GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Escherichia coli BW25113

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 15258 b1136 isocitrate dehydrogenase (NCBI)

Query= SwissProt::Q58130
         (333 letters)



>FitnessBrowser__Keio:15258
          Length = 416

 Score =  159 bits (402), Expect = 1e-43
 Identities = 120/366 (32%), Positives = 169/366 (46%), Gaps = 65/366 (17%)

Query: 7   IEGDGIGKEVVPATIQVLEATGLP----------FEFVYAEAGDEVYKRTGKALPEETIE 56
           IEGDGIG +V PA ++V++A               E    E   +VY +    LP ET++
Sbjct: 32  IEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWMEIYTGEKSTQVYGQD-VWLPAETLD 90

Query: 57  TALDCDAVLFGA----AGETAADVIVKLRHILDTYANIRPVKAYKGVKC--LRPDI-DYV 109
              +    + G      G     + V LR  LD Y  +RPV+ Y+G       P++ D V
Sbjct: 91  LIREYRVAIKGPLTTPVGGGIRSLNVALRQELDLYICLRPVRYYQGTPSPVKHPELTDMV 150

Query: 110 IVRENTEGLYKGIEAEID-----------------------EGITIATRVITEKACERIF 146
           I REN+E +Y GIE + D                       E   I  +  +E+  +R+ 
Sbjct: 151 IFRENSEDIYAGIEWKADSADAEKVIKFLREEMGVKKIRFPEHCGIGIKPCSEEGTKRLV 210

Query: 147 RFAFNLARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVAEEY-------------- 192
           R A   A    +      VT  HK N++K T+G FK   Y++A E               
Sbjct: 211 RAAIEYAIANDR----DSVTLVHKGNIMKFTEGAFKDWGYQLAREEFGGELIDGGPWLKV 266

Query: 193 ------DDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSA 246
                  +I  +D   DA    I+ +P  +DV+   NL GD +SD  A  VGG+G+AP A
Sbjct: 267 KNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIACMNLNGDYISDALAAQVGGIGIAPGA 326

Query: 247 NIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVLAL 306
           NIGDE  LFE  HG+AP  AG+   NP + ILSA +MLR++G  EAAD + K +E  +  
Sbjct: 327 NIGDECALFEATHGTAPKYAGQDKVNPGSIILSAEMMLRHMGWTEAADLIVKGMEGAINA 386

Query: 307 GLTTPD 312
              T D
Sbjct: 387 KTVTYD 392


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: 336
Number of extensions: 24
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: 416
Length adjustment: 30
Effective length of query: 303
Effective length of database: 386
Effective search space:   116958
Effective search space used:   116958
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