Alignments for a candidate for ilvD in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Polaromonas naphthalenivorans CJ2

Align Dihydroxy-acid dehydratase 2; DAD 2; EC 4.2.1.9 (uncharacterized)
to candidate WP_011802359.1 PNAP_RS14935 phosphogluconate dehydratase

Query= curated2:Q5YX61
         (629 letters)



>NCBI__GCF_000015505.1:WP_011802359.1
          Length = 613

 Score =  236 bits (601), Expect = 3e-66
 Identities = 193/592 (32%), Positives = 274/592 (46%), Gaps = 78/592 (13%)

Query: 35  KPVVAVANSFTEFVPGHTHLQPVGRIVGDAIRR-------AGGIPREFNTIAVDDGIAMG 87
           +P + +  S+ + +  HT L     ++ D  R+       AGG+P      A+ DG+  G
Sbjct: 67  RPNIGIVTSYNDMLSAHTPLLSYPALIKDEARKHGATAQVAGGVP------AMCDGVTQG 120

Query: 88  HQGMLYSLPSRDLIADSIEYMVQAHCADALVCISNCDKITPGMLLAAMRLD-IPTVFVSG 146
             GM  SL SRD+IA      +     DA + +  CDKI PG+L+ A++   +P VFV  
Sbjct: 121 TSGMELSLFSRDVIAMGTAVALSHDMFDAALLLGVCDKIVPGLLIGALQFGHLPMVFVPA 180

Query: 147 GPMEGGRATLADGTVRRLDLITAMSEAVNDATSDADLATIEENACPTCGSCAGMFTANSM 206
           GPM  G        +R      A      DA  + +L +         G+C    TANS 
Sbjct: 181 GPMPSGLPNKEKARIREQ---AAQGLVGRDALLEGELKSYHSP-----GTCTFYGTANSN 232

Query: 207 NCLVEALGLALPGNGTTLATHTARRDLYEAAGATIMAITR-RYYDRDDATVLPRAIASRA 265
             L+EA+GL +PG          R +L   A  T++ IT+ + +      V  RAI    
Sbjct: 233 QMLMEAMGLHVPGTAFVQPGDMLRDELTREAARTVLGITKSKRFAPIGHVVDERAIV--- 289

Query: 266 AFDNAMALDLAMGGSTNTVLHLLAAAHEAGLDYTLADIEKRSRAVPCLCKVAPNGSHLME 325
              NAM   LA GGSTN ++H +A A  AG+     D    S  VP L  V PNGS  + 
Sbjct: 290 ---NAMVALLATGGSTNHLIHWVAVAQSAGIVIDWNDFSALSDVVPLLTHVYPNGSADVN 346

Query: 326 DVHRAGGIPAILGELRRGGHLHTTVRAVHSESLDGWLAEWDVRGPNPAQAAVDLFHAAPG 385
               AGG   ++ EL   G +H  V  V +    G + E+         A+V     A  
Sbjct: 347 QFQAAGGPGLVIRELLDAGFMHEDVLTVRA----GGIREY---------ASVPALEGA-- 391

Query: 386 GVRSATAFSQSARWAALDLDAESGCIRDVAHAYSEDGGLAVLRGNLAVDGAVVKSAGVPA 445
                     +  W A+    +   +R     +S  GGL +L GNL    +V+K + VP 
Sbjct: 392 ----------ALAWHAVGDSKDEAIVRPAGRPFSATGGLKLLTGNLG--RSVIKVSAVPD 439

Query: 446 DLHVFTGEAVVAESQEEAVTAVLSGRVR--------PGTVLVIRYEGPR--GGPGMQEML 495
           D HV    A V +SQE+ + A  SG +          G V V+R++GP+  G P + ++ 
Sbjct: 440 DRHVIEAPARVFDSQEDLLLAFNSGELERLCNETAARGVVCVVRWQGPQANGMPELHKLT 499

Query: 496 YPTAYLKGRGLAGSVAVVTDGRFSGGSSGLSIG-HVSPEAAAGGTIAAVTDGDPITIDIP 554
            P A L+G+G    VA+VTDGR SG S  +    HVSPEAAAGG +A V DGD + +D  
Sbjct: 500 PPLAVLQGKGF--MVALVTDGRMSGASGKVPAAIHVSPEAAAGGPLAKVVDGDVVRVDAL 557

Query: 555 SRTLRLEVDDAEIARRLAH------RRRTGYRPRSRHRPLSTALRAYALLAQ 600
           +  LR+ VD+AE A R A       RR+ G       R L T +R +AL A+
Sbjct: 558 TGELRVLVDEAEWAARPASIMPDELRRQNGV---GMGRGLFTGMRRHALTAE 606


Lambda     K      H
   0.319    0.134    0.395 

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: 1001
Number of extensions: 61
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 629
Length of database: 613
Length adjustment: 37
Effective length of query: 592
Effective length of database: 576
Effective search space:   340992
Effective search space used:   340992
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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
the source code
instructions for running GapMind on your computer
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