RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16685
(99 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 38.9 bits (91), Expect = 7e-06
Identities = 14/25 (56%), Positives = 19/25 (76%)
Query: 28 SLNTHRRIHSGEKPHQCQVCGKRFT 52
+L H R H+GEKP++C VCGK F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
Score = 23.1 bits (50), Expect = 7.3
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 5 LRVLISEKPHVCSVCSKGFST 25
+R EKP+ C VC K FS+
Sbjct: 6 MRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 36.0 bits (83), Expect = 7e-04
Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 3 YILRVLISE--KPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYH 60
Y+ ++L S+ P+VC +C FS+S SL H I E C VCGK F + + H
Sbjct: 61 YLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQH--IRYTEHSKVCPVCGKEFRNTDSTLDH 118
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 34.3 bits (78), Expect = 0.005
Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 21/76 (27%)
Query: 7 VLISEKPHVCSV--CSKGFSTSSSLNTHRR-------------------IHSGEKPHQCQ 45
+ KP+ C V C+K + + L H + +KP++C+
Sbjct: 343 KVKDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCE 402
Query: 46 VCGKRFTASSNLYYHR 61
VC KR+ + L YHR
Sbjct: 403 VCDKRYKNLNGLKYHR 418
Score = 26.2 bits (57), Expect = 2.9
Identities = 9/27 (33%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 38 GEKPHQCQV--CGKRFTASSNLYYHRM 62
KP++C V C K++ + L YH +
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHML 372
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 32.7 bits (74), Expect = 0.019
Identities = 22/55 (40%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 12 KPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQV--CGKRFTASSNLYYHRMTH 64
+P C C+ FS L H R H+GEKP QC C K F+ L H TH
Sbjct: 32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTH 86
Score = 27.0 bits (59), Expect = 1.6
Identities = 23/65 (35%), Positives = 30/65 (46%), Gaps = 6/65 (9%)
Query: 12 KPHVCSVCSKGFSTSSSLNTHRR--IHSGE--KPHQC--QVCGKRFTASSNLYYHRMTHI 65
P C+ FS SS L H R HSGE KP C +CGK F+ + L H + H
Sbjct: 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHT 347
Query: 66 KVNDD 70
++
Sbjct: 348 SISPA 352
>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 = 30.0 bits (68), Expect = 0.024
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 15 VCSVCSKGFSTSSSLNTHRRIH 36
C C K FS S+L H R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 29.6 bits (67), Expect = 0.032
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 43 QCQVCGKRFTASSNLYYHRMTH 64
+C CGK F+ SNL H TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 29.7 bits (67), Expect = 0.029
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 14 HVCSVCSKGFSTSSSLNTHRRIH 36
+ C C K F + S+L H R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 28.2 bits (63), Expect = 0.096
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 42 HQCQVCGKRFTASSNLYYHRMTH 64
++C CGK F + S L H TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>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 = 29.4 bits (66), Expect = 0.24
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 42 HQCQVCGKRFTASSNLYYH-RMTH 64
+ C VC F++ L H R TH
Sbjct: 74 YVCNVCMAEFSSMDQLAEHQRTTH 97
Score = 28.6 bits (64), Expect = 0.53
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 7 VLISEKPHVCSVCSKGFSTSSSLNTHRRI-HS 37
I+ +VC+VC FS+ L H+R HS
Sbjct: 67 TPINPSSYVCNVCMAEFSSMDQLAEHQRTTHS 98
>gnl|CDD|235183 PRK03976, rpl37ae, 50S ribosomal protein L37Ae; Reviewed.
Length = 90
Score = 28.4 bits (64), Expect = 0.28
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 16/54 (29%)
Query: 5 LRVLISE------KPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFT 52
+R +++ HVC VC + +R+ +G +C+ CG +F
Sbjct: 22 IRKRVADIEEKMRAKHVCPVCGRP--------KVKRVGTG--IWECRKCGAKFA 65
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 26.8 bits (60), Expect = 0.35
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 42 HQCQVCGKRFTASSNLYYHRMTH 64
H C VCGK F++ L H+ +H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
Score = 26.8 bits (60), Expect = 0.37
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 14 HVCSVCSKGFSTSSSLNTHRRIH 36
H C VC K FS+ +L H++ H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
>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 = 1.0
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 14 HVCSVCSKGFSTSSSLNTHRRIH 36
C +C K FS+ +L H R H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 24.5 bits (53), Expect = 2.3
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 42 HQCQVCGKRFTASSNLYYHRMTH 64
+C +CGK F++ L H H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|222704 pfam14353, CpXC, CpXC protein. This presumed domain is
functionally uncharacterized. This domain is found in
bacteria and archaea, and is typically between 122 and
134 amino acids in length. It contains four conserved
cysteines forming two CpXC motifs.
