GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaQ in Pseudomonas simiae WCS417

Align RhaQ (characterized, see rationale)
to candidate GFF3462 PS417_17725 ribose ABC transporter permease

Query= uniprot:Q7BSH2
         (337 letters)



>FitnessBrowser__WCS417:GFF3462
          Length = 330

 Score =  164 bits (415), Expect = 3e-45
 Identities = 107/313 (34%), Positives = 171/313 (54%), Gaps = 10/313 (3%)

Query: 16  RLGTPLRRIAASWEVLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMAL 75
           RL   L R+  S     F   V++ +   LAS  FL A NLS+     +  A+IA  M  
Sbjct: 18  RLRLNLARLVRSPAFYPFVGLVVVTLVMILASDTFLTASNLSNIARQVSINAIIAVGMTC 77

Query: 76  LVISGEIDLSVAAIIALASTAMGAAVQIGIGTPGLVL-IGIGTGLACGVFNGVLVSVLKL 134
           ++++G IDLSV  ++AL+ T     +  G+  PGL +  G+  G+A G+ NG+ V+ L +
Sbjct: 78  VILTGGIDLSVGPVMALSGTLTAGLMVAGL-PPGLAIGAGMLIGVAFGIGNGLFVAYLHM 136

Query: 135 PSIVVTIGTMSLFRGISYIVLGDQAYGKYPADFAYFGQGYVVWVFSFEFVLFIVLAVLFA 194
           P I+VT+ TM + RG+  +          P  FA+FG+  +  +     ++ +   V + 
Sbjct: 137 PPIIVTLATMGIARGLGLMYTDGYPISGLPDWFAFFGRESLFGIQVPILIMLLTYLVAYV 196

Query: 195 ILLHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRP 254
           +L H T  GR +YAIG N+ A R SG+   R K +++ ++G+ + IA + LTSRL S +P
Sbjct: 197 LLQH-TRIGRYIYAIGGNEEAVRLSGVRAARFKLLVYGISGLTAAIAGLVLTSRLMSGQP 255

Query: 255 SIAQGWELEVVTMVVLGGISILGGFRHDRGVFV---IAAFVMGLVTFGLGLLNLPGIVMS 311
           +    +EL+ +  VVLGG SI GG    RGV V   + A ++G++  GL +L +   V S
Sbjct: 256 NAGVSFELDAIAAVVLGGASIAGG----RGVIVGTLLGAMLLGVLNNGLNMLGVSPYVQS 311

Query: 312 IFIGLLIIVTIAI 324
           +  G +I++ I I
Sbjct: 312 VIKGGIILLAIFI 324


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: 334
Number of extensions: 25
Number of successful extensions: 4
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: 330
Length adjustment: 28
Effective length of query: 309
Effective length of database: 302
Effective search space:    93318
Effective search space used:    93318
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 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