RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy1718
         (142 letters)



>gnl|CDD|201631 pfam01158, Ribosomal_L36e, Ribosomal protein L36e. 
          Length = 95

 Score = 93.8 bits (234), Expect = 4e-26
 Identities = 37/53 (69%), Positives = 43/53 (81%)

Query: 2  RPSRLKGIQTKNTKFTRDLVREVCGHAPYEKRAMELLKVSKDKRALKFLKRRV 54
          RPSR KG  +K TKF RD++REV G APYEKR +ELLKV KDKRALKF K+R+
Sbjct: 20 RPSRRKGKLSKRTKFVRDIIREVAGFAPYEKRVIELLKVGKDKRALKFAKKRL 72


>gnl|CDD|185509 PTZ00196, PTZ00196, 60S ribosomal protein L36; Provisional.
          Length = 98

 Score = 66.6 bits (163), Expect = 2e-15
 Identities = 29/53 (54%), Positives = 41/53 (77%)

Query: 1  MRPSRLKGIQTKNTKFTRDLVREVCGHAPYEKRAMELLKVSKDKRALKFLKRR 53
            PS+ KG+ +K  +  +D++REVCG +PYE+R +ELLKV KDKRALK+ K+R
Sbjct: 22 PSPSKRKGLLSKRKRLVKDVIREVCGFSPYERRMIELLKVGKDKRALKYAKKR 74


>gnl|CDD|227384 COG5051, RPL36A, Ribosomal protein L36E [Translation, ribosomal
          structure and biogenesis].
          Length = 97

 Score = 56.1 bits (135), Expect = 3e-11
 Identities = 28/53 (52%), Positives = 40/53 (75%)

Query: 2  RPSRLKGIQTKNTKFTRDLVREVCGHAPYEKRAMELLKVSKDKRALKFLKRRV 54
          RPSR KG  +K T+F R +VRE+ G +PYE+R +EL++ S+DKRA K  K+R+
Sbjct: 25 RPSRKKGQLSKRTEFVRSIVREIAGLSPYERRVIELIRNSQDKRARKLAKKRL 77


>gnl|CDD|239548 cd03465, URO-D_like, The URO-D _like protein superfamily includes
           bacterial and eukaryotic uroporphyrinogen decarboxylases
           (URO-D), coenzyme M methyltransferases and other
           putative bacterial methyltransferases. Uroporphyrinogen
           decarboxylase (URO-D) decarboxylates the four acetate
           side chains of uroporphyrinogen III (uro-III) to create
           coproporphyrinogen III, an important branching point of
           the tetrapyrrole biosynthetic pathway. The
           methyltransferases represented here are important for
           ability of methanogenic organisms to use other compounds
           than carbon dioxide for reduction to methane.
          Length = 330

 Score = 28.8 bits (65), Expect = 1.0
 Identities = 15/73 (20%), Positives = 24/73 (32%), Gaps = 10/73 (13%)

Query: 29  PYEKRAMELLKVSKDKRALKFLKRRVSLYVLRSAVVLCPTKSRKFDRATRDIIRDRESSH 88
           P    A+ LLK        + L  RV +           +      +    +  D E  H
Sbjct: 109 PELLEAIRLLK--------EELGDRVPVIGAVGGPFTLASLLMGASKFLMLLYTDPELVH 160

Query: 89  FQLSQKIPTTFVK 101
            +L +K  T F+ 
Sbjct: 161 -KLLEKC-TEFII 171


>gnl|CDD|211397 cd11559, W2_eIF4G1_like, C-terminal W2 domain of eukaryotic
          translation initiation factor 4 gamma 1 and similar
          proteins.  eIF4G1 is a component of the multi-subunit
          eukaryotic translation initiation factor 4F, which
          facilitates recruitment of the mRNA to the ribosome, a
          rate-limiting step during translation initiation. This
          C-terminal domain, whose structure resembles that of a
          set of concatenated HEAT repeats, has been associated
          with binding to/recruiting the kinase Mnk1, which
          phosphorylates eIF4E.
          Length = 134

 Score = 26.5 bits (59), Expect = 3.5
 Identities = 16/57 (28%), Positives = 21/57 (36%), Gaps = 5/57 (8%)

Query: 15 KFTRDLVREVCGHAPYEKRAMELLKVSKDKRA---LKFLKRRVS--LYVLRSAVVLC 66
           F R L+  V  +A  EK   E  K   +K A    K+L       L  L +   L 
Sbjct: 40 GFVRALMTAVLKYAIEEKSLPEKEKALLEKYAPLLQKYLDDDEQLQLQALYALQALV 96


>gnl|CDD|212677 cd10235, HscC_like_NBD, Nucleotide-binding domain of Escherichia
           coli HscC and similar proteins.  This subfamily
           includes Escherichia coli HscC (also called heat shock
           cognate protein C, Hsc62, or YbeW) and the the putative
           DnaK-like protein Escherichia coli ECs0689. It belongs
           to the heat shock protein 70 (Hsp70) family of
           chaperones that assist in protein folding and assembly
           and can direct incompetent "client" proteins towards
           degradation. Typically, Hsp70s have a nucleotide-binding
           domain (NBD) and a substrate-binding domain (SBD). The
           nucleotide sits in a deep cleft formed between the two
           lobes of the NBD. The two subdomains of each lobe change
           conformation between ATP-bound, ADP-bound, and
           nucleotide-free states. ATP binding opens up the
           substrate-binding site; substrate-binding increases the
           rate of ATP hydrolysis. Hsp70 chaperone activity is
           regulated by various co-chaperones: J-domain proteins
           and nucleotide exchange factors (NEFs). Two genes in the
           vicinity of the HscC gene code for potential
           cochaperones: J-domain containing proteins, DjlB/YbeS
           and DjlC/YbeV. HscC and its co-chaperone partners may
           play a role in the SOS DNA damage response. HscC does
           not appear to require a NEF.
          Length = 339

