GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components

Query= TCDB::Q9RQ06
         (407 letters)



>FitnessBrowser__Cola:Echvi_1022
          Length = 345

 Score =  145 bits (367), Expect = 1e-39
 Identities = 83/224 (37%), Positives = 125/224 (55%), Gaps = 11/224 (4%)

Query: 44  VYDTNFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKEDLLQV 103
           V D + EI EG +  I+G +GSGK+TLL+L+  L  P  G+I    Q +  +N +  L  
Sbjct: 21  VKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKGEIVFSGQTI--VNGKSALPA 78

Query: 104 RRKSMSMVFQNFGLFPHRTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFKDQ--- 160
            ++ + ++FQ + LFP  T+LEN    L       +E R   + A+D+  L   +D    
Sbjct: 79  NQREVGVIFQEYALFPQMTLLENVREALH------QESRNARQIAMDSLALAGLEDSFSA 132

Query: 161 YPKQLSGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTIIF 220
           YP QLS G +QR  LARALA+ P++LL+D+ F +LD   + E+ +++ ++      T I 
Sbjct: 133 YPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEISEDIRDIVKATGITAIV 192

Query: 221 VSHDLNEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKTF 264
            SH   +AL + D IAI+  G + Q+GT  EI   PAN YV  F
Sbjct: 193 ASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVANF 236


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: 300
Number of extensions: 18
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: 345
Length adjustment: 30
Effective length of query: 377
Effective length of database: 315
Effective search space:   118755
Effective search space used:   118755
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