GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS04815 BPHYT_RS04815
           dihydroxy-acid dehydratase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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