GapMind for catabolism of small carbon sources

 

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

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 3607842 Dshi_1250 ABC transporter related (RefSeq)

Query= TCDB::P96483
         (377 letters)



>FitnessBrowser__Dino:3607842
          Length = 351

 Score =  322 bits (824), Expect = 1e-92
 Identities = 185/376 (49%), Positives = 233/376 (61%), Gaps = 28/376 (7%)

Query: 1   MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60
           M+ +T   A + Y   +   V  +D++I DGEF V VGPSGCGKST LRM+AGLE+ + G
Sbjct: 1   MSGITLRGAVKRY--GETQVVHGVDLSIADGEFCVFVGPSGCGKSTLLRMIAGLEETSEG 58

Query: 61  AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120
           +I IG RDVT L P +R +AMVFQ YALYPHMTVA+NMGF LK+ GVPKAEI+ KV  A+
Sbjct: 59  SIHIGARDVTRLDPSERGVAMVFQTYALYPHMTVAENMGFGLKMNGVPKAEIKAKVAAAS 118

Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180
           +IL L  YL RKPKALSGGQRQRVA+GRAIVR P+VFL DEPLSNLDA+LRV  R +IA 
Sbjct: 119 EILKLDDYLARKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIAR 178

Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240
           L + +G T +YVTHDQVEAMT+ D++ VL+ G ++QV +P  +Y  P N+FVAGFIGSPA
Sbjct: 179 LHKEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGAPLELYRDPDNVFVAGFIGSPA 238

Query: 241 MNLVEVPITDGGVKF-GNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASL 299
           MN ++  I +  V   G   +PV       A      VTVGVRP+H              
Sbjct: 239 MNFLDGRIENDAVHLAGLPPLPV-----PGAAGRSGPVTVGVRPQHI------------- 280

Query: 300 SKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVP 359
               A  P G    V + E LG   Y+Y     G +   L V         +G+ + +  
Sbjct: 281 ----ALEPGGDGYLVELTESLGGVSYLYLR---GADGSRLTVEAGEEDPIAEGTPVGLSL 333

Query: 360 RPGETHVFSTSTGERL 375
            P    +F   TG+RL
Sbjct: 334 APDRVMLFEAETGQRL 349


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: 397
Number of extensions: 22
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: 351
Length adjustment: 29
Effective length of query: 348
Effective length of database: 322
Effective search space:   112056
Effective search space used:   112056
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