RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= 537021.9.peg.74_1
         (196 letters)



>gnl|CDD|153108 cd01049, RNRR2, Ribonucleotide Reductase, R2/beta subunit,
           ferritin-like diiron-binding domain.  Ribonucleotide
           Reductase, R2/beta subunit (RNRR2) is a member of a
           broad superfamily of ferritin-like diiron-carboxylate
           proteins. The RNR protein catalyzes the conversion of
           ribonucleotides to deoxyribonucleotides and is found in
           all eukaryotes, many prokaryotes, several viruses, and
           few archaea. The catalytically active form of RNR is a
           proposed alpha2-beta2 tetramer. The homodimeric alpha
           subunit (R1) contains the active site and redox active
           cysteines as well as the allosteric binding sites. The
           beta subunit (R2) contains a diiron cluster that, in its
           reduced state, reacts with dioxygen to form a stable
           tyrosyl radical and a diiron(III) cluster. This
           essential tyrosyl radical is proposed to generate a
           thiyl radical, located on a cysteine residue in the R1
           active site that initiates ribonucleotide reduction. The
           beta subunit is composed of 10-13 helices, the 8 longest
           helices form an alpha-helical bundle; some have 2
           addition beta strands. Yeast is unique in that it
           assembles both homodimers and heterodimers of RNRR2. The
           yeast heterodimer, Y2Y4, contains R2 (Y2) and a R2
           homolog (Y4) that lacks the diiron center and is
           proposed to only assist in cofactor assembly, and
           perhaps stabilize R1 (Y1) in its active conformation.
          Length = 288

 Score =  165 bits (420), Expect = 7e-42
 Identities = 57/144 (39%), Positives = 79/144 (54%), Gaps = 5/144 (3%)

Query: 32  NQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFAS 91
             L P+KY WAWE Y  A  N W P E+ +  DL  W+    LT+ ER  IKR L F A+
Sbjct: 1   FNLNPIKYPWAWELYKKAEANFWTPEEIDLSKDLKDWEK---LTEAERHFIKRVLAFLAA 57

Query: 92  SESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDE--GELFNMY 149
            +S+V  N+V    RH+  PE R +   QAF E +HS ++ YI+ +LG DE   ELF   
Sbjct: 58  LDSIVGENLVELFSRHVQIPEARAFYGFQAFMENIHSESYSYILDTLGKDEERDELFEAI 117

Query: 150 REVPSITAKANWALQYTQTLSSPS 173
              P++  KA+W L++   L   +
Sbjct: 118 ETDPALKKKADWILRWYDNLDDNT 141


>gnl|CDD|30557 COG0208, NrdF, Ribonucleotide reductase, beta subunit [Nucleotide
           transport and metabolism].
          Length = 348

 Score =  148 bits (376), Expect = 7e-37
 Identities = 47/158 (29%), Positives = 74/158 (46%), Gaps = 4/158 (2%)

Query: 14  EKRVNVDDKRMLNARS-DVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKN 72
            K   +++ ++ N    +     P+KY WA E Y     N W+P E+ + +D+  WK   
Sbjct: 8   TKNDELEEPKIFNGNPTNAINWNPIKYPWALELYKKLTANFWLPEEIDLSNDIKDWKK-- 65

Query: 73  GLTDDERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQ 132
            L+DDE+ +I R L F    +S+ ANN V A+   ++ PE    L  QAF EA+H+ ++ 
Sbjct: 66  -LSDDEKDLIIRVLAFLTLLDSIQANNGVPALSPLVTTPEEEAVLTNQAFMEAIHARSYS 124

Query: 133 YIITSLGLDEGELFNMYREVPSITAKANWALQYTQTLS 170
           YI  +LG  E E       V +       A    +   
Sbjct: 125 YIFDTLGPTEDEDEVFDDWVATNEILQEKAEIILRYYD 162


>gnl|CDD|36780 KOG1567, KOG1567, KOG1567, Ribonucleotide reductase, beta subunit
           [Nucleotide transport and metabolism].
          Length = 344

