GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Pseudomonas fluorescens FW300-N2C3

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 AO356_09255 AO356_09255 glycine/betaine ABC transporter

Query= TCDB::Q9RQ06
         (407 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_09255
          Length = 372

 Score =  297 bits (761), Expect = 3e-85
 Identities = 164/357 (45%), Positives = 233/357 (65%), Gaps = 18/357 (5%)

Query: 3   VKVKIEHLTKIFGKRIKTAL-TMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIMG 61
           V V  +++ KIFG+    A+  +V+QG  K  IL+     VGV + + ++  GEIF IMG
Sbjct: 11  VLVDCQNVWKIFGESAPAAMQAVVQQGLTKTRILQDYSCVVGVSNVSLQVRRGEIFCIMG 70

Query: 62  LSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPHR 121
           LSGSGKSTL+RLLN+LI P+SGK+ +  +D++TL+   L +VR + + MVFQ+  L P+R
Sbjct: 71  LSGSGKSTLIRLLNKLITPSSGKVLVKGKDLSTLSAAQLREVRARHIGMVFQSVALLPNR 130

Query: 122 TILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALAN 181
           T+LENT +GLEVQ + K ER K AE+AL    L ++  +YP +LSGGMQQRVGLARA+  
Sbjct: 131 TVLENTAFGLEVQGIGKAERYKVAERALAKVGLSEWSQRYPSELSGGMQQRVGLARAITA 190

Query: 182 DPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKDG 241
           DPE++LMDE FSALDPLIRR++QDE  +L  +  K+ +F++HDL+EA+RIGDRIAIMKDG
Sbjct: 191 DPEVILMDEPFSALDPLIRRQLQDEFRQLTKELGKSAVFITHDLDEAIRIGDRIAIMKDG 250

Query: 242 KIMQIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIMIPALTTNIDVDGPSVA--LKK 299
            I+Q+GT EEI+  PA+DYV  FV  + R  ++ A ++M P         G  +A  +K 
Sbjct: 251 VIIQVGTAEEIVLKPADDYVAEFVAGISRLHLVKAHSVMTPVAPFKAANPGCDIARLIKT 310

Query: 300 MKTEEVSSLMAVDRKRQFRGVVTSEQAIAARKNNQSLKDVMTTDVGTVTKEMLVRDI 356
               +++ L+ +         V SE+   A  +N    DV+   VG +T   L+R +
Sbjct: 311 RLDADINELIGL--------TVKSERDALAVVDN----DVV---VGIITPRDLLRGV 352


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: 376
Number of extensions: 13
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: 372
Length adjustment: 30
Effective length of query: 377
Effective length of database: 342
Effective search space:   128934
Effective search space used:   128934
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