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 3607559 Dshi_0971 ABC transporter related (RefSeq)

Query= TCDB::P96483
         (377 letters)



>FitnessBrowser__Dino:3607559
          Length = 334

 Score =  302 bits (773), Expect = 1e-86
 Identities = 171/378 (45%), Positives = 228/378 (60%), Gaps = 46/378 (12%)

Query: 1   MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60
           M  +  ++ T+ +   D   +  LD+ IEDGEF V VGPSGCGKST LR++AGLED+  G
Sbjct: 1   MGQIKLNQVTKSF--GDVEVIPPLDLTIEDGEFAVFVGPSGCGKSTLLRLIAGLEDITSG 58

Query: 61  AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120
            I I  +D T++PP  R +AMVFQ+YALYPHM+V  N+ F +K+AG+ +AE +++++ AA
Sbjct: 59  HIEIDGKDATNVPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIDEAEQQRRIDAAA 118

Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180
           K L+LT YLDR+P  LSGGQRQRVA+GRAIVREP  FL DEPLSNLDA LRV  R +I+ 
Sbjct: 119 KALNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISE 178

Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240
           L +RL  T +YVTHDQVEAMTM D++ VL+ G ++QV SP  +Y  P N FVAGFIGSP 
Sbjct: 179 LHKRLETTMIYVTHDQVEAMTMADKIVVLRAGHIEQVGSPLELYHSPRNEFVAGFIGSPK 238

Query: 241 MNLVEVPITDGGVKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLS 300
           MNL+                    +   AA  G    T+G+RPEH DV    G       
Sbjct: 239 MNLI--------------------KGAEAAKHG--VATIGIRPEHTDVSTTEGLWEG--- 273

Query: 301 KDSADAPAGLAVSVNVVEELGADGY--VYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVV 358
                        V V E LG+D +  ++G      +   + VRV+G    + G  + + 
Sbjct: 274 ------------RVGVAEHLGSDTFLHIHGVP----DCDPMTVRVDGELPVKHGDKIFLT 317

Query: 359 PRPGETHVFSTSTGERLS 376
           P+  + H F  + G R+S
Sbjct: 318 PQLDKLHKFD-AQGLRVS 334


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: 351
Number of extensions: 12
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: 334
Length adjustment: 29
Effective length of query: 348
Effective length of database: 305
Effective search space:   106140
Effective search space used:   106140
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