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 3607646 Dshi_1055 ABC transporter related (RefSeq)

Query= SwissProt::P54537
         (240 letters)



>FitnessBrowser__Dino:3607646
          Length = 366

 Score =  154 bits (388), Expect = 3e-42
 Identities = 88/236 (37%), Positives = 135/236 (57%), Gaps = 6/236 (2%)

Query: 2   IKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITIK 61
           ++V+ LSK +G  + L+ +  TIA GE   ++GPSG GK+T LR +    +P  G + + 
Sbjct: 9   VEVKGLSKHYGPVKALRQVDLTIAAGEYFVLLGPSGGGKTTLLRTIGGFHRPTEGQVLLH 68

Query: 62  DTEITKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQEKAEDLL 121
             +++    +    +    MVFQ + LFPH TVL+N+ Y  + V    K  AQEKA  ++
Sbjct: 69  GRDMSHLPPD----KRPTTMVFQAYALFPHMTVLQNVSYG-LKVAGMDKATAQEKAAAMM 123

Query: 122 RKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQVMKE 181
             VGL       P+ LSGGQ+QRV +ARAL ++ DI+L DEP +ALD ++ K++   +K 
Sbjct: 124 DVVGLAGFAERKPHELSGGQQQRVQLARALVLDRDILLLDEPLAALDAQLRKDMCLELKH 183

Query: 182 LVE-TGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDFL 236
           L E  G+T + VTH    A  VADR+  +  G +VE G  ++ + +P  K    F+
Sbjct: 184 LQEKVGITFIHVTHNQEEAMTVADRIALVADGQLVEQGAARDIYRAPIKKFTAGFV 239


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: 191
Number of extensions: 11
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: 366
Length adjustment: 26
Effective length of query: 214
Effective length of database: 340
Effective search space:    72760
Effective search space used:    72760
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: 48 (23.1 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