GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Sphingomonas koreensis DSMZ 15582

Align Fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate Ga0059261_0725 Ga0059261_0725 Fructose-1,6-bisphosphate aldolase

Query= curated2:B2RLG9
         (293 letters)



>FitnessBrowser__Korea:Ga0059261_0725
          Length = 301

 Score =  313 bits (803), Expect = 2e-90
 Identities = 163/286 (56%), Positives = 213/286 (74%), Gaps = 3/286 (1%)

Query: 8   QMRQAPGFVGALDQSGGSTPKALKAYGIQPDAYQSEEEMFDLIHQMRTRMITSPAFATGK 67
           ++ +  GF+ ALDQSGGSTPKALK YGI+ DAY  +EEMFDLIH MR+R+ITSP+F   K
Sbjct: 9   KIAEGNGFIAALDQSGGSTPKALKGYGIEEDAYSGDEEMFDLIHAMRSRIITSPSFNGDK 68

Query: 68  IIGVILFERTMRGKIEGMPTADFLWEKRHIVPFLKVDKGLQDEANGVQLMKPFPELGKLC 127
           +IG ILFERTM G+++G PT   L E R +VPF+K+DKGL+ E NGVQLMKP PEL  L 
Sbjct: 69  VIGAILFERTMDGQVDGEPTPQALIE-RGVVPFIKIDKGLEAEENGVQLMKPMPELDALL 127

Query: 128 EEAVGYHVFGTKMRSVIKQANEQGIRDIVEQQFQWGKEILSHGLVPILEPEVDIHCPEKA 187
             A G  VFGTK RSV+  AN QGI  IV QQF+ G+++L+ GL+PILEPEV+I  PE+A
Sbjct: 128 ARAKGLGVFGTKERSVVNLANAQGIAAIVAQQFEVGRQVLAAGLMPILEPEVNIKSPERA 187

Query: 188 KAEEILKRELLAQLDKMT--EPVMLKITIPTVDNFYKEIIEHPMMLRVVALSGGYSREQA 245
           +A+ IL+ E+L  LD MT  + VMLK++IP     +  +++HP +LRVVALSGG+ R +A
Sbjct: 188 QADAILRDEILKHLDAMTGDDKVMLKLSIPAQPGLFDALVDHPRVLRVVALSGGFKRPEA 247

Query: 246 NELLSRNHGVIASFSRALVEGLSVQQTDAEFNAMLEASIEDVYQAS 291
              L++N G+IASFSRAL+E L    TDAEF+A L A+I++++ AS
Sbjct: 248 CAELAKNRGMIASFSRALLEDLRHGMTDAEFDASLGAAIDEIHAAS 293


Lambda     K      H
   0.318    0.135    0.384 

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: 280
Number of extensions: 11
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: 293
Length of database: 301
Length adjustment: 26
Effective length of query: 267
Effective length of database: 275
Effective search space:    73425
Effective search space used:    73425
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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