GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Pedobacter sp. GW460-11-11-14-LB5

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate CA265_RS04345 CA265_RS04345 lipoprotein-releasing system ATP-binding protein LolD

Query= SwissProt::P54537
         (240 letters)



>FitnessBrowser__Pedo557:CA265_RS04345
          Length = 216

 Score =  160 bits (405), Expect = 2e-44
 Identities = 93/218 (42%), Positives = 134/218 (61%), Gaps = 5/218 (2%)

Query: 1   MIKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITI 60
           M+K   + KS+G  ++LK ++  + +GE+V++IGPSG+GKST L  L  L+KP+ G++ +
Sbjct: 1   MLKATGIRKSYGNLQILKGVNFEVQKGEIVSIIGPSGAGKSTLLHILGTLDKPDDGSVQL 60

Query: 61  KDTEITKPKTNTLKV--RENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQEKAE 118
           K T I K   + L     +NIG VFQ  HL P  + +ENI   P  + K +K+ A+ +A 
Sbjct: 61  KGTVINKLNGDLLSTFRNQNIGFVFQFHHLLPEFSAIENICI-PAFIAKTNKKQAETRAF 119

Query: 119 DLLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQV 178
           +LL   GL ++    PN+LSGG++QRVAIARAL  NP I+L DEP+  LD E    + Q+
Sbjct: 120 ELLDLFGLKDRAQHKPNQLSGGEQQRVAIARALINNPSIILADEPSGNLDSENAAGLHQL 179

Query: 179 MKELVET-GMTMVIVTHEMGFAKEVADRVLFMDQGMIV 215
              L +    T VIVTH    AK  +DRV+ M  G+IV
Sbjct: 180 FVSLRDNFHQTFVIVTHNEHLAK-TSDRVVSMKDGLIV 216


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: 134
Number of extensions: 6
Number of successful extensions: 3
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: 216
Length adjustment: 23
Effective length of query: 217
Effective length of database: 193
Effective search space:    41881
Effective search space used:    41881
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