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_085545006.1 B9Y55_RS08890 ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>NCBI__GCF_900177735.1:WP_085545006.1
          Length = 512

 Score =  452 bits (1163), Expect = e-131
 Identities = 230/495 (46%), Positives = 325/495 (65%), Gaps = 1/495 (0%)

Query: 6   IEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKIN 65
           +E++ ITK F   VAN+ +++ ++KGE+ ALLGENGAGK+TLM +L G+     G I ++
Sbjct: 12  VELKGITKYFPGTVANEDVHISVKKGEVLALLGENGAGKTTLMRILYGMYRQDQGKILVD 71

Query: 66  GSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKAL 125
           GS+V IDSP  +  LGIGM+HQHF LV   +V EN++LG     +  LDL++   E++ L
Sbjct: 72  GSSVRIDSPQDAMALGIGMIHQHFSLVPVHSVAENVVLGLGSSMDR-LDLERVSSELREL 130

Query: 126 SEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMK 185
             +YGL VDP  K+  + VG QQRVEI+K LYR A ILI DEPTAVLTP E + L   ++
Sbjct: 131 GSRYGLEVDPYGKVGQLPVGMQQRVEIVKALYRKARILIMDEPTAVLTPQETERLGEFVR 190

Query: 186 SLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSVSFT 245
               +G S+ILITHKL E+ ++AD VTV+R GK + +V  + ++ ++LA MMVGR +   
Sbjct: 191 EFTSQGNSVILITHKLGEVMAMADSVTVMRAGKVVGSVSTAESSERELARMMVGRDLELV 250

Query: 246 IEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAIT 305
                  P E +LS+ DL V ++RG  A+ GLSL V  GEI GIAG+ GNGQ EL +AI 
Sbjct: 251 SGHREGLPGEPVLSVLDLTVKDDRGSIALNGLSLTVGRGEIFGIAGVSGNGQQELAEAIC 310

Query: 306 GLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTYYKA 365
           GLR    G +T+ G+D+T LS ++I    VG++P DRH+DGL+L++++ EN  L+     
Sbjct: 311 GLRAPVDGSITLNGRDITGLSVKEIIASGVGYIPADRHKDGLVLDMSVEENFILKNSGDR 370

Query: 366 PLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLI 425
           P   +GV++   I EHG  L+  F ++  +    AK  SGGNQQK +IARE+     LL+
Sbjct: 371 PYFRSGVMDGGSIGEHGAALVGRFSIKAPSPSTKAKALSGGNQQKVVIAREIGLGSSLLV 430

Query: 426 VSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVT 485
             QP RGLD+GA +Y+H  L+ ER +GKA+LL+S EL E+L LSDR+ VI+ G+I  ++ 
Sbjct: 431 AVQPIRGLDLGAADYVHSVLMEERSKGKAILLISTELSEVLTLSDRVGVIYGGRILDVLD 490

Query: 486 PETTNKQELGILMAG 500
               +   +G+LMAG
Sbjct: 491 RSDMDVDRIGLLMAG 505



 Score = 72.4 bits (176), Expect = 4e-17
 Identities = 56/238 (23%), Positives = 115/238 (48%), Gaps = 15/238 (6%)

Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329
           G  A + + + VK GE++ + G +G G++ L++ + G+ +   G + + G  V   S + 
Sbjct: 23  GTVANEDVHISVKKGEVLALLGENGAGKTTLMRILYGMYRQDQGKILVDGSSVRIDSPQD 82

Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLAL---QTYYKAPLSHNGVLNYSKINEHGRHLM 386
              L +G + +      L+   ++AEN+ L    +  +  L        S++ E G    
Sbjct: 83  AMALGIGMIHQ---HFSLVPVHSVAENVVLGLGSSMDRLDLERVS----SELRELGSRYG 135

Query: 387 QEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLI 446
            E D  G    +P      G QQ+  I + + R   +LI+ +PT  L     E + + + 
Sbjct: 136 LEVDPYGKVGQLPV-----GMQQRVEIVKALYRKARILIMDEPTAVLTPQETERLGEFVR 190

Query: 447 AERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAGGSIE 504
               +G +V+L++ +L E++ ++D + V+  G++ G V+   ++++EL  +M G  +E
Sbjct: 191 EFTSQGNSVILITHKLGEVMAMADSVTVMRAGKVVGSVSTAESSERELARMMVGRDLE 248


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: 664
Number of extensions: 34
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: 512
Length adjustment: 35
Effective length of query: 475
Effective length of database: 477
Effective search space:   226575
Effective search space used:   226575
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