GapMind for catabolism of small carbon sources

 

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

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

Query= SwissProt::Q8G845
         (340 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_524
          Length = 340

 Score =  150 bits (379), Expect = 5e-41
 Identities = 101/330 (30%), Positives = 178/330 (53%), Gaps = 34/330 (10%)

Query: 20  RQMIPTLAAVVIFILMIIMGQALFGTYIR-LGFISS------LFIDHAYLIILAVAMTLP 72
           R+ +PT  ++ + ++ I +   +FG  +R   F+ +      + +  + + +LA+ +T  
Sbjct: 17  RRRLPTELSIFLVLIGIGLVFEMFGWIMRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQV 76

Query: 73  ILTGGIDLSVGAIVAITAVVGLKLANAG------------VPAFLVMIIMLLIGAVFGLL 120
           I+T GIDLS G+++A++A++   LA               +P ++ ++  L +G + G +
Sbjct: 77  IITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVVAGLGVGLLAGAI 136

Query: 121 AGTLIEEFNMQPFIATLSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISN 180
            G++I    + PFIATL  M  ARGLA         + +G   S +S+    I +  +  
Sbjct: 137 NGSIIAITGIPPFIATLGMMVSARGLARY-------YTEGQPVSMLSDSYTAIGHGAMP- 188

Query: 181 DLSFNVGVIIALVVVVFGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSA 240
                  VII LVV V  ++ L +T+ G+  YAIGG+  +A   G+ VKR   I+Y  + 
Sbjct: 189 -------VIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAG 241

Query: 241 TLAALASIVYTANIGSAKNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSIL 300
            LA LA +V +A   + +  +G+ +ELDA+A+ VIGGT + GG G + G+V+G+L+  ++
Sbjct: 242 LLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVM 301

Query: 301 DPLTSDFGVPAEWTTIVIGLMILVFVVLQR 330
               +  GV A    I+ GL+I+V VV+ +
Sbjct: 302 ASGFTFVGVDAYIQDIIKGLIIVVAVVIDQ 331


Lambda     K      H
   0.327    0.142    0.400 

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: 262
Number of extensions: 12
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: 340
Length of database: 340
Length adjustment: 28
Effective length of query: 312
Effective length of database: 312
Effective search space:    97344
Effective search space used:    97344
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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