RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8224
(766 letters)
>gnl|CDD|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH
domains) [General function prediction only].
Length = 194
Score = 181 bits (462), Expect = 6e-53
Identities = 61/164 (37%), Positives = 94/164 (57%), Gaps = 1/164 (0%)
Query: 31 MRKVPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAA 90
V +P R G L W ++ I E +++R + K+ +V IR + +TED L KA
Sbjct: 9 SEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKAR 68
Query: 91 DFVKAFVYGFDVDDALALLRLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTI 150
D VKA GF + AL LL D+ ++E ++KDV TL GDHL R GR+ G+ G+T+ I
Sbjct: 69 DVVKAIGRGFPPEKALKLLE-DDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAI 127
Query: 151 ENITKTRIVIADSKIHVLGSYQNVQVALKALSNLILGSPPNKVY 194
E +T I + + ++G ++ V++A +A+ LI G+P KVY
Sbjct: 128 EELTGVYISVYGKTVAIIGGFEQVEIAREAVEMLINGAPHGKVY 171
>gnl|CDD|211858 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain
protein. This family of proteins is universal among the
41 archaeal genomes analyzed in and is not observed
outside of the archaea. The proteins contain a single KH
domain (pfam00013) which is likely to confer the ability
to bind RNA.
Length = 172
Score = 99.2 bits (248), Expect = 4e-24
Identities = 43/135 (31%), Positives = 73/135 (54%), Gaps = 2/135 (1%)
Query: 60 KLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVDDALALLRLDNLFIESF 119
+ V+ ++ S E+++ E ED + KA + VKA GF + AL LL D+ +E
Sbjct: 26 RTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKLLD-DDYMLEVI 84
Query: 120 EIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIVIADSKIHVLGSYQNVQVALK 179
++K+ + L R GR+ G+GG+T+ IE +T I + + ++G + VQ+A +
Sbjct: 85 DLKEY-GKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYGKTVGIIGDPEQVQIARE 143
Query: 180 ALSNLILGSPPNKVY 194
A+ LI G+P VY
Sbjct: 144 AIEMLIEGAPHGTVY 158
>gnl|CDD|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional.
Length = 180
Score = 95.7 bits (239), Expect = 8e-23
Identities = 50/162 (30%), Positives = 80/162 (49%), Gaps = 5/162 (3%)
Query: 34 VPVPNHRYGPLKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSP-ETEDISNLQKAADF 92
V +P R G L + I E + V+ + S E+ + P + ED + KA D
Sbjct: 7 VKIPKDRIGVLIGKKGETKKEIEE--RTGVKLEIDSETGEVIIEPTDGEDPLAVLKARDI 64
Query: 93 VKAFVYGFDVDDALALLRLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIEN 152
VKA GF + AL LL D+ +E ++ D + L R GR+ G+GG+T+ IE
Sbjct: 65 VKAIGRGFSPEKALRLLD-DDYVLEVIDLSDY-GDSPNALRRIKGRIIGEGGKTRRIIEE 122
Query: 153 ITKTRIVIADSKIHVLGSYQNVQVALKALSNLILGSPPNKVY 194
+T I + + ++G + V++A +A+ LI G+P VY
Sbjct: 123 LTGVDISVYGKTVAIIGDPEQVEIAREAIEMLIEGAPHGTVY 164
>gnl|CDD|201954 pfam01753, zf-MYND, MYND finger.
Length = 39
Score = 55.5 bits (134), Expect = 3e-10
Identities = 17/39 (43%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 317 CEVC--KVAASLKCGGCNQVFYCSKSHQKQHWKEHKPGC 353
C VC + L+C C V+YCSK QK W HK C
Sbjct: 1 CAVCGKEALKLLRCSRCKSVYYCSKECQKADWPYHKKEC 39
>gnl|CDD|215657 pfam00013, KH_1, KH domain. KH motifs bind RNA in vitro.
Autoantibodies to Nova, a KH domain protein, cause
paraneoplastic opsoclonus ataxia.
