GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Brucella inopinata BO1

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_008510542.1 BIBO1_RS17490 ABC transporter ATP-binding protein

Query= TCDB::P96483
         (377 letters)



>NCBI__GCF_000182725.1:WP_008510542.1
          Length = 333

 Score =  295 bits (754), Expect = 2e-84
 Identities = 165/344 (47%), Positives = 204/344 (59%), Gaps = 40/344 (11%)

Query: 24  LDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDIAMVF 83
           +++ + DGEF++ VGPSGCGKST LR +AGLEDV+ G + I   DVT  PP  R IAMVF
Sbjct: 22  INLEVNDGEFIIFVGPSGCGKSTLLRSIAGLEDVSAGQVLINGEDVTVTPPSRRGIAMVF 81

Query: 84  QNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGGQRQR 143
           Q+YALYPH+TV  NMG  LK AG PK EI  +V +A+ +L L  YL R+P  LSGGQRQR
Sbjct: 82  QSYALYPHLTVKANMGLGLKQAGAPKDEIEGRVAKASAMLALEPYLARRPAELSGGQRQR 141

Query: 144 VAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAMTMG 203
           VA+GRA+VR P++FL DEPLSNLDA LRV TR +IA L R L  T +YVTHDQVEAMT+ 
Sbjct: 142 VAIGRALVRNPELFLFDEPLSNLDAALRVQTRLEIAKLHRELKATMIYVTHDQVEAMTLA 201

Query: 204 DRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFGNSVVPVN 263
           DR+ VL  G ++Q+ SP  +Y++P NLFVAGFIGSP MN +                   
Sbjct: 202 DRIVVLNAGRIEQIGSPMELYNRPDNLFVAGFIGSPQMNFI------------------- 242

Query: 264 REALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNVVEELGAD 323
            EA      G R  T+G+RPEH  V    G                    V   E LGAD
Sbjct: 243 -EAARIGATGAR--TIGIRPEHLSVSRESGTWKG---------------KVIHAEHLGAD 284

Query: 324 GYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVF 367
             +Y   E  G V     R+ G Q   +   + + P  G+TH F
Sbjct: 285 TILYVETETAGLV---TARLFGEQHYNEDDVIFLTPEEGKTHYF 325


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: 335
Number of extensions: 15
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: 333
Length adjustment: 29
Effective length of query: 348
Effective length of database: 304
Effective search space:   105792
Effective search space used:   105792
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 24 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