GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Dinoroseobacter shibae DFL-12

Align 3-isopropylmalate/3-methylmalate dehydrogenase; 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; IPMDH; Beta-IPM dehydrogenase; D-malate dehydrogenase [decarboxylating]; EC 1.1.1.85; EC 1.1.1.n5; EC 1.1.1.83 (characterized)
to candidate 3610012 Dshi_3393 3-isopropylmalate dehydrogenase (RefSeq)

Query= SwissProt::Q58130
         (333 letters)



>FitnessBrowser__Dino:3610012
          Length = 357

 Score =  233 bits (594), Expect = 5e-66
 Identities = 148/354 (41%), Positives = 209/354 (59%), Gaps = 29/354 (8%)

Query: 4   ICVIEGDGIGKEVVPATIQVLE-----ATGLPFEFVYAEAGDEVYKRTGKALPEETIETA 58
           I V +GDGIG E++  T+ +L      A      F     G   Y +TG+ALP  +++ A
Sbjct: 6   ITVFDGDGIGPEIMAPTLGLLRKLAGTAATYDLNFDSHPMGAGHYAQTGQALPRASLDAA 65

Query: 59  LDCDAVLFGAAG--------ETAADVIVKLRHILDTYANIRPVKAYKGVKC---LRPDID 107
              DA+L  A G         T     + +R  LD YA +RPV+   G          +D
Sbjct: 66  RASDAILLSAMGLPDIRYPDGTEITPQIDIRIALDLYAGVRPVRIVPGHPTPLHAPGPVD 125

Query: 108 YVIVRENTEGLY--KGIEAEIDEGITIATRVITEKACERIFRFAFNLARERKKMGK-EGK 164
           +V++RE+TEGL+  KG +  + +     T  IT    E++FRFAF LA +RK  G+ EG+
Sbjct: 126 FVLIRESTEGLFHTKG-KGTVTKDHATETLQITRDTSEKLFRFAFALAAQRKASGRGEGR 184

Query: 165 VTCAHKANVLKLTDGLFKKIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFDVVVTSNL 224
           VTC  KANV +     F++IF   A  + D+ A+  Y+DAM ++++T+PQ FDV+VT N+
Sbjct: 185 VTCVDKANVFRAF-AFFREIFDAEAARHPDLIADHAYVDAMALWMVTRPQTFDVMVTENM 243

Query: 225 FGDILSDGAAGTVGGLGLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLML 284
           FGDILSD  AG +GGLGLAPSA+IGD++ +F+P HG+APDIAG+ IANP A ILSA +ML
Sbjct: 244 FGDILSDLGAGLMGGLGLAPSADIGDDNAVFQPCHGTAPDIAGRGIANPLAMILSAAMML 303

Query: 285 RYLG----EYEAA---DKVEKALEEVLALG-LTTPDLGGNLNTFEMAEEVAKRV 330
            +L       E A    ++ +A+E VL  G + T DLGGN +T E A  VA ++
Sbjct: 304 DWLALRGQNAELATDGQRLREAVEAVLTEGRVLTRDLGGNASTEEAAAAVAAKL 357


Lambda     K      H
   0.318    0.138    0.390 

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: 288
Number of extensions: 14
Number of successful extensions: 8
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: 333
Length of database: 357
Length adjustment: 29
Effective length of query: 304
Effective length of database: 328
Effective search space:    99712
Effective search space used:    99712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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