GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ in Sinorhizobium meliloti 1021

Align PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate SMc03865 SMc03865 amino-acid transport system permease ABC transporter protein

Query= TCDB::Q88NY3
         (248 letters)



>FitnessBrowser__Smeli:SMc03865
          Length = 273

 Score =  115 bits (289), Expect = 7e-31
 Identities = 68/224 (30%), Positives = 122/224 (54%), Gaps = 15/224 (6%)

Query: 26  ITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRLVSGIATAYVELFRNVPLLVQLF--- 82
           + GLG T+ + +  +++A +LG  + +M    + ++  IA  Y E+ R VP+LV LF   
Sbjct: 47  LKGLGVTVFVTLVGFVLATVLGLGVALMALSEHVVLRQIARFYTEVIRGVPILVLLFYIA 106

Query: 83  ---------IWYFLVPDLLPEGLQEWFKQDLNPTTSALISVVICLGLFTAARVCEQVRTG 133
                    +  F+   L+  G   W +  +    S +   ++ L +  +A + E  R G
Sbjct: 107 FVGAPALVTVANFVAAPLISAG---WIEPFVVRDVSLMWRAIMALMIGYSAFIAEVFRAG 163

Query: 134 IQALPKGQEAAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLME 193
           IQ++ KGQ  AA+A+G S  Q +  V+ PQA R+I+PPL ++F+ + K+SS+ S++G+ +
Sbjct: 164 IQSVDKGQVEAAKALGLSRYQRFRLVVFPQAIRVILPPLGNDFVAMVKDSSLVSVLGVAD 223

Query: 194 LLAQTKQTAEFSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKV 237
           +    K  A  S   FE +++   +Y  L +GL L +R VE+++
Sbjct: 224 ITQMGKVYASGSFRFFETYSIVAYVYLVLTIGLSLALRAVERRL 267


Lambda     K      H
   0.325    0.139    0.425 

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: 122
Number of extensions: 8
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: 273
Length adjustment: 24
Effective length of query: 224
Effective length of database: 249
Effective search space:    55776
Effective search space used:    55776
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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