RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16828
(372 letters)
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 36.2 bits (83), Expect = 0.022
Identities = 23/79 (29%), Positives = 33/79 (41%), Gaps = 9/79 (11%)
Query: 105 VHSGKEYPCE--QCDRKFTNGYKLKQHMLT-HMQKDTSISIDVIS------EIKKFKCDQ 155
V GK Y C C++K+ N LK HML H + + + K ++C+
Sbjct: 344 VKDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEV 403
Query: 156 CDYATKDKYNLGTHIKRRH 174
CD K+ L H K H
Sbjct: 404 CDKRYKNLNGLKYHRKHSH 422
Score = 35.8 bits (82), Expect = 0.031
Identities = 22/97 (22%), Positives = 38/97 (39%), Gaps = 12/97 (12%)
Query: 137 DTSISIDVISEIKKFKCD--QCDYATKDKYNLGTHIKRRHTKEYSVLCTQCGFGCYTNRE 194
DT + + + K +KC C+ K++ L H+ H + N
Sbjct: 336 DTPSRMLKVKDGKPYKCPVEGCNKKYKNQNGLKYHMLHGH----------QNQKLHENPS 385
Query: 195 LEEHQILTHGAEPYHCKYCDKTFTKRMNVKTHERMKH 231
E+ I + +PY C+ CDK + +K H + H
Sbjct: 386 PEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKHSH 422
Score = 33.9 bits (77), Expect = 0.12
Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 20/95 (21%)
Query: 228 RMKHENHKPYECYI--CNKILVSRGRLNEHLNQVHLAQRFECKLCHKTIVSEKTFKKHMA 285
+K ++ KPY+C + CNK ++ L H+ H Q+ H+ EK
Sbjct: 341 MLKVKDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKL-----HENPSPEK----MNI 391
Query: 286 LHSDAKPFVCNICGKDFK----LKYYVNLHMRTHT 316
+ KP+ C +C K +K LKY+ R H+
Sbjct: 392 FSAKDKPYRCEVCDKRYKNLNGLKYH-----RKHS 421
Score = 31.2 bits (70), Expect = 0.98
Identities = 26/89 (29%), Positives = 37/89 (41%), Gaps = 20/89 (22%)
Query: 289 DAKPFVCNI--CGKDFK----LKYYVNLHMRTHTRIRPTFECDVCHQIFPTDFRTKHMLV 342
D KP+ C + C K +K LKY+ LH + ++ + IF
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYH-MLHGHQNQKLHENPSPEK-MNIFSAK-------- 395
Query: 343 HDVEKSHLCFVCGAGFVNDAGLKVHMRKH 371
+K + C VC + N GLK H RKH
Sbjct: 396 ---DKPYRCEVCDKRYKNLNGLKYH-RKH 420
Score = 30.1 bits (67), Expect = 2.2
Identities = 18/80 (22%), Positives = 27/80 (33%), Gaps = 20/80 (25%)
Query: 202 THGAEPYHCKY--CDKTFTKRMNVKTHERMKHEN------------------HKPYECYI 241
+PY C C+K + + +K H H+N KPY C +
Sbjct: 344 VKDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEV 403
Query: 242 CNKILVSRGRLNEHLNQVHL 261
C+K + L H H
Sbjct: 404 CDKRYKNLNGLKYHRKHSHD 423
>gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional.
Length = 325
Score = 35.0 bits (81), Expect = 0.051
Identities = 19/52 (36%), Positives = 24/52 (46%), Gaps = 9/52 (17%)
Query: 279 TFKKHMALHSDAKPFVCNICGKDFKLKYYVNLHMRTHTRIRPTFECDVCHQI 330
T + HMA+H KP V + Y + H R HTR+R E HQI
Sbjct: 194 TKRTHMAVHPMGKPAVTH---------YRIMEHFRVHTRLRLRLETGRTHQI 236
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 33.5 bits (76), Expect = 0.20
Identities = 22/108 (20%), Positives = 37/108 (34%), Gaps = 17/108 (15%)
Query: 150 KFKC--DQCDYATKDKYNLGTHIKRRHTKEYSVLCTQ------CGFGCYTNRELEEHQIL 201
FKC +C L H K +H C + + L +H+
Sbjct: 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNG 210
Query: 202 THGAEPYH----CKYCDKTFTKRMNVKTHERMKHENHKPYECYICNKI 245
E + C +C F ++ H R++HE C+IC+ +
Sbjct: 211 GLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRHE-----ACHICDMV 253
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 29.2 bits (65), Expect = 0.41
Identities = 8/26 (30%), Positives = 20/26 (76%)
Query: 23 ECPVCGKVLSRKSKLVSHMRSFHTSV 48
ECP+CG++ ++ +++H+R +T++
Sbjct: 7 ECPICGEIYIKRKSMITHLRKHNTNL 32
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 28.1 bits (63), Expect = 0.61
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 280 FKKHMALHSDAKPFVCNICGKDFK 303
++HM H+ KP+ C +CGK F
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 26.6 bits (59), Expect = 2.1
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 194 ELEEHQILTHGAEPYHCKYCDKTFT 218
L H G +PY C C K+F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 25.0 bits (55), Expect = 7.0
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 338 KHMLVHDVEKSHLCFVCGAGFVN 360
+HM H EK + C VCG F +
Sbjct: 4 RHMRTHTGEKPYKCPVCGKSFSS 26
Score = 24.7 bits (54), Expect = 8.6
Identities = 11/21 (52%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 311 HMRTHTRIRPTFECDVCHQIF 331
HMRTHT +P ++C VC + F
Sbjct: 5 HMRTHTGEKP-YKCPVCGKSF 24
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 31.6 bits (71), Expect = 0.64
Identities = 43/229 (18%), Positives = 67/229 (29%), Gaps = 24/229 (10%)
Query: 42 RSFHTSVTPEAGGDNNDTSGHMSQIQTMLMLDHKKPKSRAPVECSYCGKVLSRKDKLTRH 101
+S + S S K C SR LTRH
Sbjct: 251 SDSSSSASESPRSSLPTASSQSSSPNESDSSSEKGFSLPIK--SKQCNISFSRSSPLTRH 308