Length = 59
Score = 42.9 bits (102), Expect = 1e-05
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 133 SRAIGRLAGKGGRTKFTIENITKTRIVIADSK---IHVLGSYQNVQVALKAL 181
+GR+ GKGG I T +I I D + + + G+ + V+ A + +
Sbjct: 8 PDKVGRIIGKGGSNIKEIREETGVKIRIPDDRDDTVTISGTPEQVEKAKELI 59
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 40.4 bits (95), Expect = 2e-04
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 133 SRAIGRLAGKGGRTKFTIENITKTRIVI-----ADSKIHVLGSYQNVQVALKALSNLI 185
+ +G + GKGG T IE T +I I + + + G +NV+ A + + ++
Sbjct: 11 ADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELILEIL 68
>gnl|CDD|216155 pfam00856, SET, SET domain. SET domains are protein lysine
methyltransferase enzymes. SET domains appear to be
protein-protein interaction domains. It has been
demonstrated that SET domains mediate interactions with
a family of proteins that display similarity with
dual-specificity phosphatases (dsPTPases). A subset of
SET domains have been called PR domains. These domains
are divergent in sequence from other SET domains, but
also appear to mediate protein-protein interaction. The
SET domain consists of two regions known as SET-N and
SET-C. SET-C forms an unusual and conserved knot-like
structure of probably functional importance.
Additionally to SET-N and SET-C, an insert region
(SET-I) and flanking regions of high structural
variability form part of the overall structure.
Length = 113
Score = 38.2 bits (89), Expect = 0.002
Identities = 16/64 (25%), Positives = 26/64 (40%)
Query: 365 GRHMVATKDIREGEIILEEKPLVVGPKTASVPLCLGCHRTLKPTSMEENEPLSFYKCSDC 424
GR + AT+DI +GE+I+E ++ P+ A L L+ + LS
Sbjct: 1 GRGLFATRDIPKGELIIEYVGELITPEEAEERELLYNKEELRGLLSDLELFLSRLDSEYD 60
Query: 425 GWPL 428
Sbjct: 61 IDAT 64
Score = 33.6 bits (77), Expect = 0.093
Identities = 12/43 (27%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 624 TAMLSHNCKPN--TKHVIVNEDFSLQLIALVNIRKGDIISTTY 664
++H+C+PN + V VN + + AL +I+ G+ ++ Y
Sbjct: 70 ARFINHSCEPNCEVRFVFVNGGDRIVVRALRDIKPGEELTIDY 112
Score = 33.2 bits (76), Expect = 0.10
Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 2/95 (2%)
Query: 508 IYRVNLVRFIKDVLHMDVSEETILRIAGILDTNAFDIRRSVGKIKIRGIYMKTAMLSHNC 567
Y L+ + + + LR S I G+ ++H+C
Sbjct: 18 EYVGELITPEEAEERELLYNKEELRGLLSDLELFLSRLDSEYDIDATGLGNVARFINHSC 77
Query: 568 KPN--TKHVIVNEDFSLQLIALVNICKGDIISTTY 600
+PN + V VN + + AL +I G+ ++ Y
Sbjct: 78 EPNCEVRFVFVNGGDRIVVRALRDIKPGEELTIDY 112
>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA. There are two different KH domains that belong
to different protein folds, but they share a single KH
motif. The KH motif is folded into a beta alpha alpha
beta unit. In addition to the core, type II KH domains
(e.g. ribosomal protein S3) include N-terminal extension
and type I KH domains (e.g. hnRNP K) contain C-terminal
extension.
Length = 64
Score = 32.9 bits (76), Expect = 0.045
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 7/56 (12%)
Query: 133 SRAIGRLAGKGGRTKFTIENITKTRIVIADSK-------IHVLGSYQNVQVALKAL 181
S +GR+ GKGG T I T +I I DS + + G+ + V+ A + +
Sbjct: 8 SSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63
>gnl|CDD|214614 smart00317, SET, SET (Su(var)3-9, Enhancer-of-zeste, Trithorax)
domain. Putative methyl transferase, based on outlier
plant homologues.
