GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Shewanella amazonensis SB2B

Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)

Query= TCDB::P96483
         (377 letters)



>FitnessBrowser__SB2B:6938538
          Length = 378

 Score =  219 bits (559), Expect = 7e-62
 Identities = 110/234 (47%), Positives = 155/234 (66%), Gaps = 2/234 (0%)

Query: 17  DKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKD 76
           D  AVD + + I  GE   L+G SG GKST LRMLAG E    G I +  +D+T LPP +
Sbjct: 32  DVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYLDGQDITDLPPYE 91

Query: 77  RDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKAL 136
           R I M+FQ+YAL+PHMTV  N+ F LK   + KA+I Q+V+E  K++ + QY  RKP  L
Sbjct: 92  RPINMMFQSYALFPHMTVEQNIAFGLKQDKMSKADISQRVQEMLKLVHMEQYAKRKPHQL 151

Query: 137 SGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQ 196
           SGGQRQRVA+ R++ + P++ L+DEP+  LD KLR   + ++  +  R+G+T V VTHDQ
Sbjct: 152 SGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERVGVTCVMVTHDQ 211

Query: 197 VEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITD 250
            EAMTM  R+A++ DG + QV SP ++Y+ P +  +A FIG+  +NL +  I +
Sbjct: 212 EEAMTMAGRIAIMSDGWIAQVGSPMDIYESPNSRMIAEFIGT--VNLFDCEIIE 263


Lambda     K      H
   0.317    0.135    0.379 

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: 336
Number of extensions: 11
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: 377
Length of database: 378
Length adjustment: 30
Effective length of query: 347
Effective length of database: 348
Effective search space:   120756
Effective search space used:   120756
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: 50 (23.9 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