GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-B in Marinobacter adhaerens HP15

Align PTS system, fructose-specific, IIB subunnit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate GFF3783 HP15_3725 PTS system, fructose-specific IIBC component

Query= TCDB::D2RXA4
         (150 letters)



>FitnessBrowser__Marino:GFF3783
          Length = 587

 Score = 89.7 bits (221), Expect = 7e-23
 Identities = 48/115 (41%), Positives = 70/115 (60%), Gaps = 4/115 (3%)

Query: 2   KFVAVTSCPTGIAHSQMAAENLEQTATDRGHEIDVEVQGAMGQENELSSDAIAEADAVII 61
           + VAVT+CPTG+AH+ MAAE L   A   GH+I VE QG++G ++ L+ + IA AD VI+
Sbjct: 128 RIVAVTACPTGVAHTFMAAEALTAAAQSAGHKIRVETQGSVGAQDPLTEEEIAAADVVIL 187

Query: 62  AADTSVNQDRFEGKPV----VTAPVKDAVNDVEDLLERAIAAADGETSTADSAQS 112
           A D  V+  RF GK V      A +K   + + D LE+A+    G+  T+ ++ S
Sbjct: 188 ACDIEVDPGRFSGKRVWRTSTGAALKKPADTIRDALEQAVVLNAGQKKTSGASGS 242



 Score = 66.2 bits (160), Expect = 8e-16
 Identities = 43/122 (35%), Positives = 63/122 (51%), Gaps = 1/122 (0%)

Query: 1   MKFVAVTSCPTGIAHSQMAAENLEQTATDRGHEIDVEVQGAMGQ-ENELSSDAIAEADAV 59
           M  + VT+CP G+A   +AA  LE+ A  RG  +  + +G  G+ +N+ S  AI +AD V
Sbjct: 1   MNLIIVTACPQGVATRFLAARALERAANRRGWSVTTDTRGPDGKTDNKPSEAAIQQADLV 60

Query: 60  IIAADTSVNQDRFEGKPVVTAPVKDAVNDVEDLLERAIAAADGETSTADSAQSEGAADAS 119
           I A    VN D + GK ++  PV  A+ D + +L RA A A        S +S   + A 
Sbjct: 61  IAAVGIPVNLDVYAGKRLLQIPVTAALPDPDAILTRAQAEATPWDPAMASQESIATSTAV 120

Query: 120 AS 121
            S
Sbjct: 121 GS 122


Lambda     K      H
   0.307    0.122    0.323 

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: 150
Number of extensions: 4
Number of successful extensions: 2
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: 150
Length of database: 587
Length adjustment: 26
Effective length of query: 124
Effective length of database: 561
Effective search space:    69564
Effective search space used:    69564
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 48 (23.1 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