Length = 128
Score = 26.9 bits (60), Expect = 1.2
Identities = 6/23 (26%), Positives = 6/23 (26%)
Query: 42 HQCQVCGKRFTASSNLYYHRMTH 64
C CG F YH
Sbjct: 39 FTCPSCGHEFRLDYPFLYHDPEK 61
>gnl|CDD|234774 PRK00464, nrdR, transcriptional regulator NrdR; Validated.
Length = 154
Score = 27.0 bits (61), Expect = 1.3
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 43 QCQVCGKRFT 52
+C CGKRFT
Sbjct: 30 ECLACGKRFT 39
>gnl|CDD|224508 COG1592, COG1592, Rubrerythrin [Energy production and conversion].
Length = 166
Score = 26.5 bits (59), Expect = 2.1
Identities = 13/38 (34%), Positives = 15/38 (39%), Gaps = 13/38 (34%)
Query: 11 EKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCG 48
K VC VC G+ H GE P C +CG
Sbjct: 132 GKVWVCPVC--GY-----------THEGEAPEVCPICG 156
>gnl|CDD|181037 PRK07569, PRK07569, bidirectional hydrogenase complex protein HoxU;
Validated.
Length = 234
Score = 26.5 bits (59), Expect = 2.3
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 4 ILRVLISEKPHVCSVC 19
I+ +L +E HVC+VC
Sbjct: 88 IVELLFAEGNHVCAVC 103
>gnl|CDD|227515 COG5188, PRP9, Splicing factor 3a, subunit 3 [RNA processing and
modification].
Length = 470
Score = 26.5 bits (58), Expect = 2.4
Identities = 15/58 (25%), Positives = 18/58 (31%), Gaps = 5/58 (8%)
Query: 16 CSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRFTASSNLYYHRMTHIKVNDDFKE 73
C C + FS S H K H + GK S HR + D E
Sbjct: 241 CVKCGREFSRSKVFEYHLE----GKRHCKEGQGKEEFVYSEYVLHRYLKY-LGDPVSE 293
>gnl|CDD|223048 PHA03333, PHA03333, putative ATPase subunit of terminase;
Provisional.
Length = 752
Score = 26.7 bits (59), Expect = 2.6
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 59 YHRMTHIKVNDDFKEILNL 77
HI V++ KE+LNL
Sbjct: 378 VFCPDHITVDEGLKELLNL 396
>gnl|CDD|223965 COG1034, NuoG, NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75
kD subunit (chain G) [Energy production and conversion].
Length = 693
Score = 26.2 bits (58), Expect = 3.9
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 3 YILRVLISEKPHVCSVCSKG 22
++ L+ P C VC KG
Sbjct: 85 GVMEFLLINHPLDCPVCDKG 104
>gnl|CDD|233315 TIGR01213, pseudo_Pus10arc, tRNA pseudouridine(54/55) synthase.
Members of this family show twilight-zone similarity to
several predicted RNA pseudouridine synthases. All
trusted members of this family are archaeal. Several
eukaryotic homologs lack N-terminal homology including
two CXXC motifs [Hypothetical proteins, Conserved].
