GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araVsh in Pseudomonas putida KT2440

Align ABC transporter related (characterized, see rationale)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__Putida:PP_2759
          Length = 512

 Score =  313 bits (801), Expect = 1e-89
 Identities = 183/497 (36%), Positives = 283/497 (56%), Gaps = 8/497 (1%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           +LEL+ I K +   +AL+  SLR+ AG VH L+GENGAGKSTL+KV+ G    D G +L 
Sbjct: 5   VLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLLL 64

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123
            G+P    +P   ++ GI  ++QE  L    TV + LF G+E R   L+  +    +A  
Sbjct: 65  DGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQQREAAR 124

Query: 124 VLTQ-FKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182
           +L   F L +  +A + + S A QQ++ I R + +  +VLV DEP+ +L  +EV+ L  I
Sbjct: 125 LLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLLRI 184

Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242
           + +L+  G+AIV+I+H+L ++  + DR+TVLRNG+ + E         ++   M+ R + 
Sbjct: 185 VQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVNREVG 244

Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302
           E         +    A A+LL +  +    + Q ++L V +G+ VGL GL+GSG  E+  
Sbjct: 245 ELY------PKVAVPAGALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKELLR 298

Query: 303 AVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQ 362
           ++FGL   DSG + L GQ L+L  P +A++ G+AL PE+R+  G+   LS++EN  LA  
Sbjct: 299 SLFGLAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAAL 358

Query: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422
           +R      LS  R++      I++L+I    A   + QLSGGNQQKV LA+W A    L 
Sbjct: 359 SRFVRLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLY 418

Query: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVREL 482
           +LDEP+ GID+GA  EI +LI  L  EG  +L+ SS+L EL+   +++ V+         
Sbjct: 419 LLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARF 478

Query: 483 SGAELTSQHVMQAIAEG 499
           +  E  S  ++ A+A G
Sbjct: 479 AAGEANSDRLL-AVATG 494


Lambda     K      H
   0.319    0.136    0.377 

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: 616
Number of extensions: 29
Number of successful extensions: 7
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: 499
Length of database: 512
Length adjustment: 34
Effective length of query: 465
Effective length of database: 478
Effective search space:   222270
Effective search space used:   222270
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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:

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