GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Shewanella sp. ANA-3

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate 7026373 Shewana3_3515 ABC transporter related (RefSeq)

Query= reanno::Dino:3607124
         (338 letters)



>FitnessBrowser__ANA3:7026373
          Length = 349

 Score =  192 bits (489), Expect = 8e-54
 Identities = 99/237 (41%), Positives = 147/237 (62%), Gaps = 6/237 (2%)

Query: 4   IKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIG 63
           + + +++  Y   Q L  ++L +  GE +  +GPSGCGK+TLLR +AGL+ +S G I+I 
Sbjct: 5   LNLHQVHSDYQGQQVLKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEIQIN 64

Query: 64  GRDVTT----VEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAAR 119
           G+ V+     V    R + M+FQ YAL+PH+TV EN+ FG  V    P  RK R+ +   
Sbjct: 65  GKTVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFG--VAKLTPAQRKARLDDMLA 122

Query: 120 VLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGL 179
           +++LE    R P +LSGGQ+QRV+I RA+   P + L DEP SN+DA++R  M  E+  +
Sbjct: 123 LVKLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAEIRSI 182

Query: 180 HKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGS 236
            KQ   + ++VTH + EA   AD + + N+G I Q G   +LY  PNSR+VA+F+GS
Sbjct: 183 LKQRNVSAVFVTHSKDEAFVFADTLAIFNQGVIVQHGRAENLYAAPNSRYVADFLGS 239


Lambda     K      H
   0.320    0.139    0.396 

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: 269
Number of extensions: 14
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: 338
Length of database: 349
Length adjustment: 29
Effective length of query: 309
Effective length of database: 320
Effective search space:    98880
Effective search space used:    98880
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 (21.8 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