GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_12065 in Pseudomonas simiae WCS417

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 GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>lcl|FitnessBrowser__WCS417:GFF2332 PS417_11890 D-ribose transporter
           ATP-binding protein
          Length = 517

 Score =  393 bits (1010), Expect = e-114
 Identities = 219/495 (44%), Positives = 312/495 (63%), Gaps = 1/495 (0%)

Query: 1   MARPLLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDA 60
           +  P LL+  +++K + GV AL D +L +R G+V AL G NGAGKST + I+ GI Q DA
Sbjct: 18  LEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDA 77

Query: 61  GSILLNGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKAL 120
           G I L G P+ F  P  A  AGIAMI QEL  +P+M++AENIW+GRE   +  +V+++ +
Sbjct: 78  GEIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREM 137

Query: 121 NRRTRELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQ 180
           +R T ELL  L  ++D    +  LS+A+ Q+VEIAKA S+D  ++IMDEPTSAI E E  
Sbjct: 138 HRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVA 197

Query: 181 TLFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIV 240
            LF  I  L +QG GIVY++H+++E+  IAD+ ++FRDG ++   R   ++ D L+  +V
Sbjct: 198 HLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMV 257

Query: 241 GQELTRIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLN 300
           G+EL+++   +      +  L V +L+  G F D+S  L  GEILGI GLMGSGR+    
Sbjct: 258 GRELSQL-FPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAE 316

Query: 301 CIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAY 360
            I+G+T + SG +TL GK + I  P   I  G +L+TEDRK SGL    S+L N+ ++  
Sbjct: 317 TIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL 376

Query: 361 KRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCL 420
              +    I  +    L EDM K+L++KT SLE  + ++SGGNQQK +LA+ L T P  L
Sbjct: 377 PHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLL 436

Query: 421 LCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTIS 480
           + DEPTRGID GAK EIY L+      G A I++SSE PE+L +SDR+ V   G L+   
Sbjct: 437 ILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTL 496

Query: 481 TDTALSQEALLRLAS 495
             +  +QE +++LAS
Sbjct: 497 DRSEATQEKVMQLAS 511


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: 572
Number of extensions: 26
Number of successful extensions: 6
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: 495
Length of database: 517
Length adjustment: 34
Effective length of query: 461
Effective length of database: 483
Effective search space:   222663
Effective search space used:   222663
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 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, 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