GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Alkalihalobacterium alkalinitrilicum DSM 22532

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 WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein

Query= TCDB::P96483
         (377 letters)



>NCBI__GCF_002019605.1:WP_078429421.1
          Length = 351

 Score =  221 bits (563), Expect = 2e-62
 Identities = 126/305 (41%), Positives = 176/305 (57%), Gaps = 28/305 (9%)

Query: 1   MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60
           M+ + FD  T+ Y  +  PAVDQL++ I +GE + L+GPSGCGK+T+LRMLAG E    G
Sbjct: 1   MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60

Query: 61  AIRIGDR----DVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKV 116
            IRIGD     D   LPP+ R I MVFQ+YAL+PH+T+  N+ F L        + +++ 
Sbjct: 61  KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLN--RWKNRDKKKRA 118

Query: 117 EEAAKILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRT 176
           +E  +++ L ++  R P  LSGGQ+QRVA+ RA+   P+V LMDEP SNLDA LR   R 
Sbjct: 119 QEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178

Query: 177 QIASLQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFI 236
            + ++ R+   T + VTHDQ +A  + DRV V+ +G++QQ+ +P+ MY  PAN FVA F+
Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFV 238

Query: 237 GS---------PAMNLVEVPITDGGVKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFD 287
           G          P +  VE  I       G   +P         DK    V V +RPE   
Sbjct: 239 GKTNLISGTLCPDLKHVETHI-------GRVCLP------QETDKVIENVMVSIRPEGCR 285

Query: 288 VVELG 292
           + E G
Sbjct: 286 LAEKG 290


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: 292
Number of extensions: 9
Number of successful extensions: 3
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 Apr 09 2024. 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