GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Malonomonas rubra DSM 5091

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_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= TCDB::Q9RQ06
         (407 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  369 bits (946), Expect = e-106
 Identities = 194/405 (47%), Positives = 278/405 (68%), Gaps = 9/405 (2%)

Query: 2   PVKVKIEHLTKIFGKRIKTALTMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIMG 61
           PVK+++++L KIFG + K A+ +++QG  K  I +KT  TVGV D +FEI +GEIFVIMG
Sbjct: 4   PVKIEVKNLYKIFGPQPKKAMALLKQGLDKEAIFEKTETTVGVQDASFEIFKGEIFVIMG 63

Query: 62  LSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPHR 121
           LSGSGKST++R+LNRLIEPTSG++ ID +D+  +N + L++VRR  +SMVFQ+F L PH 
Sbjct: 64  LSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKVRRAKLSMVFQSFALMPHM 123

Query: 122 TILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALAN 181
           T+L+N  +GLE+  V K+ R +RA +AL+   L  + +  P +LSGGMQQRVGLAR LA 
Sbjct: 124 TVLQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAESMPDELSGGMQQRVGLARGLAV 183

Query: 182 DPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKDG 241
           DP+ILLMDEAFSALDPLIR EMQDELL+LQAK ++TI+F+SHDL+EA+RIGDRIAIM+ G
Sbjct: 184 DPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISHDLDEAMRIGDRIAIMEGG 243

Query: 242 KIMQIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIMIPALTTNIDVDG--PSVALKK 299
           +++Q+GT EEIL NPA+DYV+ F   VD   ++TA +I      T    DG  P   L++
Sbjct: 244 RVVQVGTPEEILQNPADDYVRAFFRGVDPTNILTAGDIATQTQVTIPITDGKNPRAGLQR 303

Query: 300 MKTEEVSSLMAVDRKRQFRGVVTSEQAIAARKNN---QSLKDVMTTDVGTVTKEMLVRDI 356
           +   +      +D ++ F+GVV+++      +N+     + +    +V    K+  ++DI
Sbjct: 304 LVKNDRDYAYVLDSEKTFKGVVSTDSLRDMLENDNVPHLIPNAYLEEVVAAHKDDSLQDI 363

Query: 357 LPIIYDAPTPLAVVDDQGYLKGILIRGIVLEAL----ADIPDEVE 397
           LP +   P PL ++DD G   G + + + L+ L    +D P ++E
Sbjct: 364 LPKVAAHPWPLPILDDDGRYLGAISKNLFLKTLHRNQSDEPADME 408


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: 482
Number of extensions: 17
Number of successful extensions: 2
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: 415
Length adjustment: 31
Effective length of query: 376
Effective length of database: 384
Effective search space:   144384
Effective search space used:   144384
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