Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate HSERO_RS16560 HSERO_RS16560 2-hydroxyacid dehydrogenase
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__HerbieS:HSERO_RS16560 Length = 468 Score = 194 bits (494), Expect = 4e-54 Identities = 147/469 (31%), Positives = 230/469 (49%), Gaps = 22/469 (4%) Query: 11 IAAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIP 70 + A + I A V + D+ G +++ + EV+ +++ + +P Sbjct: 5 LQACRAAIGAPHVLTDAHDTAGYLTDQRGRYTGRALAVLRPADSAEVAAVVRLCAQFAVP 64 Query: 71 VVVRGSGTGLVGACVPLFGG--IMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEE 128 +V +G TGLV VP G ++L +N I +D N T+TVE G +L L + Sbjct: 65 LVPQGGNTGLVLGSVPDQQGNAVVLSLRRLNRIRAVDALNNTITVESGCVLQHLQEQAAA 124 Query: 129 NDLFYPPD-PGEKSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIV 187 +P E S TI GN+STNAGG ++YG TR+ GL VV A GEI+ + Sbjct: 125 AGRLFPLSLAAEGSCTIGGNLSTNAGGTGVLRYGNTRELCLGLEVVTAQGEIMSSLKGLR 184 Query: 188 KNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSK 247 K+++GY L+DL IG+EGTL VIT A++KL P P+ ++ L + + A ++ ++ ++ Sbjct: 185 KDNTGYDLRDLFIGAEGTLGVITAAVMKLFPQPRAQVTALAALPHPAQALQLL-QLAQAH 243 Query: 248 AIP--TAIEFMERQTILFAEDFLGKKFP------DSSSNAYILLTF-DGNTKEQVEAEYE 298 P T E M F + K FP D Y+LL D ++E A +E Sbjct: 244 CGPALTGFELMSD----FCLQLVRKHFPEQRLPFDRPHPQYVLLELSDSESEEHARALFE 299 Query: 299 TVANLCLAEG-AKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDECDVVVPRNRIAEF 357 + L +G D I ++ + ++W R + + + +A + + D+ VP +RIAEF Sbjct: 300 GLIGTALEQGLVDDAVIAASLAQSRALWRLRES-ISSAQAHEGKNIKHDISVPISRIAEF 358 Query: 358 IEFTHDLAKEM--DVRIPSFGHAGDGNLHIYVCRDE-LCQADWEAKLAEAMDRMYAKALT 414 I T L ++ R+ +FGH GDGNLH V E + D+ A+ A ++ Sbjct: 359 IAATDVLVQQAAPGCRMVTFGHLGDGNLHYNVSPPEGVADRDFIARQAAINRVVHDSVDR 418 Query: 415 FEGLVSGEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKV 463 F G +S EHG+G KR+ + L LM IK DP+ L+NP KV Sbjct: 419 FGGSISAEHGLGALKREEITRYKSPVELQLMRAIKLALDPQQLMNPGKV 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: 446 Number of extensions: 16 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: 468 Length adjustment: 33 Effective length of query: 433 Effective length of database: 435 Effective search space: 188355 Effective search space used: 188355 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