RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780136|ref|YP_003064549.1| ribonucleotide-diphosphate
reductase subunit beta [Candidatus Liberibacter asiaticus str. psy62]
         (125 letters)



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

 Score =  130 bits (328), Expect = 1e-31
 Identities = 47/120 (39%), Positives = 70/120 (58%), Gaps = 1/120 (0%)

Query: 1   MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
           +RDE+LHL F   +I ++  ENP LWT E + +   +  EA  LE  YA    P    GL
Sbjct: 218 IRDEALHLYFIGYLIQRLVAENPELWTAELKDEIYDLFKEAVELEKEYAEYLYPGIL-GL 276

Query: 61  NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120
                +QY+++ AN+R   +GLEPL+   ENP PW+   +   ++ +FFE RV+ YQ+G+
Sbjct: 277 TEDLVKQYIRYNANKRLQNLGLEPLYPAEENPIPWIELSLSADEKTDFFEGRVSSYQKGS 336


>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 =  107 bits (270), Expect = 8e-25
 Identities = 42/102 (41%), Positives = 65/102 (63%), Gaps = 1/102 (0%)

Query: 1   MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
            RDESLH +F   +I ++  ENP L+T+EF+++   ++ EA  LE  +A + +P G +GL
Sbjct: 187 SRDESLHGDFACLLIRELLNENPELFTEEFKEEVYELIKEAVELEKEFARDLLPDGILGL 246

Query: 61  NAPSCEQYMQFIANRRCHQIGLEPLFK-YTENPFPWMSEVID 101
           N    +QY++++ANRR   +GLE LF    +NPF WM  + D
Sbjct: 247 NKEDMKQYIEYVANRRLENLGLEKLFNVEDKNPFDWMELISD 288


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

 Score = 72.7 bits (178), Expect = 3e-14
 Identities = 40/117 (34%), Positives = 63/117 (53%), Gaps = 9/117 (7%)

Query: 2   RDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLN 61
           RDE LH +F         +   HL  K  +++   ++ EA  +E  +  E +P   +G+N
Sbjct: 219 RDEGLHCDFAC-------LLFSHLKKKPNEERIEEIITEAVEIEQEFLTEALPVNLIGMN 271

Query: 62  APSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQ 118
                QY++F+A+R   ++G E  +   ENPF +M E I L  + NFFE RV+EYQ+
Sbjct: 272 CDLMSQYIEFVADRLLVELGNEKYYN-AENPFDFM-ENISLAGKTNFFEKRVSEYQK 326


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

 Score = 51.2 bits (123), Expect = 8e-08
 Identities = 27/96 (28%), Positives = 44/96 (45%), Gaps = 6/96 (6%)

Query: 2   RDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLN 61
           RDE+LH +    + N           K   ++   +  EA  +EI +     P    G+N
Sbjct: 192 RDEALHTDAACLLYNNYLGLE-----KPEPKRIYKLFREAVEIEIEFIEAAAPVDVHGMN 246

Query: 62  APSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMS 97
             + +QY++F A+R    IG +PLF    NPF  ++
Sbjct: 247 VRAIKQYIEFSADRLLVAIGYKPLFN-VPNPFFPLA 281


>gnl|CDD|176781 cd08803, Death_ank3, Death domain of Ankyrin-3.  Death Domain
          (DD) of the human protein ankyrin-3 (ANK-3) and related
          proteins. Ankyrins are modular proteins comprising
          three conserved domains, an N-terminal membrane-binding
          domain containing ANK repeats, a spectrin-binding
          domain and a C-terminal DD. ANK-3, also called
          anykyrin-G (for general or giant), is found in neurons
          and at least one splice variant has been shown to be
          essential for propagation of action potentials as a
          binding partner to neurofascin and voltage-gated sodium
          channels. It is required for maintaining axo-dendritic
          polarity, and may be a genetic risk factor associated
          with bipolar disorder. ANK-3 may also play roles in
          other cell types. Mutations affecting ANK-3 pathways
          for Na channel localization are associated with Brugada
          syndrome, a potentially fata arrythmia. 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 = 84

 Score = 29.6 bits (66), Expect = 0.23
 Identities = 11/22 (50%), Positives = 16/22 (72%)

Query: 8  LNFGIDVINQIKIENPHLWTKE 29
          LNF +D INQI++ENP+    +
Sbjct: 25 LNFSVDEINQIRVENPNSLIAQ 46


>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 = 28.5 bits (64), Expect = 0.57
 Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 2/81 (2%)

Query: 3   DESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNA 62
           DES H+ +G     ++   +   W   F+++   ++  A  L I    E   +   GL+ 
Sbjct: 189 DESRHIAWGTFTCRRLVAADDANWDV-FEERMNELVPHALGL-IDEIFELYDEMPFGLDP 246

