GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gci in Burkholderia phytofirmans PsJN

Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate BPHYT_RS28240 BPHYT_RS28240 L-rhamnonate dehydratase

Query= BRENDA::A9CEQ8
         (378 letters)



>FitnessBrowser__BFirm:BPHYT_RS28240
          Length = 392

 Score =  143 bits (360), Expect = 9e-39
 Identities = 108/344 (31%), Positives = 163/344 (47%), Gaps = 30/344 (8%)

Query: 32  VLVEIECDDGTVGWGECLGPARPNAAVVQAYSGWLIGQDPRQTEKIWAVLYNALRDQGQR 91
           ++VEIE  DGTVG+    G       V +  + +L GQ     EK+W  +Y +    G++
Sbjct: 59  LVVEIEASDGTVGFAVTTGGEIGAFIVEKHLARFLEGQLVTDIEKMWDQMYFSTLYYGRK 118

Query: 92  GLSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYATGSFKRDNVDRVSDNASE 151
           G+ L  +SG+D+ALWD+  K     +  LLGG  R+ +  YATG+          D A E
Sbjct: 119 GVVLNTISGVDLALWDLLAKVRKEPVYQLLGGPVRDELVFYATGA--------RPDLAKE 170

Query: 152 MAERRAEGFHACKIKIGF-------GVEEDLRVIAAVREAIGPDMRLMIDANHGYTVTEA 204
           M      GF   K+ +         G++++L  +A +R  +G D  LM D      V  A
Sbjct: 171 M------GFIGGKLPLQHGPAEGEAGLKQNLEKLADMRSRVGDDFWLMYDCWMSLDVPYA 224

Query: 205 ITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQP--IPVAGGETWHGRYGMWQALSAGA 262
             L   A  +G+ W EE + P+    YA +R   P  + V+ GE    R+G    L    
Sbjct: 225 TRLAQAAHEYGLKWIEECLPPDDYWGYAELRRNVPRGMMVSTGEHEATRWGFRMLLEMQC 284

Query: 263 VDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIAAALQFMAAMTPDPVRVN 322
            D++QPD+  CGG +E+ KI+ LA  H V +VPH  G+ V    +  F+      P    
Sbjct: 285 CDLIQPDVGWCGGITELIKISALADAHNVMVVPH--GSSVY---SYHFVVTRHNSPF-AE 338

Query: 323 PIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEIN 366
            +    + D     F   +L EP+  VNG + +PD PG G+ +N
Sbjct: 339 FLMMAPKADEVVPMFTPLLLDEPV-PVNGRMKVPDTPGFGVRLN 381


Lambda     K      H
   0.321    0.138    0.431 

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: 425
Number of extensions: 25
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: 378
Length of database: 392
Length adjustment: 30
Effective length of query: 348
Effective length of database: 362
Effective search space:   125976
Effective search space used:   125976
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 (21.9 bits)
S2: 50 (23.9 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