GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Burkholderia phytofirmans PsJN

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 BPHYT_RS15730 BPHYT_RS15730 isocitrate dehydrogenase

Query= SwissProt::Q58130
         (333 letters)



>FitnessBrowser__BFirm:BPHYT_RS15730
          Length = 418

 Score =  156 bits (394), Expect = 1e-42
 Identities = 122/368 (33%), Positives = 176/368 (47%), Gaps = 69/368 (18%)

Query: 7   IEGDGIGKEVVPATIQVLEATGLPFEFVYAE----------AGDEVYKRTGKA--LPEET 54
           IEGDG G ++ P  I+V++A     E  YA           AG++  K  G    LPEET
Sbjct: 34  IEGDGTGLDITPVMIKVVDAA---VEKAYAGKKKIHWMEIYAGEKSTKVYGPDVWLPEET 90

Query: 55  I----ETALDCDAVLFGAAGETAADVIVKLRHILDTYANIRPVKAYKGVKC--LRPD-ID 107
           +    E  +     L    G     + V LR  LD Y  +RPV+ +KGV      P+  +
Sbjct: 91  LQVLKEYVVSIKGPLTTPVGGGIRSLNVALRQELDLYVCLRPVQYFKGVPSPVREPEKTN 150

Query: 108 YVIVRENTEGLYKGIE--AEIDE------------GIT---------IATRVITEKACER 144
            VI REN+E +Y GIE  AE ++            G+          I  + ++ +  ER
Sbjct: 151 MVIFRENSEDIYAGIEWPAESEQAKKVIKFLREEMGVKKIRFPDTSGIGIKPVSREGTER 210

Query: 145 IFRFAFNLARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVAEEY------------ 192
           + R A   A + ++      VT  HK N++K T+G F+   Y +A++             
Sbjct: 211 LVRKAIQYAIDNERRS----VTLVHKGNIMKFTEGAFRDYGYALAQKEFAAELIDGGPWM 266

Query: 193 --------DDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAP 244
                    DI  +D   DA    I+ +P  +DV+ T NL GD +SD  A  VGG+G+AP
Sbjct: 267 KIKNPKTGGDIVLKDVIADAFLQQILLRPAEYDVIATLNLNGDYVSDALAAQVGGIGIAP 326

Query: 245 SANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVL 304
            AN+ D   +FE  HG+AP  AGK   NP + ILSA +MLR+LG  EAAD + K++E+ +
Sbjct: 327 GANMSDSVAMFEATHGTAPKYAGKDYVNPGSEILSAEMMLRHLGWTEAADLIIKSMEKSI 386

Query: 305 ALGLTTPD 312
                T D
Sbjct: 387 LQKRVTYD 394


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: 337
Number of extensions: 22
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: 333
Length of database: 418
Length adjustment: 30
Effective length of query: 303
Effective length of database: 388
Effective search space:   117564
Effective search space used:   117564
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: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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