Alignments for a candidate for PS417_12065 in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_12065 in Pseudomonas putida KT2440

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit

Query= uniprot:A0A1N7TX47
         (495 letters)



>FitnessBrowser__Putida:PP_2759
          Length = 512

 Score =  287 bits (735), Expect = 5e-82
 Identities = 173/491 (35%), Positives = 265/491 (53%), Gaps = 3/491 (0%)

Query: 6   LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65
           +L+   + K +    AL    L + AGSVH L G NGAGKST + +L GI + DAGS+LL
Sbjct: 5   VLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLLL 64

Query: 66  NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125
           +G P     P +    GI  I QE       TV E ++ G E RR G ++D ++  R   
Sbjct: 65  DGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHE-RRFGPLLDRRSQQREAA 123

Query: 126 ELLDS-LEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184
            LLD      + A + +  LS A+ Q+V+I +A     +V++ DEP+ A+ + E + L +
Sbjct: 124 RLLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLLR 183

Query: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244
            ++RL   G  IVY+SH L E+  + D  ++ R+G  V      +   + + R +V +E+
Sbjct: 184 IVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVNREV 243

Query: 245 TRIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYG 304
             +  KV     A   L V  L RA  +  I LQ+R+GEI+G+ GL+GSG  E L  ++G
Sbjct: 244 GELYPKVAVPAGA-LLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKELLRSLFG 302

Query: 305 LTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLS 364
           L   DSG V L G+P+ +  P+  +  G++L+ E+R+  G+ L  S+  N  L+A  R  
Sbjct: 303 LAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAALSRFV 362

Query: 365 SWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDE 424
              L++  +E     ++++RL+IK       V  +SGGNQQKV LAK  +      L DE
Sbjct: 363 RLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLYLLDE 422

Query: 425 PTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTA 484
           P+ GID GAK EIY L+ + V+ G   +++SS+ PEL+ L DRI V   G +        
Sbjct: 423 PSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARFAAGE 482

Query: 485 LSQEALLRLAS 495
            + + LL +A+
Sbjct: 483 ANSDRLLAVAT 493



 Score = 82.4 bits (202), Expect = 3e-20
 Identities = 64/236 (27%), Positives = 107/236 (45%), Gaps = 11/236 (4%)

Query: 13  AKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQF 72
           A+AY G+       L +R G +  L G  G+G    L  L G+   D+G + L+G P+  
Sbjct: 267 ARAYQGID------LQVRRGEIVGLTGLVGSGAKELLRSLFGLAPPDSGEVRLDGQPLSL 320

Query: 73  NRPSEALAAGIAMITQELEPIPY---MTVAENIWLGREPRRAGCIVDNKALNRRTR-ELL 128
             P EA+A G+A++ +E         ++V EN  L    R     + + A  R T  EL+
Sbjct: 321 RSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAALSRFVRLGLLSPARERHTTLELI 380

Query: 129 DSLEFDVD-ATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIR 187
           + L      A + + +LS    Q V +AK F+    + ++DEP+  I       +++ I 
Sbjct: 381 ERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLYLLDEPSVGIDVGAKVEIYRLIG 440

Query: 188 RLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQE 243
            L  +GAG++ +S  L EL  + D   +   GA        + + D L+    G +
Sbjct: 441 ELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARFAAGEANSDRLLAVATGAQ 496


Lambda     K      H
   0.319    0.135    0.381 

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: 520
Number of extensions: 19
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 495
Length of database: 512
Length adjustment: 34
Effective length of query: 461
Effective length of database: 478
Effective search space:   220358
Effective search space used:   220358
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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 (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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources