RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

Searching..................................................done

Query= psy13876
         (118 letters)



>gnl|CDD|214631 smart00350, MCM, minichromosome maintenance proteins. 
          Length = 509

 Score = 81.2 bits (201), Expect = 3e-19
 Identities = 34/77 (44%), Positives = 45/77 (58%), Gaps = 7/77 (9%)

Query: 49  TYIEAQRIQCLSKA---LEDDKPAGTLSEEEMAEL----GGDQFYSKLAASLAPEIYGHE 101
           TYIEA  ++ L       +      +LS+EE  E+         Y +LA SLAP IYGHE
Sbjct: 150 TYIEANHVRKLDYKRSFEDSSFSVQSLSDEEEEEIRKLSKDPDIYERLARSLAPSIYGHE 209

Query: 102 DVKKALLLLLVGGVDRS 118
           D+KKA+LLLL GGV ++
Sbjct: 210 DIKKAILLLLFGGVHKN 226


>gnl|CDD|224162 COG1241, MCM2, Predicted ATPase involved in replication control,
           Cdc46/Mcm family [DNA replication, recombination, and
           repair].
          Length = 682

 Score = 72.4 bits (178), Expect = 3e-16
 Identities = 30/80 (37%), Positives = 44/80 (55%), Gaps = 9/80 (11%)

Query: 43  PGLLSDTYIEAQRIQCLSKALEDDKPAGTLSEEEMAEL----GGDQFYSKLAASLAPEIY 98
            G + + Y+EA  ++ L K     +    ++EE+  E+         Y  L  S+AP IY
Sbjct: 235 KGPVFEIYLEANSVEKLDK-----REEVEITEEDEEEIKELAKRPDIYDILIKSIAPSIY 289

Query: 99  GHEDVKKALLLLLVGGVDRS 118
           GHEDVKKA+LL L GGV ++
Sbjct: 290 GHEDVKKAILLQLFGGVKKN 309


>gnl|CDD|215947 pfam00493, MCM, MCM2/3/5 family. 
          Length = 327

 Score = 66.0 bits (162), Expect = 4e-14
 Identities = 29/46 (63%), Positives = 34/46 (73%), Gaps = 1/46 (2%)

Query: 74  EEEMAELGGD-QFYSKLAASLAPEIYGHEDVKKALLLLLVGGVDRS 118
           EEE+ EL  D   Y KLA S+AP IYGHEDVKKA+LL L GGV ++
Sbjct: 2   EEEIRELAKDPDIYDKLARSIAPSIYGHEDVKKAILLQLFGGVKKN 47


>gnl|CDD|173403 PTZ00111, PTZ00111, DNA replication licensing factor MCM4;
           Provisional.
          Length = 915

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 1/55 (1%)

Query: 61  KALEDDKPAGTLSEEEMAELGGD-QFYSKLAASLAPEIYGHEDVKKALLLLLVGG 114
           K L ++     L   ++ EL  +   Y  L  S AP I    +VK  LL  L  G
Sbjct: 415 KYLGNENDFSDLQVYKILELSRNPMIYRILLDSFAPSIKARNNVKIGLLCQLFSG 469


>gnl|CDD|163562 TIGR03850, bind_CPR_0540, carbohydrate ABC transporter
           substrate-binding protein, CPR_0540 family.  Members of
           this protein are the substrate-binding protein of a
           predicted carbohydrate transporter operon, together with
           permease subunits of ABC transporter homology families.
           This substrate-binding protein frequently co-occurs in
           genomes with a family of disaccharide phosphorylases,
           TIGR02336, suggesting that the molecule transported will
           include
           beta-D-galactopyranosyl-(1->3)-N-acetyl-D-glucosamine
           and related carbohydrates. Members of this family are
           sporadically strain by strain, often in species with a
           human host association, including Propionibacterium
           acnes and Clostridium perfringens, and Bacillus cereus
           [Transport and binding proteins, Carbohydrates, organic
           alcohols, and acids].
          Length = 437

 Score = 29.3 bits (66), Expect = 0.44
 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)

