GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gci in Pseudomonas fluorescens FW300-N2C3

Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate AO356_26155 AO356_26155 rhamnonate dehydratase

Query= BRENDA::A9CEQ8
         (378 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26155
          Length = 394

 Score =  147 bits (372), Expect = 4e-40
 Identities = 112/372 (30%), Positives = 176/372 (47%), Gaps = 30/372 (8%)

Query: 9   HLLEHRLDTPFES-ASMRFDRRAH-------VLVEIECDDGTVGWGECLGPARPNAAVVQ 60
           H ++  + TP       R  RR+        ++VEIE +DGTVG+    G   P A +V+
Sbjct: 28  HWIDDHIATPMSKYPDYRQSRRSFGINVLGTLVVEIEANDGTVGFAVTTG-GEPAAYIVE 86

Query: 61  AYSGWLI-GQDPRQTEKIWAVLYNALRDQGQRGLSLTALSGIDIALWDIKGKHYGASISM 119
            +    + G      EKIW  +Y +    G++GL +  +SG+D+ALWD+ GK     +  
Sbjct: 87  KHLARFVEGARVTDIEKIWDQMYQSTLYYGRKGLVINTISGVDLALWDLLGKIRQEPVHQ 146

Query: 120 LLGGRWRESVRAYATGSFKRDNVDRVSDNASEMAERR--AEGFHACKIKIGFGVEEDLRV 177
           LLGG  R+ ++ YATG+ + D   ++     +M      AEG          G+ ++L  
Sbjct: 147 LLGGAVRDELQFYATGA-RPDLAQKMGFIGGKMPLHHGPAEGEE--------GLRKNLEA 197

Query: 178 IAAVREAIGPDMRLMIDANHGYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAG 237
           +A +RE +GPD  LM+D      +  A  L   A   G+ W EE + P+    YA +R  
Sbjct: 198 LATMRERVGPDFWLMLDCWMSLDLNYATKLAVGAHEHGLKWIEEALPPDDYWGYAALRKN 257

Query: 238 QP--IPVAGGETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQKIATLATLHGVRIVP 295
            P  + V  GE    R+G    L  G  DI+QPD+  CGG +E+ KI+ LA  H   ++P
Sbjct: 258 VPKGMLVTTGEHEATRWGFRMLLEMGCCDIIQPDVGWCGGLTELVKISALADAHNALVIP 317

Query: 296 HVWGTGVQIAAALQFMAAMTPDPVRVNPIEPIMEFDRTHNPFRQAVLREPLEAVNGV-VT 354
           H  G+ V    +  F+A     P     +    + D     F   +L EP+     + ++
Sbjct: 318 H--GSSVY---SYHFVATRHNSPF-AEFLMMAPKADEVVPMFHPQLLGEPVPVQGRMRLS 371

Query: 355 IPDGPGLGIEIN 366
           + D PG G+ +N
Sbjct: 372 VLDQPGFGVTLN 383


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: 449
Number of extensions: 26
Number of successful extensions: 3
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: 394
Length adjustment: 30
Effective length of query: 348
Effective length of database: 364
Effective search space:   126672
Effective search space used:   126672
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