GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xad in Acidovorax sp. GW101-3H11

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate Ac3H11_954 Dihydroxy-acid dehydratase (EC 4.2.1.9)

Query= reanno::pseudo5_N2C3_1:AO356_28760
         (594 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_954
          Length = 567

 Score =  277 bits (709), Expect = 7e-79
 Identities = 182/531 (34%), Positives = 277/531 (52%), Gaps = 26/531 (4%)

Query: 30  RYMNYGMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHP 89
           R M Y M  EE    +P++G+A   S +TPCN    +LA    AGI +AGG    F    
Sbjct: 28  RSMYYAMGYEEGDFVKPMVGVANGHSTITPCNSGLQKLADAAIAGIEEAGGNAQVFGTPT 87

Query: 90  IAEQSRRPTAALDRNLAYLGLVE-----ILHGYPLDGVVLTTGCDKTTPACLMAAATTDL 144
           I++     T  +  +L    ++       + G  +DGV++  GCDK  P  LM     ++
Sbjct: 88  ISDGMAMGTEGMKYSLVSREVISDCIETCVGGQWMDGVLVVGGCDKNMPGGLMGMLRANV 147

Query: 145 PAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTM 204
           PAI + GG +L GH++G+ +   +V + A    AAG++      E+   A P  G C  M
Sbjct: 148 PAIYVYGGTILPGHYQGKDLNIVSV-FEAVGENAAGKLSDFDLKEIEKRAIPGTGSCGGM 206

Query: 205 GTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICELVLQDIRPSQIMTRQAF 264
            TA +M++  EALG+SLP  +++  P+ E+   A  + K + E + +DI+P  I+T+++ 
Sbjct: 207 YTANTMSSAFEALGISLPYSSTMANPHDEKMNSAKESAKVLIEAIKKDIKPRDIVTKKSI 266

Query: 265 ENAIAVASALGASSNCPPHLIAIARHMGVELSLDDWQRIGEDVPLLVNCMPAGKYLGEGF 324
           ENA+AV  A G S+N   H +AIA   GVE S+DD++R+    P+L +  P+GKYL    
Sbjct: 267 ENAVAVIMATGGSTNAVLHFLAIAHAAGVEWSIDDFERVRVKTPVLCDLKPSGKYLAVDL 326

Query: 325 HRAGGVPSVMHELQKAGRLHEDCATVSGRTIGEI---VSSSLTSNADVIHPFDTPLKHRA 381
           HRAGG+P VM  L  AG LH DC T+ G+T+ E+   V     ++ DVI P + P+  + 
Sbjct: 327 HRAGGIPQVMKVLLNAGLLHGDCLTIEGKTVAEVLKDVPDQPRADQDVIRPINNPMYAQG 386

Query: 382 GFIVLSGNFFDSAIMKMSVVGEAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPAL 441
              +L GN        +S  G   + T L  P         A VFE  +     I   A 
Sbjct: 387 HLAILKGN--------LSPEGAVAKITGLKNP----VITGPARVFEDEQSALEAI--LAG 432

Query: 442 DIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSIL 500
            I    ++V+R +G  G PG  E+  +AP  ALI  G+ +S+  + DGR SG +    + 
Sbjct: 433 KIKAGDVMVLRYLGPKGGPGMPEM--LAPTGALIGAGLGESVGLITDGRFSGGTWGMVVG 490

Query: 501 NMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMARRRLEWTPNIP 551
           +++PEAA GG +A +   D + +D     + L + +EE+ARRR  WT   P
Sbjct: 491 HVAPEAAAGGTIAFVHEGDSITIDARQLLLELNVSEEEIARRRAAWTAPAP 541


Lambda     K      H
   0.319    0.135    0.407 

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: 834
Number of extensions: 43
Number of successful extensions: 5
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: 594
Length of database: 567
Length adjustment: 36
Effective length of query: 558
Effective length of database: 531
Effective search space:   296298
Effective search space used:   296298
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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