 Score = 82.7 bits (204), Expect = 5e-17
 Identities = 48/155 (30%), Positives = 72/155 (46%), Gaps = 6/155 (3%)

Query: 21  DKRMLNARSDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERL 80
           D+ +L        + P+KY   W+ Y  A  + W   EV +  DL  W+    L DDER 
Sbjct: 24  DEPLLMENPRRFVMFPIKYHDIWQMYKKAEASFWTAEEVDLSKDLDDWEK---LNDDERH 80

Query: 81  MIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGL 140
            I   L FFA+S+ +V  N+V    + +  PE R +   Q   E +HS  +  +I +   
Sbjct: 81  FISHVLAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQIAIENIHSEMYSLLIDTYIR 140

Query: 141 DEGE---LFNMYREVPSITAKANWALQYTQTLSSP 172
           D  E   LFN    +P +  KA+WAL++     S 
Sbjct: 141 DPKEREFLFNAIETIPEVKKKADWALRWISDKDSL 175


>gnl|CDD|144013 pfam00268, Ribonuc_red_sm, Ribonucleotide reductase, small chain. 
          Length = 281

 Score = 80.1 bits (198), Expect = 4e-16
 Identities = 37/132 (28%), Positives = 56/132 (42%), Gaps = 6/132 (4%)

Query: 36  PLKYGWAWEKYLSACNNHWMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSESL 95
           P+++   WE Y  A  N W+  EV +  D+  W+    L + ER        F A+++ +
Sbjct: 13  PIQHPDIWELYKKAEANRWLAEEVDLSKDIPDWEK---LNEAEREFYSFVFAFLAAADGI 69

Query: 96  VANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGE---LFNMYREV 152
           V  N+   +       +   Y   Q   E VHS  +  I  +L  DE E    FN     
Sbjct: 70  VNENLAERLSAEFQQKDILHYYGEQIAIENVHSEVYSLIQLTLFNDEKERDAYFNAIETD 129

Query: 153 PSITAKANWALQ 164
           P+I  KA W L+
Sbjct: 130 PAIQRKAQWLLR 141


>gnl|CDD|153120 cd07911, RNRR2_Rv0233_like, Ribonucleotide Reductase R2-like
           protein, Mn/Fe-binding domain.  Rv0233 is a
           Mycobacterium tuberculosis ribonucleotide reductase R2
           protein with a  heterodinuclear
           manganese/iron-carboxylate cofactor located in its metal
           center. The Rv0233-like family may represent a
           structural/functional counterpart of the evolutionary
           ancestor of the RNRR2's (Ribonucleotide Reductase,
           R2/beta subunit) and the bacterial multicomponent
           monooxygenases.  RNRR2s belong to a broad superfamily of
           ferritin-like diiron-carboxylate proteins. The RNR
           protein catalyzes the conversion of ribonucleotides to
           deoxyribonucleotides and is found in prokaryotes and
           archaea. The catalytically active form of RNR is a
           proposed alpha2-beta2 tetramer. The homodimeric alpha
           subunit (R1) contains the active site and redox active
           cysteines as well as the allosteric binding sites.
          Length = 280

 Score = 33.9 bits (78), Expect = 0.034
 Identities = 21/92 (22%), Positives = 40/92 (43%), Gaps = 5/92 (5%)

Query: 54  WMPTEVPMQDDLALWKSKNGLTDDERLMIKRNLGFFASSESLVANNI--VLAIYRHLSNP 111
           W P ++    D   W     L+++ER +  R    F + E  V  ++  ++         
Sbjct: 22  WNPADIDFSQDREDW---EQLSEEERDLALRLCAGFIAGEEAVTLDLLPLMMAMAAEGRL 78

Query: 112 ECRQYLLRQAFEEAVHSHTFQYIITSLGLDEG 143
           E   YL +  FEEA H+  F+  + ++G+ + 
Sbjct: 79  EEEMYLTQFLFEEAKHTDFFRRWLDAVGVSDD 110


