Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate RR42_RS33755 RR42_RS33755 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >FitnessBrowser__Cup4G11:RR42_RS33755 Length = 358 Score = 356 bits (913), Expect = e-103 Identities = 184/359 (51%), Positives = 247/359 (68%), Gaps = 10/359 (2%) Query: 2 MKTMRIAAIPGDGIGKEVLPEGIRVLQA-AAERWGFALSFEQMEWASCEYYSHHGKMMPD 60 M+ +IAAIPGDGIG EV+ G++VL+ A + GF L E W+S +YY G +P+ Sbjct: 1 MREYKIAAIPGDGIGPEVISAGLQVLETLAGQDGGFKLGVEHFPWSS-DYYLEKGYYIPE 59 Query: 61 DWHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLA 120 E+L +FDAI+FGAVG + VPDH+SLWG L + FDQY N+RP R+ PGV PLA Sbjct: 60 GGLERLKQFDAIFFGAVGALN-VPDHVSLWGLRLPIAQGFDQYANVRPARVLPGVKSPLA 118 Query: 121 GKQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQS 180 + DID+ ++REN+EGEY+ GGR + G E + +VFTR GV+RI R+AFE+AQ Sbjct: 119 NGK--DIDWVIIRENSEGEYAGNGGRTHRGLPIETGTETAVFTRAGVERIHRFAFEIAQK 176 Query: 181 RPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVV 240 RPRK LT TKSN M WDE +A++YP+++ D++ +D + R V++P DVV Sbjct: 177 RPRKHLTLVTKSNAQRFGMVMWDEIFYEVAKDYPDVKVDRELVDAVTTRMVLKPHTLDVV 236 Query: 241 VASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIAT 300 VA+NL DILSDL A +G++GIAP+ANLNPER FPS+FEP+HGSA DI GK +ANPIAT Sbjct: 237 VATNLHADILSDLAAALSGSLGIAPTANLNPERLFPSMFEPIHGSAFDITGKGVANPIAT 296 Query: 301 IWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHGPKTPDMKGNATTPQVADAICKII 359 W AMML+ LG + A ++AAIE++ A+G TPD+ G+ATT V +AICK++ Sbjct: 297 FWTAAMMLEHLGE-----KPAAERLMAAIEQITANGVFTPDLGGHATTASVTEAICKVL 350 Lambda K H 0.321 0.138 0.432 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: 405 Number of extensions: 18 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: 361 Length of database: 358 Length adjustment: 29 Effective length of query: 332 Effective length of database: 329 Effective search space: 109228 Effective search space used: 109228 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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