GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Desulfoscipio geothermicus DSM 3669

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_092482139.1 BM299_RS03860 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= TCDB::Q9RQ06
         (407 letters)



>NCBI__GCF_900115975.1:WP_092482139.1
          Length = 390

 Score =  403 bits (1036), Expect = e-117
 Identities = 199/390 (51%), Positives = 294/390 (75%), Gaps = 2/390 (0%)

Query: 1   MPVKVKIEHLTKIFGKRIKTALTMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIM 60
           MPVKV++++LTKIFG+  K  L  V+QG  K +IL+ TG TVG+ + +F++ EGE+FVIM
Sbjct: 1   MPVKVEVKNLTKIFGRNPKAILEKVKQGMSKEKILEDTGHTVGIRNASFQVEEGEVFVIM 60

Query: 61  GLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPH 120
           GLSGSGKSTL+R LN L +PT+G+I++D  ++   +K+ L + R++ ++MVFQ+FGL  H
Sbjct: 61  GLSGSGKSTLIRCLNLLNKPTAGEIYVDGDNILEYDKKQLKKFRQEKVAMVFQHFGLLSH 120

Query: 121 RTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALA 180
           RT++ N EYGLEV+ +PK ER + A+KA+ NA L  ++++ P +LSGGMQQRVGLARALA
Sbjct: 121 RTVIGNVEYGLEVKKIPKNERCEIAKKAIANAGLAGWENKMPNELSGGMQQRVGLARALA 180

Query: 181 NDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKD 240
           NDP+ILLMDE FSALDPLIRR+MQ EL+ELQ++ +KTIIF++HD+NEA +IGDR+A+MKD
Sbjct: 181 NDPDILLMDEPFSALDPLIRRDMQYELMELQSRLKKTIIFITHDINEAFKIGDRVAVMKD 240

Query: 241 GKIMQIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIMI-PALTTNIDVDGPSVALKK 299
           G I QIGT EE+L +P ++Y++ FV+D+DR+KV+ A+++M  P +  +I  +G   A+ +
Sbjct: 241 GVIEQIGTPEELLASPESEYIENFVKDIDRSKVLQAKHVMFKPTVLVSIK-EGLKAAMME 299

Query: 300 MKTEEVSSLMAVDRKRQFRGVVTSEQAIAARKNNQSLKDVMTTDVGTVTKEMLVRDILPI 359
           MK+  +SS+  VD +++ +G+VT +  I A K N++L++++  D  T   E  ++D++P 
Sbjct: 300 MKSNGISSVFVVDSEKRLQGIVTIDDTIKAIKENKTLREILKHDYYTTDCEAFLQDLIPK 359

Query: 360 IYDAPTPLAVVDDQGYLKGILIRGIVLEAL 389
             D   PLAV+D+ G L G++ R  VL AL
Sbjct: 360 ATDTKYPLAVIDEDGKLLGLISRVSVLSAL 389


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: 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: 390
Length adjustment: 31
Effective length of query: 376
Effective length of database: 359
Effective search space:   134984
Effective search space used:   134984
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 Apr 09 2024. 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