RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4830
(292 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 38.5 bits (90), Expect = 9e-05
Identities = 18/26 (69%), Positives = 20/26 (76%)
Query: 80 NLEVHMRTHTGERPYQCEVCNKRFSQ 105
NL HMRTHTGE+PY+C VC K FS
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 36.2 bits (84), Expect = 7e-04
Identities = 14/26 (53%), Positives = 20/26 (76%)
Query: 172 SHQVHMRTHTGERPFQCAVCSKRFTQ 197
+ + HMRTHTGE+P++C VC K F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 35.1 bits (81), Expect = 0.001
Identities = 16/26 (61%), Positives = 19/26 (73%)
Query: 24 YLEIHMRTHTGERPFQCVVCLKRFSQ 49
L HMRTHTGE+P++C VC K FS
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 35.1 bits (81), Expect = 0.002
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 200 SLNTHKRVHTGERPYACDICDKRFA 224
+L H R HTGE+PY C +C K F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 26.2 bits (58), Expect = 1.8
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 5/31 (16%)
Query: 108 SLNTHKRIHINYLHTEDKPYHCTGCDAAFSR 138
+L H R H T +KPY C C +FS
Sbjct: 1 NLRRHMRTH-----TGEKPYKCPVCGKSFSS 26
Score = 25.8 bits (57), Expect = 2.8
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 1 MKLHSGNKPYHCTACDASF 19
M+ H+G KPY C C SF
Sbjct: 6 MRTHTGEKPYKCPVCGKSF 24
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 39.4 bits (92), Expect = 0.002
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 6/47 (12%)
Query: 224 AVKSYVTSHRWSHVGDKPFGCTSCHLTFTSKSQFAVHLRTHHTVGAN 270
K + S+V C C F+S Q A H RT H++GA+
Sbjct: 62 QSKKATPINPSSYV------CNVCMAEFSSMDQLAEHQRTTHSIGAS 102
Score = 29.4 bits (66), Expect = 2.6
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 269 ANHVCNVCGRSFVRDSYLIRHQ 290
+++VCNVC F L HQ
Sbjct: 72 SSYVCNVCMAEFSSMDQLAEHQ 93
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 35.8 bits (82), Expect = 0.023
Identities = 45/210 (21%), Positives = 67/210 (31%), Gaps = 40/210 (19%)
Query: 8 KPYHCTACDASFCRKPYLEIHMRT--HTGE--RPFQCVV--CLKRFSQKSALNTHKRMHI 61
P C+ SF R L H+R+ H+GE +PF C C K FS+ AL
Sbjct: 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKR------ 341
Query: 62 PYIQYYCDACDATFTTKQNLEVHMRTHTGERPYQC--EVCNKRFSQKSSLNTHKRIHINY 119
H+ HT P + + +FS + + +
Sbjct: 342 ----------------------HILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYK 379
Query: 120 LHTEDKPYHCT--GCDAAFSRKQYLEVNHTTVLAVMQPSLGNNTWSAKFLTSLFSHQVHM 177
DK C F R L H +P N +K ++ H
Sbjct: 380 DLKNDKKSETLSNSCIRNFKRDSNLS-LHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHK 438
Query: 178 RTHTGERPFQCAVCSKRFTQKSSLNTHKRV 207
+ HT P C+ K F + L+ H +
Sbjct: 439 KIHTNHAPLLCS-ILKSFRRDLDLSNHGKD 467
Score = 34.7 bits (79), Expect = 0.045
Identities = 42/203 (20%), Positives = 72/203 (35%), Gaps = 17/203 (8%)
Query: 48 SQKSALNTHKRMHIPYIQYYCDACDATFTTKQNLEVHMRTHTGER-PYQCEVCNKRFSQK 106
S S ++ A+ + E + G P + + CN FS+
Sbjct: 244 SPSSLSSSDSSSSAS-ESPRSSLPTASSQSSSPNESDSSSEKGFSLPIKSKQCNISFSRS 302
Query: 107 SSLNTHKRIHINYLHT--EDKPYHCT--GCDAAFSRKQYL---EVNHTTVLAVMQPSLGN 159
S L H R + H+ KP+ C C FSR L + HT++ + L +
Sbjct: 303 SPLTRHLR---SVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNS 359
Query: 160 NTWSAKFLTSL-FSHQVHMRTHTGERPFQCAV--CSKRFTQKSSLNTHKRVHTGERPYAC 216
++ + L + + ++ + C + F + S+L+ H H RPY C
