GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Dinoroseobacter shibae DFL-12

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate 3606891 Dshi_0321 ABC transporter related (RefSeq)

Query= SwissProt::P54537
         (240 letters)



>FitnessBrowser__Dino:3606891
          Length = 258

 Score =  264 bits (674), Expect = 1e-75
 Identities = 129/239 (53%), Positives = 174/239 (72%)

Query: 2   IKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITIK 61
           I+++K++K +G+  VL++I+ T+  GE + + GPSGSGKST +RC+N LE+   G+IT+ 
Sbjct: 18  IEIDKMNKWYGQFHVLRDINLTVYRGERIVICGPSGSGKSTLIRCINALEEHQAGSITVD 77

Query: 62  DTEITKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQEKAEDLL 121
            T ++    N   +R  +GM FQHF+LFPH T+LEN   AP+ V+K  K+ A+  A   L
Sbjct: 78  GTLLSSDLKNIDTIRSEVGMCFQHFNLFPHLTILENCTLAPIWVRKTPKKEAEATAMHFL 137

Query: 122 RKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQVMKE 181
            KV + ++ N YP +LSGGQ+QRVAIAR+L M P IMLFDEPTSALDPEM+KEVL  M E
Sbjct: 138 EKVKIPDQANKYPGQLSGGQQQRVAIARSLCMRPRIMLFDEPTSALDPEMIKEVLDTMIE 197

Query: 182 LVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDFLEKIL 240
           L E GMTM+ VTHEMGFA++VA+RV+FMD G IVE   P+EFF +P+S R + FL +IL
Sbjct: 198 LAEEGMTMICVTHEMGFARQVANRVIFMDAGQIVEQNEPEEFFGNPQSDRTKLFLSQIL 256


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: 178
Number of extensions: 5
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: 240
Length of database: 258
Length adjustment: 24
Effective length of query: 216
Effective length of database: 234
Effective search space:    50544
Effective search space used:    50544
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: 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