RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4803
(235 letters)
>gnl|CDD|215272 PLN02492, PLN02492, ribonucleoside-diphosphate reductase.
Length = 324
Score = 214 bits (546), Expect = 6e-69
Identities = 80/128 (62%), Positives = 97/128 (75%), Gaps = 5/128 (3%)
Query: 113 GLHCEFACLMFKHLVNKPSEERIKSIVLDAVLVEQEFLTEALPVKLIGMNCDLMKQYIEY 172
GLHC+FACL++ L NK SEER+K IV +AV +E+EF+ +ALP L+GMN DLM QYIE+
Sbjct: 197 GLHCDFACLLYSLLKNKLSEERVKEIVCEAVEIEKEFVCDALPCALVGMNADLMSQYIEF 256
Query: 173 VADRLLVDLGCSKHYFAENPFDFMENISLEGKTNFFERKVGEYQKSSVMA-----DQDNQ 227
VADRLLV LG K Y NPFD+ME ISL+GKTNFFE++VGEYQK+ VM+ DN
Sbjct: 257 VADRLLVALGYEKVYNVVNPFDWMELISLQGKTNFFEKRVGEYQKAGVMSSLNGGGADNH 316
Query: 228 VFRLDEQF 235
VF LDE F
Sbjct: 317 VFSLDEDF 324
Score = 30.4 bits (69), Expect = 0.67
Identities = 10/14 (71%), Positives = 13/14 (92%)
Query: 7 SLLIDTYIKDQEER 20
SLL+DTYIKD +E+
Sbjct: 108 SLLLDTYIKDPKEK 121
>gnl|CDD|240315 PTZ00211, PTZ00211, ribonucleoside-diphosphate reductase small
subunit; Provisional.
Length = 330
Score = 205 bits (523), Expect = 2e-65
Identities = 74/123 (60%), Positives = 98/123 (79%)
Query: 113 GLHCEFACLMFKHLVNKPSEERIKSIVLDAVLVEQEFLTEALPVKLIGMNCDLMKQYIEY 172
GLH +FACL++ HL NK ER++ I+ +AV +E+EF+ +ALPV LIGMN LM QYIE+
Sbjct: 208 GLHTDFACLLYSHLKNKLPRERVQEIIKEAVEIEREFICDALPVDLIGMNSRLMAQYIEF 267
Query: 173 VADRLLVDLGCSKHYFAENPFDFMENISLEGKTNFFERKVGEYQKSSVMADQDNQVFRLD 232
VADRLLV LG K Y ++NPFD+M+ ISL+GKTNFFE++VGEYQK+ VMA++ ++VF LD
Sbjct: 268 VADRLLVALGVPKIYNSKNPFDWMDMISLQGKTNFFEKRVGEYQKAGVMAERTSKVFSLD 327
Query: 233 EQF 235
F
Sbjct: 328 ADF 330
Score = 30.1 bits (68), Expect = 1.0
Identities = 11/14 (78%), Positives = 13/14 (92%)
Query: 7 SLLIDTYIKDQEER 20
SLLIDTYI D+EE+
Sbjct: 119 SLLIDTYITDEEEK 132
>gnl|CDD|144013 pfam00268, Ribonuc_red_sm, Ribonucleotide reductase, small chain.
Length = 281
Score = 117 bits (295), Expect = 5e-32
Identities = 35/87 (40%), Positives = 51/87 (58%), Gaps = 2/87 (2%)
Query: 113 GLHCEFACLMFKHLV--NKPSEERIKSIVLDAVLVEQEFLTEALPVKLIGMNCDLMKQYI 170
LH + ACL++ + + KP +RI + +AV +E EF+ A PV + GMN +KQYI
Sbjct: 195 ALHTDAACLLYNNYLGLEKPEPKRIYKLFREAVEIEIEFIEAAAPVDVHGMNVRAIKQYI 254
Query: 171 EYVADRLLVDLGCSKHYFAENPFDFME 197
E+ ADRLLV +G + NPF +
Sbjct: 255 EFSADRLLVAIGYKPLFNVPNPFFPLA 281
>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 = 112 bits (282), Expect = 7e-30
Identities = 40/98 (40%), Positives = 62/98 (63%), Gaps = 9/98 (9%)
Query: 113 GLHCEFACLMFKHLVNK-------PSEERIKSIVLDAVLVEQEFLTEALPVKLIGMNCDL 165
LH +FACL+ + L+N+ +E + ++ +AV +E+EF + LP ++G+N +
Sbjct: 191 SLHGDFACLLIRELLNENPELFTEEFKEEVYELIKEAVELEKEFARDLLPDGILGLNKED 250
Query: 166 MKQYIEYVADRLLVDLGCSKHY--FAENPFDFMENISL 201
MKQYIEYVA+R L +LG K + +NPFD+ME IS
Sbjct: 251 MKQYIEYVANRRLENLGLEKLFNVEDKNPFDWMELISD 288
>gnl|CDD|223286 COG0208, NrdF, Ribonucleotide reductase, beta subunit [Nucleotide
transport and metabolism].