Query: 63  PSCEQYMQFIANRRCHQIGLE 83
               QY      RR   I   
Sbjct: 247 DELMQYAVDQFQRRLGYIERA 267


>gnl|CDD|176732 cd08317, Death_ank, Death domain associated with Ankyrins.  Death
          Domain (DD) associated with Ankyrins. Ankyrins are
          modular proteins comprising three conserved domains, an
          N-terminal membrane-binding domain containing ANK
          repeats, a spectrin-binding domain and a C-terminal DD.
          Ankyrins function as adaptor proteins and they
          interact, through ANK repeats, with structurally
          diverse membrane proteins, including ion
          channels/pumps, calcium release channels, and cell
          adhesion molecules. They play critical roles in the
          proper expression and membrane localization of these
          proteins. In mammals, this family includes ankyrin-R
          for restricted (or ANK1), ankyrin-B for broadly
          expressed (or ANK2) and ankyrin-G for general or giant
          (or ANK3). They are expressed in different combinations
          in many tissues and play non-overlapping functions. 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 = 84

 Score = 28.0 bits (63), Expect = 0.64
 Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 4/33 (12%)

Query: 7  HLNFGIDVINQIKIENPHLWTKEFQQKSRTMLH 39
           L      I+ IK ENP+       Q+++ ML 
Sbjct: 24 ELGVSETDIDLIKAENPN----SLAQQAQAMLK 52


>gnl|CDD|34330 COG4714, COG4714, Uncharacterized membrane-anchored protein
          conserved in bacteria [Function unknown].
          Length = 303

 Score = 27.3 bits (60), Expect = 1.3
 Identities = 8/23 (34%), Positives = 12/23 (52%)

Query: 53 MPKGFVGLNAPSCEQYMQFIANR 75
          +P G + + A    QYM+ I N 
Sbjct: 67 LPAGMIFIPAEEANQYMELIGNN 89


>gnl|CDD|144063 pfam00330, Aconitase, Aconitase family (aconitate hydratase). 
          Length = 464

 Score = 26.2 bits (58), Expect = 2.7
 Identities = 9/23 (39%), Positives = 11/23 (47%), Gaps = 5/23 (21%)

Query: 77  CHQIGLEPLFKYTENPFPWMSEV 99
            HQIGLE  F       P ++ V
Sbjct: 109 VHQIGLENGFT-----LPGLTLV 126


>gnl|CDD|176783 cd08805, Death_ank1, Death domain of Ankyrin-1.  Death Domain
          (DD) of the human protein ankyrin-1 (ANK-1) and related
          proteins. Ankyrins are modular proteins comprising
          three conserved domains, an N-terminal membrane-binding
          domain containing ANK repeats, a spectrin-binding
          domain and a C-terminal DD. ANK-1, also called
          ankyrin-R (for restricted), is found in brain, muscle,
          and erythrocytes and is thought to function in linking
          integral membrane proteins to the underlying
          cytoskeleton. It plays a critical nonredundant role in
          erythroid development and is associated with hereditary
          spherocytosis (HS), a common disorder of the red cell
          membrane. The small alternatively-spliced variant,
          sANK-1, found in striated muscle and concentrated in
          the sarcoplasmic reticulum (SR) binds obscurin and
          titin, which facilitates the anchoring of the network
          SR to the contractile apparatus. 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 = 84

 Score = 25.3 bits (55), Expect = 4.7
 Identities = 8/17 (47%), Positives = 14/17 (82%)

Query: 8  LNFGIDVINQIKIENPH 24
          L F ++ IN+I++ENP+
Sbjct: 25 LQFSVEDINRIRVENPN 41


>gnl|CDD|144343 pfam00703, Glyco_hydro_2, domain.  This family contains
          beta-galactosidase, beta-mannosidase and
          beta-glucuronidase activities.
          Length = 108

 Score = 24.8 bits (54), Expect = 6.0
 Identities = 5/15 (33%), Positives = 11/15 (73%)

Query: 13 DVINQIKIENPHLWT 27
            I +++++NP LW+
Sbjct: 64 TTILELEVKNPKLWS 78


>gnl|CDD|36375 KOG1160, KOG1160, KOG1160, Fe-S oxidoreductase [Energy production
           and conversion].
          Length = 601

 Score = 25.0 bits (54), Expect = 6.6
 Identities = 13/51 (25%), Positives = 18/51 (35%), Gaps = 3/51 (5%)

Query: 71  FIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAE 121
           FI  +     G   L   T    PW  EV++   E       + EY+   E
Sbjct: 476 FIEVKGVTYCGESELSNLTMTNVPWHEEVVEFVFE---LVDLLQEYEIACE 523


>gnl|CDD|32321 COG2138, COG2138, Uncharacterized conserved protein [Function
          unknown].
          Length = 245

 Score = 24.6 bits (53), Expect = 6.7
 Identities = 10/31 (32%), Positives = 16/31 (51%)

Query: 56 GFVGLNAPSCEQYMQFIANRRCHQIGLEPLF 86
           F+ L  PS  + +Q +  R   +I + PLF
Sbjct: 40 AFLELAEPSLREALQALVARGVDRIVVVPLF 70


  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    0.135    0.421 

Gapped
Lambda     K      H
   0.267   0.0643    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,556,887
Number of extensions: 71162
Number of successful extensions: 154
Number of sequences better than 10.0: 1
Number of HSP's gapped: 150
Number of HSP's successfully gapped: 18
Length of query: 125
Length of database: 6,263,737
Length adjustment: 82
Effective length of query: 43
Effective length of database: 4,491,799
Effective search space: 193147357
Effective search space used: 193147357
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: 51 (23.6 bits)