Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate N515DRAFT_1999 N515DRAFT_1999 D-lactate dehydrogenase
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__Dyella79:N515DRAFT_1999 Length = 456 Score = 261 bits (666), Expect = 4e-74 Identities = 153/424 (36%), Positives = 231/424 (54%), Gaps = 9/424 (2%) Query: 42 HSYPEVLIKVTSTEEVSKIMKYAYEHNIPVVVRGSGTGLVGACVPLFGGIMLETTLMNNI 101 ++ P+ ++ TS E+ +++ EH +P+V RG GT GA VP+ GG++ MN I Sbjct: 38 NALPDAVVFPTSHEQTEALVRACREHRVPLVARGRGTNTTGATVPVDGGVVASFERMNRI 97 Query: 102 LELDTENLTVTVEPGVLLMELSKFVEENDLFYPPDPGEKS-ATIAGNISTNAGGMRAVKY 160 L +D +N VEPGVL +L + ++ + F+PPDP +I GN++ N+ G R VKY Sbjct: 98 LRIDPDNRLAVVEPGVLNGDLQQALKPHGFFWPPDPTSSPWCSIGGNLACNSAGPRTVKY 157 Query: 161 GVTRDYVRGLTVVLANGEIIELGGKIVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLP 220 G R+ GL V G G K S+GY L L+IGSEGTL +IT+A LKL P P Sbjct: 158 GSPRENTLGLRAVAGTGVGFRCGTYTSKGSTGYDLTRLLIGSEGTLALITEATLKLTPKP 217 Query: 221 KMTLSLLIPFENISDAAGIVPKIIKSKAIPTAIEFMERQTILFAEDFLGKKFPDSSSNAY 280 +L + ++S AA V +I+ P A+EF++ + A D G P + A Sbjct: 218 SGLRTLRATYRDVSAAARAVARIMAQPVTPCALEFIDDVALKLARDHGGDSVP--VAGAM 275 Query: 281 ILLTFDGNTKEQVEAEYETVANLCLAEGAKDVYIVDTVERKDSVWSARGAFLEAIKASTT 340 +++ DG + + E V+ +G + + + + E ++WSAR A A + + Sbjct: 276 LMIEVDGE-PDTLAGAVEAVSRAARGDGLESLQVAQSAEETQALWSARKALSPAQRTISP 334 Query: 341 EMDECDVVVPRNRIAEFIEFTHDLAKEMDVRIPSFGHAGDGNLHIYVC-RDELCQADWEA 399 DVVVP +R+ E ++ LA + DV I SFGHAG+GNLH+ + RDE + A Sbjct: 335 NKINEDVVVPVSRLPELVDGIKALAAKHDVLIVSFGHAGNGNLHVNLLPRDEAERERAHA 394 Query: 400 KLAEAMDRMYAKALTFEGLVSGEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLN 459 LAE ++A + +G +SGEHGIG KR+++ E L LM G+K FDP +LN Sbjct: 395 CLAE----VFALVIRLDGTLSGEHGIGLVKREFMPLALQPETLGLMRGVKAAFDPDGILN 450 Query: 460 PKKV 463 P+K+ Sbjct: 451 PRKL 454 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: 453 Number of extensions: 19 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: 456 Length adjustment: 33 Effective length of query: 433 Effective length of database: 423 Effective search space: 183159 Effective search space used: 183159 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