>gnl|CDD|37956 KOG2745, KOG2745, KOG2745, Mitochondrial carrier protein [General
           function prediction only].
          Length = 321

 Score = 30.3 bits (68), Expect = 0.35
 Identities = 19/92 (20%), Positives = 30/92 (32%), Gaps = 2/92 (2%)

Query: 86  LGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDEGEL 145
            GFFA     +  ++++     L      +Y+L   F +    H  QY           L
Sbjct: 192 AGFFAGLVPRLLGDLLVLWGCSLLAHLINRYILDSEFGDTKDVH--QYNHAVTQFAVSSL 249

Query: 146 FNMYREVPSITAKANWALQYTQTLSSPSFHYW 177
                 V +  A     L       SPS++ W
Sbjct: 250 TYPLSVVSTCMAVNGSGLAAGLPPYSPSYNNW 281


>gnl|CDD|37643 KOG2432, KOG2432, KOG2432, Uncharacterized conserved protein
           [Function unknown].
          Length = 565

 Score = 29.6 bits (66), Expect = 0.57
 Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 158 KANWALQYTQTLSSPSFHYWNKRRRSRILTRSLRFLCR 195
           K +W   Y + L SP+F  W   RR R L ++L+ L  
Sbjct: 459 KGDWKGLYRRFLRSPNFRGWFGARR-RELQQTLQDLQL 495


>gnl|CDD|39857 KOG4658, KOG4658, KOG4658, Apoptotic ATPase [Signal transduction
           mechanisms].
          Length = 889

 Score = 28.4 bits (63), Expect = 1.4
 Identities = 17/85 (20%), Positives = 31/85 (36%), Gaps = 12/85 (14%)

Query: 47  LSACNNHWMPTEVPMQD---DLALWKSKNGLTDDERLMIKRNLGFFASSESL-------- 95
           L    +      V M D   ++ALW + +    +E  ++   +G     +          
Sbjct: 469 LIEERDEGRKETVKMHDVVREMALWIASDFGKQEENQIVSDGVGLSEIPQVKSWNSVRRM 528

Query: 96  -VANNIVLAIYRHLSNPECRQYLLR 119
            + NN +  I     NP+ R  LL+
Sbjct: 529 SLMNNKIEHIAGSSENPKLRTLLLQ 553


>gnl|CDD|36427 KOG1213, KOG1213, KOG1213, Sister chromatid cohesion complex
           Cohesin, subunit RAD21/SCC1 [Cell cycle control, cell
           division, chromosome partitioning].
          Length = 614

 Score = 28.1 bits (62), Expect = 1.4
 Identities = 16/94 (17%), Positives = 28/94 (29%), Gaps = 4/94 (4%)

Query: 8   SPIQAGEKRVNVDDKRMLNARSDVNQLLPLKYGWAWEKYLSACNNHWMPTEVPMQDDLAL 67
             I   +++++VD   +L+      QL                    MP E    + L  
Sbjct: 305 DSILRRKRKLSVDGVTLLSEEEFKEQLADFSDILTSLDLAPPTRVLMMPKETGRVEKLFS 364

Query: 68  WKSKNGLTDDERLMIKRNLGFFASSESLVANNIV 101
               +   +      +     F S ESL   + V
Sbjct: 365 SPEPDLFANRLLFTGR----LFLSLESLKPEDSV 394


>gnl|CDD|36726 KOG1513, KOG1513, KOG1513, Nuclear helicase MOP-3/SNO (DEAD-box
            superfamily) [Transcription, Signal transduction
            mechanisms].
          Length = 1300

 Score = 27.7 bits (61), Expect = 2.4
 Identities = 15/39 (38%), Positives = 19/39 (48%)

Query: 144  ELFNMYREVPSITAKANWALQYTQTLSSPSFHYWNKRRR 182
             L   Y +V S  AK +W  QY  +L+  S  YWN   R
Sbjct: 1179 SLSKKYHKVSSEEAKEHWEQQYDLSLNMCSHAYWNGNCR 1217


