RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5350
(377 letters)
>gnl|CDD|238007 cd00048, DSRM, Double-stranded RNA binding motif. Binding is not
sequence specific but is highly specific for double
stranded RNA. Found in a variety of proteins including
dsRNA dependent protein kinase PKR, RNA helicases,
Drosophila staufen protein, E. coli RNase III, RNases
H1, and dsRNA dependent adenosine deaminases.
Length = 68
Score = 80.8 bits (200), Expect = 2e-19
Identities = 29/68 (42%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVN-VYKEEGMGKSKKIAKREA 225
NP LQE R P P YE E G H FTV V EG G SKK AK+ A
Sbjct: 1 NPKSLLQELAQKRGKPLPEYELVEEEGPDHAPRFTVEVTVGGKITGEGEGSSKKEAKQNA 60
Query: 226 ALNMLKFL 233
A L+ L
Sbjct: 61 AEAALRKL 68
Score = 63.1 bits (154), Expect = 6e-13
Identities = 29/71 (40%), Positives = 42/71 (59%), Gaps = 4/71 (5%)
Query: 77 TPVSLMQELLSRRGTA-PKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAK 135
P SL+QEL +RG P+YEL++ EG + P F +++ + G G SKKEAK
Sbjct: 1 NPKSLLQELAQKRGKPLPEYELVEEEGPDHAPRFTVEVTVGGK---ITGEGEGSSKKEAK 57
Query: 136 HNAAKSVLDQL 146
NAA++ L +L
Sbjct: 58 QNAAEAALRKL 68
>gnl|CDD|214634 smart00358, DSRM, Double-stranded RNA binding motif.
Length = 67
Score = 71.1 bits (175), Expect = 8e-16
Identities = 28/68 (41%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 168 PVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVN-VYKEEGMGKSKKIAKREAA 226
P LQE RK PP YE + G H FTV V EG G SKK AK+ AA
Sbjct: 1 PKSLLQELAQKRKLPP-EYELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAA 59
Query: 227 LNMLKFLE 234
L+ L+
Sbjct: 60 EAALRSLK 67
Score = 63.8 bits (156), Expect = 3e-13
Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 78 PVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHN 137
P SL+QEL +R P+YEL++ EG + P F + + + G G SKKEAK
Sbjct: 1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGK---RTGEGEGSSKKEAKQR 57
Query: 138 AAKSVLDQL 146
AA++ L L
Sbjct: 58 AAEAALRSL 66
>gnl|CDD|215670 pfam00035, dsrm, Double-stranded RNA binding motif. Sequences
gathered for seed by HMM_iterative_training Putative
motif shared by proteins that bind to dsRNA. At least
some DSRM proteins seem to bind to specific RNA targets.
Exemplified by Staufen, which is involved in
localisation of at least five different mRNAs in the
early Drosophila embryo. Also by interferon-induced
protein kinase in humans, which is part of the cellular
response to dsRNA.
Length = 66
Score = 60.4 bits (147), Expect = 5e-12
Identities = 30/67 (44%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 168 PVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYK-EEGMGKSKKIAKREAA 226
P LQE +K P P YE E G PH FTV VN K G G SKK AK+ AA
Sbjct: 1 PKSLLQE-LCQKKGPKPPYEYVEEEGPPHSPTFTVTVTVNGKKYGTGTGSSKKEAKQLAA 59
Query: 227 LNMLKFL 233
L+ L
Sbjct: 60 EKALQKL 66
Score = 56.5 bits (137), Expect = 1e-10
Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 78 PVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHN 137
P SL+QEL ++G P YE ++ EG + P F +++T + Y G+G SKKEAK
Sbjct: 1 PKSLLQELCQKKGPKPPYEYVEEEGPPHSPTF--TVTVTVNGKKY-GTGTGSSKKEAKQL 57
Query: 138 AAKSVLDQL 146
AA+ L +L
Sbjct: 58 AAEKALQKL 66
>gnl|CDD|234633 PRK00102, rnc, ribonuclease III; Reviewed.