Query: 77  MAELGGDQFYSKLAASLAPEIYGHEDVKKAL 107
           +AE GGD F++K A +    I+  E+ KKA 
Sbjct: 215 LAEAGGDDFFNK-AMNYEEGIWDTEEAKKAF 244


>gnl|CDD|217045 pfam02452, PemK, PemK-like protein.  PemK is a growth inhibitor in
           E. coli known to bind to the promoter region of the Pem
           operon, auto-regulating synthesis. This Pfam family
           consists of the PemK protein in addition to ChpA, ChpB
           and other PemK-like proteins.
          Length = 110

 Score = 28.0 bits (63), Expect = 0.72
 Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 1/37 (2%)

Query: 44  GLLSDTYIEAQRIQCLSKALEDDKPAGTLSEEEMAEL 80
             L  + +   +I+ + KA    K  G LS+E+M E+
Sbjct: 67  NGLKPSVVLLDQIRTVDKAR-LGKKIGRLSDEDMEEV 102


>gnl|CDD|233870 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit.
           Cobaltochelatase is responsible for the insertion of
           cobalt into the corrin ring of coenzyme B12 during its
           biosynthesis. Two versions have been well described.
           CbiK/CbiX is a monomeric, anaerobic version which acts
           early in the biosynthesis (pfam06180). CobNST is a
           trimeric, ATP-dependent, aerobic version which acts late
           in the biosynthesis (TIGR02257/TIGR01650/TIGR01651). A
           number of genomes (actinobacteria, cyanobacteria,
           betaproteobacteria and pseudomonads) which apparently
           biosynthesize B12, encode a cobN gene but are
           demonstrably lacking cobS and cobT. These genomes do,
           however contain a homolog (modelled here) of the
           magnesium chelatase subunits BchI/BchD family. Aside
           from the cyanobacteria (which have a separate magnesium
           chelatase trimer), these species do not make chlorins,
           so do not have any use for a magnesium chelatase.
           Furthermore, in nearly all cases the members of this
           family are proximal to either CobN itself or other genes
           involved in cobalt transport or B12 biosynthesis.
          Length = 633

 Score = 27.7 bits (62), Expect = 1.4
 Identities = 13/23 (56%), Positives = 14/23 (60%), Gaps = 4/23 (17%)

Query: 97  IYGHEDVKKALLLLLV----GGV 115
           I G ED+K ALLL  V    GGV
Sbjct: 6   IVGQEDLKLALLLNAVDPRIGGV 28


>gnl|CDD|205323 pfam13142, DUF3960, Domain of unknown function (DUF3960).  This
           presumed domain is functionally uncharacterized. This
           domain family is found in bacteria, and is typically
           between 72 and 89 amino acids in length.
          Length = 89

 Score = 25.2 bits (55), Expect = 4.9
 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 3/63 (4%)

Query: 44  GLLSDTYIEAQRIQCLSKALEDDKPAGTLSEEEMAELGGDQFYSKLAASLAPEI-YGHED 102
            L++DTY+E      L   L    P G   E  +      +FY +   +L P I YG   
Sbjct: 11  NLVTDTYVEPNNFADLFSLLVPCHPKGEGKERTILVWKEKEFYKE--ENLIPFILYGMNK 68

Query: 103 VKK 105
            K+
Sbjct: 69  AKE 71


>gnl|CDD|179895 PRK04930, PRK04930, glutathione-regulated potassium-efflux system
           ancillary protein KefG; Provisional.
          Length = 184

 Score = 25.3 bits (56), Expect = 8.6
 Identities = 9/28 (32%), Positives = 16/28 (57%), Gaps = 3/28 (10%)

Query: 7   ASMVGKHWILGLLRYW---QNPTMLQNY 31
           A+M   HW+  ++ YW   Q+P  L ++
Sbjct: 140 AAMCRMHWLSPIIIYWARRQSPEELASH 167


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.320    0.137    0.411 

Gapped
Lambda     K      H
   0.267   0.0754    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,080,930
Number of extensions: 518992
Number of successful extensions: 448
Number of sequences better than 10.0: 1
Number of HSP's gapped: 447
Number of HSP's successfully gapped: 16
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.1 bits)