GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Lactobacillus silagei IWT126

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_089136535.1 CES79_RS05345 methionine ABC transporter ATP-binding protein

Query= TCDB::Q9RQ06
         (407 letters)



>NCBI__GCF_002217945.1:WP_089136535.1
          Length = 344

 Score =  196 bits (498), Expect = 9e-55
 Identities = 113/275 (41%), Positives = 166/275 (60%), Gaps = 5/275 (1%)

Query: 24  MVEQGEPKNEILKKTGATVGVYDTNFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSG 83
           M+E          K G    V D N  I++GEI+ I+G SG+GKSTL R+LN L  PTSG
Sbjct: 1   MIEFKNVTKTFTTKDGDVTAVSDVNLNIDDGEIYGIVGYSGAGKSTLTRMLNGLETPTSG 60

Query: 84  KIFIDDQDVATLNKEDLLQVRRKSMSMVFQNFGLFPHRTILENTEYGLEVQNVPKEERRK 143
           +I I+   +  L+  +L + R+K + M+FQ+F L   RT+++N  + LEV  V + +R+K
Sbjct: 61  EIDINGDPITALSGPELRKKRQK-IGMIFQHFNLLWSRTVIQNIMFPLEVAGVSRSDRKK 119

Query: 144 RAEKALDNANLLDFKDQYPKQLSGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREM 203
           +A+  +D   L   +  YP +LSGG +QRVG+ARALANDPEIL+ DEA SALDP    E+
Sbjct: 120 KAQHLVDLVGLTGREHSYPSELSGGQKQRVGVARALANDPEILISDEATSALDPQTTDEV 179

Query: 204 QDELLELQAKFQKTIIFVSHDLNEALRIGDRIAIMKDGKIMQIGTGEEILTNPANDYVKT 263
            D LLE+  K   +I+ ++H+++   +I D +A+M DGK+++ GT   +  NP     K 
Sbjct: 180 LDLLLEINKKMNLSIVLITHEMHAIRKICDHVAVMDDGKVVEQGTVFNVFRNPKKQITKR 239

Query: 264 FV-EDVDRAKVITAENIMIPALTTNIDVDGPSVAL 297
           FV E+VD A  +T  N ++  L  +   DG  V L
Sbjct: 240 FVSEEVDPA--LTDTNSIVEDLIKSYP-DGTIVQL 271


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: 349
Number of extensions: 15
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: 344
Length adjustment: 30
Effective length of query: 377
Effective length of database: 314
Effective search space:   118378
Effective search space used:   118378
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 24 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