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

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis