GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Escherichia coli BW25113

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 18063 b4035 fused maltose transport subunit, ATP-binding component of ABC superfamily/regulatory protein (NCBI)

Query= TCDB::P96483
         (377 letters)



>FitnessBrowser__Keio:18063
          Length = 371

 Score =  292 bits (747), Expect = 1e-83
 Identities = 166/373 (44%), Positives = 230/373 (61%), Gaps = 24/373 (6%)

Query: 1   MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60
           MA+V     T+ +   +      +++ I +GEF+V VGPSGCGKST LRM+AGLE +  G
Sbjct: 1   MASVQLQNVTKAW--GEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSG 58

Query: 61  AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120
            + IG++ +   PP +R + MVFQ+YALYPH++VA+NM F LK+AG  K  I Q+V + A
Sbjct: 59  DLFIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVA 118

Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180
           ++L L   LDRKPKALSGGQRQRVA+GR +V EP VFL+DEPLSNLDA LRV  R +I+ 
Sbjct: 119 EVLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISR 178

Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240
           L +RLG T +YVTHDQVEAMT+ D++ VL  G + QV  P  +Y  PA+ FVAGFIGSP 
Sbjct: 179 LHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPK 238

Query: 241 MNLVEVPITDGGVKFGNSVVPV-NREAL-----SAADKGDRTVTVGVRPEHFDVVELGGA 294
           MN + V +T   +      +P+ NR+ +     S   +    +++G+RPEH         
Sbjct: 239 MNFLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHL-------- 290

Query: 295 VAASLSKDSADAPAGLAVSVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGST 354
               L  D AD    L   V VVE+LG +  ++   ++    ++LV R N   + E+G+T
Sbjct: 291 ----LPSDIADVI--LEGEVQVVEQLGNETQIH--IQIPSIRQNLVYRQNDVVLVEEGAT 342

Query: 355 LHVVPRPGETHVF 367
             +   P   H+F
Sbjct: 343 FAIGLPPERCHLF 355


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: 367
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: 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.

Links

Downloads

Related tools

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