Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate Pf6N2E2_1497 D-2-hydroxyglutarate dehydrogenase
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1497 Length = 474 Score = 201 bits (512), Expect = 3e-56 Identities = 152/465 (32%), Positives = 224/465 (48%), Gaps = 14/465 (3%) Query: 13 AIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPVV 72 A++ L+ A V G E + D+ G + STEEV+ +++ + PVV Sbjct: 8 ALQALVGARHVQDGEEAAP-YLTDKQGRYVGQVIAAVHPASTEEVAAVVRACAAADTPVV 66 Query: 73 VRGSGTGLVGACVPLFGG--IMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEEND 130 V+G TGL+G P G ++L MN + +DT+N T+TVE G +L + E Sbjct: 67 VQGGNTGLMGGATPDASGRAVLLLLDRMNRVRAVDTDNDTLTVEAGCILQTVQDVAREAG 126 Query: 131 LFYPPDPG-EKSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKN 189 +P G E S T+ GN+ TNAGG ++YG TR+ GL VV A GEI + K+ Sbjct: 127 RLFPLSLGAEGSCTLGGNLGTNAGGTAVLRYGNTRELTLGLEVVTAQGEIWNGLRGLRKD 186 Query: 190 SSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKS-KA 248 ++GY L+DL IGSEGTL +IT A LKL PLPK + L+ F+++ A ++ A Sbjct: 187 NTGYDLRDLFIGSEGTLGIITAATLKLFPLPKARATALLAFDSLEQAVALLSHARAGFGA 246 Query: 249 IPTAIEFMERQTI-LFAEDFLGKKFPDSSSN---AYILLTFDGNTKEQVEAEYETVANLC 304 TA E + + + L E F P S + +L D +++ + +E V Sbjct: 247 SLTAFELLSAECLALLREQFPDGPRPFSGTRWPWFALLELSDNHSESRAREVFEQVLGEA 306 Query: 305 LAEG-AKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHD 363 + D I + + + + W R +A K + M D+ VP +++ F+ T Sbjct: 307 FEQQLLADALIAENLVQSQAFWQLRENMSDAQKRAGRNMKH-DISVPISQVVAFVAHTDA 365 Query: 364 LAKE--MDVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRM-YAKALTFEGLVS 420 L ++ VR +FGH GDGNLH V D A+ ++ + A G +S Sbjct: 366 LLQQHFPGVRHYTFGHLGDGNLHYNVAHPLDSTVDAHMAHYPALSQLVHDSAHAHGGSIS 425 Query: 421 GEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKVCQ 465 EHGIG K L L LM IKQ DP+NLLNP KV + Sbjct: 426 AEHGIGQRKVNVLGRYKSAVELDLMHRIKQALDPRNLLNPGKVLE 470 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: 435 Number of extensions: 19 Number of successful extensions: 6 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: 474 Length adjustment: 33 Effective length of query: 433 Effective length of database: 441 Effective search space: 190953 Effective search space used: 190953 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