Length = 124
Score = 34.6 bits (80), Expect = 0.045
Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 623 KTAMLSHNCKPNT--KHVIVNEDFSLQLIALVNIRKGDIISTTYTQPFWGT 671
++H+C+PN V VN D + + AL +I+ G+ ++ Y +
Sbjct: 74 LARFINHSCEPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDYGSDYANE 124
Score = 33.5 bits (77), Expect = 0.12
Identities = 19/84 (22%), Positives = 31/84 (36%), Gaps = 3/84 (3%)
Query: 526 SEETILRIAGILDTNAFDIRRSVGKIKIRGIYMKTAMLSHNCKPNT--KHVIVNEDFSLQ 583
G FDI + I R ++H+C+PN V VN D +
Sbjct: 42 ERPKAYDTDGAKAFYLFDIDSDL-CIDARRKGNLARFINHSCEPNCELLFVEVNGDDRIV 100
Query: 584 LIALVNICKGDIISTTYTQPFWGT 607
+ AL +I G+ ++ Y +
Sbjct: 101 IFALRDIKPGEELTIDYGSDYANE 124
Score = 31.5 bits (72), Expect = 0.56
Identities = 13/57 (22%), Positives = 23/57 (40%)
Query: 354 AKYKVVRNDILGRHMVATKDIREGEIILEEKPLVVGPKTASVPLCLGCHRTLKPTSM 410
K +V ++ G + AT+DI +GE I E ++ + A K +
Sbjct: 1 NKLEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDTDGAKAFYL 57
>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'. All proteins in this
family for which functions are known are components of
the primosome which is involved in replication, repair,
and recombination.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 505
Score = 35.4 bits (82), Expect = 0.13
Identities = 14/32 (43%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 416 LSFYKCSDCGWPLCAPRCK-SLPSHQKECKLM 446
C CG+ LC P C SL H+KE KL
Sbjct: 211 SKNLLCRSCGYILCCPNCDVSLTYHKKEGKLR 242
>gnl|CDD|222400 pfam13824, zf-Mss51, Zinc-finger of mitochondrial splicing
suppressor 51. Mss51 regulates the expression of
cytochrome oxidase, so this domain is probably
DNA-binding.
Length = 55
Score = 30.8 bits (70), Expect = 0.24
Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 316 KCEVCK----VAASLKCGGCNQVFYCSKSHQKQHWKEHKPGCAKYKVVRND 362
C CK + +C C +CS+ H + ++EH+ C + V D
Sbjct: 1 LCPHCKHDLPARVNFECPDCGIPTHCSEEHWEDDYEEHRELCETLRQVNED 51
>gnl|CDD|225491 COG2940, COG2940, Proteins containing SET domain [General function
prediction only].
Length = 480
Score = 34.0 bits (78), Expect = 0.29
Identities = 18/96 (18%), Positives = 42/96 (43%), Gaps = 4/96 (4%)
Query: 602 QPFWGTMDRRLHLRMSKWIYMKTAMLSHNCKPNTKHVIVNED--FSLQLIALVNIRKGDI 659
+ +G ++ + +R S+ ++H+C PN + + + F + + A+ +I+ G+
Sbjct: 384 EFSFGLLEDKDKVRDSQKAGDVARFINHSCTPNCEASPIEVNGIFKISIYAIRDIKAGEE 443
Query: 660 ISTTYTQPFW-GTMDRRLHLRMSKCFDCTCDRCKDP 694
++ Y ++L + C C DRC
Sbjct: 444 LTYDYGPSLEDNRELKKLLEKRWGC-ACGEDRCSHT 478
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 30.8 bits (70), Expect = 3.3
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 137 GRLAGKGGRTKFTIENITKTRIVIADSKIHVLGSYQN---VQVALKALSNLIL 186
GR+ G+ GR E +T ++I D+ V+ S N ++A L L+
Sbjct: 211 GRIIGREGRNIRAFEGLTGVDLIIDDTPEAVVISSFNPIRREIARLTLEKLLA 263
>gnl|CDD|226714 COG4263, NosZ, Nitrous oxide reductase [Energy production and
conversion].