 Score = 26.3 bits (59), Expect = 5.6
 Identities = 9/40 (22%), Positives = 18/40 (45%)

Query: 16  FTRDLVREVCGHAPYEKRAMELLKVSKDKRALKFLKRRVS 55
           FTR L          +   ++  ++++  RA +  KR +S
Sbjct: 200 FTRALAEAFLKKHGLDFEKLDPSELARLLRAAERAKRALS 239


>gnl|CDD|213369 cd12835, EcCorA-like_1, Escherichia coli Mg2+ transporter CorA_like
           subgroup.  A bacterial subgroup of the Escherichia coli
           CorA-Salmonella typhimurium ZntB_like (EcCorA_ZntB-like)
           family of the MIT superfamily of essential membrane
           proteins involved in transporting divalent cations
           (uptake or efflux) across membranes. This subgroup
           includes the Mg2+ transporters Escherichia coli CorA and
           Salmonella typhimurium CorA (which can also transport
           Co2+, and Ni2+). Structures of the intracellular domain
           of Vibrio parahaemolyticus and Salmonella typhimurium
           ZntB form funnel-shaped homopentamers, the tip of the
           funnel is formed from two C-terminal transmembrane (TM)
           helices from each monomer, and the large opening of the
           funnel from the N-terminal cytoplasmic domains. The GMN
           signature motif of the MIT superfamily occurs just after
           TM1, mutation within this motif is known to abolish Mg2+
           transport through Salmonella typhimurium CorA, and
           Mrs2p. Natural variants such as GVN and GIN, such as
           occur in some ZntB family proteins, may be associated
           with the transport of different divalent cations, such
           as zinc and cadmium. The functional diversity of MIT
           transporters may also be due to minor structural
           differences regulating gating, substrate selection, and
           transport.
          Length = 287

 Score = 25.7 bits (57), Expect = 8.9
 Identities = 19/54 (35%), Positives = 23/54 (42%), Gaps = 16/54 (29%)

Query: 45  RALKFLKRRVSLYVLRSAVVLCPTKSRKFDRATRDIIRDRES--SHFQ-LSQKI 95
           RAL FL R   L               + + A R+I+RD ES   H Q L  KI
Sbjct: 168 RALSFLLRTRRL------------SDEQLEDA-REILRDIESLLPHTQFLFDKI 208


>gnl|CDD|200463 cd11324, AmyAc_Amylosucrase, Alpha amylase catalytic domain found
           in Amylosucrase.  Amylosucrase is a glucosyltransferase
           that catalyzes the transfer of a D-glucopyranosyl moiety
           from sucrose onto an acceptor molecule. When the
           acceptor is another saccharide, only alpha-1,4 linkages
           are produced. Unlike most amylopolysaccharide synthases,
           it does not require any alpha-D-glucosyl nucleoside
           diphosphate substrate. In the presence of glycogen it
           catalyzes the transfer of a D-glucose moiety onto a
           glycogen branch, but in its absence, it hydrolyzes
           sucrose and synthesizes polymers, smaller
           maltosaccharides, and sucrose isoforms. The
           Alpha-amylase family comprises the largest family of
           glycoside hydrolases (GH), with the majority of enzymes
           acting on starch, glycogen, and related oligo- and
           polysaccharides. These proteins catalyze the
           transformation of alpha-1,4 and alpha-1,6 glucosidic
           linkages with retention of the anomeric center. The
           protein is described as having 3 domains: A, B, C. A is
           a (beta/alpha) 8-barrel; B is a loop between the beta 3
           strand and alpha 3 helix of A; C is the C-terminal
           extension characterized by a Greek key. The majority of
           the enzymes have an active site cleft found between
           domains A and B where a triad of catalytic residues
           (Asp, Glu and Asp) performs catalysis. Other members of
           this family have lost the catalytic activity as in the
           case of the human 4F2hc, or only have 2 residues that
           serve as the catalytic nucleophile and the acid/base,
           such as Thermus A4 beta-galactosidase with 2 Glu
           residues (GH42) and human alpha-galactosidase with 2 Asp
           residues (GH31). The family members are quite extensive
           and include: alpha amylase, maltosyltransferase,
           cyclodextrin glycotransferase, maltogenic amylase,
           neopullulanase, isoamylase, 1,4-alpha-D-glucan
           maltotetrahydrolase, 4-alpha-glucotransferase,
           oligo-1,6-glucosidase, amylosucrase, sucrose
           phosphorylase, and amylomaltase.
          Length = 536

 Score = 26.0 bits (58), Expect = 9.5
 Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 1/26 (3%)

Query: 102 CESFYHNSIM-LTWYKLSTKPQRLFT 126
           CE  Y+NS+M L W  L+T+  RL  
Sbjct: 322 CELAYNNSLMALLWSALATRDTRLLR 347


  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
   0.325    0.134    0.416 

Gapped
Lambda     K      H
   0.267   0.0567    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,914,425
Number of extensions: 577661
Number of successful extensions: 611
Number of sequences better than 10.0: 1
Number of HSP's gapped: 611
Number of HSP's successfully gapped: 14
Length of query: 142
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 55
Effective length of database: 7,078,804
Effective search space: 389334220
Effective search space used: 389334220
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.9 bits)