GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Sinorhizobium meliloti 1021

Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate SMa1846 SMa1846 3-isopropylmalate dehydrogenase

Query= BRENDA::P76251
         (361 letters)



>FitnessBrowser__Smeli:SMa1846
          Length = 347

 Score =  329 bits (843), Expect = 8e-95
 Identities = 183/354 (51%), Positives = 222/354 (62%), Gaps = 12/354 (3%)

Query: 2   MKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDD 61
           MK+  IA IPGDGIG++V     +VL   A   GF L+     W SC +Y   G MMP D
Sbjct: 1   MKSYSIALIPGDGIGQDVTDAAWQVLSTVARHSGFTLTGTSFPW-SCAFYKETGAMMPAD 59

Query: 62  WHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAG 121
             E L  FDAI  G+VGWP  VPD ISL G LL  R+ F QY N+RP RL  GV  PL  
Sbjct: 60  GIEALRPFDAILLGSVGWPAEVPDSISLHGLLLPIRKAFVQYANIRPHRLLSGVEGPL-- 117

Query: 122 KQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQSR 181
            +  D D   VRENTEGEYS  GGRV++GT  EV ++ S+FTR GV+RILR+AFE A+ R
Sbjct: 118 -KASDFDILCVRENTEGEYSGAGGRVHQGTADEVAVETSIFTRAGVERILRFAFEQARQR 176

Query: 182 PRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVVV 241
            R  L S TKSN    SM +WDE    +A+ YP++     HID + AR VM PE  DVVV
Sbjct: 177 -RGKLASVTKSNAQKHSMVFWDEVTRQLADEYPDVEVTSYHIDAMAARVVMAPESLDVVV 235

Query: 242 ASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIATI 301
           ASNLFGDIL+DLG A  G +G A SAN+NP+R+ PS+FEPVHGSAPDI    IANPIA I
Sbjct: 236 ASNLFGDILTDLGAAIQGGLGFAASANINPDRSAPSMFEPVHGSAPDIAHLGIANPIAAI 295

Query: 302 WAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHGPKTPDMKGNATTPQVADAI 355
           W+GAMML+ LG      ++A   I+AA+E     G  T  + G   T  +  A+
Sbjct: 296 WSGAMMLEHLGE-----REAAGMIMAALERTTIRGIGT--VPGKDRTRSITAAV 342


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: 362
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: 347
Length adjustment: 29
Effective length of query: 332
Effective length of database: 318
Effective search space:   105576
Effective search space used:   105576
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