Length = 637
Score = 30.3 bits (68), Expect = 4.5
Identities = 14/67 (20%), Positives = 23/67 (34%), Gaps = 4/67 (5%)
Query: 248 KTEPTGLEMFLDKFQAQDSVLHDQNQHIVQAKLAL----LQIYETSVEDQKCQLNVDDQK 303
K PT +F D+ Q + V A+ L L + L +D Q
Sbjct: 341 KLSPTFTVIFDDRIQDLFDGKLAPPRDAVVAEPELGLGPLHTTFDGRGNAYTTLFIDSQI 400
Query: 304 CQLNVDK 310
+ N++
Sbjct: 401 VKWNIED 407
>gnl|CDD|188819 cd09435, LIM3_Zyxin, The third LIM domain of Zyxin. The third LIM
domain of Zyxin: Zyxin exhibits three copies of the LIM
domain, an extensive proline-rich domain and a nuclear
export signal. Localized at sites of cellsubstratum
adhesion in fibroblasts, Zyxin interacts with
alpha-actinin, members of the cysteine-rich protein
(CRP) family, proteins that display Src homology 3 (SH3)
domains and Ena/VASP family members. Zyxin and its
partners have been implicated in the spatial control of
actin filament assembly as well as in pathways important
for cell differentiation. In addition to its functions
at focal adhesion plaques, recent work has shown that
zyxin moves from the sites of cell contacts to the
nucleus, where it directly participates in the
regulation of gene expression. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 67
Score = 27.5 bits (61), Expect = 4.6
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 400 GCHRTLKPTSMEENEPLSFYKCSDCGWPL 428
G T++ ++E+N + YKC DCG PL
Sbjct: 13 GRDETVRVVALEKNFHMKCYKCEDCGRPL 41
>gnl|CDD|225824 COG3286, COG3286, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 204
Score = 29.4 bits (66), Expect = 5.5
Identities = 21/86 (24%), Positives = 33/86 (38%), Gaps = 7/86 (8%)
Query: 44 LKENWMKIFTPIVEHLKLQVRFNLKSRNVEIRLSPETEDISNLQKAADFVKAFVYGFDVD 103
++ +K P E ++L L E R P T + L A + VYG D D
Sbjct: 107 VRGGELKTNAPWSEVVELVRE--LSEVYREARFQPLTRQVRKLVVAV----SIVYGLDPD 160
Query: 104 DALALLRLDNLFIESFEIKDVKTLKG 129
DA ++ +E E + +K
Sbjct: 161 DAAEEA-VELGLLEEGEDGLRELIKN 185
>gnl|CDD|234331 TIGR03724, arch_bud32, Kae1-associated kinase Bud32. Members of
this protein family are the Bud32 protein associated
with Kae1 (kinase-associated endopeptidase 1) in the
Archaea. In many Archaeal genomes, Kae1 and Bud32 are
fused. The complex is homologous to the Kae1 and Bud32
subunits of the eukaryotic KEOPS complex, an apparently
ancient protein kinase-containing molecular machine
[Unknown function, General].
Length = 199
Score = 29.1 bits (66), Expect = 6.2
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 100 FDVDDALALLRLDNLFIESFEIKDVKTLKGDHLSRAIGRLAGKGGRTKFTIENITKTRIV 159
+DVD + ++ +IE +KDV D L R IGRL GK + ++T + I+
Sbjct: 65 YDVDPDNKTIVME--YIEGKPLKDVIEEGNDELLREIGRLVGKLHKAGIVHGDLTTSNII 122
Query: 160 IADSKI 165
+ D K+
Sbjct: 123 VRDDKL 128
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 29.6 bits (67), Expect = 8.5
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 1/27 (3%)
Query: 421 CSDCGWPLCAPRC-KSLPSHQKECKLM 446
C DCG+ P C L H+ +L
Sbjct: 438 CRDCGYIAECPNCDSPLTLHKATGQLR 464
>gnl|CDD|181924 PRK09514, zntR, zinc-responsive transcriptional regulator;
Provisional.
Length = 140
Score = 28.0 bits (63), Expect = 9.8
Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 153 ITKTRIVIADSKIHVLGSYQNVQVALKALSNLILGSPPNKVYGGIL 198
I ++ ++KI L Q+++ +L+ L++ G+ + VY IL
Sbjct: 85 IVDEKLAEVEAKIAEL---QHMRRSLQRLNDACCGTAHSAVYCSIL 127
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
0.321 0.135 0.406
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 37,162,922
Number of extensions: 3577346
Number of successful extensions: 2988
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2978
Number of HSP's successfully gapped: 29
Length of query: 766
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 662
Effective length of database: 6,324,786
Effective search space: 4187008332
Effective search space used: 4187008332
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: 63 (28.0 bits)