GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Sphingomonas koreensis DSMZ 15582

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate Ga0059261_3653 Ga0059261_3653 phosphate ABC transporter ATP-binding protein, PhoT family (TC 3.A.1.7.1)

Query= SwissProt::P54537
         (240 letters)



>FitnessBrowser__Korea:Ga0059261_3653
          Length = 276

 Score =  143 bits (360), Expect = 4e-39
 Identities = 85/236 (36%), Positives = 135/236 (57%), Gaps = 12/236 (5%)

Query: 11  FGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNG-----GTITIKDTEI 65
           +G+ + ++++S  +    V A IGPSG GKSTFLR LN +          G IT+    I
Sbjct: 38  YGEKQAIRDVSIDVDMENVTAFIGPSGCGKSTFLRTLNRMNDTVASARVEGEITLDGENI 97

Query: 66  TKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAP-VNVKKESKQAAQEKAEDLLRKV 124
                + +++R  +GMVFQ  + FP K++ EN+ Y P ++    +K    +  E  L++ 
Sbjct: 98  YDKSMDVVQLRARVGMVFQKPNPFP-KSIYENVAYGPRIHGLARAKGDMDQIVERSLKRA 156

Query: 125 GLFE----KRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQVMK 180
           GL+E    + ND    LSGGQ+QR+ IARA+A++P+++L DEP SALDP    ++ +++ 
Sbjct: 157 GLWEEVKDRLNDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDPIATAKIEELIH 216

Query: 181 ELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDFL 236
           EL      +VIVTH M  A  V+ R  F   G +VE G   + F +P+ +R +D++
Sbjct: 217 EL-RGRYAIVIVTHNMQQAARVSQRTAFFHLGTLVEYGETDQIFTAPRQERTKDYI 271


Lambda     K      H
   0.317    0.134    0.368 

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: 139
Number of extensions: 8
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: 240
Length of database: 276
Length adjustment: 24
Effective length of query: 216
Effective length of database: 252
Effective search space:    54432
Effective search space used:    54432
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 (21.6 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