GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaQ in Tistlia consotensis USBA 355

Align RhaQ (characterized, see rationale)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease

Query= uniprot:Q7BSH2
         (337 letters)



>NCBI__GCF_900177295.1:WP_085121058.1
          Length = 335

 Score =  142 bits (358), Expect = 1e-38
 Identities = 96/319 (30%), Positives = 167/319 (52%), Gaps = 17/319 (5%)

Query: 18  GTPLRRIAASWEVLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLV 77
           G  L+++A S E+ +  +A++I    SL SPYFL   N+ +         +++  M  ++
Sbjct: 22  GRLLKQLATSLELRMLGLALVIGAVLSLLSPYFLTESNIFNILDQSVVIGILSIGMTFVI 81

Query: 78  ISGEIDLSVAAIIALASTAMGAAVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSI 137
           ++G IDLSV ++  L+   +G A++     P  +L+G+ TG   G+ +G+L+   +L + 
Sbjct: 82  LTGGIDLSVGSVAGLSGIVLGLALK-DYPIPVAILLGVLTGAGVGLVSGILIGYFRLAAF 140

Query: 138 VVTIGTMSLFRGISYIVLGDQAYGKYPADFAYFGQGYVVWVFSFEF---VLFIVLAVLFA 194
           VVT+G M++ R ++YI  G  A   +P+D +      +V+   F     VLF+  A L A
Sbjct: 141 VVTLGMMAIGRSLAYIFSGQTAISGFPSDLSS-----IVYTDVFGIPTNVLFLGFAYLLA 195

Query: 195 I-LLHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTR 253
              L  T  GR +YAIG+N  AAR +G+ V     + ++++G ++ +A     +++ S  
Sbjct: 196 WGYLTYTKGGRTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVD 255

Query: 254 PSIAQGWELEVVTMVVLGGISILGGFRHDRGVFV---IAAFVMGLVTFGLGLLNLPGIVM 310
           P    G EL+ +  VV+GG S+ GG    RG  V   I   +M ++  GL LL +     
Sbjct: 256 PLTGNGMELDAIAAVVIGGASLYGG----RGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQ 311

Query: 311 SIFIGLLIIVTIAIPIIAR 329
              IG +II+ + +  + R
Sbjct: 312 GSAIGSIIIMALLVERLVR 330


Lambda     K      H
   0.330    0.145    0.423 

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: 343
Number of extensions: 26
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: 337
Length of database: 335
Length adjustment: 28
Effective length of query: 309
Effective length of database: 307
Effective search space:    94863
Effective search space used:    94863
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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