GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Bacteroides clarus YIT 12056

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 WP_009122826.1 BUB52_RS04605 ABC transporter ATP-binding protein

Query= TCDB::Q9RQ06
         (407 letters)



>NCBI__GCF_900129655.1:WP_009122826.1
          Length = 256

 Score =  132 bits (331), Expect = 1e-35
 Identities = 74/238 (31%), Positives = 137/238 (57%), Gaps = 6/238 (2%)

Query: 46  DTNFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRR 105
           D N     G+  +I+G SGSGK+ L++ +  L+ P  G++  D ++  T+ K++   +RR
Sbjct: 19  DINATFENGKTNLIIGQSGSGKTVLMKCIVGLLTPEKGELLYDHRNFLTMGKKEKKALRR 78

Query: 106 KSMSMVFQNFGLFPHRTILENTEYGLEV-QNVPKEERRKRAEKALDNANLLDFKDQYPKQ 164
           + M M+FQ+  LF   T+L+N  + L +  +    +R +RA   L+  NL++ KD++P +
Sbjct: 79  E-MGMIFQSAALFDSMTVLDNVMFPLNMFSSDTLRDRTRRAMFCLERVNLIEAKDKFPGE 137

Query: 165 LSGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHD 224
           +SGGMQ+RV +ARA+A +P+ L  DE  S LDP     + + + ++  ++  T +  +HD
Sbjct: 138 ISGGMQKRVAIARAIALNPQYLFCDEPNSGLDPKTSLVIDELIQDITREYNMTTLINTHD 197

Query: 225 LNEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKTFVEDVD---RAKVITAENI 279
           +N  + IG++I  + +G     G+ ++I T+  N+ +  F+   D   + K +  +NI
Sbjct: 198 MNSVMGIGEKIIYIYEGHKEWEGSKDDIFTS-TNERLNNFIFASDLFRKVKEVEIQNI 254


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: 236
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: 256
Length adjustment: 28
Effective length of query: 379
Effective length of database: 228
Effective search space:    86412
Effective search space used:    86412
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: 48 (23.1 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