GapMind for catabolism of small carbon sources

 

Aligments for a candidate for araG in Pseudomonas simiae WCS417

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



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

 Score =  372 bits (956), Expect = e-107
 Identities = 203/493 (41%), Positives = 312/493 (63%), Gaps = 6/493 (1%)

Query: 6   PYL-SFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64
           PYL     I K FPGV AL D+      G V ALMGENGAGKSTL+KI++G Y P  G +
Sbjct: 21  PYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEI 80

Query: 65  VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLG--QLPHKGGIVNRSLLNY 122
            + G+ + F    AA  AG+A+I+QEL+L+P M++AENI++G  QL     + +R +   
Sbjct: 81  RLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRC 140

Query: 123 EAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNL 182
            A L L  L +++DP+  +  LSI + QMVEIAKA++ ++ I+  DEPTS+++ +E+ +L
Sbjct: 141 TAEL-LARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHL 199

Query: 183 FRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVG 242
           F +I +L+ +G+ I+Y++H+M E+FA++D + VF+DG Y+        ++ D+L+  MVG
Sbjct: 200 FSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIG-LQRADSMNSDSLISMMVG 258

Query: 243 RDIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGM 302
           R++  ++  +    G+  L +  +   GV   +S  + +GEI+G+ GL+G+GR+ + + +
Sbjct: 259 RELSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETI 318

Query: 303 FGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRK 362
           FG T  ++GQ+ +D + + I  P  AI  G  L  EDRK  G+ P  SV +N+ ++    
Sbjct: 319 FGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL-P 377

Query: 363 HVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVIL 422
           H  G   I         +   + L +KTP  EQ I  LSGGNQQKA+L RWL    ++++
Sbjct: 378 HYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLI 437

Query: 423 LDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELL 482
           LDEPTRGIDVGAK EIY +I  LA++G+AV+  SS+LPEVLG++DR++VM EGE+ G L 
Sbjct: 438 LDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLD 497

Query: 483 HEQADERQALSLA 495
             +A + + + LA
Sbjct: 498 RSEATQEKVMQLA 510


Lambda     K      H
   0.319    0.136    0.391 

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: 27
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: 504
Length of database: 517
Length adjustment: 35
Effective length of query: 469
Effective length of database: 482
Effective search space:   226058
Effective search space used:   226058
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 (21.7 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 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