GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Rhodobacter viridis JA737

Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate WP_110804905.1 C8J30_RS06530 amino acid ABC transporter permease

Query= reanno::pseudo1_N1B4:Pf1N1B4_772
         (248 letters)



>NCBI__GCF_003217355.1:WP_110804905.1
          Length = 262

 Score =  100 bits (249), Expect = 3e-26
 Identities = 66/212 (31%), Positives = 112/212 (52%), Gaps = 9/212 (4%)

Query: 28  GLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWYFL 87
           G+G T+ + + A+  AL+LG +L V     + I   +A  Y E+ R VP++V L    F 
Sbjct: 43  GIGITVFVTLFAFAGALVLGLVLAVASLSRHLIWRQLARFYTEVIRGVPIIVMLLYVAFA 102

Query: 88  VPDLLPADIQEWYKQDLNPTTSA-----FLSVVVCLGLFTTARVCEQVRTGIQALPRGQE 142
              L+PA +  W    L P  S          V+ L L   A + E  R G+ ++ RGQ 
Sbjct: 103 ---LVPAVVAGWNALGL-PEASVRDFPLLARAVLALILAYAAFLAEVFRAGLLSVERGQI 158

Query: 143 AAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTA 202
            AA+A+G      +  ++ PQA+R ++PPL ++F+ + K+SS+ S++G+ ++    K TA
Sbjct: 159 EAAKALGLNGWLRFRLIIFPQAFRTVLPPLGNDFVAMVKDSSLVSVLGVADITQLGKVTA 218

Query: 203 EFSANLFEAFTLATLIYFTLNMSLMLLMRSVE 234
             +   FE + +  LIY  + ++L L +R +E
Sbjct: 219 AGNFRYFETYNVVALIYLAMTVTLSLALRKLE 250


Lambda     K      H
   0.326    0.140    0.433 

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: 146
Number of extensions: 7
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: 248
Length of database: 262
Length adjustment: 24
Effective length of query: 224
Effective length of database: 238
Effective search space:    53312
Effective search space used:    53312
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 (21.7 bits)
S2: 47 (22.7 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