GapMind for catabolism of small carbon sources

 

Alignments for a candidate for leuT in Oceanisphaera arctica V1-41

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_104485326.1 UN63_RS03140 sodium-dependent transporter

Query= TCDB::O67854
         (513 letters)



>NCBI__GCF_002936955.1:WP_104485326.1
          Length = 445

 Score =  181 bits (460), Expect = 4e-50
 Identities = 140/475 (29%), Positives = 238/475 (50%), Gaps = 48/475 (10%)

Query: 5   REHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWA 64
           REH+ +R G I+A AG AVGLGN   FP QAA NGGGAF+I Y++  +++  P++ +E A
Sbjct: 2   REHFGSRFGFIMAAAGAAVGLGNIWGFPTQAASNGGGAFLIAYLVLVMMLAFPMLVMEVA 61

Query: 65  MGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLV 124
           +GRYG A    +   +     +   A ++G  G+ +P +V  +Y  +  W L F    + 
Sbjct: 62  IGRYGQANPVDSVRKLGRTPLQKTIASLVGYAGMLVPSLVLSFYAIVAGWLLAFLAAAVT 121

Query: 125 GLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILI 184
            +                         +G     E +    L   IV+ +  ++   +++
Sbjct: 122 RI-------------------------LGWDAATEWLEAFGLGRNIVWTLVFYLLTILVV 156

Query: 185 R-GISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGV 243
           + G+ +GIER++   MP LF+L  FL++  ++L T +G A  GL     PDF K+ +PG+
Sbjct: 157 QAGVRRGIERWSARLMPALFVL--FLLLFFYIL-TQDG-AMTGLKHYLVPDFSKVLEPGL 212

Query: 244 WIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAV 303
            I+A+GQ FF+L++G  +++ Y SY+ K+++I  +     TL +     L G + +PA  
Sbjct: 213 LISAMGQAFFSLTIGGCSMLMYGSYLNKNENIPRTAF-QVTLLDTGVAFLAGLVILPA-- 269

Query: 304 AFFGVANAVAI-AKAGAF----NLGFITLPAIFSQTAG--GTFLGFLWFFLLFFAGLTSS 356
            F  + N V I A+ G+      L F+ LPA+F  T G  G  +  ++F L+  A LTSS
Sbjct: 270 MFVAMKNGVTIFAEDGSLLSSDTLVFVVLPALF-DTMGPIGLVMALVFFVLMGIAALTSS 328

Query: 357 IAIMQPMIAFLEDELKLSRKHAV-LWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFF 415
           I++++  +++  +  K SR     L   A+  FS  + +        +   +        
Sbjct: 329 ISMLEVPVSYTTERFKASRPLMTWLLGGALALFSVAICLNFGALFGFVIRLSTQNIQPLV 388

Query: 416 GLTELIIFFWIFGADKAWEEINRGGIIKVP----RIYYYVMRYITPAFLAVLLVV 466
           GL   ++  W++G  K +EE+ +G          RI+ + +R + P  L VLLV+
Sbjct: 389 GLGFCVLGGWMWGRAKLFEELVQGSPELAGSVFWRIWPWYVRIVCP--LLVLLVI 441


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: 733
Number of extensions: 41
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
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