RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7988
(73 letters)
>gnl|CDD|215272 PLN02492, PLN02492, ribonucleoside-diphosphate reductase.
Length = 324
Score = 88.2 bits (219), Expect = 7e-23
Identities = 33/56 (58%), Positives = 40/56 (71%), Gaps = 5/56 (8%)
Query: 23 QHYFAENPFDFMENISLEGKTNFFERKVGEYQKSSVMA-----DQDNQVFRLDEQF 73
+ Y NPFD+ME ISL+GKTNFFE++VGEYQK+ VM+ DN VF LDE F
Sbjct: 269 KVYNVVNPFDWMELISLQGKTNFFEKRVGEYQKAGVMSSLNGGGADNHVFSLDEDF 324
>gnl|CDD|240315 PTZ00211, PTZ00211, ribonucleoside-diphosphate reductase small
subunit; Provisional.
Length = 330
Score = 87.1 bits (216), Expect = 2e-22
Identities = 30/51 (58%), Positives = 43/51 (84%)
Query: 23 QHYFAENPFDFMENISLEGKTNFFERKVGEYQKSSVMADQDNQVFRLDEQF 73
+ Y ++NPFD+M+ ISL+GKTNFFE++VGEYQK+ VMA++ ++VF LD F
Sbjct: 280 KIYNSKNPFDWMDMISLQGKTNFFEKRVGEYQKAGVMAERTSKVFSLDADF 330
>gnl|CDD|223286 COG0208, NrdF, Ribonucleotide reductase, beta subunit [Nucleotide
transport and metabolism].
Length = 348
Score = 41.9 bits (99), Expect = 4e-06
Identities = 16/33 (48%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 28 ENPFDFMEN-ISLEGKTNFFERKVGEYQKSSVM 59
ENP ++E +S + KT+FFE +V YQK SV
Sbjct: 306 ENPIPWIELSLSADEKTDFFEGRVSSYQKGSVA 338
>gnl|CDD|235968 PRK07209, PRK07209, ribonucleotide-diphosphate reductase subunit
beta; Validated.
Length = 369
Score = 36.9 bits (86), Expect = 2e-04
Identities = 16/29 (55%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 27 AENPFDFM-ENISLEGKTNFFERKVGEYQ 54
ENPF +M E I L+ + NFFE +V EYQ
Sbjct: 333 TENPFPWMSEMIDLKKEKNFFETRVIEYQ 361
>gnl|CDD|236591 PRK09614, nrdF, ribonucleotide-diphosphate reductase subunit beta;
Reviewed.
Length = 324
Score = 28.6 bits (65), Expect = 0.22
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 42 KTNFFERKVGEYQKSSVMADQD 63
+FFE K Y K + A +D
Sbjct: 298 NHDFFEGKGTSYVKGATEATED 319
>gnl|CDD|178113 PLN02497, PLN02497, probable pectinesterase.
Length = 331
Score = 26.8 bits (59), Expect = 0.83
Identities = 11/43 (25%), Positives = 14/43 (32%), Gaps = 3/43 (6%)
Query: 6 GKSRTHDLALTRYCFVLQHYFAENPFDFMEN---ISLEGKTNF 45
G R + CF L H PF + + G NF
Sbjct: 2 GTHRIIIGLIALCCFCLPHLIEAKPFGVYQQQVFVDQSGHGNF 44
>gnl|CDD|224531 COG1615, COG1615, Uncharacterized conserved protein [Function
unknown].
