Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_011654905.1 RL_RS30530 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >NCBI__GCF_000009265.1:WP_011654905.1 Length = 363 Score = 358 bits (920), Expect = e-104 Identities = 180/358 (50%), Positives = 235/358 (65%), Gaps = 8/358 (2%) Query: 3 KTMRIAAIPGDGIGKEVLPEGIRVLQAAAERW-GFALSFEQMEWASCEYYSHHGKMMPDD 61 +T +IAAIP DGIG EV+ G+ VL A +R G Q +W S +YY HGKMMP+D Sbjct: 8 RTHKIAAIPADGIGPEVIGAGLEVLHALQQRSDGLRFEITQFDWGS-DYYREHGKMMPED 66 Query: 62 WHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAG 121 QL + DAIYFGAVG PD + DHI+LWG L + FDQY N+RP R+ PG+P PL Sbjct: 67 GLAQLRKHDAIYFGAVGAPD-IADHITLWGLRLPICQGFDQYANVRPTRILPGIPTPLRD 125 Query: 122 KQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQSR 181 + GD+D+ +VREN+EGEYS GGR + G EV + ++FTR GV RI+R+AF +AQSR Sbjct: 126 RGVGDLDWVIVRENSEGEYSGHGGRAHRGLPEEVATEVAIFTRVGVTRIMRFAFRIAQSR 185 Query: 182 PRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVVV 241 PRK LT TKSN + WDE ++ +P+++WDK +D + R + PE D +V Sbjct: 186 PRKLLTVVTKSNAQRFGLVLWDEIAAEVSTEFPDVKWDKVLVDAMTVRMTLHPESLDTIV 245 Query: 242 ASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIATI 301 A+NL DILSDL A G++G+AP+AN++PER FPS+FEP+HGSA DI GK IANPIA+ Sbjct: 246 ATNLHADILSDLAGALAGSLGVAPTANIDPERRFPSMFEPIHGSAFDITGKGIANPIASF 305 Query: 302 WAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHGPKTPDMKGNATTPQVADAICKII 359 W MLD LG +A ++ AIE V + G TPD+ G ATT +V DA+ K I Sbjct: 306 WTACQMLDHLGEA-----EASARLMKAIETVCSAGISTPDVGGTATTREVTDAVIKAI 358 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: 442 Number of extensions: 16 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: 361 Length of database: 363 Length adjustment: 29 Effective length of query: 332 Effective length of database: 334 Effective search space: 110888 Effective search space used: 110888 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