GapMind for catabolism of small carbon sources

 

Aligments for a candidate for opuBA in Shewanella amazonensis SB2B

Align BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized)
to candidate 6939439 Sama_3531 molybdenum ABC transporter, ATP-binding protein (RefSeq)

Query= TCDB::Q9RQ06
         (407 letters)



>lcl|FitnessBrowser__SB2B:6939439 Sama_3531 molybdenum ABC
           transporter, ATP-binding protein (RefSeq)
          Length = 370

 Score =  150 bits (378), Expect = 8e-41
 Identities = 83/216 (38%), Positives = 127/216 (58%), Gaps = 2/216 (0%)

Query: 46  DTNFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRR 105
           + +F    GE   ++G SG GK+TLLR++  L +P +G I    +     ++      + 
Sbjct: 20  EADFSCRAGEFLAVVGPSGGGKTTLLRMIAGLAKPENGSIRCGKRIWFDSDEGIHCSPQN 79

Query: 106 KSMSMVFQNFGLFPHRTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQL 165
           + +  V Q+FGLFP  + L N    L+  ++P +ERR RA  AL+  NL    D+ P QL
Sbjct: 80  RHIGFVPQHFGLFPKLSALGNIMAALD--HLPSQERRPRALAALEKVNLHGLTDRLPSQL 137

Query: 166 SGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDL 225
           SGG +QRV LARALA +P +LL+DE FSA+D   R  +  EL  L+A+    +I V+HDL
Sbjct: 138 SGGQKQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKAELNIPVIMVTHDL 197

Query: 226 NEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYV 261
           NEAL + D + ++  G ++Q GT +++ + P N+ V
Sbjct: 198 NEALLLADSMLLISQGHMLQHGTPQDVFSRPRNEAV 233


Lambda     K      H
   0.316    0.135    0.364 

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: 261
Number of extensions: 12
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: 407
Length of database: 370
Length adjustment: 30
Effective length of query: 377
Effective length of database: 340
Effective search space:   128180
Effective search space used:   128180
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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