Length = 229
Score = 62.8 bits (154), Expect = 2e-11
Identities = 27/65 (41%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 171 QLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKE-EGMGKSKKIAKREAALNM 229
+LQE R P P YE + G H++ FTV VN + EG G SKK A++ AA
Sbjct: 163 RLQELLQGRGLPLPEYELVKEEGPAHDKEFTVEVTVNGKELGEGTGSSKKEAEQAAAKQA 222
Query: 230 LKFLE 234
LK L+
Sbjct: 223 LKKLK 227
Score = 56.7 bits (138), Expect = 2e-09
Identities = 27/85 (31%), Positives = 44/85 (51%), Gaps = 4/85 (4%)
Query: 63 AARLEVMRLNTGDRTPVSLMQELL-SRRGTAPKYELIQIEGAINEPIFKYRISLTSESRL 121
R+E + L + + +QELL R P+YEL++ EG ++ F +++ +
Sbjct: 145 EPRIEEIDLGDLVKDYKTRLQELLQGRGLPLPEYELVKEEGPAHDKEFTVEVTVNGKEL- 203
Query: 122 YVAIGSGKSKKEAKHNAAKSVLDQL 146
G+G SKKEA+ AAK L +L
Sbjct: 204 --GEGTGSSKKEAEQAAAKQALKKL 226
>gnl|CDD|233772 TIGR02191, RNaseIII, ribonuclease III, bacterial. This family
consists of bacterial examples of ribonuclease III. This
enzyme cleaves double-stranded rRNA. It is involved in
processing ribosomal RNA precursors. It is found even in
minimal genones such as Mycoplasma genitalium and
Buchnera aphidicola, and in some cases has been shown to
be an essential gene. These bacterial proteins contain a
double-stranded RNA binding motif (pfam00035) and a
ribonuclease III domain (pfam00636). Eukaryotic homologs
tend to be much longer proteins with additional domains,
localized to the nucleus, and not included in this
family [Transcription, RNA processing].
Length = 220
Score = 56.8 bits (138), Expect = 2e-09
Identities = 25/66 (37%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNV-YKEEGMGKSKKIAKREA 225
+ LQE R P P Y + G H++ FTV VN EG GKSKK A++ A
Sbjct: 153 DYKTALQEWAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNA 212
Query: 226 ALNMLK 231
A L+
Sbjct: 213 AKAALE 218
Score = 56.8 bits (138), Expect = 2e-09
Identities = 26/68 (38%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 80 SLMQELL-SRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNA 138
+ +QE +R P+Y LI+ EG ++ F +S+ E G GKSKKEA+ NA
Sbjct: 156 TALQEWAQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGE---PYGEGKGKSKKEAEQNA 212
Query: 139 AKSVLDQL 146
AK+ L++L
Sbjct: 213 AKAALEKL 220
>gnl|CDD|223644 COG0571, Rnc, dsRNA-specific ribonuclease [Transcription].
Length = 235
Score = 56.1 bits (136), Expect = 4e-09
Identities = 29/99 (29%), Positives = 44/99 (44%), Gaps = 6/99 (6%)
Query: 137 NAAKSVLDQLIGRDDEKLMCQKENLFKVEPNPVGQLQEACMTRKWPPPVYETEETTGLPH 196
AA+ + +L E++ + FK +P +LQE + P Y + G H
Sbjct: 137 EAARKFILKLFLPRLEEI--DAGDQFK---DPKTRLQELLQAQGLVLPEYRLVKEEGPAH 191
Query: 197 ERMFTVCAYVN-VYKEEGMGKSKKIAKREAALNMLKFLE 234
++ FTV V G G+SKK A++ AA LK L
Sbjct: 192 DKEFTVEVAVGGKELGTGKGRSKKEAEQAAAEQALKKLG 230
Score = 44.9 bits (107), Expect = 2e-05
Identities = 26/83 (31%), Positives = 45/83 (54%), Gaps = 4/83 (4%)
Query: 65 RLEVMRLNTGDRTPVSLMQELLSRRG-TAPKYELIQIEGAINEPIFKYRISLTSESRLYV 123
RLE + + P + +QELL +G P+Y L++ EG ++ F +++ + +
Sbjct: 150 RLEEIDAGDQFKDPKTRLQELLQAQGLVLPEYRLVKEEGPAHDKEFTVEVAVGGK---EL 206
Query: 124 AIGSGKSKKEAKHNAAKSVLDQL 146
G G+SKKEA+ AA+ L +L
Sbjct: 207 GTGKGRSKKEAEQAAAEQALKKL 229
>gnl|CDD|234517 TIGR04238, seadorna_dsRNA, seadornavirus double-stranded
RNA-binding protein. This protein family occurs in the
seadornavirus virus group, with an N-terminal domain for
binding double-stranded RNA, is designated VP12 in Banna
virus, VP8 in Kadipiro virus, and VP11 in Liao ning
virus.