Length = 388
Score = 25.9 bits (57), Expect = 3.9
Identities = 7/24 (29%), Positives = 10/24 (41%)
Query: 28 SLNTHRRIHSGEKPHQCQVCGKRF 51
+L R + + C VCG F
Sbjct: 40 ALELGRPVKEFVESEPCDVCGGIF 63
>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 = 24.1 bits (53), Expect = 3.9
Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 4/31 (12%)
Query: 13 PHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQ 43
C C K F + ++L H + K H+
Sbjct: 1 QFYCVACDKYFKSENALENHLK----SKKHK 27
>gnl|CDD|239124 cd02659, peptidase_C19C, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 334
Score = 25.7 bits (57), Expect = 4.4
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 8/34 (23%)
Query: 49 KRFTASSNLY-YHRMTHIKVND--DFKEILNLEP 79
KRF + + M IK+ND +F L++EP
Sbjct: 201 KRFE-----FDFETMMRIKINDRFEFPLELDMEP 229
>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 = 23.7 bits (52), Expect = 5.0
Identities = 5/21 (23%), Positives = 9/21 (42%)
Query: 12 KPHVCSVCSKGFSTSSSLNTH 32
C +C+ F+ S+ H
Sbjct: 2 GGFYCKLCNVTFTDEISVEAH 22
>gnl|CDD|218738 pfam05766, NinG, Bacteriophage Lambda NinG protein. NinG or Rap
is involved in recombination. Rap (recombination adept
with plasmid) increases lambda-by-plasmid recombination
catalyzed by Escherichia coli's RecBCD pathway.
Length = 188
Score = 25.4 bits (56), Expect = 5.1
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 40 KPHQCQVCGKRFT 52
KP +C+VCG F
Sbjct: 5 KPKKCKVCGVYFV 17
>gnl|CDD|214499 smart00064, FYVE, Protein present in Fab1, YOTB, Vac1, and EEA1.
The FYVE zinc finger is named after four proteins where
it was first found: Fab1, YOTB/ZK632.12, Vac1, and
EEA1. The FYVE finger has been shown to bind two Zn2+
ions. The FYVE finger has eight potential zinc
coordinating cysteine positions. The FYVE finger is
structurally related to the PHD finger and the RING
finger. Many members of this family also include two
histidines in a motif R+HHC+XCG, where + represents a
charged residue and X any residue. The FYVE finger
functions in the membrane recruitment of cytosolic
proteins by binding to phosphatidylinositol 3-phosphate
(PI3P), which is prominent on endosomes. The R+HHC+XCG
motif is critical for PI3P binding.
Length = 68
Score = 23.9 bits (52), Expect = 7.7
Identities = 13/42 (30%), Positives = 17/42 (40%), Gaps = 12/42 (28%)
Query: 10 SEKPHVCSVCSKGFSTSSSLNTHRRIHSGEKPHQCQVCGKRF 51
E+ C C K F+ T RR H C+ CG+ F
Sbjct: 7 DEEVSNCMGCGKEFN-----LTKRRHH-------CRNCGRIF 36
>gnl|CDD|204520 pfam10588, NADH-G_4Fe-4S_3, NADH-ubiquinone oxidoreductase-G
iron-sulfur binding region.
Length = 41
Score = 23.2 bits (51), Expect = 8.9
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 4 ILRVLISEKPHVCSVCSKG 22
IL +L++ P C C K
Sbjct: 4 ILELLLANHPLDCPTCDKN 22
>gnl|CDD|220438 pfam09845, DUF2072, Zn-ribbon containing protein (DUF2072). This
archaeal protein has no known function.
Length = 121
Score = 24.4 bits (53), Expect = 9.1
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 41 PHQCQVCGKRFTASS 55
PH+C CGK F S
Sbjct: 1 PHRCTKCGKIFEDGS 15
>gnl|CDD|225899 COG3364, COG3364, Zn-ribbon containing protein [General function
prediction only].
Length = 112
Score = 24.5 bits (53), Expect = 9.2
Identities = 8/17 (47%), Positives = 9/17 (52%)
Query: 41 PHQCQVCGKRFTASSNL 57
PHQC CG+ F S
Sbjct: 2 PHQCTRCGEVFDDGSEE 18
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
0.320 0.132 0.392
Gapped
Lambda K H
0.267 0.0759 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,619,000
Number of extensions: 345514
Number of successful extensions: 388
Number of sequences better than 10.0: 1
Number of HSP's gapped: 378
Number of HSP's successfully gapped: 55
Length of query: 99
Length of database: 10,937,602
Length adjustment: 65
Effective length of query: 34
Effective length of database: 8,054,592
Effective search space: 273856128
Effective search space used: 273856128
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 (21.8 bits)
S2: 53 (24.1 bits)