GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaQ in Pantoea rwandensis LMG 26275

Align RhaQ (characterized, see rationale)
to candidate WP_084931761.1 HA51_RS02830 hypothetical protein

Query= uniprot:Q7BSH2
         (337 letters)



>NCBI__GCF_002095475.1:WP_084931761.1
          Length = 323

 Score =  167 bits (423), Expect = 3e-46
 Identities = 98/289 (33%), Positives = 160/289 (55%), Gaps = 4/289 (1%)

Query: 37  VLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISGEIDLSVAAIIALASTA 96
           ++I V  S  SP F    NL +     +  A+IA  M L++ISG IDLSV    AL S  
Sbjct: 31  LIIVVTFSFLSPVFFTVPNLLNILQQSSINALIALGMTLVIISGGIDLSVGPTAAL-SAV 89

Query: 97  MGAAVQI-GIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSIVVTIGTMSLFRGISYIVL 155
           +GA + + G+  P  +L  +G G  CGVF+G+LV+   L   +VT+G +SLFR I+ I  
Sbjct: 90  LGATLMVAGVPVPVAILATLGIGALCGVFSGMLVAYAGLQPFIVTLGGLSLFRAIALIYT 149

Query: 156 GDQAYGKYPADFAYFGQGYVVWVFSFEFVLFIVLAVLFAILLHATNFGRQVYAIGNNDFA 215
           G       P +F       V  +     ++  V+A++  ++++ T  G  + A+G N+ A
Sbjct: 150 GGNPVFGIPMEFRSIINSDVFGI-PTPIIIVAVIALVLWLVMNKTPLGEYILAVGGNEEA 208

Query: 216 ARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRPSIAQGWELEVVTMVVLGGISI 275
           AR +G+PV+R K  +F+++G ++ +A++ L  RLG+  P+I   WEL+ +    +GG S+
Sbjct: 209 ARVAGVPVKRTKVTVFIISGTLASLASLILIGRLGAAEPTIGNLWELDAIAAAAIGGASL 268

Query: 276 LGGFRHDRGVFVIAAFVMGLVTFGLGLLNLPGIVMSIFIGLLIIVTIAI 324
           +GG     G  +I A ++G +  GL LLN+      +  GL+II+ + I
Sbjct: 269 MGGKGSIVGT-IIGAIILGALRNGLTLLNIQAFYQLLATGLIIIIAMLI 316


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: 281
Number of extensions: 14
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: 323
Length adjustment: 28
Effective length of query: 309
Effective length of database: 295
Effective search space:    91155
Effective search space used:    91155
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