GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Marinobacter adhaerens HP15

Align Extracellular solute-binding protein, family 7 (characterized, see rationale)
to candidate GFF3854 HP15_3795 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component

Query= uniprot:Q48AL6
         (362 letters)



>FitnessBrowser__Marino:GFF3854
          Length = 341

 Score =  164 bits (415), Expect = 3e-45
 Identities = 101/334 (30%), Positives = 165/334 (49%), Gaps = 11/334 (3%)

Query: 26  AHADDDKKYRWKLAETWGPNFPIFGDATKNMAKMVKEMSNGRLTIRIDSSNKHKSALGIF 85
           A ADD    RWK+   +  N P  G     +A  +   S+G + +R+    K      I 
Sbjct: 12  AFADD---LRWKMPVAFATNLPGLGSPAAWVADNLTTASDGSIQVRVYEPGKLVPPFDIL 68

Query: 86  DFVKSGQYQMGHSASYYWKGKNFNTMFFTTVPFGMIASEQHAWFYYGGGMELMKKVYDQY 145
             V  G+   G++   Y +GK      F  VPFGM       W+Y+GGG E++++ Y   
Sbjct: 69  QSVSDGKVSAGYTWIGYDQGKVPAIPLFAAVPFGMKPPAYIGWYYFGGGHEMLQETYANK 128

Query: 146 G--IMSFPGGNTGNQMGGWFKKEINSVEDLKGLKMRIPGFAGEVLAKLGAKPTNIPSGEL 203
           G  + +   G  G +  GW+ + I ++ED KGLK+R  G  G+VL KLGA  T +P GEL
Sbjct: 129 GFNVHAQLCGIIGPETAGWYSEPIETLEDYKGLKIRFAGLGGKVLEKLGASVTMMPGGEL 188

Query: 204 YTALERNTIDALEWVGPSLDLRMGFHKIAPY-YYTGWHEPGTELQFMVNQKAYNSLPKDL 262
           Y ALE+ TIDA E+  P++D  +GF+++  Y  + GWH+  T    ++N+  +    +  
Sbjct: 189 YQALEKGTIDATEFSMPAIDQILGFNQVVKYNLFPGWHQQFTAQYMLINKDEWARATEAQ 248

Query: 263 QKILTVAMKAAAYDMYSQSMHASGVNLASLKKDYPNVQMRSFPKPVMEAIVQANDELLEE 322
           + ++  +  AA     ++  + +G  LA  +     VQ    P+ V+  + +   E+LEE
Sbjct: 249 KALVEASCTAATTRGLAEGEYKNGKVLAEFQD--KGVQADQIPRDVLLKLREVTQEVLEE 306

Query: 323 FAAKDPMTAEILKSLNDYKHQIRAWTNLSDRAYL 356
            A+KD     + +S  ++    + W     RAY+
Sbjct: 307 EASKDADFKRVYESQQEFMESYKIW---DTRAYV 337


Lambda     K      H
   0.318    0.133    0.402 

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: 330
Number of extensions: 18
Number of successful extensions: 4
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: 362
Length of database: 341
Length adjustment: 29
Effective length of query: 333
Effective length of database: 312
Effective search space:   103896
Effective search space used:   103896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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