Sbjct: 360 SSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNC 419
Query: 217 D--ICDKRFAVKSYVTSHRWSHV 237
C K F + H+ H
Sbjct: 420 KNPPCSKSFNRHYNLIPHKKIHT 442
Score = 33.9 bits (77), Expect = 0.10
Identities = 26/119 (21%), Positives = 43/119 (36%), Gaps = 14/119 (11%)
Query: 185 PFQCAVCSKRFTQKSSLNTHKR--VHTGE--RPYACDI--CDKRFAVKSYVTSHRWSHVG 238
P + C+ F++ S L H R H+GE +P++C C K F+ + H H
Sbjct: 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTS 348
Query: 239 DKPFGCTSCHLT------FTSKSQFAVHLRTHHTVGANHVCNV--CGRSFVRDSYLIRH 289
P + + ++ ++ C R+F RDS L H
Sbjct: 349 ISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLH 407
Score = 30.8 bits (69), Expect = 0.91
Identities = 36/205 (17%), Positives = 57/205 (27%), Gaps = 35/205 (17%)
Query: 37 PFQCVVCLKRFSQKSALNTHKRMHI----PYIQYYCDA--CDATFTTKQNLEVHMRTHTG 90
P + C FS+ S L H R + C C F+ L+ H+ HT
Sbjct: 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTS 348
Query: 91 ERPYQC--EVCNKRFSQKSSLNTHKRIHINYLHTEDKPYHCTGCDAAFSRKQYLEVNHTT 148
P + + +FS + + + DK
Sbjct: 349 ISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLS----------------- 391
Query: 149 VLAVMQPSLGNNTWSAKFLTSLFSHQVHMRTHTGERPFQCAVCSKRFTQKSSLNTHKRVH 208
S N L+ + R + + CSK F + +L HK++H
Sbjct: 392 ------NSCIRNFKRDSNLSLHIITHLSFRPY----NCKNPPCSKSFNRHYNLIPHKKIH 441
Query: 209 TGERPYACDICDKRFAVKSYVTSHR 233
T P C I +
Sbjct: 442 TNHAPLLCSILKSFRRDLDLSNHGK 466
Score = 29.7 bits (66), Expect = 2.0
Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 7 NKPYHCTACDASFCRKPYLEIHMRTHTGERPFQCVV--CLKRFSQKSALNTHKRMH 60
+P C C SF R +L H+R+HTGE+P QC C K FS+ L+ H R H
Sbjct: 31 PRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTH 86
Score = 28.9 bits (64), Expect = 3.1
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 65 QYYCDACDATFTTKQNLEVHMRTHTGERPYQCEV--CNKRFSQKSSLNTHKRIH 116
C C +F+ ++L H+R+HTGE+P QC C+K FS+ L+ H R H
Sbjct: 33 PDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTH 86
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus,
particularly the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 30.6 bits (70), Expect = 0.060
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 65 QYYCDACDATFTTKQNLEVHMRT 87
Q+YC ACD F ++ LE H+++
Sbjct: 1 QFYCVACDKYFKSENALENHLKS 23
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 33.9 bits (77), Expect = 0.080
Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 11/82 (13%)
Query: 34 GERPFQCVV--CLKRFSQKSALNTHKRMHIPYIQYYCDACDATFTTKQNLEVHMRTHTGE 91
+P++C V C K++ ++ L H + + E +
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLH---------GHQNQKLHENPSPEKMNIFSAKD 396
Query: 92 RPYQCEVCNKRFSQKSSLNTHK 113
+PY+CEVC+KR+ + L H+
Sbjct: 397 KPYRCEVCDKRYKNLNGLKYHR 418
Score = 33.5 bits (76), Expect = 0.11
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 16/60 (26%)
Query: 90 GERPYQCEV--CNKRFSQKSSLNTHKR--------------IHINYLHTEDKPYHCTGCD 133
+PY+C V CNK++ ++ L H +N +DKPY C CD
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCD 405
Score = 30.8 bits (69), Expect = 0.84
Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 21/73 (28%)
Query: 182 GERPFQCAV--CSKRFTQKSSLNTHKR-------------------VHTGERPYACDICD 220
+P++C V C+K++ ++ L H ++PY C++CD
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCD 405
