GapMind for catabolism of small carbon sources

 

Alignments for a candidate for opuBA in Methanospirillum stamsii Pt1

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_109939593.1 DLD82_RS02795 ABC transporter ATP-binding protein

Query= TCDB::Q9RQ06
         (407 letters)



>NCBI__GCF_003173335.1:WP_109939593.1
          Length = 263

 Score =  154 bits (390), Expect = 2e-42
 Identities = 84/210 (40%), Positives = 127/210 (60%), Gaps = 11/210 (5%)

Query: 39  GATVGVYDTNFEINEGEIFVIMGLSGSGKSTLLRLLNRLIEPTSGKIFIDDQDVATLNKE 98
           G  V + D N  I + E    +G SG GK+TLLR++  L    SG++ +D +        
Sbjct: 19  GRVVALSDVNLTIADDEFVSFVGPSGCGKTTLLRIIAGLDTANSGEVRVDGE-------- 70

Query: 99  DLLQVRRKSMSMVFQNFGLFPHRTILENTEYGLEVQNVPKEERRKRAEKALDNANLLDFK 158
            L+    + + MVFQ + LFP + +L N  +GL ++ + KEER   A+K +    L  F+
Sbjct: 71  -LITGPGQKVGMVFQEYSLFPWQNVLTNVAFGLRMRGIGKEERYSIAKKFIALVGLTQFE 129

Query: 159 DQYPKQLSGGMQQRVGLARALANDPEILLMDEAFSALDPLIRREMQDELLELQAKFQKTI 218
           + YP +LSGGM+QRV +ARALA DP++LLMDE F ALD   R  MQ ELL++    +KTI
Sbjct: 130 ESYPYELSGGMRQRVAIARALATDPDLLLMDEPFGALDAQTRNHMQCELLDIWGTKKKTI 189

Query: 219 IFVSHDLNEALRIGDRIAIM--KDGKIMQI 246
           +FV+H  +EA+ + DR+ ++  + G+I +I
Sbjct: 190 LFVTHSCDEAVFLSDRVVVLSPRPGRIREI 219


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: 241
Number of extensions: 7
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: 263
Length adjustment: 28
Effective length of query: 379
Effective length of database: 235
Effective search space:    89065
Effective search space used:    89065
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: 48 (23.1 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