GapMind for catabolism of small carbon sources

 

Alignments 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 GFF3976 HP15_3916 sodium-dependent transporter family protein

Query= TCDB::O67854
         (513 letters)



>FitnessBrowser__Marino:GFF3976
          Length = 465

 Score =  170 bits (431), Expect = 9e-47
 Identities = 139/478 (29%), Positives = 221/478 (46%), Gaps = 60/478 (12%)

Query: 8   WATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWAMGR 67
           W++RL  ILA  G+AVGLGN  +FP    ENGGGAF++ Y++   ++GIP+M  E  +GR
Sbjct: 19  WSSRLAFILAATGSAVGLGNIWKFPYVTGENGGGAFVLVYLLCIAVIGIPIMMAEVFIGR 78

Query: 68  YGGAQGHGTTPAIFYLLWRNRFA---KILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLV 124
            G    H    ++  +  RN  A   +I  + G+    V+  +Y  I  W   +     V
Sbjct: 79  NG---RHNPITSMRLVAERNLSAPGWRISAIIGMIAAFVILSFYSVIGGWAASY-----V 130

Query: 125 GLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILI 184
           G            DSI   F   L S        + +L  ++F  +V L        ++ 
Sbjct: 131 GHAAMGDFTGGTADSIGELFGGLLAS------PGQLLLWHTIFMALVIL--------VVS 176

Query: 185 RGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVW 244
           +G+  G+ER   I MP LF+L +  V       T  G   + ++FL+TPDF  L   GV 
Sbjct: 177 QGLKGGLERAVTILMPALFLLLLVAV----GYATTTGHFGEAVSFLFTPDFGALTINGVL 232

Query: 245 IAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVA 304
           I A+G  FFTLSLG   ++ Y SY+ +D  I   G TA ++      I+   +++ A +A
Sbjct: 233 I-ALGHAFFTLSLGMAIMMAYGSYLGRDVSI---GRTAVSV-----AIMDTVVALLAGLA 283

Query: 305 FFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMI 364
            F V  A  +       L F TLP  F     G   G L+F LL FA  TS I++++P++
Sbjct: 284 IFPVVFANGLEAGAGPGLIFQTLPLAFGNMPMGGLFGTLFFILLLFAAWTSGISLLEPVV 343

Query: 365 AFLEDELKLSRKHA------VLWTAAIVFF--------SAHLVMFL----NKSLDEMDFW 406
            ++E++  L+R  +      + W   I            A L MF         D +DF+
Sbjct: 344 EWVEEKTSLARTGSSILVGVLCWALGIASILSLNVWADVAPLAMFERFEGKTIFDLLDFF 403

Query: 407 AGTIGVVFFGLTELIIFFWIFGADKAWEEIN-RGGIIKVPRIYYYVMRYITPAFLAVL 463
              + +   GL   +   W    +    ++  +GG      ++Y ++R++TP  +A++
Sbjct: 404 TANVLLPLSGLLTAVFVGWFVAKESLKSDLALQGGAF---TLWYNLIRFVTPIAVAIV 458


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: 740
Number of extensions: 41
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: 465
Length adjustment: 34
Effective length of query: 479
Effective length of database: 431
Effective search space:   206449
Effective search space used:   206449
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:

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