GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21720 in Rhodobacter viridis JA737

Align ABC transporter for D-glucosamine, permease component 2 (characterized)
to candidate WP_110806870.1 C8J30_RS16145 ABC transporter permease subunit

Query= reanno::pseudo3_N2E3:AO353_21720
         (220 letters)



>NCBI__GCF_003217355.1:WP_110806870.1
          Length = 232

 Score = 92.0 bits (227), Expect = 8e-24
 Identities = 64/210 (30%), Positives = 103/210 (49%), Gaps = 11/210 (5%)

Query: 18  LWSGFLTSVQCSVLAIMLGTLIGIVAGLVLTYGTLWMRAPFRFYVDLIRGTPVFVLVLAC 77
           L  G  T++  + L   L  +      L+  +G    +   R Y+  +RGTP+   +   
Sbjct: 14  LLDGAETTLILTGLGAALAAVFSPGLALIRLFGPTPAKMLLRAYISFVRGTPLLAQLFLV 73

Query: 78  FYMA-------PALG-WQI--DAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASKA 127
           FY +         LG W    D F   VL   +   ++  EI+RG ++A+P G++EA++A
Sbjct: 74  FYGSGQFRAELTGLGLWSFFRDPFNCAVLVFVINSCAYQTEILRGGIEAVPPGEIEAARA 133

Query: 128 IGLTFYQALAYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTFM 187
           IG+T  + LA V+ P A R   P   N    ++KAS L S++ V +L+  T+QI +R+F 
Sbjct: 134 IGMTRARVLARVIFPHAYRIAWPALGNEVILLMKASALASIVTVFDLMGRTRQIFSRSF- 192

Query: 188 TLEFYLFAGFLFFIINYAIELLGRHIEKRV 217
               Y  A  L+ +I      L R IE+R+
Sbjct: 193 EFSVYFEAAALYLLITVVFVFLWRQIERRL 222


Lambda     K      H
   0.330    0.142    0.440 

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: 123
Number of extensions: 8
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: 220
Length of database: 232
Length adjustment: 22
Effective length of query: 198
Effective length of database: 210
Effective search space:    41580
Effective search space used:    41580
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 (21.9 bits)
S2: 46 (22.3 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