>gnl|CDD|40030 KOG4833, KOG4833, KOG4833, Uncharacterized conserved protein
           [Function unknown].
          Length = 573

 Score = 27.4 bits (60), Expect = 2.4
 Identities = 10/36 (27%), Positives = 17/36 (47%)

Query: 103 AIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITSL 138
           A  RH    E    ++ +AFE A+  + F+ +   L
Sbjct: 256 AEERHFLMDEDHSSVVHKAFEAAILLNFFEILQRLL 291


>gnl|CDD|36693 KOG1480, KOG1480, KOG1480, Netrin transmembrane receptor unc-5
           [Signal transduction mechanisms].
          Length = 909

 Score = 27.0 bits (59), Expect = 3.3
 Identities = 13/65 (20%), Positives = 25/65 (38%), Gaps = 2/65 (3%)

Query: 78  ERLMIKRNLGFFASSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYIITS 137
           ++L + R L +FA+  S  A  ++L ++     P+     L  A EE         + + 
Sbjct: 842 QKLHLDRYLSYFATKPSPTA--VILDLWEARHQPDGDLSSLAAALEEMGRPDAVLSLASE 899

Query: 138 LGLDE 142
                
Sbjct: 900 GQCFP 904


>gnl|CDD|33462 COG3664, XynB, Beta-xylosidase [Carbohydrate transport and
           metabolism].
          Length = 428

 Score = 26.8 bits (59), Expect = 3.6
 Identities = 10/48 (20%), Positives = 23/48 (47%)

Query: 125 AVHSHTFQYIITSLGLDEGELFNMYREVPSITAKANWALQYTQTLSSP 172
            + +  ++    S+ L  G+L+N++ E+ +       +L Y Q  + P
Sbjct: 347 PLKTGRYKDGSFSIDLTNGDLYNVWAEMGARYGPDKSSLDYLQEATQP 394


>gnl|CDD|145853 pfam02915, Rubrerythrin, Rubrerythrin.  This domain has a
           ferritin-like fold.
          Length = 137

 Score = 26.2 bits (58), Expect = 6.3
 Identities = 10/64 (15%), Positives = 19/64 (29%), Gaps = 3/64 (4%)

Query: 85  NLGFFASSESLVANNIVLAIYRHL--SNPECRQYLLRQAFEEAVHSHTFQYIITSLGLDE 142
            L +  + ES  A      +        P+  +     A EE  H+     ++  L    
Sbjct: 2   ILEYAIAGESS-ARRRYKELAEKAKGEGPQIAELFEEMAEEERRHAGFLNKLLKDLFPGL 60

Query: 143 GELF 146
             + 
Sbjct: 61  EPVI 64


>gnl|CDD|176779 cd08801, Death_UNC5D, Death domain found in Uncoordinated-5D.
           Death Domain (DD) found in Uncoordinated-5D (UNC5D).
           UNC5D is part of the UNC-5 homolog family. It is a
           receptor for the secreted netrin-1 and plays a role in
           axonal guidance, angiogenesis, and apoptosis. UNC5
           proteins are transmembrane proteins with an
           extracellular domain consisting of two immunoglobulin
           repeats, two thrombospondin type-I modules and an
           intracellular region containing a ZU-5 domain, UPA
           domain and a DD. In general, DDs are protein-protein
           interaction domains found in a variety of domain
           architectures. Their common feature is that they form
           homodimers by self-association or heterodimers by
           associating with other members of the DD superfamily
           including CARD (Caspase activation and recruitment
           domain), DED (Death Effector Domain), and PYRIN. They
           serve as adaptors in signaling pathways and can recruit
           other proteins into signaling complexes.
          Length = 98

