GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Tistlia consotensis USBA 355

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_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>NCBI__GCF_900177295.1:WP_085124759.1
          Length = 518

 Score =  306 bits (785), Expect = 9e-88
 Identities = 167/493 (33%), Positives = 277/493 (56%), Gaps = 4/493 (0%)

Query: 2   AQHVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGS 61
           A  ++E+R ++++F   +A D ++  LR GE+H L GENGAGKST+++M+AG L P+ G 
Sbjct: 20  AAPLLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGE 79

Query: 62  IKINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQE 121
            +  G  V ++S   +  LGI  V Q F LV   TV EN+ LG E  + G+LD +     
Sbjct: 80  FRFRGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTRLGLLDRRALHDR 139

Query: 122 IKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELM 181
             A+ ++ G  + P  ++  ++   QQ VEI K       +LI DEPTA LT  E  +L 
Sbjct: 140 ADAILKRLGFPLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLF 199

Query: 182 TIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRS 241
            +++ +  +G  +I ITH+L EIR + DR+TV+R G+ + TV+   T   +L  +M GR 
Sbjct: 200 KLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMTGRV 259

Query: 242 VSFTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELV 301
                 K   KP   +LS++ L       + A    SL V AGEI+G+AG+ G+G+SE+ 
Sbjct: 260 YDELFPKVRFKPGRELLSVERLTTASGSVVEA----SLSVCAGEIVGLAGLVGSGKSEVA 315

Query: 302 QAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQT 361
           +A  GL KI  GH+ +KG++VT    +++ +    +VP DR  +GL++   + EN++L +
Sbjct: 316 RACFGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPS 375

Query: 362 YYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDP 421
              AP  +  +L+     +  R L ++ +++        + FSGGNQQK ++A+   R  
Sbjct: 376 LTLAPFGNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPV 435

Query: 422 DLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQ 481
            +    +PT G+DVG    I++ +    + G  +LL+S +L E+LNLS+R  V + G++Q
Sbjct: 436 QVFAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQ 495

Query: 482 GIVTPETTNKQEL 494
             +  +   ++++
Sbjct: 496 AELAGDEITEEKV 508



 Score = 72.0 bits (175), Expect = 5e-17
 Identities = 56/233 (24%), Positives = 109/233 (46%), Gaps = 12/233 (5%)

Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329
           G+ A+  +  +++ GE+  + G +G G+S ++  I G  +   G    +G+ V   S   
Sbjct: 35  GVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFRFRGEPVELNSVHH 94

Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQE- 388
              L +  V ++     L+ ++T+ ENL L     A  +  G+L+   +++    +++  
Sbjct: 95  ARGLGISAVFQEF---SLVPQMTVEENLFLG----AESTRLGLLDRRALHDRADAILKRL 147

Query: 389 -FDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIA 447
            F +R  + ++     +   QQ   IA+    +  +LI+ +PT  L       + K +  
Sbjct: 148 GFPLRPRDRVLH---LTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLFKLIEQ 204

Query: 448 ERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAG 500
            + +G  V+ ++  L EI  + DRI V+ DG+    V  +TT + EL  LM G
Sbjct: 205 VKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMTG 257


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: 545
Number of extensions: 29
Number of successful extensions: 5
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: 518
Length adjustment: 35
Effective length of query: 475
Effective length of database: 483
Effective search space:   229425
Effective search space used:   229425
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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