Length = 348
Score = 98.1 bits (245), Expect = 4e-24
Identities = 42/118 (35%), Positives = 63/118 (53%), Gaps = 10/118 (8%)
Query: 113 GLHCEFACLMFKHLVNKPSEER-------IKSIVLDAVLVEQEFLTEALPVKLIGMNCDL 165
LH F + + LV + E I + +AV +E+E+ P ++G+ DL
Sbjct: 222 ALHLYFIGYLIQRLVAENPELWTAELKDEIYDLFKEAVELEKEYAEYLYP-GILGLTEDL 280
Query: 166 MKQYIEYVADRLLVDLGCSKHYFAE-NPFDFMEN-ISLEGKTNFFERKVGEYQKSSVM 221
+KQYI Y A++ L +LG Y AE NP ++E +S + KT+FFE +V YQK SV
Sbjct: 281 VKQYIRYNANKRLQNLGLEPLYPAEENPIPWIELSLSADEKTDFFEGRVSSYQKGSVA 338
>gnl|CDD|201070 pfam00191, Annexin, Annexin. This family of annexins also
includes giardin that has been shown to function as an
annexin.
Length = 66
Score = 72.1 bits (178), Expect = 5e-17
Identities = 25/62 (40%), Positives = 33/62 (53%)
Query: 36 EARRGELMLGTDESTFNAILCTRSYPQLAEVFSQYYTLTGHELDEAIGREFSGDIKEGLI 95
R LGTDE T IL TRS QL + Y L G +L++ I E SGD ++ L+
Sbjct: 5 LLRAAMKGLGTDEDTLIRILATRSNAQLQAIREAYKKLYGKDLEKDIKSETSGDFEKLLL 64
Query: 96 AI 97
A+
Sbjct: 65 AL 66
>gnl|CDD|235968 PRK07209, PRK07209, ribonucleotide-diphosphate reductase subunit
beta; Validated.
Length = 369
Score = 75.0 bits (185), Expect = 7e-16
Identities = 32/94 (34%), Positives = 54/94 (57%), Gaps = 2/94 (2%)
Query: 125 HLVNKPSEERIKSIVLDAVLVEQEFLTEALPVKLIGMNCDLMKQYIEYVADRLLVDLGCS 184
HL + I+ ++ +AV +E + + +P ++G+N + K Y+ ++A+R L +G
Sbjct: 268 HLWTAEFQAEIRELIKEAVELEYRYARDTMPRGVLGLNASMFKDYLRFIANRRLQQIGLK 327
Query: 185 KHYF-AENPFDFM-ENISLEGKTNFFERKVGEYQ 216
Y ENPF +M E I L+ + NFFE +V EYQ
Sbjct: 328 PQYPGTENPFPWMSEMIDLKKEKNFFETRVIEYQ 361
>gnl|CDD|197661 smart00335, ANX, Annexin repeats.
Length = 53
Score = 66.7 bits (164), Expect = 6e-15
Identities = 21/53 (39%), Positives = 30/53 (56%)
Query: 45 GTDESTFNAILCTRSYPQLAEVFSQYYTLTGHELDEAIGREFSGDIKEGLIAI 97
GTDE T IL +RS QL + Y G +L++ I E SGD ++ L+A+
Sbjct: 1 GTDEKTLIEILASRSNAQLQAIKQAYKKRYGKDLEDDIKSETSGDFEKLLLAL 53
>gnl|CDD|236591 PRK09614, nrdF, ribonucleotide-diphosphate reductase subunit beta;
Reviewed.
