GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xad in Burkholderia phytofirmans PsJN

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate BPHYT_RS04815 BPHYT_RS04815 dihydroxy-acid dehydratase

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



>FitnessBrowser__BFirm:BPHYT_RS04815
          Length = 557

 Score =  249 bits (636), Expect = 2e-70
 Identities = 173/529 (32%), Positives = 274/529 (51%), Gaps = 32/529 (6%)

Query: 30  RYMNYGMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHP 89
           R M Y +  E+    +P+IGIA   S +TPCN     LA    A I+ A   P  F    
Sbjct: 20  RSMYYALGYEKADFDKPMIGIANGHSTITPCNAGLQRLADAAVAAIKGADANPQIFGTPT 79

Query: 90  IAEQSRRPTAALDRNLAYLGLVE-----ILHGYPLDGVVLTTGCDKTTPACLMAAATTDL 144
           I++     T  +  +L    ++       + G  +DGVV+  GCDK  P  ++    T++
Sbjct: 80  ISDGMSMGTEGMKYSLVSREVISDCIETCVQGQWMDGVVVIGGCDKNMPGGMIGMLRTNV 139

Query: 145 PAIVLSGGPMLDGHHKGELIGSGTVL--WHARNLMAAGEIDYEGFMEMTTAASPSVGHCN 202
           P+I + GG +  G+ KG  +   T++  + A     AG +  E F  +   A PS G C 
Sbjct: 140 PSIYVYGGTIRPGNWKGTDL---TIVSSFEAVGEFTAGRMSQEDFDGIEQNACPSTGSCG 196

Query: 203 TMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICELVLQDIRPSQIMTRQ 262
            M TA +M++  EALGMSL   +++  P +E+   A  + + + E V +D++P  I+T++
Sbjct: 197 GMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVESVKKDLKPRDIVTKK 256

Query: 263 AFENAIAVASALGASSNCPPHLIAIARHMGVELSLDDWQRIGEDVPLLVNCMPAGKYLGE 322
           + ENA+AV  A G S+N   H +AIA    VE S+DD++R+ + VP++ N  P+G+++  
Sbjct: 257 SIENAVAVIMATGGSTNAVLHFLAIAHAAEVEWSIDDFERMRKKVPVICNLKPSGQFVAT 316

Query: 323 GFHRAGGVPSVMHELQKAGRLHEDCATVSGRTIGE---IVSSSLTSNADVIHPFDTPLKH 379
             H+AGG+P VM  L  AG LH DC T++GRTI E    V     ++  VI P D  L  
Sbjct: 317 DLHKAGGIPQVMKILLDAGLLHGDCITITGRTIAEELKDVPGKPRADQQVIFPIDQALYK 376

Query: 380 RAGFIVLSGNFFDSAIMKMSVVGEAFRKTYLSEPGAENSFEARAIVFEGPED-YHARIDD 438
                +L GN        ++V G   + T L  P         A VF+  +    A + D
Sbjct: 377 EGHLAILKGN--------LAVDGAVAKITGLKNP----VITGPARVFDDEQSALEAILAD 424

Query: 439 PALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASP 497
             +  D   ++V+R +G  G PG  E+  +AP +A+I +G+ +S+  + DGR SG +   
Sbjct: 425 KIVAGD---VVVLRYLGPKGGPGMPEM--LAPTSAIIGKGLGESVGLITDGRFSGGTWGM 479

Query: 498 SILNMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMARRRLEW 546
            + +++PEA VGG +A +Q  D + +D +   + L ID+ E+ RRR  W
Sbjct: 480 VVGHVAPEAFVGGTIAFVQEGDSITIDAHKLLLQLNIDNAELERRRAAW 528


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: 806
Number of extensions: 42
Number of successful extensions: 4
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: 557
Length adjustment: 36
Effective length of query: 558
Effective length of database: 521
Effective search space:   290718
Effective search space used:   290718
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