GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fru2-IIB in Marinobacter adhaerens HP15

Align PTS system, fructose-specific, IIB component, component of D-allose/D-ribose transporting Enzyme II complex (Fru2; IIA/IIB/IIC) (Patron et al. 2017). This system is similar to Frz of E. coli (TC#4.A.2.1.9) which is involved in environmental sensing, host adaptation and virulence (characterized)
to candidate GFF3783 HP15_3725 PTS system, fructose-specific IIBC component

Query= TCDB::Q3JZE2
         (103 letters)



>FitnessBrowser__Marino:GFF3783
          Length = 587

 Score = 94.7 bits (234), Expect = 1e-24
 Identities = 46/100 (46%), Positives = 69/100 (69%), Gaps = 1/100 (1%)

Query: 2   KIVGVAACTVGIAHTYIAQEKLENASKAAGHDVKIETQGTIGIENQLTSEEIAAADIVLL 61
           +IV V AC  G+AHT++A E L  A+++AGH +++ETQG++G ++ LT EEIAAAD+V+L
Sbjct: 128 RIVAVTACPTGVAHTFMAAEALTAAAQSAGHKIRVETQGSVGAQDPLTEEEIAAADVVIL 187

Query: 62  AVDVKIAGEERFEGKKVVKVPTEVAIKSPNKLIAKLVEVA 101
           A D+++    RF GK+V +  T  A+K P   I   +E A
Sbjct: 188 ACDIEV-DPGRFSGKRVWRTSTGAALKKPADTIRDALEQA 226



 Score = 52.0 bits (123), Expect = 1e-11
 Identities = 27/97 (27%), Positives = 54/97 (55%), Gaps = 2/97 (2%)

Query: 1  MKIVGVAACTVGIAHTYIAQEKLENASKAAGHDVKIETQGTIG-IENQLTSEEIAAADIV 59
          M ++ V AC  G+A  ++A   LE A+   G  V  +T+G  G  +N+ +   I  AD+V
Sbjct: 1  MNLIIVTACPQGVATRFLAARALERAANRRGWSVTTDTRGPDGKTDNKPSEAAIQQADLV 60

Query: 60 LLAVDVKIAGEERFEGKKVVKVPTEVAIKSPNKLIAK 96
          + AV + +   + + GK+++++P   A+  P+ ++ +
Sbjct: 61 IAAVGIPV-NLDVYAGKRLLQIPVTAALPDPDAILTR 96


Lambda     K      H
   0.311    0.128    0.332 

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: 110
Number of extensions: 5
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 103
Length of database: 587
Length adjustment: 23
Effective length of query: 80
Effective length of database: 564
Effective search space:    45120
Effective search space used:    45120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 46 (22.3 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