Query: 221 KRFAVKSYVTSHR 233
KR+ + + HR
Sbjct: 406 KRYKNLNGLKYHR 418
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 29.4 bits (66), Expect = 0.15
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 94 YQCEVCNKRFSQKSSLNTHKRIH 116
Y+C C K F KS+L H R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 27.0 bits (60), Expect = 0.95
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 186 FQCAVCSKRFTQKSSLNTHKRVH 208
++C C K F KS+L H R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 27.0 bits (60), Expect = 1.2
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 66 YYCDACDATFTTKQNLEVHMRTH 88
Y C C F +K L HMRTH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 25.9 bits (57), Expect = 2.3
Identities = 11/23 (47%), Positives = 11/23 (47%)
Query: 10 YHCTACDASFCRKPYLEIHMRTH 32
Y C C F K L HMRTH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 25.5 bits (56), Expect = 3.4
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 38 FQCVVCLKRFSQKSALNTHKRMH 60
++C C K F KSAL H R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 29.2 bits (66), Expect = 0.18
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 95 QCEVCNKRFSQKSSLNTHKRIH 116
+C C K FS+KS+L H R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 27.3 bits (61), Expect = 0.88
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 187 QCAVCSKRFTQKSSLNTHKRVH 208
+C C K F++KS+L H R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 26.5 bits (59), Expect = 1.5
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 39 QCVVCLKRFSQKSALNTHKRMH 60
+C C K FS+KS L H R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 25.8 bits (57), Expect = 2.6
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 68 CDACDATFTTKQNLEVHMRTH 88
C C +F+ K NL+ H+RTH
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
Score = 25.0 bits (55), Expect = 5.1
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 244 CTSCHLTFTSKSQFAVHLRTH 264
C C +F+ KS HLRTH
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
Score = 24.6 bits (54), Expect = 6.6
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 272 VCNVCGRSFVRDSYLIRHQNK 292
C CG+SF R S L RH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRT 21
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 27.6 bits (62), Expect = 0.71
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 66 YYCDACDATFTTKQNLEVHMRTH 88
+ C C TF++ Q L H ++H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a
zinc-finger domain with the CxxCx(12)Hx(6)H motif,
found in multiple copies in a wide range of proteins
from plants to metazoans. Some member proteins,
particularly those from plants, are annotated as being
RNA-binding.
Length = 25
Score = 26.7 bits (60), Expect = 1.6
Identities = 9/21 (42%), Positives = 16/21 (76%)
Query: 66 YYCDACDATFTTKQNLEVHMR 86
+YC+ C+ TFT++ L+ H+R
Sbjct: 1 FYCELCNVTFTSESQLKSHLR 21
Score = 25.2 bits (56), Expect = 4.2
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 94 YQCEVCNKRFSQKSSLNTHKR 114
+ CE+CN F+ +S L +H R
Sbjct: 1 FYCELCNVTFTSESQLKSHLR 21
>gnl|CDD|227480 COG5151, SSL1, RNA polymerase II transcription
initiation/nucleotide excision repair factor TFIIH,
subunit SSL1 [Transcription / DNA replication,
recombination, and repair].
