GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Pedobacter sp. GW460-11-11-14-LB5

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 CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein

Query= TCDB::Q9RQ06
         (407 letters)



>FitnessBrowser__Pedo557:CA265_RS07485
          Length = 252

 Score =  132 bits (332), Expect = 1e-35
 Identities = 82/221 (37%), Positives = 122/221 (55%), Gaps = 15/221 (6%)

Query: 48  NFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKS 107
           + +IN+GE   +MG SGSGKSTL+ +L  L  P+SG   ++  +V+ ++ + L +VR + 
Sbjct: 29  SLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGTYVLNGTNVSHMSDDALAEVRNQE 88

Query: 108 MSMVFQNFGLFPHRTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSG 167
           +  VFQ F L P  T L+N    L      K++R  RA +AL+N  L +  D  P +LSG
Sbjct: 89  IGFVFQTFNLLPRSTSLDNVALPLIYAGTSKKDRDARAARALENVGLGNRMDHKPNELSG 148

Query: 168 GMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNE 227
           G +QRV +ARAL N+P I+L DE    LD     E+   L E+ +K   TII V+H+  +
Sbjct: 149 GQRQRVAVARALINNPSIILADEPTGNLDTKTSIEIMGLLEEIHSK-GNTIILVTHE-ED 206

Query: 228 ALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKTFVEDV 268
             +   RI  M+DG I              NDY+ T +++V
Sbjct: 207 IAQHAHRIVRMRDGLI-------------ENDYLNTDIKNV 234


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: 219
Number of extensions: 12
Number of successful extensions: 1
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: 252
Length adjustment: 28
Effective length of query: 379
Effective length of database: 224
Effective search space:    84896
Effective search space used:    84896
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 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 (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