GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Burkholderia phytofirmans PsJN

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 BPHYT_RS05040 BPHYT_RS05040 sugar ABC transporter ATPase

Query= TCDB::P96483
         (377 letters)



>FitnessBrowser__BFirm:BPHYT_RS05040
          Length = 371

 Score =  302 bits (773), Expect = 1e-86
 Identities = 178/384 (46%), Positives = 241/384 (62%), Gaps = 21/384 (5%)

Query: 1   MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60
           MA+++     + YP    P +  ++I IEDG+FL+LVG SGCGKST L M+AGLE V  G
Sbjct: 1   MASLSIRDVYKTYPNG-VPVLKGVNIDIEDGQFLILVGGSGCGKSTLLNMIAGLETVTKG 59

Query: 61  AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120
            I+I  + V +L PKDRDIAMVFQ+YALYP MTV +N+ F L I  VPK E  Q V+  +
Sbjct: 60  EIQIDGKTVNNLSPKDRDIAMVFQSYALYPSMTVRENISFGLNIRKVPKNEQTQIVDRVS 119

Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180
             L +T  LDRKP  LSGGQRQRVAMGRA+ R+P +FL DEPLSNLDAKLR+  R++I  
Sbjct: 120 NTLQITHLLDRKPGQLSGGQRQRVAMGRALARDPVMFLFDEPLSNLDAKLRIEMRSEIKL 179

Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240
           L +RLG T VYVTHDQ+EAMT+GDR+AV+KDG++QQ  +P+ +YD P+NLFVAGFIG+P 
Sbjct: 180 LHQRLGTTIVYVTHDQIEAMTLGDRIAVMKDGIVQQFGAPQEIYDSPSNLFVAGFIGAPP 239

Query: 241 MNLVEVPITDGGVKFGNSV-VPVNREALS-------AADKGDRTVTVGVRPEHFDVVELG 292
           MN ++  + + G      +   V R AL+             R V +G+RPE   + +  
Sbjct: 240 MNFIQGKLVEQGAGVALELDTGVARTALNLPFDSAKVRSHVGREVILGLRPER--ITDAR 297

Query: 293 GAVAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKG 352
           GA       D+A     + V V+V+E  G D  V+  A+V G  K +V RV+    P+  
Sbjct: 298 GA-----HGDNAKLQP-IEVKVDVIEPTGPDTLVF--AQVNG--KRIVSRVHPASNPQPL 347

Query: 353 STLHVVPRPGETHVFSTSTGERLS 376
           +   ++    +  +F  S  ER++
Sbjct: 348 ANTTLLFDTSKAVLFDPSNEERIA 371


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: 400
Number of extensions: 14
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: 371
Length adjustment: 30
Effective length of query: 347
Effective length of database: 341
Effective search space:   118327
Effective search space used:   118327
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