GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaQ in Burkholderia phytofirmans PsJN

Align RhaQ (characterized, see rationale)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease

Query= uniprot:Q7BSH2
         (337 letters)



>FitnessBrowser__BFirm:BPHYT_RS16055
          Length = 335

 Score =  169 bits (429), Expect = 7e-47
 Identities = 104/304 (34%), Positives = 166/304 (54%), Gaps = 5/304 (1%)

Query: 21  LRRIAASWEVLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISG 80
           L+R    +  +   V  ++ VF   AS  FL   N+ +     +  A+IA  M  ++++G
Sbjct: 31  LKRSTLFYPFIGLLVVCIVMVF---ASDSFLSGANIENVLRQVSINAIIAVGMTCVILTG 87

Query: 81  EIDLSVAAIIALASTAMGAAVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSIVVT 140
            IDLSV +++ALA T     +  G+     + IGI  GL  G  NG  V+   +P I+VT
Sbjct: 88  GIDLSVGSVMALAGTLAAGLMVAGMNAVAALAIGIAVGLGFGAANGFFVAFAGMPPIIVT 147

Query: 141 IGTMSLFRGISYIVLGDQAYGKYPADFAYFGQGYVVWVFSFEFVLFIVLAVLFAILLHAT 200
           + TM + RG++ I  G       P   ++FG G ++ V +   V+  V+ V+  +LL   
Sbjct: 148 LATMGIARGLALIYTGGYPIDGLPDWVSFFGSGKILGVQA-PVVIMAVIYVIAWVLLERM 206

Query: 201 NFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRPSIAQGW 260
            FGR VYAIG N+ A R SG+ V RVK I++ + G+ S  AA+ LT+RL S +P+   G+
Sbjct: 207 PFGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSGQPNAGVGF 266

Query: 261 ELEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNLPGIVMSIFIGLLIIV 320
           EL+ +  VV+GG SI GG     G  +I A ++G++  GL ++ +   V ++  G +I++
Sbjct: 267 ELDAIAAVVMGGTSISGGRGSIIGT-LIGALLLGVLNNGLNMVGVNPYVQNVIKGGIILL 325

Query: 321 TIAI 324
            I I
Sbjct: 326 AIYI 329


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: 331
Number of extensions: 23
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 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