GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruK in Pseudomonas putida KT2440

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit

Query= SwissProt::Q8G847
         (513 letters)



>lcl|FitnessBrowser__Putida:PP_2759 PP_2759 ribose ABC transporter -
           ATP-binding subunit
          Length = 512

 Score =  313 bits (802), Expect = 9e-90
 Identities = 177/508 (34%), Positives = 290/508 (57%), Gaps = 20/508 (3%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           P++ ++GI   F   +ALDG  L +  G VH L+GENGAGKST+IK L G+++ +AGS++
Sbjct: 4   PVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLL 63

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKR-GPFGIDWKKTHEAA 124
           +DG+P         +  GI  ++QE  L    +VGE +  GHE+R GP      +  EAA
Sbjct: 64  LDGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQQREAA 123

Query: 125 KKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLF 184
           +      GL  +  +  +  +S A QQ+V I RA++I  +VL+ DEP+ +L   EV  L 
Sbjct: 124 RLLDDYFGLR-LPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLL 182

Query: 185 AIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKS 244
            I++++RD G+AI+++SH+L +I  + DR+T+LRNG+ + EV  ++T  +++  +M+ + 
Sbjct: 183 RIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVNRE 242

Query: 245 AAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTE 304
             EL         +   P    ++DV+GLG+      +D+ + +GE+VG  GL+GSG  E
Sbjct: 243 VGELYP-------KVAVPAGALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKE 295

Query: 305 LGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILI 364
           L R L+G   PDSG   L+G+ +++  P  A+   +A   E RR +G+  DL+V++N  +
Sbjct: 296 LLRSLFGLAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTL 355

Query: 365 ALQA---TRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLA 421
           A  +     G+  P  ++       + ++ L ++       V+ LSGGNQQKV + +W A
Sbjct: 356 AALSRFVRLGLLSPARERHTTL---ELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFA 412

Query: 422 THPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEV---- 477
               L +LDEP+ GID+GAK EI +++ +L  +G GV+ +SS+L E++ L D I V    
Sbjct: 413 RCSSLYLLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRG 472

Query: 478 -LKDRHKIAEIENDDTVSQATIVETIAN 504
            +  R    E  +D  ++ AT  +   N
Sbjct: 473 AIAARFAAGEANSDRLLAVATGAQRAQN 500


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: 609
Number of extensions: 28
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: 512
Length adjustment: 35
Effective length of query: 478
Effective length of database: 477
Effective search space:   228006
Effective search space used:   228006
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.

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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 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