GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Pantoea rwandensis LMG 26275

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 WP_084935209.1 HA51_RS14055 sugar ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>NCBI__GCF_002095475.1:WP_084935209.1
          Length = 494

 Score =  304 bits (779), Expect = 4e-87
 Identities = 170/494 (34%), Positives = 282/494 (57%), Gaps = 6/494 (1%)

Query: 1   MAQHVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSG 60
           M    +E   I+K F    A D+++L ++ G +HAL+GENGAGKSTLM  L G+  P  G
Sbjct: 1   MTAFALEAEGISKFFPGVKALDNVSLRIKPGSVHALMGENGAGKSTLMKCLIGMYRPDKG 60

Query: 61  SIKINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQ 120
           +I+I G  V       + + GI M+HQ   LV   TV ENI LG E +K G +D  K  +
Sbjct: 61  TIRIKGEPVQFQDTMDALRSGISMIHQELNLVPYMTVAENIWLGREPMKYGFVDHGKLNK 120

Query: 121 EIKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQEL 180
           + + L  +  + +  +  + ++S+ AQQ VEI K +   +DI+I DEPT+ LT +E+  L
Sbjct: 121 QTQELLNRLNIRLKADRMVGELSIAAQQMVEIAKAVSWNSDIVIMDEPTSALTETEVAHL 180

Query: 181 MTIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGR 240
            TI++ L ++GK+II I+HK+DEI ++ D +++ R G  + +   S  T Q L   MVGR
Sbjct: 181 FTIIRDLREQGKAIIYISHKMDEIFTITDEISIFRDGTWVGSNNTSEFTRQSLITQMVGR 240

Query: 241 SVSFTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSEL 300
            ++    K   +    +L++++L   +         ++  V+ GEI+G+AG+ G G+SE+
Sbjct: 241 ELTQLFPKFNGEIGADVLTVRNLTCKDR-----FTDINFTVRKGEILGVAGLVGAGRSEV 295

Query: 301 VQAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQ 360
           ++++ G+    SG + I G  V   S     E  +  + EDR + GL L L++ EN+++ 
Sbjct: 296 MESLFGMESFDSGEVLIDGVPVKIDSPSTAIEKGMAFLTEDRKKSGLFLVLSVMENMSI- 354

Query: 361 TYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRD 420
                 +S  G +++ K+ +     +++ +++           SGGNQQK +IAR +   
Sbjct: 355 VNMPDYVSKAGFVSHMKMAQDCMEQIRKLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQ 414

Query: 421 PDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQI 480
           P +LI+ +PTRG+DVGA   I++ +    + G A+++VS EL EIL +SDR+ V+H G+I
Sbjct: 415 PKILILDEPTRGIDVGAKAEIYRLISELANRGVAIIMVSSELPEILGMSDRVMVMHGGRI 474

Query: 481 QGIVTPETTNKQEL 494
            GI+  E  N++ +
Sbjct: 475 TGILDKEEANQETI 488



 Score = 91.3 bits (225), Expect = 7e-23
 Identities = 58/231 (25%), Positives = 119/231 (51%), Gaps = 8/231 (3%)

Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329
           G+ A+  +SL +K G +  + G +G G+S L++ + G+ +   G + IKG+ V    T  
Sbjct: 17  GVKALDNVSLRIKPGSVHALMGENGAGKSTLMKCLIGMYRPDKGTIRIKGEPVQFQDTMD 76

Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEF 389
                +  + ++ +   L+  +T+AEN+ L    + P+ + G +++ K+N+  + L+   
Sbjct: 77  ALRSGISMIHQELN---LVPYMTVAENIWLG---REPMKY-GFVDHGKLNKQTQELLNRL 129

Query: 390 DVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAER 449
           ++R   + +  +  S   QQ   IA+ V  + D++I+ +PT  L    + ++   +   R
Sbjct: 130 NIRLKADRMVGE-LSIAAQQMVEIAKAVSWNSDIVIMDEPTSALTETEVAHLFTIIRDLR 188

Query: 450 DEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAG 500
           ++GKA++ +S ++DEI  ++D I++  DG   G        +Q L   M G
Sbjct: 189 EQGKAIIYISHKMDEIFTITDEISIFRDGTWVGSNNTSEFTRQSLITQMVG 239


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: 573
Number of extensions: 32
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: 510
Length of database: 494
Length adjustment: 34
Effective length of query: 476
Effective length of database: 460
Effective search space:   218960
Effective search space used:   218960
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 24 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