GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Synechococcus elongatus PCC 7942

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate Synpcc7942_0249 Synpcc7942_0249 ATPase

Query= SwissProt::P54537
         (240 letters)



>FitnessBrowser__SynE:Synpcc7942_0249
          Length = 261

 Score =  251 bits (640), Expect = 1e-71
 Identities = 129/241 (53%), Positives = 170/241 (70%), Gaps = 1/241 (0%)

Query: 1   MIKVEKLSKSFGKH-EVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTIT 59
           MI  E + K +G   + L  +S T+  GEVV ++GPSGSGKSTFLR LN LE    G I 
Sbjct: 21  MIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIW 80

Query: 60  IKDTEITKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQEKAED 119
           I+   ++  + +   +R+ +GMVFQ F+LFPH TVL+N+M APV V++     A+  A  
Sbjct: 81  IEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQ 140

Query: 120 LLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQVM 179
           LL +V + E+ + YP +LSGGQ+QRVAIARALAM P I+LFDEPTSALDPEMV+EVL VM
Sbjct: 141 LLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVM 200

Query: 180 KELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDFLEKI 239
           ++L   GMTM++ THE+GFA+EVADRV+ M  G IVE+  P  FF +P+S RA+ FL +I
Sbjct: 201 RDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQI 260

Query: 240 L 240
           L
Sbjct: 261 L 261


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: 181
Number of extensions: 3
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: 261
Length adjustment: 24
Effective length of query: 216
Effective length of database: 237
Effective search space:    51192
Effective search space used:    51192
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