Length = 201
Score = 50.7 bits (121), Expect = 2e-07
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 1/82 (1%)
Query: 167 NPVGQLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEEGMGKSKKIAKREAA 226
N VG LQE + R PVYE G H FT+ N + SKK A++ AA
Sbjct: 1 NVVGMLQELAVKRGLELPVYEKVGKEGPDHAPTFTIKLTANDIEVIEAASSKKQAEKLAA 60
Query: 227 LNML-KFLETVPIEIPEKKQGE 247
+ E +E+ + ++
Sbjct: 61 ATIYEDMKENGLLEVHDTRKSV 82
>gnl|CDD|171444 PRK12371, PRK12371, ribonuclease III; Reviewed.
Length = 235
Score = 40.1 bits (94), Expect = 0.001
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 171 QLQEACMTRKWPPPVYETEETTGLPHERMFTVCAYVNVYKEE-GMGKSKKIAKREAALNM 229
+LQE + PVY + +G H+ FTV V + E G G+SK+ A++ AA M
Sbjct: 166 ELQEWAHAQFGVTPVYRVDSRSGPDHDPRFTVEVEVKGFAPETGEGRSKRAAEQVAAEKM 225
Query: 230 LK 231
L+
Sbjct: 226 LE 227
Score = 31.2 bits (71), Expect = 0.75
Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 90 GTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNAAKSVL 143
G P Y + G ++P F + + G G+SK+ A+ AA+ +L
Sbjct: 176 GVTPVYRVDSRSGPDHDPRFTVEVEV---KGFAPETGEGRSKRAAEQVAAEKML 226
>gnl|CDD|222987 PHA03103, PHA03103, double-strand RNA-binding protein; Provisional.
Length = 183
Score = 32.8 bits (75), Expect = 0.15
Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 98 IQIE--GAINEPIFKYRISLTSESRLYVAIGSGKSKKEAKHNAAKSVLDQLIG 148
I I G + P F + S + AIGS +KKEAK+NAAK +D+++
Sbjct: 128 INITSSGPSHSPTF-TASVIISGIKFKPAIGS--TKKEAKNNAAKLAMDKILN 177
>gnl|CDD|177482 PHA02701, PHA02701, ORF020 dsRNA-binding PKR inhibitor;
Provisional.
Length = 183
Score = 29.9 bits (67), Expect = 1.3
Identities = 27/80 (33%), Positives = 37/80 (46%), Gaps = 5/80 (6%)
Query: 68 VMRLNTGDRTPVSLMQELLSRRGTAPKYELIQIEGAINEPIFKYRISLTSESRLYVAIGS 127
VMRL T PVS + E R ++ + G + P+F I ++ + VA S
Sbjct: 102 VMRLKT--LNPVSAVNEFCMRTHRPLEFCETRSGGHDHCPLFTCTIVVSGKV---VATAS 156
Query: 128 GKSKKEAKHNAAKSVLDQLI 147
G SKK A+H A L LI
Sbjct: 157 GCSKKLARHAACADALTILI 176
>gnl|CDD|216847 pfam02016, Peptidase_S66, LD-carboxypeptidase.
Muramoyl-tetrapeptide carboxypeptidase hydrolyses a
peptide bond between a di-basic amino acid and the
C-terminal D-alanine in the tetrapeptide moiety in
peptidoglycan. This cleaves the bond between an L- and a
D-amino acid. The function of this activity is in murein
recycling. This family also includes the microcin c7
self-immunity protein. This family corresponds to Merops
family S66.
Length = 281
Score = 29.4 bits (67), Expect = 3.0
Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 9/62 (14%)
Query: 268 TPQILKKIQQYHTVFSQKTKGPL-------LEKLLSTRNLIDEVEDPILYLEDLSDELKY 320
++ + + K +G L L LL T L D + IL+LED E Y
Sbjct: 146 EEKLTEPNGPLKLLGPGKAEGRLIGGNLTVLASLLGTPYLPD-TKGKILFLED-VGEAPY 203
Query: 321 RV 322
R+
Sbjct: 204 RI 205
>gnl|CDD|107281 cd06286, PBP1_CcpB_like, Ligand-binding domain of a novel
transcription factor implicated in catabolite repression
in Bacillus and Clostridium species. This group
includes the ligand-binding domain of a novel
transcription factor implicated in catabolite repression
in Bacillus and Clostridium species. CcpB is 30%
identical in sequence to CcpA which functions as the
major transcriptional regulator of carbon catabolite
repression/regulation (CCR), a process in which enzymes
necessary for the metabolism of alternative sugars are
inhibited in the presence of glucose. Like CcpA, the
DNA-binding protein CcpB exerts its
catabolite-repressing effect by a mechanism dependent on
the presence of HPr(Ser-P), the small phosphocarrier
proteins of the phosphoenolpyruvate-sugar
phosphotransferase system, but with a less significant
degree.
