GapMind for catabolism of small carbon sources

 

Aligments for a candidate for leuT in Marinobacter adhaerens HP15

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 GFF878 HP15_857 sodium-dependent transporter family protein

Query= TCDB::O67854
         (513 letters)



>lcl|FitnessBrowser__Marino:GFF878 HP15_857 sodium-dependent
           transporter family protein
          Length = 460

 Score =  191 bits (484), Expect = 6e-53
 Identities = 142/476 (29%), Positives = 231/476 (48%), Gaps = 52/476 (10%)

Query: 8   WATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGR 67
           W++R+  ILA AG+AVGLGN  +FP    ENGGGAF++ Y+    L+G+P++  E  +GR
Sbjct: 15  WSSRMAFILAAAGSAVGLGNIWKFPYITGENGGGAFVLIYLACIFLIGVPVLIAETMIGR 74

Query: 68  YGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLVGLV 127
            GG     T   +       R  + +G  G+    +V  +Y  I  W L +  K   GL 
Sbjct: 75  RGGQSPVATMRTLTKTEGTARGWRAIGWNGVIASFLVLSFYAVIGGWALVYIGKAATGLF 134

Query: 128 PEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILIRGI 187
                   D ++I   F   L          E ++  S+F  IV        V I+ RGI
Sbjct: 135 -----TGADAEAIGGQFGGLL------ANPWELLMWHSVFMVIV--------VFIVGRGI 175

Query: 188 SKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVWIAA 247
             G+E+   + MP LF+L V +VI        +G+    ++F+++PDF KL   GV + A
Sbjct: 176 RSGLEKAVNMLMPLLFVLLVAMVIYAM----NSGSFGRAVSFMFSPDFSKLTTAGV-LTA 230

Query: 248 VGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVAFFG 307
           +G   FTLS+G G ++ Y SY+ K  +I  + +T A        ++  S+++ A +A F 
Sbjct: 231 LGHAAFTLSIGIGVLMAYGSYLPKTVNIARTAMTIA--------VVDTSVALLAGLAIFP 282

Query: 308 VANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMIAFL 367
           +  A  +       L F+TLP  F Q +GG   G ++F LL  A +TS+I++++P++ +L
Sbjct: 283 LVFANGLEPGAGPGLIFVTLPLAFGQMSGGALFGTIFFALLLVAAITSAISMLEPVVEWL 342

Query: 368 EDELKLSR-KHAV-----LWTAAI-------VFFSAHLVMFL-----NKSLDEMDFWAGT 409
           E+   +SR K A+     +W   I       V+ S H + F+         D +DF    
Sbjct: 343 EEHKGVSRAKSAIGGGLAIWFIGIGTVLSFNVWESVHPLGFIPFFEGKTVFDLLDFLVSN 402

Query: 410 IGVVFFGLTELIIFFWIFGADKAWEEINRGGIIKVPRIYYYVMRYITPAFLAVLLV 465
           + +   GL   +   W    +    +I   G     + + +V+RY+TPA +AV+ +
Sbjct: 403 LMMPLGGLAIALFAGWAMKRESLPADIGLQG--SSYKAFMFVLRYLTPAGIAVVFL 456


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: 717
Number of extensions: 53
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: 460
Length adjustment: 34
Effective length of query: 479
Effective length of database: 426
Effective search space:   204054
Effective search space used:   204054
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: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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