Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_106718830.1 CU100_RS22300 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >NCBI__GCF_003010935.1:WP_106718830.1 Length = 358 Score = 364 bits (935), Expect = e-105 Identities = 188/361 (52%), Positives = 237/361 (65%), Gaps = 9/361 (2%) Query: 2 MKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWG-FALSFEQMEWASCEYYSHHGKMMPD 60 MKT +IAAIPGDGIGKEV+ G+RVL+A + R G F L W S +YY HG +MP+ Sbjct: 1 MKTYKIAAIPGDGIGKEVVAAGLRVLEACSSRDGNFKLDVADFPWGS-DYYKAHGVLMPE 59 Query: 61 DWHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLA 120 ++L FDAIYFGAVG PD VPDH++LWG L + FDQY N+RP R+ PG+ PL Sbjct: 60 GGIDELKAFDAIYFGAVGAPD-VPDHLTLWGLRLAICQPFDQYANVRPTRILPGIESPLR 118 Query: 121 GKQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQS 180 G D+D+ +VREN+EGEY+ GGR + G EV + S+FTR GV RI+R+AF+LAQS Sbjct: 119 GVTARDLDWVIVRENSEGEYAGQGGRSHRGLPEEVATEVSIFTRAGVSRIMRFAFQLAQS 178 Query: 181 RPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVV 240 RPRK LT TKSN M WDE +A ++P++ WDK +D + R + P D + Sbjct: 179 RPRKLLTVVTKSNAQRHGMVLWDEIAREVANDFPDVIWDKMLVDAMTVRMTLNPGSLDTI 238 Query: 241 VASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIAT 300 VA+NL DILSDL A G+IGIAP+ANLNPE FPS+FEP+HGSA DI GK IANP+ T Sbjct: 239 VATNLHADILSDLAAALAGSIGIAPTANLNPEGRFPSMFEPIHGSAFDITGKGIANPVGT 298 Query: 301 IWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAH-GPKTPDMKGNATTPQVADAICKII 359 W+ MML+ LG A ++ AIE V A TPD++GNATT V A+C I Sbjct: 299 FWSAVMMLEHLGEA-----SAAARLMRAIERVTADPALHTPDLRGNATTEMVTQAVCAAI 353 Query: 360 L 360 L Sbjct: 354 L 354 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: 423 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: 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 Jul 26 2024. The underlying query database was built on Jul 25 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