GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaQ in Rhodobacter johrii JA192

Align RhaQ (characterized, see rationale)
to candidate WP_108223269.1 C8J29_RS11820 ABC transporter permease

Query= uniprot:Q7BSH2
         (337 letters)



>NCBI__GCF_003046325.1:WP_108223269.1
          Length = 363

 Score =  141 bits (356), Expect = 2e-38
 Identities = 93/310 (30%), Positives = 155/310 (50%), Gaps = 16/310 (5%)

Query: 30  VLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISGEIDLSVAAI 89
           V L  + V + +F +L    F  A+ L+          ++  A  L+V++  IDLSV AI
Sbjct: 46  VPLIVLVVSVSIFGALLGQKFFSAFTLTLILQQVAIVGIVGAAQTLVVLTAGIDLSVGAI 105

Query: 90  IALASTAMGA-AVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSIVVTIGTMSLFR 148
           + L+S  MG    + GI  P  VL G+  G   G  NG LV+ +KLP  +VT+G   +  
Sbjct: 106 MVLSSVIMGQFTFRYGIPAPLSVLCGLAAGAGIGFVNGTLVARMKLPPFIVTLGMWQIVL 165

Query: 149 GISYI-----VLGDQAYGKYPADFAYFGQGYVVW---------VFSFEFVLFIVLAVLFA 194
             +++      +  Q          +FG  + +          VF++  VL I+L ++ A
Sbjct: 166 AANFLYSANETIRSQDISAQAPILQFFGNTFRLGADEAGRGGAVFTYGAVLLILLVLVIA 225

Query: 195 ILLHATNFGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRP 254
            +L  T +GR VYA+G++  AA  +G+    V   ++ L+G++  +A   +  RLGS  P
Sbjct: 226 YVLRQTAWGRHVYAVGDDPDAAELAGVQTRNVLVTVYTLSGLICALAGWVMIGRLGSVSP 285

Query: 255 SIAQGWELEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNLPGIVMSIFI 314
           +  Q   +E +T VV+GGIS+ GG     G+ +  A ++G+ + GL L+        + I
Sbjct: 286 TAGQFANIESITAVVIGGISLFGGRGSVLGM-LFGALIVGVFSLGLKLMGTDPQWTYLLI 344

Query: 315 GLLIIVTIAI 324
           G+LII  +A+
Sbjct: 345 GMLIIAAVAV 354


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: 321
Number of extensions: 14
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: 337
Length of database: 363
Length adjustment: 29
Effective length of query: 308
Effective length of database: 334
Effective search space:   102872
Effective search space used:   102872
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 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