGYSRSPEEIACMKAIKAVFDPN 443 Query: 456 NLLNPKKV 463 ++NP K+ Sbjct: 444 GIMNPGKI 451 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: 507 Number of extensions: 27 Number of successful extensions: 4 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: 455 Length adjustment: 33 Effective length of query: 433 Effective length of database: 422 Effective search space: 182726 Effective search space used: 182726 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