GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Pseudomonas putida KT2440

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 PP_4011 PP_4011 isocitrate dehydrogenase, NADP(+)-specific

Query= SwissProt::Q58130
         (333 letters)



>FitnessBrowser__Putida:PP_4011
          Length = 418

 Score =  159 bits (401), Expect = 2e-43
 Identities = 124/384 (32%), Positives = 179/384 (46%), Gaps = 72/384 (18%)

Query: 7   IEGDGIGKEVVPATIQVLEAT---------GLPFEFVYA-EAGDEVYKRTGKALPEETIE 56
           IEGDGIG +V P  I+V++A           + +  VYA E   +VY +    LP+ET++
Sbjct: 34  IEGDGIGVDVSPVMIKVVDAAVQKAYGGKRKIAWMEVYAGEKATQVYDQD-TWLPQETLD 92

Query: 57  TALDCDAVLFGA----AGETAADVIVKLRHILDTYANIRPVKAYKGVKC--LRP-DIDYV 109
              D    + G      G     + V LR  LD Y  +RPV  ++GV     +P D+D V
Sbjct: 93  AVRDYVVSIKGPLTTPVGGGIRSLNVALRQQLDLYVCLRPVLWFQGVPSPVKKPGDVDMV 152

Query: 110 IVRENTEGLYKGIE-----------------------AEIDEGITIATRVITEKACERIF 146
           I REN+E +Y GIE                          D+   I  + ++++  +R+ 
Sbjct: 153 IFRENSEDIYAGIEWKAGSPEANKVIKFLKEEMGVTKIRFDQDCGIGVKPVSKEGTKRLV 212

Query: 147 RFAFNLARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVAEEY-------------- 192
           R A     +  +      +T  HK N++K T+G FK   Y+VA +               
Sbjct: 213 RKALQYVVDNDRES----LTLVHKGNIMKFTEGAFKDWGYEVARDEFGAELLDGGPWMKF 268

Query: 193 ------DDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSA 246
                  ++  +D   DAM   I+ +P  +DV+ T NL GD LSD  A  VGG+G+AP A
Sbjct: 269 KNPKTGREVIVKDAIADAMLQQILLRPAEYDVIATLNLNGDYLSDALAAEVGGIGIAPGA 328

Query: 247 NIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVLAL 306
           N+ D   +FE  HG+AP  AG+   NP + ILSA +MLR++G  EAAD + K     +A 
Sbjct: 329 NLSDTVAMFEATHGTAPKYAGQDKVNPGSVILSAEMMLRHMGWTEAADLIIKGTNGAIAA 388

Query: 307 GLTTPDLGGNLNTFEMAEEVAKRV 330
              T D       FE   E AK V
Sbjct: 389 KTVTYD-------FERLMEGAKLV 405


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: 310
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