GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Acidovorax sp. GW101-3H11

Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate Ac3H11_375 Tartrate dehydrogenase (EC 1.1.1.93) @ Tartrate decarboxylase (EC 4.1.1.73) @ D-malic enzyme (EC 1.1.1.83)

Query= BRENDA::P76251
         (361 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_375
          Length = 364

 Score =  481 bits (1238), Expect = e-140
 Identities = 232/362 (64%), Positives = 286/362 (79%), Gaps = 13/362 (3%)

Query: 6   RIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDDWHEQ 65
           RIA + GDGIGKEV+PEG+RVL  AA ++G  L F+  +++S +YY  HGKM+PD+W EQ
Sbjct: 5   RIAVVAGDGIGKEVMPEGLRVLDVAARKFGIDLHFDHFDFSSWDYYEKHGKMLPDNWKEQ 64

Query: 66  LSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAGKQ-- 123
           +   +AIYFGAVGWP+ + DH+SLWGSLL FRREFDQY+NLRP RL PGV  P+  +   
Sbjct: 65  IGSHEAIYFGAVGWPEKIADHVSLWGSLLLFRREFDQYINLRPARLMPGVIAPVVRRDGS 124

Query: 124 ---PGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQS 180
              PG+ID  +VRENTEGEYSS+GGR+ EGT  E+V+QE+V +R GVDR+L++AF+LAQS
Sbjct: 125 PRLPGEIDMLIVRENTEGEYSSIGGRMYEGTPREIVMQETVMSRHGVDRVLKFAFDLAQS 184

Query: 181 RPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVV 240
           RP+K LTSATKSNG+AI+MPYWDERV  MA++YP+++ DK HIDIL A FV +P+ FDVV
Sbjct: 185 RPKKHLTSATKSNGIAITMPYWDERVAEMAKSYPDVKVDKFHIDILTAHFVQRPDFFDVV 244

Query: 241 VASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIAT 300
           VASNLFGDILSDLGPACTGTIGIAPSANLNP RT PSLFEPVHGSAPDI G+ IANPI  
Sbjct: 245 VASNLFGDILSDLGPACTGTIGIAPSANLNPTRTMPSLFEPVHGSAPDIAGQGIANPIGQ 304

Query: 301 IWAGAMMLDFLGNGDERFQQAHNGILAAIEEVI---AHGPKTPDMKGNATTPQVADAICK 357
           IW GAMMLDFLG     ++ AH+ +LAAIE V+   + GP+TPD+ G + T  V  AI +
Sbjct: 305 IWCGAMMLDFLG-----YRAAHDAVLAAIEAVLDPQSGGPRTPDLGGKSGTQDVGKAIAE 359

Query: 358 II 359
            +
Sbjct: 360 AL 361


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: 495
Number of extensions: 20
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: 364
Length adjustment: 29
Effective length of query: 332
Effective length of database: 335
Effective search space:   111220
Effective search space used:   111220
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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