GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Cupriavidus basilensis 4G11

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized)
to candidate RR42_RS36980 RR42_RS36980 amino acid ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_16285
         (248 letters)



>FitnessBrowser__Cup4G11:RR42_RS36980
          Length = 224

 Score =  107 bits (268), Expect = 2e-28
 Identities = 68/205 (33%), Positives = 104/205 (50%), Gaps = 11/205 (5%)

Query: 32  TIAIAIVAWIIALMLGSVLGVMRTVPNRLVSGIATCYVELFRNVPLLVQLFIWYFLVPDL 91
           T+A+++  +++   + +   V+   P   +   A   V L R  PLLVQLF WYF    L
Sbjct: 2   TVALSVAVFVLGCAIAAGWLVLARSPIMPLRLTARGAVGLLRRTPLLVQLFFWYFGAAQL 61

Query: 92  LPQN----LQDWYKQDLN------PTTSAYLSVVVCLGLFTAARVCEQVRTGIQALPRGQ 141
           L +     L DW    +       P+  A L+ +  +GL+ +A    ++  G+  +PRGQ
Sbjct: 62  LGEGAIGALYDWQGWRIGGWHVPAPSLEA-LASLAGIGLYASAFYARELEAGLANVPRGQ 120

Query: 142 ESAARAMGFKLPQIYWNVLLPQAYRIVIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQT 201
            +AA A+GF     +W V+LPQA RI   P+  +F    KN+S+A  IG  E+    +Q 
Sbjct: 121 GAAALALGFTPAAAFWRVVLPQALRIAARPMVGQFCQTIKNTSLAMAIGFAEMSYTARQV 180

Query: 202 AEFSANLFEAFTLATLIYFTLNMSL 226
              S   F+AF LATL+Y  L + L
Sbjct: 181 ETDSLMTFQAFGLATLLYVALILLL 205


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: 151
Number of extensions: 10
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: 224
Length adjustment: 23
Effective length of query: 225
Effective length of database: 201
Effective search space:    45225
Effective search space used:    45225
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 Sep 17 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