RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781006|ref|YP_003065419.1| 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)