Length = 421
Score = 29.6 bits (66), Expect = 2.3
Identities = 28/113 (24%), Positives = 39/113 (34%), Gaps = 16/113 (14%)
Query: 10 YHCTACDASFCRKPY------LEIHMRTHTGERPFQCVVCLKRFSQKSALNTHKRMHIPY 63
Y C C C P L++ + TH R + + LK F +K K H
Sbjct: 309 YECPVCKTKVCSLPISCPICSLQLILSTHLA-RSYHHLYPLKPFVEKPEGTNPKSTH--- 364
Query: 64 IQYYCDACDATFTTKQNLEVHMRTHTGERPYQCEVCNKRFSQKSSLNTHKRIH 116
C C F T +G YQCE+C F + H+ +H
Sbjct: 365 ----CFVCQGPFPKPPVSPFDESTSSGR--YQCELCKSTFCSDCDVFIHETLH 411
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 27.9 bits (62), Expect = 2.8
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 5/50 (10%)
Query: 241 PFGCTSCHLTFTSKSQFAVHLR-THHTVGANHVCNVCGRSFVRDSYLIRH 289
P+ C C + F+S H+R T H+ VC VCG+ F + H
Sbjct: 73 PYVCPLCLMPFSSSVSLKQHIRYTEHSK----VCPVCGKEFRNTDSTLDH 118
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 29.2 bits (66), Expect = 3.1
Identities = 12/77 (15%), Positives = 20/77 (25%), Gaps = 23/77 (29%)
Query: 56 HKRMHIPYIQYYCDACDATFTTKQNLEVHMRTHTGERPYQCEVCNKRFSQKSSLNTHKRI 115
++R + P + C C N + + H +C C
Sbjct: 428 NRRGYAPLLL--CRDCGYIAEC-PNCDSPLTLHKATGQLRCHYCG--------------- 469
Query: 116 HINYLHTEDKPYHCTGC 132
+ E P C C
Sbjct: 470 -----YQEPIPQSCPEC 481
>gnl|CDD|223349 COG0271, BolA, Stress-induced morphogen (activity unknown) [Signal
transduction mechanisms].
Length = 90
Score = 27.3 bits (61), Expect = 3.3
Identities = 11/36 (30%), Positives = 17/36 (47%)
Query: 172 SHQVHMRTHTGERPFQCAVCSKRFTQKSSLNTHKRV 207
SH+ H G F+ + S+ F KS + H+ V
Sbjct: 27 SHRHHGHAGGGGSHFKVVIVSEAFQGKSLVARHRLV 62
>gnl|CDD|128804 smart00531, TFIIE, Transcription initiation factor IIE.
Length = 147
Score = 28.1 bits (63), Expect = 3.5
Identities = 11/58 (18%), Positives = 20/58 (34%), Gaps = 9/58 (15%)
Query: 77 TKQNLEVHMRTHTGERPYQCEVCNKRFSQKSSLNTHKRIHINYLHTEDKPYHCTGCDA 134
++ LE + T Y+C C +++ + N L D + C C
Sbjct: 83 MRKRLEDKLEDETNNAYYKCPNCQSKYTF---------LEANQLLDMDGTFTCPRCGE 131
>gnl|CDD|197732 smart00451, ZnF_U1, U1-like zinc finger. Family of C2H2-type
zinc fingers, present in matrin, U1 small nuclear
ribonucleoprotein C and other RNA-binding proteins.
Length = 35
Score = 25.7 bits (57), Expect = 4.0
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 65 QYYCDACDATFTTKQNLEVHMRTH 88
+YC C+ TFT + ++E H++
Sbjct: 3 GFYCKLCNVTFTDEISVEAHLKGK 26
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 24.5 bits (53), Expect = 8.4
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 94 YQCEVCNKRFSQKSSLNTHKRIH 116
++C +C K FS K +L H R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
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
0.325 0.132 0.440
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,434,705
Number of extensions: 1117866
Number of successful extensions: 1530
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1503
Number of HSP's successfully gapped: 88
Length of query: 292
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 196
Effective length of database: 6,679,618
Effective search space: 1309205128
Effective search space used: 1309205128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 59 (26.6 bits)