GapMind for catabolism of small carbon sources

 

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

Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate 3608624 Dshi_2017 ABC transporter related (RefSeq)

Query= CharProtDB::CH_024626
         (378 letters)



>FitnessBrowser__Dino:3608624
          Length = 333

 Score =  248 bits (633), Expect = 2e-70
 Identities = 130/282 (46%), Positives = 183/282 (64%), Gaps = 22/282 (7%)

Query: 20  LAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLDNE 79
           L  ++K F   +VI  + + +  GEF+ ++GPSGCGK+T+LR++AGLETV SG + +D  
Sbjct: 6   LDNVKKSFGKTDVIHGVSIDVTEGEFIVIVGPSGCGKSTLLRMVAGLETVSSGEVRIDGR 65

Query: 80  DITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLET 139
            +  +   +R +  VFQ+YAL+PHM+VF+N+A+GL++ K P AEI  RV  A +++QLE 
Sbjct: 66  VVNTLEPMDRDIAMVFQNYALYPHMSVFDNMAYGLKIAKVPKAEIADRVAVAAKLLQLEP 125

Query: 140 FAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLGI 199
           +  RKP +LSGGQ+QRVA+ RA+V KP + L DE LS LD KLR QM+ E+KALQR+LG+
Sbjct: 126 YLGRKPKELSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEIKALQRELGV 185

Query: 200 TFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNATVI 259
           T ++VTHDQ EA+T++DR++VM  G  +Q G P E+Y  P+  FVAGFIG      +   
Sbjct: 186 TSLYVTHDQVEAMTLADRMIVMNGGVADQIGAPLEVYANPQTAFVAGFIG------SPPT 239

Query: 260 ERLDEQRVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRV 301
             L    VRA   G++  I                RPE LRV
Sbjct: 240 NFLPADMVRAGPAGQQVGI----------------RPEHLRV 265


Lambda     K      H
   0.319    0.136    0.385 

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: 331
Number of extensions: 10
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: 378
Length of database: 333
Length adjustment: 29
Effective length of query: 349
Effective length of database: 304
Effective search space:   106096
Effective search space used:   106096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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