GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Pseudomonas fluorescens FW300-N1B4

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate Pf1N1B4_4621 L-arabonate dehydratase (EC 4.2.1.25)

Query= curated2:B9MPM8
         (552 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4621
          Length = 578

 Score =  370 bits (949), Expect = e-106
 Identities = 218/544 (40%), Positives = 322/544 (59%), Gaps = 20/544 (3%)

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 NIPAILISGGPMLAGKI-GDKVCDLNSVFEGVGAYSAGKISEEDLYALEENACPGCGSCS 192
           ++PAI+++GGPML GK  G  +     V++      AG I+ +D  A E       G+C+
Sbjct: 139 DVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTITLDDFLAAEGGMSRSAGTCN 198

Query: 193 GMFTANTMNCLSEVLGLALPGNGTIPAVMAARIRLAKMAGMKIVELVEKDIKPSDILTVE 252
            M TA+TM C++E LG +LP N  IPAV A R  LA M+GM+ VE+V +D+K S ILT E
Sbjct: 199 TMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMRAVEMVREDLKLSKILTKE 258

Query: 253 AFENALAVDMALGGSTNTILHLPAIANEVGIKLNLDIINAISDRTPNLCKLSPAGQHHIE 312
           AFENA+ V+ A+GGSTN ++HL AIA  +G++L+LD  + I    P +  L P+G+  +E
Sbjct: 259 AFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWSRIGRGMPTIVDLQPSGRFLME 318

Query: 313 DLYFAGGVQAVMNELSKKGLL-HLNLMTVTGKTVGENIKDANVKNYN-VIRPIDNPYSET 370
           + Y+AGG+ AV+  L +  L+ + N +TV GKT+GEN KDA +   + VIR +DNP    
Sbjct: 319 EFYYAGGLPAVLRRLGEANLIPNPNALTVNGKTIGENTKDAPIYGQDEVIRTLDNPIRAD 378

Query: 371 GGLVIVRGNLAPDGAVVKKSAVPPKLMKHRGPARVFESGEEVFEAILKG---KIQKGDVI 427
           GG+ ++RGNLAP GAV+K SA   +LM+HRG A VFE+  ++++A +      +    ++
Sbjct: 379 GGICVLRGNLAPLGAVLKPSAASAELMQHRGRAVVFEN-FDMYKARINDPELDVDANSIL 437

Query: 428 VIRYEGPKGGPGMRE---MLSPTSALAGVGLIEDVALITDGRFSGATRGACFGHVSPEAA 484
           V++  GPKG PGM E   M  P   LA    + D+  I+D R SG   G    HV+PEAA
Sbjct: 438 VMKNCGPKGYPGMAEVGNMGLPAKLLAQG--VTDMVRISDARMSGTAYGTVVLHVAPEAA 495

Query: 485 ERGPIAAVQDGDMISIDIENKTLTLEVPEEEIKRRLEILPPFEPKVKKGYLYRYSKLVRS 544
             GP+A V++GD I +D  N  L L++P+ E+  R+  L P +  +  GY   Y   V  
Sbjct: 496 AGGPLATVKEGDWIELDCANGRLHLDIPDAELAARMADLQPPQQLIVGGYRQLYIDHVLQ 555

Query: 545 ASTG 548
           A  G
Sbjct: 556 ADQG 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: 777
Number of extensions: 42
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