GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlG in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for D-mannitol and D-mannose, permease component 2 (characterized)
to candidate AO353_25890 AO353_25890 sugar ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_25890
         (276 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25890
          Length = 276

 Score =  546 bits (1406), Expect = e-160
 Identities = 276/276 (100%), Positives = 276/276 (100%)

Query: 1   MTLQQTRRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYL 60
           MTLQQTRRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYL
Sbjct: 1   MTLQQTRRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYL 60

Query: 61  HVNERSGYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWMLSTKMLPP 120
           HVNERSGYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWMLSTKMLPP
Sbjct: 61  HVNERSGYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWMLSTKMLPP 120

Query: 121 VGVLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMIYTYFKDIPKDILEAARLDGAT 180
           VGVLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMIYTYFKDIPKDILEAARLDGAT
Sbjct: 121 VGVLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMIYTYFKDIPKDILEAARLDGAT 180

Query: 181 LWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSKAAPLTALIASYSSPEGLF 240
           LWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSKAAPLTALIASYSSPEGLF
Sbjct: 181 LWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSKAAPLTALIASYSSPEGLF 240

Query: 241 WAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276
           WAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK
Sbjct: 241 WAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276


Lambda     K      H
   0.327    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: 481
Number of extensions: 10
Number of successful extensions: 1
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: 276
Length of database: 276
Length adjustment: 25
Effective length of query: 251
Effective length of database: 251
Effective search space:    63001
Effective search space used:    63001
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 (21.8 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