GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SOT in Bacteroides clarus YIT 12056

Align Sorbitol (D-Glucitol):H+ co-transporter, SOT1 (Km for sorbitol of 0.64 mM) of 509 aas and 12 TMSs (Gao et al. 2003). SOT1 of P. cerasus is expressed throughout fruit development, but especially when growth and sorbitol accumulation rates are highest. In leaves, PcSOT1 expression is highest in young, expanding tissues, but substantially less in mature leaves (characterized)
to candidate WP_009122015.1 BUB52_RS10060 sugar porter family MFS transporter

Query= TCDB::AIU41385.1
         (509 letters)



>NCBI__GCF_900129655.1:WP_009122015.1
          Length = 479

 Score =  268 bits (684), Expect = 4e-76
 Identities = 155/479 (32%), Positives = 255/479 (53%), Gaps = 41/479 (8%)

Query: 31  AILASMTSILLGYDIGVMSGASIYIQEDLKISDVEVEILIGILNLYSLIGSAAAGRTSDW 90
           AI+A+   +L G+D GV+SGA  ++Q+D  I D  +E++     + ++ G+   G+ +D+
Sbjct: 17  AIIAATGGLLFGFDTGVISGAIPFLQKDFGIDDGVIELITTAGLVGAIAGALFCGKVTDY 76

Query: 91  IGRRYTIVFAGAIFFTGALLMGFATNYAFLMVGRFVAGIGVGYALMIAPVYNAEVSPASS 150
           +GR+  I+ +  IF  GA+  G A +   L++ R   GI +G +    P+Y AE+SP + 
Sbjct: 77  LGRKKVILASAVIFAIGAVWSGIAPDSTNLILARLFLGIAIGVSSFAVPLYIAEISPTNI 136

Query: 151 RGALTSFPEVFVNIGILLGYVANYAFSGLPINLGWRLMLGVGVFPSVILAVGVLTMPESP 210
           RG L S  ++ V +G+L+ Y+++  F+       WR M   G+ P++IL +G+  MPESP
Sbjct: 137 RGTLVSMFQLMVTLGVLVSYLSDLFFADEVDVTCWRPMFYAGILPALILLIGMFCMPESP 196

Query: 211 RWLVMQGRLGDAKHVLDKTSDSLEEAQLRLADIKEAAGIPEHCTEDV-VQVPKHSHGEEV 269
           RWL+ +GR   A  +L+K                E  G  E     +  ++ K  +    
Sbjct: 197 RWLMSKGRKQKAMLILNKI---------------EGHGAAEEVAHSINEEIEKSKNEISK 241

Query: 270 WKELLLHPTPPVRHILIAAVGFHFFQQMSGIDALVLYSPRIFRASGITDSSTLLLATVAV 329
           W EL+    P +R  L  A+G  FFQQ  GI+ ++ YSP+IF  +G   + + + A V V
Sbjct: 242 WSELI---KPTLRTPLFIAIGIMFFQQFVGINTVIYYSPKIFFMAGFDGAVSAIWAAVGV 298

Query: 330 GFSKTIFTLIAIGFLDRVGRRPLLLTSVAGMIASLLCLGTSLTIVDHEKEKMMWASVVCL 389
           G    + TL++I F+DR+GRR L  T + G+I SL+ L  S   V+       W +V+  
Sbjct: 299 GVVNVVATLVSIYFVDRLGRRKLYFTGLTGIILSLITLSLSFVFVNELGNAGQWLTVI-- 356

Query: 390 TMVLAYVGFFSIGMGPIAWVYSSEIFPLKLRAQGCSMGTAVNRIMSGVLTMTFITLYKAI 449
             +  YV FF+I +GP+ W+  SE+FP K+R  G S+G+    + + +++ TF  +  A+
Sbjct: 357 -FMFLYVAFFAISIGPLGWLIISEVFPQKVRGLGASVGSLSVWVFNSIVSFTFFKIVNAL 415

Query: 450 TMGGT---------------FFLYGAIATVGWVFFYTMLPETQGRTLEDMEVLFGKFWR 493
           T+ GT               F  YG IA +  ++ Y  +PET+G +LE +E     +WR
Sbjct: 416 TIPGTEIMVDGEQVGNPAGAFGFYGLIALLALIWGYFYVPETKGISLEKIE----DYWR 470


Lambda     K      H
   0.326    0.140    0.424 

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: 718
Number of extensions: 49
Number of successful extensions: 5
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: 509
Length of database: 479
Length adjustment: 34
Effective length of query: 475
Effective length of database: 445
Effective search space:   211375
Effective search space used:   211375
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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