GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Pseudomonas fluorescens GW456-L13

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate PfGW456L13_3320 L-arabonate dehydratase (EC 4.2.1.25)

Query= curated2:B9MPM8
         (552 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3320
          Length = 578

 Score =  367 bits (941), Expect = e-106
 Identities = 219/546 (40%), Positives = 324/546 (59%), Gaps = 24/546 (4%)

Query: 16  RSLFKAMGYTDEEIR-RPLIAVVNSWNEVVPGHIHLDRIAEAVKAGIRLAGATPMEFNVI 74
           RS  K  G  D +   +P+I + N+W+E+ P + H  +IAE VK G+  AG  P+EF V 
Sbjct: 25  RSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHFRQIAEHVKRGVIEAGGFPVEFPVF 84

Query: 75  GVCDGIAMGHIGMK-YSLITRELIADSIEAMVMAHQFDGMVLIPNCDKIVPGMLIAAARV 133
                 + G   ++  +++TR L +  +E  +  +  DG+VL+  CDK  P +L+ AA  
Sbjct: 85  ------SNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVLLTGCDKTTPALLMGAASC 138

Query: 134 NIPAILISGGPMLAGKIGDKVCDLNS---VFEGVGAYSAGKISEEDLYALEENACPGCGS 190
           ++PAI+++GGPML GK   K  D+ S   V++      AG IS +D  A E       G+
Sbjct: 139 DVPAIVVTGGPMLNGKHKGK--DIGSGTVVWQLSEQVKAGTISIDDFLAAEGGMSRSAGT 196

Query: 191 CSGMFTANTMNCLSEVLGLALPGNGTIPAVMAARIRLAKMAGMKIVELVEKDIKPSDILT 250
           C+ M TA+TM C++E LG +LP N  IPAV A R  LA M+GM+ VE+V +D+K S ILT
Sbjct: 197 CNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMRAVEMVREDLKLSKILT 256

Query: 251 VEAFENALAVDMALGGSTNTILHLPAIANEVGIKLNLDIINAISDRTPNLCKLSPAGQHH 310
            EAFENA+ V+ A+GGSTN ++HL AIA  +G++L+LD    I    P +  L P+G+  
Sbjct: 257 KEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWTRIGRGMPTIVDLQPSGRFL 316

Query: 311 IEDLYFAGGVQAVMNELSKKGLL-HLNLMTVTGKTVGENIKDANVKNYN-VIRPIDNPYS 368
           +E+ Y+AGG+ AV+  L +  L+ + N +TV GK++GEN +DA +   + VIR +DNP  
Sbjct: 317 MEEFYYAGGLPAVLRRLGEANLIPNPNALTVNGKSIGENTRDAPIYGEDEVIRTLDNPIR 376

Query: 369 ETGGLVIVRGNLAPDGAVVKKSAVPPKLMKHRGPARVFESGEEVFEAILKG---KIQKGD 425
             GG+ ++RGNLAP GAV+K SA  P+LM+HRG A VFE+  ++++A +      +    
Sbjct: 377 ADGGICVLRGNLAPLGAVLKPSAATPELMQHRGRAVVFEN-FDMYKARINDPELDVDANS 435

Query: 426 VIVIRYEGPKGGPGMRE---MLSPTSALAGVGLIEDVALITDGRFSGATRGACFGHVSPE 482
           ++V++  GPKG PGM E   M  P   LA    + D+  I+D R SG   G    HV+PE
Sbjct: 436 ILVMKNCGPKGYPGMAEVGNMGLPAKLLAQG--VTDMVRISDARMSGTAYGTVVLHVAPE 493

Query: 483 AAERGPIAAVQDGDMISIDIENKTLTLEVPEEEIKRRLEILPPFEPKVKKGYLYRYSKLV 542
           AA  GP+AAV++GD I +D  +  L L++ + E+  R+  L P +  +  GY   Y   V
Sbjct: 494 AAAGGPLAAVKEGDWIELDCASGRLHLDIADTELAARMADLQPPQNLIVGGYRQLYIDHV 553

Query: 543 RSASTG 548
             A  G
Sbjct: 554 LQADQG 559


Lambda     K      H
   0.318    0.137    0.394 

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: 788
Number of extensions: 45
Number of successful extensions: 7
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: 552
Length of database: 578
Length adjustment: 36
Effective length of query: 516
Effective length of database: 542
Effective search space:   279672
Effective search space used:   279672
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: 53 (25.0 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