GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Sinorhizobium meliloti 1021

Align BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized)
to candidate SMa0576 SMa0576 Leu or Leu/Val/Ile transport binding protein

Query= TCDB::Q9L3M3
         (381 letters)



>FitnessBrowser__Smeli:SMa0576
          Length = 363

 Score =  325 bits (834), Expect = 9e-94
 Identities = 169/357 (47%), Positives = 227/357 (63%), Gaps = 3/357 (0%)

Query: 3   KSLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGIN 62
           + L +A AL   LA    A  +VLI VAGP++G  A  G QL++GAE A A+INAAGG+ 
Sbjct: 2   RHLFTAAALAFALASQSEA--EVLIGVAGPMSGKLAWTGTQLRRGAEMAVANINAAGGVL 59

Query: 63  GEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPG 122
           G+Q+++ + DD  DP+Q ++ A K  ADG  FVIGH+ SG SIPAS++YA  G+L+  P 
Sbjct: 60  GQQVRLIVADDFCDPRQALAAAEKLVADGAVFVIGHYCSGASIPASKIYAAAGVLQISPS 119

Query: 123 RDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKK 182
              P L   G  N FR C RDD QG  AG YLADH+ D+KIA++HD T YG+GLADETKK
Sbjct: 120 STNPMLTEQGHANVFRVCSRDDAQGHKAGNYLADHWGDSKIAILHDNTTYGKGLADETKK 179

Query: 183 AMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKA 242
            +N  GVTE +Y+    G  D+S  +A ++ A ++++Y GG HTEA L++R A D+    
Sbjct: 180 QLNMRGVTEAVYQSYTPGKDDYSVEVAALQTAHIAVLYLGGYHTEAALMVRAARDRAYPV 239

Query: 243 TLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEAYTLYSY 302
            L+SGD   +     IAG A  GTL TF  DP  N    E+VE+F+A  F P+++TL+SY
Sbjct: 240 QLISGDDTATEAFGLIAGPAAEGTLFTFVADPRRNAEAAEVVERFRAENFEPDSWTLHSY 299

Query: 303 AAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWK 359
            A +  A A   A SLD +AV  A++E   F TVLG I FD+KGD  +  ++ Y WK
Sbjct: 300 GAAEIWAQAVTKANSLDLQAVIAALRE-DQFDTVLGRIDFDKKGDLTVQSWVWYVWK 355


Lambda     K      H
   0.314    0.132    0.383 

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: 375
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: 381
Length of database: 363
Length adjustment: 30
Effective length of query: 351
Effective length of database: 333
Effective search space:   116883
Effective search space used:   116883
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 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