Aligments for a candidate for ilvD in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Aligments for a candidate for ilvD in Pseudomonas simiae WCS417

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate GFF2156 PS417_11000 dihydroxy-acid dehydratase

Query= curated2:B9MPM8
         (552 letters)



>FitnessBrowser__WCS417:GFF2156
          Length = 578

 Score =  369 bits (948), Expect = e-106
 Identities = 217/544 (39%), Positives = 321/544 (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 AFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWTRIGRGMPTIVDLQPSGRFLME 318

Query: 313 DLYFAGGVQAVMNELSKKGLL-HLNLMTVTGKTVGENIKDANVKNYN-VIRPIDNPYSET 370
           + Y+AGG+ AV+  L +  L+ H N +TV GK++GEN +D+ +   + VIR +DNP    
Sbjct: 319 EFYYAGGLPAVLRRLGEANLIPHPNALTVNGKSLGENTQDSPIYGQDEVIRTLDNPIRAD 378

Query: 371 GGLVIVRGNLAPDGAVVKKSAVPPKLMKHRGPARVFESGEEVFEAILKG---KIQKGDVI 427
           GG+ ++RGNLAP GAV+K SA  P LM+HRG A VFE+  ++++A +      +    ++
Sbjct: 379 GGICVLRGNLAPLGAVLKPSAASPALMQHRGRAVVFEN-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 AGGPLATVKEGDWIELDCANGRLHLDIPDAELAARMADLAPPQKLIVGGYRQLYIDHVLQ 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: 792
Number of extensions: 43
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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