GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Desulfoscipio geothermicus DSM 3669

Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1 (characterized)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4771
         (248 letters)



>NCBI__GCF_900115975.1:WP_092487756.1
          Length = 234

 Score =  118 bits (295), Expect = 1e-31
 Identities = 77/214 (35%), Positives = 115/214 (53%), Gaps = 11/214 (5%)

Query: 28  GLAWTIGIAIAAWIIALTLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWYFL 87
           G   T+ I I +  I   LG I G+ R    +++  +AT YV+ FR  PLLVQ+FI YF 
Sbjct: 15  GAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFIVYFG 74

Query: 88  VPDLLPADLQEWYKQDLNPTTSA-------FLSVVVCLGLFTTARVCEQVRTGIQALPKG 140
           +P LL  DLQ +       T  A       FL+ V+   L + A V E  R G+Q++ +G
Sbjct: 75  IPKLL-MDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFRAGVQSIERG 133

Query: 141 QESAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNTSVASLIGLMELLAQTKQ 200
           Q  AAR++G    Q    V+LPQA++ +IPPL +EF+ + K+TS+ S+IG  EL   T+ 
Sbjct: 134 QMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAEL---TRN 190

Query: 201 TAEFSANLFEAFTLATLIYFTLNMSLMLLMRVVE 234
                A  +E+F +   + F   +    L R+V+
Sbjct: 191 GQLIIARTYESFAIWLTVGFIYLIMTFTLSRIVD 224


Lambda     K      H
   0.326    0.139    0.432 

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: 133
Number of extensions: 4
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: 234
Length adjustment: 23
Effective length of query: 225
Effective length of database: 211
Effective search space:    47475
Effective search space used:    47475
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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