Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate AO356_24000 AO356_24000 hydroxyacid dehydrogenase
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24000 Length = 474 Score = 208 bits (529), Expect = 4e-58 Identities = 156/464 (33%), Positives = 228/464 (49%), Gaps = 14/464 (3%) Query: 14 IKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPVVV 73 ++ L+ A+ V G+E + D+ G + STEEV+ +++ + PVVV Sbjct: 9 LQALVGAKHV-QGSEDAAPYLTDKQGRYVGQVIAAVHPASTEEVAAVVRACAATDTPVVV 67 Query: 74 RGSGTGLVGACVPLFGG--IMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEENDL 131 +G TGL+G P G ++L MN + +DT+N T+TVE G +L + E Sbjct: 68 QGGNTGLIGGATPDSSGRAMLLLLDRMNRVRAVDTDNDTLTVEAGCILQTVQDVAREAGR 127 Query: 132 FYPPDPG-EKSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNS 190 +P G E S T+ GN+ TNAGG ++YG TR+ GL VV A GE+ + + K++ Sbjct: 128 LFPLSLGAEGSCTLGGNLGTNAGGTAVLRYGNTRELTLGLEVVTARGEVWDGLRGLRKDN 187 Query: 191 SGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKS-KAI 249 +GY L+DL IGSEGTL +IT A LKL PLPK + L+ F+++ A ++ A Sbjct: 188 TGYDLRDLFIGSEGTLGIITAATLKLFPLPKAQATALLAFDSLEQAVALLSHARAGFGAS 247 Query: 250 PTAIEFMERQTI-LFAEDFLGKKFPDSSSNA--YILLTFDGNTKEQVEAE-YETVANLCL 305 TA E + + + L E F P +S+ + LL N E E +E V Sbjct: 248 LTAFELLSAECLALLREQFPDGPRPFASARQPWFALLELSDNHSESHAREVFEQVLGEAF 307 Query: 306 AEG-AKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDL 364 + D I +++ + + W R +A K + M D+ VP +++ F+ T L Sbjct: 308 EQHLLADALIAESLVQSQAFWQLRENMSDAQKRAGRNMKH-DISVPISQVVAFVAHTDAL 366 Query: 365 AKEM--DVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAMDRM-YAKALTFEGLVSG 421 +E VR +FGH GDGNLH V D A+ R+ + A G +S Sbjct: 367 LQEQFPGVRHYTFGHLGDGNLHYNVAHPLDSTVDAHMGHYAALSRLVHDSAHAHGGSISA 426 Query: 422 EHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKVCQ 465 EHGIG K L T L LM IKQ DP+NLLNP KV + Sbjct: 427 EHGIGQRKVNELGRYKSTVELDLMHRIKQALDPRNLLNPGKVLE 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: 426 Number of extensions: 18 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: 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