GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_4681 L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1)

Query= TCDB::Q9RQ06
         (407 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4681
          Length = 392

 Score =  277 bits (709), Expect = 3e-79
 Identities = 145/280 (51%), Positives = 200/280 (71%), Gaps = 4/280 (1%)

Query: 5   VKIEHLTKIFGKRIKTALTMVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIMGLSG 64
           ++ E +  IF  R K AL ++++G  + EIL++TG  VGV   +  I +GEI V+MGLSG
Sbjct: 4   IRFEDVDVIFSNRPKAALDLLDKGLSRPEILQQTGLIVGVEKASLSIEKGEICVLMGLSG 63

Query: 65  SGKSTLLRLLNRLIEPTSGKIFIDDQ----DVATLNKEDLLQVRRKSMSMVFQNFGLFPH 120
           SGKS+LLR +N L   + GK+F++ +    D+A+ +  +L  +R K ++MVFQ F L P 
Sbjct: 64  SGKSSLLRCINGLNTVSRGKLFVEHEGRQIDIASCSPAELKMMRTKRIAMVFQKFALMPW 123

Query: 121 RTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALA 180
            T+ EN  +GLE+Q  P++ERRK  ++ L+   L  ++++ P +LSGGMQQRVGLARALA
Sbjct: 124 LTVRENISFGLEMQGRPEKERRKLVDEKLELVGLTQWRNKKPDELSGGMQQRVGLARALA 183

Query: 181 NDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKD 240
            D +ILLMDE FSALDPLIR+ +QDELLELQ K QKTI+FVSHDL+EAL++G RIAIMKD
Sbjct: 184 MDADILLMDEPFSALDPLIRQGLQDELLELQRKLQKTIVFVSHDLDEALKLGTRIAIMKD 243

Query: 241 GKIMQIGTGEEILTNPANDYVKTFVEDVDRAKVITAENIM 280
           GKI+Q    EEI+ NPA+DYV+TFV   +   V+   ++M
Sbjct: 244 GKIIQYSKPEEIVLNPADDYVRTFVAHTNPLNVLCGRSLM 283


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: 372
Number of extensions: 10
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: 392
Length adjustment: 31
Effective length of query: 376
Effective length of database: 361
Effective search space:   135736
Effective search space used:   135736
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