Query: 102 IAAV-HSGKEY-----PCEQCDRKFTNGYKLKQHMLTHMQKDTSISIDVISEIKKFKCDQ 155
+ +V HSG+ P C + F+ LK+H+L H + + S K
Sbjct: 309 LRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPL-- 366
Query: 156 CDYATKDKYNLGTHIKRRHTKEYSVLCTQCGFGC------YTNRELEEHQILTHGAEPYH 209
+ + + + K T C +N L L+
Sbjct: 367 -----LNNEPPQSLQQYKDLKNDKKSETL-SNSCIRNFKRDSNLSLHIITHLSFRPYNCK 420
Query: 210 CKYCDKTFTKRMNVKTHERMKHENHKPYECYICNKILVSRGRLNEHLNQ 258
C K+F + N+ H+++ H NH P K L+ H
Sbjct: 421 NPPCSKSFNRHYNLIPHKKI-HTNHAPL-LCSILKSFRRDLDLSNHGKD 467
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 27.4 bits (61), Expect = 1.1
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 111 YPCEQCDRKFTNGYKLKQHMLTH 133
Y C +C + F + L++HM TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 27.0 bits (60), Expect = 1.2
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 293 FVCNICGKDFKLKYYVNLHMRTH 315
+ C CGK FK K + HMRTH
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 = 26.5 bits (59), Expect = 1.9
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 294 VCNICGKDFKLKYYVNLHMRTH 315
C CGK F K + H+RTH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 26.2 bits (58), Expect = 2.8
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 113 CEQCDRKFTNGYKLKQHMLTH 133
C C + F+ LK+H+ TH
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
Score = 26.2 bits (58), Expect = 2.8
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 23 ECPVCGKVLSRKSKLVSHMRS 43
+CP CGK SRKS L H+R+
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRT 21
>gnl|CDD|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin. The first 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 cell substratum
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 = 87
Score = 27.9 bits (62), Expect = 2.9
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 67 QTMLMLDHKKPKSRAPVE-CSYCGKVLSRKDKLTRHIAAVHSGKEYPCEQCDRK 119
Q M +DH A E C CG+ LSR R + + + C QC+++
Sbjct: 15 QLMQDMDHPPAAEAATNELCGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQ 68
>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 = 26.0 bits (58), Expect = 3.4
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 264 RFECKLCHKTIVSEKTFKKHM 284
+F C C K SE + H+
Sbjct: 1 QFYCVACDKYFKSENALENHL 21
>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 = 26.1 bits (58), Expect = 3.8
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 205 AEPYHCKYCDKTFTKRMNVKTHERMKHENHK 235
++CK C+ TFT ++V+ H + K HK
Sbjct: 1 TGGFYCKLCNVTFTDEISVEAHLKGK--KHK 29
>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 = 25.7 bits (56), Expect = 4.1
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 111 YPCEQCDRKFTNGYKLKQHMLTH 133
+ C C + F++ LK+H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|214746 smart00614, ZnF_BED, BED zinc finger. DNA-binding domain in
chromatin-boundary-element-binding proteins and
transposases.
Length = 50
Score = 26.2 bits (58), Expect = 4.2
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 12 IEPKPSKYIKVECPVCGKVLSRKSK-----LVSHMRSFHTSV 48
I K + + +C CGK LSR SK L H+R H +
Sbjct: 9 ILEKDNGKQRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHPAR 50
Score = 25.9 bits (57), Expect = 5.8
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 5/38 (13%)
Query: 75 KKPKSRAPVECSYCGKVLSRKDK-----LTRHIAAVHS 107
+K + +C YCGK LSR K L RH+ H
Sbjct: 11 EKDNGKQRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48
>gnl|CDD|235516 PRK05582, PRK05582, DNA topoisomerase I; Validated.
Length = 650
Score = 29.0 bits (66), Expect = 4.4
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 5/29 (17%)
Query: 9 TEAIEPKPSKYIKVECPVC-GKVLSRKSK 36
T+ I K I V+CP C G+++ RKSK
Sbjct: 603 TKPIV----KEIGVKCPKCGGQIVERKSK 627
>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 = 25.2 bits (56), Expect = 5.6
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 265 FECKLCHKTIVSEKTFKKHMA 285
F C+LC+ T SE K H+
Sbjct: 1 FYCELCNVTFTSESQLKSHLR 21
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 0.135 0.428
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,528,463
Number of extensions: 1558486
Number of successful extensions: 2145
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2125
Number of HSP's successfully gapped: 96
Length of query: 372
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 274
Effective length of database: 6,590,910
Effective search space: 1805909340
Effective search space used: 1805909340
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: 40 (21.5 bits)
S2: 60 (27.0 bits)