Length = 324
Score = 51.4 bits (124), Expect = 8e-08
Identities = 25/123 (20%), Positives = 53/123 (43%), Gaps = 14/123 (11%)
Query: 114 LHCEFACLMFKHLVNKPSE-------ERIKSIVLDAVLVEQEFLTEALPVKLIGMNCDLM 166
LH + +F+ + + E + I ++ + E+ + + +G + +
Sbjct: 200 LHGYYIGYLFQEGLEELPELEQEELKDEIYDLLYELYENEEAYTELLYDI--VG-LAEDV 256
Query: 167 KQYIEYVADRLLVDLGCSKHYFAENPFD--FMENISLEG--KTNFFERKVGEYQKSSVMA 222
K+YI Y A++ L++LG + E + ++ +S +FFE K Y K + A
Sbjct: 257 KKYIRYNANKRLMNLGLEPLFPEEEEVNPIWLNGLSNNADENHDFFEGKGTSYVKGATEA 316
Query: 223 DQD 225
+D
Sbjct: 317 TED 319
>gnl|CDD|139206 PRK12759, PRK12759, bifunctional
gluaredoxin/ribonucleoside-diphosphate reductase subunit
beta; Provisional.
Length = 410
Score = 49.3 bits (117), Expect = 5e-07
Identities = 37/110 (33%), Positives = 57/110 (51%), Gaps = 5/110 (4%)
Query: 120 CLMFKHLVNKPSEERIKSIVLDAVLVEQEFLTEALPVKLI-GMNCDLMKQYIEYVADRLL 178
C ++V+ ++ I + AV +E F+ A + I G+ D +KQYI ++ DR L
Sbjct: 297 CQENPYIVDNEFKKEIYLMASKAVELEDRFIELAYELGTIEGLKADEVKQYIRHITDRRL 356
Query: 179 VDLGCSKHYFAE-NPFDFMENISLEG--KTNFFERKVGEYQKSSVMADQD 225
LG + Y E NP ++E I L G TNFFE +V EY+ + + D
Sbjct: 357 NQLGLKEIYNIEKNPLTWLEWI-LNGADHTNFFENRVTEYEVAGLTGSWD 405
>gnl|CDD|237565 PRK13934, PRK13934, stationary phase survival protein SurE;
Provisional.
Length = 266
Score = 30.9 bits (70), Expect = 0.49
Identities = 15/34 (44%), Positives = 19/34 (55%)
Query: 68 SQYYTLTGHELDEAIGREFSGDIKEGLIAISPLT 101
YY L G L+ G + +KEG IAI+PLT
Sbjct: 205 RAYYWLYGTPLEPEPGTDVYVVLKEGNIAITPLT 238
>gnl|CDD|181647 PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta;
Reviewed.
Length = 376
Score = 28.8 bits (65), Expect = 2.6
Identities = 8/17 (47%), Positives = 14/17 (82%)
Query: 158 LIGMNCDLMKQYIEYVA 174
+IG+N D++ QY+EY+
Sbjct: 297 MIGLNKDILCQYVEYIT 313
>gnl|CDD|168145 PRK05639, PRK05639, 4-aminobutyrate aminotransferase; Provisional.
Length = 457
Score = 28.4 bits (63), Expect = 3.3
Identities = 27/101 (26%), Positives = 44/101 (43%), Gaps = 7/101 (6%)
Query: 16 DQEERMTAPGITRSVCSLWFEARRGELMLGTDESTFNAILCTR-------SYPQLAEVFS 68
++E+R+ +PGI + L + G L+ D + F L S+P+L +
Sbjct: 20 EREKRVLSPGIGVKLFPLVPKRGFGALIEDVDGNVFIDFLAGAAAASTGYSHPKLVKAVQ 79
Query: 69 QYYTLTGHELDEAIGREFSGDIKEGLIAISPLTNYKPGFGL 109
+ L H + E + + E L ISP+ N K FGL
Sbjct: 80 EQVALIQHSMIGYTHSERAIRVAEKLAEISPIENPKVLFGL 120
>gnl|CDD|130412 TIGR01345, malate_syn_G, malate synthase G. This model describes
the G isozyme of malate synthase. Isocitrate synthase
and malate synthase form the glyoxylate shunt, which
generates additional TCA cycle intermediates [Energy
metabolism, TCA cycle].
