GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruK in Sinorhizobium meliloti 1021

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>lcl|FitnessBrowser__Smeli:SM_b20713 SM_b20713 sugar uptake ABC
           transporter ATP-binding protein
          Length = 513

 Score =  348 bits (892), Expect = e-100
 Identities = 190/499 (38%), Positives = 314/499 (62%), Gaps = 11/499 (2%)

Query: 7   IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66
           ++  +G+  EFPGV ALD V+  L  G VHALMGENGAGKST++K L G+Y  + G + +
Sbjct: 23  LLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPDQGEVKL 82

Query: 67  DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDWKKTHEAAK 125
            G   +    LDA   GIA ++QE+NL   ++V EN+ +  E +  FG +D  +      
Sbjct: 83  RGAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRFGFVDHGEMRRMTA 142

Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185
           K   ++ ++ +DP   +  +S+A +Q+V IA+A+   + VLI+DEPTS+L   EV  LF 
Sbjct: 143 KLFERLKID-LDPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLFE 201

Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245
           I+R +R  G+ I++++H +++++EI D  ++ R+G++I   ++ +  RD++I MM+G+  
Sbjct: 202 IIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHLSNEVTRDDIIRMMVGR-- 259

Query: 246 AELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTEL 305
            E++Q+  K+   E+  G+  ++ VK L   G    V  D+  GE++G AGL+GSGR+ +
Sbjct: 260 -EITQMFPKE---EVPIGDV-VLSVKNLTLNGVFRDVSFDVRAGEILGVAGLVGSGRSNV 314

Query: 306 GRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIA 365
              L+G     SGT  ++GK+V I     A+++++A+ TE+R+D G +  L + +N+ IA
Sbjct: 315 AETLFGVTPASSGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDILENMQIA 374

Query: 366 LQATRGMFKP-IPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHP 424
           +   + + +  + ++E  A  ++  ++L V+  +    V+NLSGGNQQKVLIGRWL T+P
Sbjct: 375 VLQDKFVKRGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQKVLIGRWLLTNP 434

Query: 425 ELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKI 484
            +LILDEPTRGID+GAKAEI ++V +LA  G+ V+ ISSE+ EV+ +SD I V+ +  ++
Sbjct: 435 RILILDEPTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVMHE-GRV 493

Query: 485 AEIENDDTVSQATIVETIA 503
             I +    +Q  ++E  A
Sbjct: 494 TGILDRAEATQIKVMELAA 512


Lambda     K      H
   0.316    0.135    0.376 

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: 632
Number of extensions: 30
Number of successful extensions: 8
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: 513
Length adjustment: 35
Effective length of query: 478
Effective length of database: 478
Effective search space:   228484
Effective search space used:   228484
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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