Length = 260
Score = 29.1 bits (66), Expect = 3.5
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 42 FDNNEIKQIPKVSTNNLPLEE----AARLEVMRLNTGDRTPVSLMQELLSR 88
FDN I ++ ++T + P++E A L + +L + + L EL+ R
Sbjct: 210 FDNQPISELLGITTIDQPVKELGEKAFELLLNQLESEKPKQIELPLELIER 260
>gnl|CDD|218778 pfam05852, DUF848, Gammaherpesvirus protein of unknown function
(DUF848). This family consists of several
uncharacterized proteins from the Gammaherpesvirinae.
Length = 146
Score = 28.4 bits (64), Expect = 4.0
Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 5/74 (6%)
Query: 254 ESNGLKHTHDSTFLTPQILKKIQQYHTVFSQKTKGPLLEKLLSTRNL--IDEVEDPILYL 311
++ +H S ++ K+ T +K K L LL + ++ E +
Sbjct: 42 DTQKSLRSHQSLRQERELKNKVSSLETEIREKKK--ELS-LLKKFDRKKVERAEALTDRV 98
Query: 312 EDLSDELKYRVSFV 325
E+L +EL++ + +
Sbjct: 99 EELKEELEFELERL 112
>gnl|CDD|181085 PRK07691, PRK07691, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 496
Score = 29.1 bits (66), Expect = 4.4
Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 12/79 (15%)
Query: 273 KKIQQYHTVFSQKTKGPLLEKLLSTRNLIDEVEDPILYLEDLSDELKYRVSFVDIEEKSK 332
IQ+Y + G LL + + + + + I LE + + + + FV
Sbjct: 27 PIIQRYVALI-----GSLLTLVAAIILVANVYKHGIQTLELGNWKAPFGIVFV------- 74
Query: 333 ADGFQSLLQLTTTPVTVFC 351
AD F +LL LT++ +T
Sbjct: 75 ADMFAALLVLTSSIITFLV 93
>gnl|CDD|173181 PRK14718, PRK14718, ribonuclease III; Provisional.
Length = 467
Score = 29.0 bits (64), Expect = 4.8
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 80 SLMQELLSRRGTA-PKYELIQIEGAINEPIFKYRISLTSESRLYVAI-GSGKSKKEAKHN 137
+L+QE L A P Y ++ GA + F+ ++ +L + + GSG S++ A+
Sbjct: 155 TLLQEYLQGHKIALPTYTVVATHGAAHNQQFEVECTV---PKLDIKVSGSGASRRAAEQA 211
Query: 138 AAKSVLDQLIG 148
AAK LD++
Sbjct: 212 AAKKALDEVTA 222
>gnl|CDD|237081 PRK12372, PRK12372, ribonuclease III; Reviewed.
Length = 413
Score = 28.7 bits (64), Expect = 5.2
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 80 SLMQELLSRRGTA-PKYELIQIEGAINEPIFKYRISLTSESRLYVAI-GSGKSKKEAKHN 137
+L+QE L A P Y ++ GA + F+ ++ +L V + GSG S++ A+
Sbjct: 155 TLLQEYLQGHKIALPTYTVVATHGAAHNQQFEVECTV---PKLDVKVSGSGASRRAAEQA 211
Query: 138 AAKSVLDQLI 147
AAK LD+++
Sbjct: 212 AAKKALDEVM 221
>gnl|CDD|237507 PRK13790, PRK13790, phosphoribosylamine--glycine ligase;
Provisional.
Length = 379
Score = 28.2 bits (63), Expect = 7.1
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 115 LTSESRLYVAIGSGKSKKEAKHNAAKSV 142
+TS R+ +AIG G + ++A+ +A + V
Sbjct: 330 VTSGGRVILAIGKGDNVQDAQRDAYEKV 357
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
0.313 0.131 0.362
Gapped
Lambda K H
0.267 0.0754 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,903,150
Number of extensions: 1833030
Number of successful extensions: 1148
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1132
Number of HSP's successfully gapped: 30
Length of query: 377
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 279
Effective length of database: 6,590,910
Effective search space: 1838863890
Effective search space used: 1838863890
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 60 (26.8 bits)