GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xad in Leeuwenhoekiella blandensis MED217

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate WP_009780581.1 MED217_RS10920 dihydroxy-acid dehydratase

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



>NCBI__GCF_000152985.1:WP_009780581.1
          Length = 560

 Score =  267 bits (682), Expect = 1e-75
 Identities = 174/523 (33%), Positives = 273/523 (52%), Gaps = 29/523 (5%)

Query: 35  GMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQS 94
           G+T E+L+  +P+IGIA TG +  PCN H  +LA  VK G  +A  + + F    +++  
Sbjct: 27  GLTDEDLK--KPLIGIASTGYEGNPCNMHLNDLATYVKKGASNADLVGLIFNTIGVSDGI 84

Query: 95  RRPTAAL-----DRNLAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVL 149
              T  +      R++    +  ++     DG+V   GCDK  P  L+A    + P+I++
Sbjct: 85  SNGTPGMRFSLPSRDIIADSMETVVQAMSYDGLVTVVGCDKNMPGALIAQLRLNRPSILV 144

Query: 150 SGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALS 209
            GG +  G H G+ +   +  + A     AG ID   F E+   A P  G C  M TA +
Sbjct: 145 YGGTIASGCHNGKKLDIISA-FEAYGQKVAGTIDDNEFKEVVHKACPGAGACGGMYTANT 203

Query: 210 MNALAEALGMSLPGCASIPA--PYRERGQMAYATGKRICELVLQDIRPSQIMTRQAFENA 267
           M +  EALGMSLP  +S PA      + Q     G+ +  L+ QDI+PS I+T+++ ENA
Sbjct: 204 MASAIEALGMSLPFNSSNPAVTDANIKEQECIKAGEALKYLLEQDIKPSDIVTKESLENA 263

Query: 268 IAVASALGASSNCPPHLIAIARHMGVELSLDDWQRIGEDVPLLVNCMPAGKYLGEGFHRA 327
           I + + LG S+N   H +AIA+   V+ +L+D+QR+ ++ PLL +  P+GKY  E  H  
Sbjct: 264 IRLVTVLGGSTNAVLHFLAIAKAAQVDFTLEDFQRLSDNTPLLADLKPSGKYSMEDLHGV 323

Query: 328 GGVPSVMHELQKAGRLHEDCATVSGRTIGEIVSS--SLTSNADVIHPFDTPLKHRAGFIV 385
           GG+P V+  +   G LH DC TV+G+T+ E +    +L    D+I P + P+K      +
Sbjct: 324 GGIPGVLKYMLDNGMLHGDCLTVTGKTLAENLKDVPNLIDGQDIIRPLNKPIKDSGHIRI 383

Query: 386 LSGNFFDSAIMKMSVVGEAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDE 445
           L GN     +     V +   K  LS  G  N F +   V EG +    +  D       
Sbjct: 384 LFGN-----LATEGAVAKITGKEGLSFTGTANVFNSELEVNEGIKSGKVKKGD------- 431

Query: 446 RCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSP 504
             +++IR  G  G PG  E+  + P ++++  G+   +  + DGR SG S    + ++SP
Sbjct: 432 --VVIIRYEGPKGGPGMPEM--LKPTSSIMGAGLGKDVALITDGRFSGGSHGFVVGHVSP 487

Query: 505 EAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMARRRLEWT 547
           EA VGG +AL++  D + +D    T+N+ I DEE+A+RR +WT
Sbjct: 488 EAQVGGNIALVENGDVISIDAVKNTINIDITDEELAKRREKWT 530


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: 816
Number of extensions: 54
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: 1
Length of query: 594
Length of database: 560
Length adjustment: 36
Effective length of query: 558
Effective length of database: 524
Effective search space:   292392
Effective search space used:   292392
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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