GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Pseudomonas putida KT2440

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

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__Putida:PP_2759
          Length = 512

 Score =  286 bits (731), Expect = 2e-81
 Identities = 171/495 (34%), Positives = 278/495 (56%), Gaps = 8/495 (1%)

Query: 11  SVPVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGE 70
           S PV+E   + K FG+T AL+  S+RV  G  H LVG NGAGKSTL+ +L G+ +PD G 
Sbjct: 2   STPVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGS 61

Query: 71  VRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRD 130
           +   G      + R   R  +  ++Q   +    +V E LF   +   G ++D ++ +R+
Sbjct: 62  LLLDGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQQRE 121

Query: 131 ARALLD-HWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRL 189
           A  LLD ++ + +  +A  G+LS   +Q+V+I RAL    R ++ DEP+  L   E++RL
Sbjct: 122 AARLLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERL 181

Query: 190 FRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGE 249
            R +  L+ +G+  ++ISH+LQE+  +C  VTVLR+ R +  A VS  PR   +E +T  
Sbjct: 182 LRIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDV--AEVS--PRNTSLEQITRL 237

Query: 250 RGGLAVADAAARGALPADTAVALELKELTGAD-YEGVSFTVKRGEVVGLTGATSSGRTSV 308
                V +   + A+PA  A+ L+++ L  A  Y+G+   V+RGE+VGLTG   SG   +
Sbjct: 238 MVNREVGELYPKVAVPAG-ALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKEL 296

Query: 309 AEAIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMT 368
             ++ GL     G + +DG  L       ++A G+  +P++R  +G+ L  SV EN ++ 
Sbjct: 297 LRSLFGLAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLA 356

Query: 369 IARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPN 428
                 + G+ +PA++     ++I+ L I A G    V  LSGGNQQKV +A+  A   +
Sbjct: 357 ALSRFVRLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSS 416

Query: 429 VLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDDL-RTCDRVLVMFRGRVAA 487
           + +L +P+ G+DV +K  +  ++  + +EG  VL++S +L +L   CDR+ VM RG +AA
Sbjct: 417 LYLLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAA 476

Query: 488 EFPAGWQDHDLIASV 502
            F AG  + D + +V
Sbjct: 477 RFAAGEANSDRLLAV 491


Lambda     K      H
   0.318    0.134    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: 583
Number of extensions: 28
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: 510
Length of database: 512
Length adjustment: 35
Effective length of query: 475
Effective length of database: 477
Effective search space:   226575
Effective search space used:   226575
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 (21.7 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