GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Dethiosulfovibrio salsuginis USBA 82

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_085545416.1 B9Y55_RS11055 sugar ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>NCBI__GCF_900177735.1:WP_085545416.1
          Length = 504

 Score =  285 bits (728), Expect = 4e-81
 Identities = 167/496 (33%), Positives = 276/496 (55%), Gaps = 12/496 (2%)

Query: 5   VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKI 64
           V+ M +++K F    A   ++L +R G +HAL+GENGAGKSTLM  L G+    SG I++
Sbjct: 6   VLTMTKVSKAFPGVQALKDVSLSVRPGTVHALMGENGAGKSTLMKCLFGIYRMDSGKIEL 65

Query: 65  NGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKN----GILDLKKAGQ 120
           +G AV I +P  +  LGI M+HQ    +    V ENI LG   VK       LD K    
Sbjct: 66  DGKAVEIPNPKSALDLGISMIHQELHPIPHRPVMENIWLGRAPVKKLGPLSFLDCKAMEA 125

Query: 121 EIKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQEL 180
           + K L +   + +DP  +I  +SV   Q VEI K +   A I++ DEP++ LT  E+Q L
Sbjct: 126 QTKELFKDLDMDIDPRQQIRHLSVSRIQSVEIAKAVSYSAKIIVMDEPSSSLTEDEVQHL 185

Query: 181 MTIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGR 240
             I++ L   G +II I+HK++EI  ++D VT++R G  + T   S  ++ D+   MVGR
Sbjct: 186 FRIIRQLTARGIAIIYISHKIEEILQISDDVTIMRDGTLVGTWPSSELSTDDIISRMVGR 245

Query: 241 SVSFTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSEL 300
           +++        +P E I+ +       +    + K +S E+K GEI+G+ G+ G  ++EL
Sbjct: 246 TMTNRFPPRQNQPGEVIMEVSGY---SSPYPKSFKDVSFELKKGEILGVGGLVGAQRTEL 302

Query: 301 VQAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQ 360
           ++A+ GLR   SG L ++G+++   S        +  + E+R   G+   L++  NL + 
Sbjct: 303 MEAVFGLRSTSSGTLKLRGEEIDLSSPIIAKRQKMALLTEERRATGIFPVLSVQSNLVVA 362

Query: 361 TY--YKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVD 418
               YK  L   G+LN   +++     ++   V+  +     +  SGGNQQK ++AR + 
Sbjct: 363 NLAAYKGAL---GLLNSGAMSKDTDEGIKRLSVKTPSRGTLIRSLSGGNQQKVLLARWLL 419

Query: 419 RDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDG 478
            DPD+LI+ +PTRG+DVGA   I+  +     +GK+++++S EL E++ +SDRI V+ +G
Sbjct: 420 IDPDILILDEPTRGIDVGAKYEIYTIMADLAKQGKSIIMISSELPELMGMSDRIMVMSEG 479

Query: 479 QIQGIVTPETTNKQEL 494
           ++ GI+      ++++
Sbjct: 480 KLAGILNGAEATEEKI 495



 Score = 96.7 bits (239), Expect = 2e-24
 Identities = 66/223 (29%), Positives = 113/223 (50%), Gaps = 13/223 (5%)

Query: 24  INLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKINGSAVTIDSPSKSAQLGIG 83
           ++ +L+KGEI  + G  GA ++ LM  + GL   +SG++K+ G  + + SP  + +  + 
Sbjct: 279 VSFELKKGEILGVGGLVGAQRTELMEAVFGLRSTSSGTLKLRGEEIDLSSPIIAKRQKMA 338

Query: 84  MVHQHFMLVEAF---TVTENIILGNEVVKNGILDLKKAG-------QEIKALSEKYGLAV 133
           ++ +       F   +V  N+++ N     G L L  +G       + IK LS K     
Sbjct: 339 LLTEERRATGIFPVLSVQSNLVVANLAAYKGALGLLNSGAMSKDTDEGIKRLSVK---TP 395

Query: 134 DPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMKSLVKEGKS 193
                I  +S G QQ+V + + L    DILI DEPT  +      E+ TIM  L K+GKS
Sbjct: 396 SRGTLIRSLSGGNQQKVLLARWLLIDPDILILDEPTRGIDVGAKYEIYTIMADLAKQGKS 455

Query: 194 IILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEM 236
           II+I+ +L E+  ++DR+ V+  GK    +  +  T + + ++
Sbjct: 456 IIMISSELPELMGMSDRIMVMSEGKLAGILNGAEATEEKIMKL 498


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: 551
Number of extensions: 24
Number of successful extensions: 7
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: 504
Length adjustment: 34
Effective length of query: 476
Effective length of database: 470
Effective search space:   223720
Effective search space used:   223720
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