Length = 885
Score = 26.6 bits (59), Expect = 1.1
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 19 CFVLQHYFAENPFDFMENISLEGKTNFFERKVGEY 53
F+ FA+ F +I E K F R GE
Sbjct: 501 RFLFAIKFADLNFLLSLSIGSESKV-LFNRDPGER 534
>gnl|CDD|213069 cd11753, GH94N_ChvB_NdvB_2_like, Second GH94N domain of cyclic
beta 1-2 glucan synthetase and similar domains. The
glycoside hydrolase family 94 (previously known as
glycosyltransferase family 36) includes cyclic beta 1-2
glucan synthetase (EC:2.4.1.20) or ChvB (encoded by the
chromosomal chvB virulence gene). This second of two
tandemly repeated GH94-N-terminal-like domains has not
been characterized functionally. Some beta 1-2 glucan
synthetases are annotated as NdvB (nodule development
B) gene products, glycosyltransferases required for the
synthesis of cyclic beta-(1,2)-glucans, which play a
role in interactions between bacteria and plants.
Length = 336
Score = 25.2 bits (56), Expect = 2.9
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 5 AGKSRTHDLALTR 17
+G SR +DLA+TR
Sbjct: 80 SGYSRWNDLAVTR 92
>gnl|CDD|139206 PRK12759, PRK12759, bifunctional
gluaredoxin/ribonucleoside-diphosphate reductase subunit
beta; Provisional.
Length = 410
Score = 25.4 bits (55), Expect = 3.1
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 28 ENPFDFMENISLEG--KTNFFERKVGEYQKSSVMADQD 63
+NP ++E I L G TNFFE +V EY+ + + D
Sbjct: 369 KNPLTWLEWI-LNGADHTNFFENRVTEYEVAGLTGSWD 405
>gnl|CDD|130658 TIGR01597, PYST-B, Plasmodium yoelii subtelomeric family PYST-B.
This model represents a paralogous family of Plasmodium
yoelii genes preferentially located in the subtelomeric
regions of the chromosomes. There are no obvious
homologs to these genes in any other organism.
Length = 255
Score = 24.1 bits (52), Expect = 7.1
Identities = 12/30 (40%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 42 KTNFFERKVGEYQKSSVMADQDNQVFRLDE 71
+T FER + ++ + ++AD DNQ F L+E
Sbjct: 31 RTICFERNIKIFRNNRILADADNQ-FDLNE 59
>gnl|CDD|107029 PHA01351, PHA01351, putative minor structural protein.
Length = 1070
Score = 24.5 bits (53), Expect = 7.2
Identities = 9/22 (40%), Positives = 10/22 (45%)
Query: 26 FAENPFDFMENISLEGKTNFFE 47
FAE DF+ I E T E
Sbjct: 219 FAETSVDFLNEIRDELATTLKE 240
>gnl|CDD|235965 PRK07205, PRK07205, hypothetical protein; Provisional.
Length = 444
Score = 24.3 bits (53), Expect = 7.7
Identities = 6/23 (26%), Positives = 8/23 (34%)
Query: 14 ALTRYCFVLQHYFAENPFDFMEN 36
A+ R L DF+ N
Sbjct: 260 AVIRLAKALVVLEPHPALDFLAN 282
>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 = 24.1 bits (53), Expect = 8.4
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 28 ENPFDFMENISL 39
+NPFD+ME IS
Sbjct: 277 KNPFDWMELISD 288
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein. This
family includes the radial spoke head proteins RSP4 and
RSP6 from Chlamydomonas reinhardtii, and several
eukaryotic homologues, including mammalian RSHL1, the
protein product of a familial ciliary dyskinesia
candidate gene.
Length = 481
Score = 23.9 bits (52), Expect = 8.8
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 28 ENPFDFMENISLEGKTNFFERK 49
EN D E++SL K + F K
Sbjct: 40 ENAVDLFEDLSLFVKKSRFVPK 61
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
0.323 0.137 0.402
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,551,001
Number of extensions: 256617
Number of successful extensions: 189
Number of sequences better than 10.0: 1
Number of HSP's gapped: 188
Number of HSP's successfully gapped: 18
Length of query: 73
Length of database: 10,937,602
Length adjustment: 43
Effective length of query: 30
Effective length of database: 9,030,380
Effective search space: 270911400
Effective search space used: 270911400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.3 bits)