 Score = 25.8 bits (56), Expect = 7.7
 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 78  ERLMIKRNLGFFA--SSESLVANNIVLAIYRHLSNPECRQYLLRQAFEEAVHSHTFQYII 135
           ++  I RNL +FA  SS S V  ++  A ++H  + +     L  A EE   +H+ Q  I
Sbjct: 28  QKNSIDRNLSYFATQSSPSAVILSLWEARHQHDGDLDS----LACALEEIGRTHSKQSTI 83

Query: 136 TSLGLDEGELFNMYRE 151
                 E + FN  R+
Sbjct: 84  AETLDRESD-FNYSRQ 98


>gnl|CDD|35429 KOG0208, KOG0208, KOG0208, Cation transport ATPase [Inorganic ion
            transport and metabolism].
          Length = 1140

 Score = 25.7 bits (56), Expect = 9.0
 Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 11/71 (15%)

Query: 130  TFQYIITSLGLDEGE--LFNMYREVPSITAKA-----NWALQYTQTLSSPSFHYWNKRRR 182
            +FQYI  +L L +G      +++ V               L +   L    F  W   + 
Sbjct: 1035 SFQYIFIALVLSKGSPFRRPLWKNVLFKVFITVIILSTIYLLFVNYL----FIEWKLLQL 1090

Query: 183  SRILTRSLRFL 193
            + I T   RF+
Sbjct: 1091 TYIPTTFDRFI 1101


>gnl|CDD|107363 cd06368, PBP1_iGluR_non_NMDA_like, N-terminal
           leucine/isoleucine/valine-binding protein (LIVBP)-like
           domain of the non-NMDA (N-methyl-d-asparate) subtypes of
           ionotropic glutamate receptors.  N-terminal
           leucine/isoleucine/valine-binding protein (LIVBP)-like
           domain of the non-NMDA (N-methyl-d-asparate) subtypes of
           ionotropic glutamate receptors. While this N-terminal
           domain belongs to the periplasmic-binding fold type I
           superfamily, the glutamate-binding domain of the iGluR
           is structurally homologous to the periplasmic-binding
           fold type II. The LIVBP-like domain of iGluRs is thought
           to play a role in the initial assembly of iGluR
           subunits, but it is not well understood how this domain
           is arranged and functions in intact iGluR.  Glutamate
           mediates the majority of excitatory synaptic
           transmission in the central nervous system via two broad
           classes of ionotropic receptors, characterized by their
           response to glutamate agonists: N-methyl-d -aspartate
           (NMDA) and non-NMDA receptors. NMDA receptors have
           intrinsically slow kinetics, are highly permeable to
           Ca2+, and are blocked by extracellular Mg2+ in a
           voltage-dependent manner. Non-NMDA receptors have faster
           kinetics, are most often only weakly permeable to Ca2+,
           and are not blocked by extracellular Mg2+. While
           non-NMDA receptors typically mediate excitatory synaptic
           responses at resting membrane potentials, NMDA receptors
           contribute several forms of synaptic plasticity and are
           thought to play an important role in the development of
           synaptic pathways. Non-NMDA receptors include
           alpha-amino-3-hydroxy-5-methyl-4-isoxazole proprionate
           (AMPA) and kainate receptors.
          Length = 324

 Score = 25.7 bits (57), Expect = 9.4
 Identities = 10/30 (33%), Positives = 15/30 (50%)

Query: 117 LLRQAFEEAVHSHTFQYIITSLGLDEGELF 146
            L QA E  + S  + YI+T+L     +L 
Sbjct: 196 FLEQAVEVGMMSEYYHYILTNLDFHTLDLE 225


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.321    0.133    0.411 

Gapped
Lambda     K      H
   0.267   0.0691    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,429,135
Number of extensions: 119331
Number of successful extensions: 273
Number of sequences better than 10.0: 1
Number of HSP's gapped: 266
Number of HSP's successfully gapped: 20
Length of query: 196
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 107
Effective length of database: 4,340,536
Effective search space: 464437352
Effective search space used: 464437352
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 (21.9 bits)
S2: 55 (25.0 bits)