GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Desulfovibrio vulgaris Miyazaki F

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 8500289 DvMF_1045 glycine betaine/L-proline ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q9RQ06
         (407 letters)



>FitnessBrowser__Miya:8500289
          Length = 397

 Score =  402 bits (1032), Expect = e-116
 Identities = 208/390 (53%), Positives = 280/390 (71%), Gaps = 2/390 (0%)

Query: 4   KVKIEHLTKIFGKRIKTALTMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIMGLS 63
           K++I  LTKIFG   + AL MV  G+PK+EI K+T   VGV    F+++EGEI V+MGLS
Sbjct: 3   KIEIRDLTKIFGPVPEKALAMVRAGKPKDEIYKRTKHAVGVNRATFDVDEGEIVVVMGLS 62

Query: 64  GSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPHRTI 123
           GSGKSTL+R LNRLIEPT G + ID  DV TL+ +DL  +R+++  MVFQNF LFPHRT+
Sbjct: 63  GSGKSTLVRCLNRLIEPTDGTVRIDGTDVTTLSVKDLRALRQRTFGMVFQNFALFPHRTV 122

Query: 124 LENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALANDP 183
           LEN EYGLEV    K  RR +A +AL    L  ++   P QLSGGMQQRVGLARALA DP
Sbjct: 123 LENAEYGLEVMGAAKATRRDKAAEALARVGLAGWEAARPGQLSGGMQQRVGLARALALDP 182

Query: 184 EILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKDGKI 243
           +ILLMDEAFSALDPLIRR+MQDELL LQ   +KTI+F+SHDL+EAL+IGDRI +M+DG +
Sbjct: 183 DILLMDEAFSALDPLIRRDMQDELLRLQDDVRKTIVFISHDLDEALKIGDRIVLMRDGAV 242

Query: 244 MQIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIMIPA-LTTNIDVDGPSVALKKMKT 302
           +Q+GT E+ILT+PA+DYV  FV DVD A+V+TA  +M  +     + VDGP  AL+KM+ 
Sbjct: 243 VQVGTPEDILTSPADDYVARFVADVDIARVLTAGTVMKRSEAVAVLGVDGPRTALRKMRN 302

Query: 303 EEVSSLMAVDRKRQFRGVVTSEQAIA-ARKNNQSLKDVMTTDVGTVTKEMLVRDILPIIY 361
             +++L  +DR  +  G+VT++  +       + L  +M TD+ TV+ +    +++P++ 
Sbjct: 303 HAIATLFVLDRNHKLVGLVTADDIVEHLAGGERDLAAIMRTDITTVSTDAPASELIPLMA 362

Query: 362 DAPTPLAVVDDQGYLKGILIRGIVLEALAD 391
             P PLAV D++G L G+++RG++L ALA+
Sbjct: 363 GLPHPLAVTDERGRLAGVIVRGLLLGALAE 392


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: 441
Number of extensions: 14
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: 397
Length adjustment: 31
Effective length of query: 376
Effective length of database: 366
Effective search space:   137616
Effective search space used:   137616
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.

Links

Downloads

Related tools

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