GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruF in Pseudomonas fluorescens FW300-N2E2

Align Fructose import permease protein FruF (characterized)
to candidate Pf6N2E2_524 Inositol transport system permease protein

Query= SwissProt::Q8G846
         (356 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_524
          Length = 340

 Score =  143 bits (360), Expect = 8e-39
 Identities = 91/286 (31%), Positives = 157/286 (54%), Gaps = 26/286 (9%)

Query: 58  LITMLQESARYLMIATGMTLVISTAGIDLSVGSVMAVAG--AAAMQTLSN---------- 105
           L+ M+ + +   ++A G+T VI T GIDLS GSV+A++   AA++   S+          
Sbjct: 56  LVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLT 115

Query: 106 GMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFITTLIMMLAGRGMAKVITSGENTDAS 165
            + VW+ ++  L VGL  G +NG++++  G+ PFI TL MM++ RG+A+  T G      
Sbjct: 116 DLPVWIPVVAGLGVGLLAGAINGSIIAITGIPPFIATLGMMVSARGLARYYTEG------ 169

Query: 166 AVAGNEPLKWFANGF-ILGIPA-NFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRM 223
                +P+   ++ +  +G  A   +I +++ ++  +  R T  G    A+G N +A+R 
Sbjct: 170 -----QPVSMLSDSYTAIGHGAMPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAART 224

Query: 224 TGIKPKKILFLVYAISGFLAAIAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLG 283
           +GI  K+ L +VY+I+G LA +AG+ A+A          G   E+ AI A VIGGTSL G
Sbjct: 225 SGINVKRHLVIVYSIAGLLAGLAGVVASARA-ATGQAGMGMSYELDAIAAAVIGGTSLAG 283

Query: 284 GKFSLAGSAVGAVIIAMIRKTIITLGVNAEATPAFFAVVVIVICVM 329
           G   + G+ +GA+I+ ++      +GV+A        ++++V  V+
Sbjct: 284 GVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVI 329


Lambda     K      H
   0.325    0.136    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: 325
Number of extensions: 18
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: 356
Length of database: 340
Length adjustment: 29
Effective length of query: 327
Effective length of database: 311
Effective search space:   101697
Effective search space used:   101697
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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