GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nupA in Pseudomonas fluorescens GW456-L13

Align RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= TCDB::Q8DU37
         (510 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121 L-arabinose
           transport ATP-binding protein AraG (TC 3.A.1.2.2)
          Length = 514

 Score =  263 bits (673), Expect = 9e-75
 Identities = 157/485 (32%), Positives = 266/485 (54%), Gaps = 7/485 (1%)

Query: 11  ITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKINGSAVT 70
           I K F    A D+I+     G++HAL+GENGAGKSTL+ +L G   P SG+++I    + 
Sbjct: 21  IGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIGERTMD 80

Query: 71  IDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKALSEKYG 130
             S + S   G+ ++HQ   LV   TV EN+ LG+     G+++     Q+  A  +   
Sbjct: 81  FKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQALACLKGLA 140

Query: 131 LAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMKSLVKE 190
             +DP  K+  +S+G +Q VEI K L RGA ++ FDEPT+ L+  EI  LM I+  L  E
Sbjct: 141 DEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRLRDE 200

Query: 191 GKSIILITHKLDEIRSVADRVTVIRRGKSIETV-EVSGTTSQDLAEMMVGRSVSFTIEKT 249
           GK ++ ++H+++E+  + + VTV + G+ + T  ++S  T   L   MVGR +    +  
Sbjct: 201 GKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCMVGRDIQDIYDYR 260

Query: 250 PTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRK 309
           P +     L +  L+     G    + +S EV  GEI+G+ G+ G G++EL++ ++GL +
Sbjct: 261 PRQRGAVALKVDGLL-----GPGLREPVSFEVHKGEILGLFGLVGAGRTELLRLLSGLAR 315

Query: 310 IKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSH 369
             +G L ++G ++   S R      +   PEDR ++G++   ++AEN+ +     A  + 
Sbjct: 316 HSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENINISA-RGAHSTF 374

Query: 370 NGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQP 429
             +L      ++    ++   V+  N        SGGNQQKAI+ R +     +L++ +P
Sbjct: 375 GCLLRGLWEKDNAEQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434

Query: 430 TRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETT 489
           TRG+D+GA   I++ +     EG AV++VS +L E++ +SDRI V+ +G ++G ++ E  
Sbjct: 435 TRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEGALRGELSREQA 494

Query: 490 NKQEL 494
           N+  L
Sbjct: 495 NESNL 499


Lambda     K      H
   0.315    0.135    0.363 

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: 43
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: 510
Length of database: 514
Length adjustment: 35
Effective length of query: 475
Effective length of database: 479
Effective search space:   227525
Effective search space used:   227525
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: 42 (22.0 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