GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Shewanella oneidensis MR-1

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 203725 SO4655 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::P96483
         (377 letters)



>FitnessBrowser__MR1:203725
          Length = 354

 Score =  200 bits (508), Expect = 6e-56
 Identities = 107/274 (39%), Positives = 158/274 (57%), Gaps = 10/274 (3%)

Query: 20  AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDI 79
           AVD +++ I+ GE   L+GPSG GK+T LR++AGLE  + G ++    D+T     +R +
Sbjct: 17  AVDSVNLEIKTGELTALLGPSGSGKTTLLRIIAGLEQADSGIVKFNGEDITTQHVSERGV 76

Query: 80  AMVFQNYALYPHMTVADNMGFALKI----AGVPKAEIRQKVEEAAKILDLTQYLDRKPKA 135
             VFQ+YAL+ HMTV +N+ + L +        KAEI +KV    K++ L    DR P  
Sbjct: 77  GFVFQHYALFKHMTVFENVAYGLTVRPRKTRPSKAEIAEKVHSLLKLVQLDWTADRYPSQ 136

Query: 136 LSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHD 195
           LSGGQRQR+A+ RA+  EP+V L+DEP   LDAK+R   R  +  L   + +TTV+VTHD
Sbjct: 137 LSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRAELRRWLRRLHDEINVTTVFVTHD 196

Query: 196 QVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKF 255
           Q EA+ + D++ V+  G ++Q  +P  +YD P+N FV  F+G+  +NL    +  G    
Sbjct: 197 QEEALEVADKIVVMNKGRIEQQGTPEEVYDTPSNPFVYEFLGN--VNLFHARVKHGHSTI 254

Query: 256 GNSVVPVNREALSAADKGDRTVTVGVRPEHFDVV 289
           GN  +P    A     +G       VRP   +V+
Sbjct: 255 GNIHIPSPEHAGGEEQQG----LAYVRPHEIEVL 284


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: 329
Number of extensions: 13
Number of successful extensions: 2
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: 354
Length adjustment: 30
Effective length of query: 347
Effective length of database: 324
Effective search space:   112428
Effective search space used:   112428
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: 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