Length = 721
Score = 28.3 bits (63), Expect = 4.3
Identities = 31/130 (23%), Positives = 53/130 (40%), Gaps = 19/130 (14%)
Query: 113 GLHCEFACLMFKHLVNKPSEERIKSIVLDAVL------------VEQEFLTEALPVKLIG 160
GLH E + H + K IK IVL++ + V+ E L +G
Sbjct: 234 GLHIELQ-IDANHPIGKDDPAHIKDIVLESAITTIMDCEDSVAAVDAEDKI-LLYRNWLG 291
Query: 161 MNCDLMKQYIEYVADRLLVDLGCSKHYFAENPFDFMENISLEGKTNFFERKVGEYQKSSV 220
+ +++ +E +++ L +HY A N ISL G++ F R VG V
Sbjct: 292 LMQGTLQEKMEKNGRQIVRKLNDDRHYTAANG----SEISLHGRSLLFVRNVGHLMTIPV 347
Query: 221 MADQD-NQVF 229
+ D + ++
Sbjct: 348 IWDSEGEEIP 357
>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein
Musashi homolog 1 (Musashi-1) and similar proteins.
This subgroup corresponds to the RRM1 of Musashi-1. The
mammalian MSI1 gene encoding Musashi-1 (also termed
Msi1) is a neural RNA-binding protein putatively
expressed in central nervous system (CNS) stem cells and
neural progenitor cells and associated with asymmetric
divisions in neural progenitor cells. Musashi-1 is
evolutionarily conserved from invertebrates to
vertebrates. It is a homolog of Drosophila Musashi and
Xenopus laevis nervous system-specific RNP protein-1
(Nrp-1). Musashi-1 has been implicated in the
maintenance of the stem-cell state, differentiation, and
tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover, it
represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-1
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 77
Score = 25.7 bits (56), Expect = 6.6
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 88 GDIKEGLIAISPLTNYKPGFGLI 110
G++KE L+ PLT GFG +
Sbjct: 25 GEVKECLVMRDPLTKRSRGFGFV 47
>gnl|CDD|176195 cd08233, butanediol_DH_like, (2R,3R)-2,3-butanediol dehydrogenase.
(2R,3R)-2,3-butanediol dehydrogenase, a zinc-dependent
medium chain alcohol dehydrogenase, catalyzes the
NAD(+)-dependent oxidation of (2R,3R)-2,3-butanediol and
meso-butanediol to acetoin. BDH functions as a
homodimer. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Sorbitol and aldose reductase are NAD(+) binding
proteins of the polyol pathway, which interconverts
glucose and fructose. Sorbitol dehydrogenase is
tetrameric and has a single catalytic zinc per subunit.
Length = 351
Score = 27.1 bits (61), Expect = 7.7
Identities = 20/54 (37%), Positives = 24/54 (44%), Gaps = 12/54 (22%)
Query: 73 LTGHELDEAIGREFSGDIKE-GLIAISPLTNYKPG-----FGLIMCGLHCEFAC 120
LTG +G EFSG + E G S +T +K G I CG C AC
Sbjct: 59 LTGETAPVTLGHEFSGVVVEVG----SGVTGFKVGDRVVVEPTIKCG-TC-GAC 106
>gnl|CDD|215851 pfam00310, GATase_2, Glutamine amidotransferases class-II.
Length = 223
Score = 26.9 bits (60), Expect = 9.6
Identities = 13/53 (24%), Positives = 17/53 (32%), Gaps = 7/53 (13%)
Query: 34 WFEARRGELMLGTDESTFNAIL-----CTRS--YPQLAEVFSQYYTLTGHELD 79
W AR G G+D F+ +L RS F +Y D
Sbjct: 130 WMRAREGVFNSGSDSEAFDNLLELLVRAGRSPDMDPEERAFYEYLAGLMEPWD 182
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
0.322 0.139 0.410
Gapped
Lambda K H
0.267 0.0891 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,072,580
Number of extensions: 1145408
Number of successful extensions: 821
Number of sequences better than 10.0: 1
Number of HSP's gapped: 811
Number of HSP's successfully gapped: 25
Length of query: 235
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 141
Effective length of database: 6,768,326
Effective search space: 954333966
Effective search space used: 954333966
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: 57 (25.4 bits)