GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Phaeobacter inhibens BS107

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 GFF2246 PGA1_c22780 glycine betaine transport ATP-binding protein

Query= TCDB::Q9RQ06
         (407 letters)



>FitnessBrowser__Phaeo:GFF2246
          Length = 352

 Score =  270 bits (691), Expect = 4e-77
 Identities = 140/287 (48%), Positives = 195/287 (67%)

Query: 5   VKIEHLTKIFGKRIKTALTMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIMGLSG 64
           V++  L KIFG R K  L  V+ G  K E+L +    +G+ + N ++  GEI V+MGLSG
Sbjct: 6   VRLSGLYKIFGARDKDVLHHVQGGMGKEELLAQHKHVLGLNNINVDMQAGEITVVMGLSG 65

Query: 65  SGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPHRTIL 124
           SGKSTL+R LNRLIEPT+G+I +  +DV  L+++ L   R++ MSMVFQ F L PH+T+L
Sbjct: 66  SGKSTLIRHLNRLIEPTAGEIIVQGEDVMQLSEDGLRHARQEKMSMVFQKFALLPHKTVL 125

Query: 125 ENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALANDPE 184
           +N    L V+   +    + A K L+   L  F++ YP QLSGGMQQRVG+ARAL  +  
Sbjct: 126 KNAGMPLSVRGEDEATCDREAAKWLERVGLSGFENHYPAQLSGGMQQRVGIARALTANTP 185

Query: 185 ILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKDGKIM 244
           I+LMDEAFSALDPLIR +MQD LLELQ +  KTIIF++HDL+EAL++ D + I+KDG ++
Sbjct: 186 IMLMDEAFSALDPLIRTDMQDLLLELQKELHKTIIFITHDLDEALKLADHLVILKDGFVV 245

Query: 245 QIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIMIPALTTNIDVD 291
           Q G  + IL NP + Y++ FV D++RA+V+   +IM P +   +  D
Sbjct: 246 QQGEPQHILLNPNDPYIEDFVSDINRARVLRVRSIMTPLVGGKVPKD 292


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: 377
Number of extensions: 16
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: 352
Length adjustment: 30
Effective length of query: 377
Effective length of database: 322
Effective search space:   121394
Effective search space used:   121394
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 (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