GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4681 L-proline glycine
           betaine ABC transport system permease protein ProV (TC
           3.A.1.12.1)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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