GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltJ in Brucella inopinata BO1

Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate WP_008511689.1 BIBO1_RS19985 amino acid ABC transporter permease

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



>NCBI__GCF_000182725.1:WP_008511689.1
          Length = 323

 Score =  112 bits (280), Expect = 9e-30
 Identities = 64/207 (30%), Positives = 112/207 (54%), Gaps = 13/207 (6%)

Query: 32  TIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWYFLVPDL 91
           T+ I+  +  IA ++  I  + +   N ++ G++T Y  LFR +PLL+Q++I Y  +P +
Sbjct: 125 TLYISAISIAIATIIALIGAIAKLSQNGVIYGLSTFYTSLFRGLPLLMQIYIIYLGLPQI 184

Query: 92  LPADIQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTGIQALPRGQEAAARAMGFK 151
                       +    +  L++ +C G + T    E  R GI+++P GQ+ AA A+G  
Sbjct: 185 ---------GYVIGAIPAGILALSLCYGAYMT----EIFRAGIESIPHGQKEAATALGLG 231

Query: 152 LPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTAEFSANLFEA 211
             Q  W V+LPQA RIIIPP  ++F+ + K+SS+ S+IG+ EL+   +   +      E 
Sbjct: 232 SAQTMWLVILPQAMRIIIPPTGNQFIAMLKDSSLVSVIGVWELMYVARTQGQTEFRHIEM 291

Query: 212 FTLATLIYFTLNMSLMLLMRSVEKKVA 238
              A++IY+ L++S   +   +E+  A
Sbjct: 292 LITASMIYWILSISFEFIQSRIERYYA 318


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: 196
Number of extensions: 9
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: 248
Length of database: 323
Length adjustment: 26
Effective length of query: 222
Effective length of database: 297
Effective search space:    65934
Effective search space used:    65934
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