GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Pseudomonas stutzeri RCH2

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized)
to candidate GFF136 Psest_0136 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

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



>FitnessBrowser__psRCH2:GFF136
          Length = 229

 Score =  102 bits (255), Expect = 5e-27
 Identities = 73/235 (31%), Positives = 121/235 (51%), Gaps = 16/235 (6%)

Query: 7   WGVFFKSTGVGSETYLDWFITGLGWTIAIAIVAWIIALMLGSVLGVMRTVPNRLVSGIAT 66
           W +F K        +L  FI G   T+ +  V+ I  L++   LG+ R+  +  V  +  
Sbjct: 3   WEIFIK--------WLPSFIDGAWLTLQLVGVSVIAGLIVAVPLGIARSSRHLAVRALPY 54

Query: 67  CYVELFRNVPLLVQLFIWYFLVP--DLLPQNLQDWYKQDLNPTTSAYLSVVVCLGLFTAA 124
            Y+  FR  PLLVQLF+ Y+ +   D++ Q+    Y +D       Y   ++ + L TAA
Sbjct: 55  GYIFFFRGTPLLVQLFLVYYGMAQFDVVRQSALWPYLRD------PYWCAIITMTLHTAA 108

Query: 125 RVCEQVRTGIQALPRGQESAARAMGFKLPQIYWNVLLPQAYRIVIPPLTSEFLNVFKNSS 184
            + E +R  IQ +P G+  AARA+G    Q   +++LP+A RI +P  ++E + + K S+
Sbjct: 109 YIAEIIRGAIQNVPHGEIEAARALGMSRSQALLHIILPRATRIGLPAYSNEVILMLKASA 168

Query: 185 VASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRMVEKKVAV 239
           +AS I L+EL    ++ A  +    E F  A LIY  +   LM   +++E+ + V
Sbjct: 169 LASTITLLELTGMARKIAARTYLHEEMFLTAGLIYLLIAFILMQGFKLLERWLRV 223


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: 127
Number of extensions: 5
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: 229
Length adjustment: 23
Effective length of query: 225
Effective length of database: 206
Effective search space:    46350
Effective search space used:    46350
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