Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_011385541.1 AMB_RS16020 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >NCBI__GCF_000009985.1:WP_011385541.1 Length = 358 Score = 359 bits (921), Expect = e-104 Identities = 187/360 (51%), Positives = 237/360 (65%), Gaps = 9/360 (2%) Query: 2 MKTMRIAAIPGDGIGKEVLPEGIRVLQAAAER-WGFALSFEQMEWASCEYYSHHGKMMPD 60 M+ +IAAIP DGIGKEV+ G+ VL A+R GF L+ E +W S +YY HG MMP+ Sbjct: 1 MREFKIAAIPADGIGKEVVAAGLEVLDVLAKRDGGFRLNIETFDWGS-DYYKKHGTMMPE 59 Query: 61 DWHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLA 120 + E L +FDAIYFGAVG PD VPDH++LWG L + FDQY N+RP R+ PG+ PLA Sbjct: 60 NGRETLKQFDAIYFGAVGAPD-VPDHVTLWGLRLNICQPFDQYANVRPTRILPGIKSPLA 118 Query: 121 GKQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQS 180 G P +++ +VREN+EGEY+ GGR + G EV + ++FTR GV RI+R+AF+LAQS Sbjct: 119 GVGPRLLNWVIVRENSEGEYAGQGGRSHRGFPEEVATEVAIFTRAGVTRIMRFAFKLAQS 178 Query: 181 RPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVV 240 RPRK LT TKSN M WDE +A +P++ WDK +D + R ++PE D + Sbjct: 179 RPRKLLTVVTKSNAQRHGMVMWDEIAAEVAGEFPDVTWDKMLVDAMTMRMTLKPETLDTI 238 Query: 241 VASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIAT 300 VA+NL DILSDL A G++GIAP+ANLNPER FPS+FEP+HGSA DI GK IANPI T Sbjct: 239 VATNLHADILSDLAAALAGSLGIAPTANLNPERKFPSMFEPIHGSAFDITGKGIANPIGT 298 Query: 301 IWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHG-PKTPDMKGNATTPQVADAICKII 359 W MMLD LG A ++ AIE V A+ TPD+ G ATT V DA+ I Sbjct: 299 FWTACMMLDHLGE-----TAASARLMRAIERVTANPLLHTPDLGGKATTRIVTDAVIAAI 353 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: 421 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 Aug 03 2021. The underlying query database was built on Aug 03 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