GapMind for catabolism of small carbon sources

 

Alignments for a candidate for leuT in Algiphilus aromaticivorans DG1253

Align The amino acid (leucine):2 Na+ symporter, LeuTAa (Yamashita et al., 2005). LeuT possesses two ion binding sites, NA1 and NA2, both highly specific for Na+ but with differing mechanisms of binding (Noskov and Roux, 2008). X-ray structures have been determined for LeuT in substrate-free outward-open and apo inward-open states (characterized)
to candidate WP_043768573.1 U743_RS11885 sodium-dependent transporter

Query= TCDB::O67854
         (513 letters)



>NCBI__GCF_000733765.1:WP_043768573.1
          Length = 445

 Score =  194 bits (492), Expect = 7e-54
 Identities = 150/475 (31%), Positives = 236/475 (49%), Gaps = 53/475 (11%)

Query: 5   REHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWA 64
           RE+W +RLG ++A AG+AVGLGN  RFP  A ENGGGAF+I Y+    + G+ ++  E  
Sbjct: 4   RENWGSRLGFVMAAAGSAVGLGNIWRFPYTAGENGGGAFLIIYLGIIAIFGVSVLLAEIV 63

Query: 65  MGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLV 124
           +GR       G    +   +WR       G+ G+    V+  +YV +  WTL +     +
Sbjct: 64  LGRATQRNPVGAFGQLGGRIWRP-----AGLLGVITGFVILSFYVVVAGWTLAY-----L 113

Query: 125 GLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGD-EPILKPSLFAYIVFLITMFINVSIL 183
           GL      ++TDPD +   F       + +  G   P+   +LF  +V         + +
Sbjct: 114 GLSLAGGLDSTDPDLLGAQF-------VALSGGIWAPLALAALFMALV--------GATV 158

Query: 184 IRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGV 243
             GI++GIER  ++ MP LF+L V L   V+ +  P G A  G+ FL  PDF K+     
Sbjct: 159 GGGITRGIERANRVLMPLLFLLLVGLA--VYAMTLPGGGA--GVAFLLQPDFSKISG-AT 213

Query: 244 WIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAV 303
           + AA+ Q FF+LSLG G ++TY SY+R  + + ++     +L+  A ++ G  ++I   V
Sbjct: 214 FTAALAQAFFSLSLGMGCMLTYGSYLRPHERLGVATGAIISLDVVAALLAG--LAIMPVV 271

Query: 304 AFFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPM 363
             FGV+      +AG   L FITLPA F+   GG  +G  +F LL  A LTS+I+I++P 
Sbjct: 272 FAFGVS-----PEAGP-GLTFITLPAAFAAMPGGAIVGPAFFLLLSVAALTSAISILEPA 325

Query: 364 IAFLEDELKLSRKHAVLWTAAIVFFSAHLVMFLNKS------------LDEMDFWAGTIG 411
           I++L DE   SR   V W  A +  +  +   L+               + MDF A  + 
Sbjct: 326 ISWLTDEHGWSRGRTV-WVCASICLALGVPSSLSMGAAPGLQIAGMSFFNAMDFAATNVM 384

Query: 412 VVFFGLTELIIFFWIFGADKAWEEINRGGIIKV-PRIYYYVMRYITPAFLAVLLV 465
           +    L   +   W +G     E  N  G+  +  R +  ++R++ P  L ++L+
Sbjct: 385 MPVGALITAVFVGWFWGQGALEELSNTSGVAPIWARGWLLLLRFVAPPALVLILL 439


Lambda     K      H
   0.330    0.146    0.463 

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: 722
Number of extensions: 52
Number of successful extensions: 6
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: 513
Length of database: 445
Length adjustment: 34
Effective length of query: 479
Effective length of database: 411
Effective search space:   196869
Effective search space used:   196869
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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