GapMind for catabolism of small carbon sources

 

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

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate AO356_28580 AO356_28580 sugar ABC transporter permease

Query= reanno::psRCH2:GFF851
         (296 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28580
          Length = 280

 Score =  109 bits (273), Expect = 6e-29
 Identities = 70/213 (32%), Positives = 107/213 (50%), Gaps = 9/213 (4%)

Query: 87  NSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLIFQMFPPVLSLVAIYALFDQ 146
           NS+ +A     L L LS T+AYA  R++F G+ P+L  +L   MFP V  L  ++ +   
Sbjct: 74  NSLVVALCVVALALFLSLTAAYALGRVKFRGRGPVLMMVLGVSMFPQVAVLSGLFEVIRA 133

Query: 147 LGQH-VSWLGVNSHGAVIVASLGGMALHIWTIKGYFESIDASLEEAAIVDGATTWQAFFH 205
           LG +  SW  + S+      ++  +   +W +  +   +   LEEAAI+DGA+ W     
Sbjct: 134 LGLYNTSWALILSY------TIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTR 187

Query: 206 ILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTLSVGAQQYL--YPQNYLWGDF 263
           +LLP+  P L    +LAFI +  E+  A    +   + T+ V         P    WG  
Sbjct: 188 VLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDSQRTVPVAIALISGGSPHELPWGLL 247

Query: 264 AAAAVLSGLPITAVFLYCQKWIVGGLTAGGVKG 296
            AA+VL  +P+  + L  Q+ IV GLTAG +KG
Sbjct: 248 MAASVLVTVPLVILVLIFQRRIVSGLTAGALKG 280


Lambda     K      H
   0.327    0.139    0.433 

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: 241
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: 296
Length of database: 280
Length adjustment: 26
Effective length of query: 270
Effective length of database: 254
Effective search space:    68580
Effective search space used:    68580
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: 47 (22.7 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