GapMind for catabolism of small carbon sources

 

Alignments for a candidate for leuT in Bacteroides clarus YIT 12056

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_009121821.1 BUB52_RS13665 sodium-dependent transporter

Query= TCDB::O67854
         (513 letters)



>NCBI__GCF_900129655.1:WP_009121821.1
          Length = 455

 Score =  204 bits (519), Expect = 5e-57
 Identities = 151/480 (31%), Positives = 238/480 (49%), Gaps = 54/480 (11%)

Query: 4   KREHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEW 63
           +R ++ ++LG+ILA AG+AVGLGN  RFP +   +GG AF++ Y++  L++GIP+M  E+
Sbjct: 5   ERANFGSKLGVILASAGSAVGLGNIWRFPFETGNHGGAAFILIYLVCVLILGIPIMIAEF 64

Query: 64  AMGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFL 123
            +GR    +    T   +  L      + +G  G+    ++  YY  +  WTL F     
Sbjct: 65  LIGR----RSRANTAGAYQKLAPGTQWRWVGRMGVLAGFLILGYYSVVAGWTLEF----- 115

Query: 124 VGLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSIL 183
              + E   N+    S      EF+ S+ G         +P ++  +  L+T F    I+
Sbjct: 116 ---IGEAATNSFAGKSA----AEFIASFNGFVSNP---WRPVIWLIVFLLVTHF----II 161

Query: 184 IRGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGV 243
           I+G+ KGIE+ AKI MP LFIL + L I    L      A++G+ FL  PDF K+ D  V
Sbjct: 162 IKGVEKGIEKSAKIMMPMLFILLIVLAICSVSLP----GASEGIEFLLKPDFSKV-DGNV 216

Query: 244 WIAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAV 303
           ++ A+GQ FF+LSLG G + TYASY R D ++  + L  A + +    IL G I  PAA 
Sbjct: 217 FLGAMGQAFFSLSLGMGCLCTYASYFRNDTNLPKTALNVAGI-DTLVAILAGFIIFPAAF 275

Query: 304 AFFGVANAVAIAKAGAFNLGFITLPAIFSQTAG-----GTFLGFLWFFLLFFAGLTSSIA 358
                  +V I      +L FITLP +F Q  G        L  +++ LL  A LTS+I+
Sbjct: 276 -------SVGIQPDAGPSLLFITLPNVFQQAFGNIPWLAIVLSIMFYVLLALAALTSTIS 328

Query: 359 IMQPMIAFLEDELKLSR-KHAVLWTAAIVFFSAHLVMFLNKSLDEMDFWAGTIGVVFFGL 417
           + + + A+L +E K +R K A L TA  +       + L    D   F      +  F  
Sbjct: 329 LHEVVTAYLHEEFKFTRGKAARLVTAGCIILGVLCSLSLGVGKDYTIFGLNLFDLFDFVT 388

Query: 418 TELII----FF------WIFGADKAWEEINRGGI--IKVPRIYYYVMRYITPAFLAVLLV 465
            ++++    FF      W       WEE++  G   I + R+  ++++YI P  + ++ +
Sbjct: 389 AKIMLPLGGFFISLFTGWYLDKKIVWEEVSNNGTLNIHIYRLLIFILKYIAPIGIGLIFI 448


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: 677
Number of extensions: 32
Number of successful extensions: 9
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: 455
Length adjustment: 34
Effective length of query: 479
Effective length of database: 421
Effective search space:   201659
Effective search space used:   201659
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 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