RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1990
(382 letters)
>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III
members of the HMG-box superfamily of DNA-binding
proteins. These proteins bind the minor groove of DNA
in a non-sequence specific fashion and contain two or
more tandem HMG boxes. Class II members include
non-histone chromosomal proteins, HMG1 and HMG2, which
bind to bent or distorted DNA such as four-way DNA
junctions, synthetic DNA cruciforms, kinked
cisplatin-modified DNA, DNA bulges, cross-overs in
supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 47.6 bits (114), Expect = 2e-07
Identities = 20/37 (54%), Positives = 29/37 (78%)
Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 90
+VTK+LG +W +LS EKK Y ++AE DK+RY +E+K
Sbjct: 30 EVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK 66
Score = 47.2 bits (113), Expect = 2e-07
Identities = 20/36 (55%), Positives = 28/36 (77%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 36
VTK+LG +W +LS EKK Y ++AE DK+RY +E+K
Sbjct: 31 VTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK 66
>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a
variety of eukaryotic chromosomal proteins and
transcription factors. HMGs bind to the minor groove of
DNA and have been classified by DNA binding
preferences. Two phylogenically distinct groups of
Class I proteins bind DNA in a sequence specific
fashion and contain a single HMG box. One group
(SOX-TCF) includes transcription factors, TCF-1, -3,
-4; and also SRY and LEF-1, which bind four-way DNA
junctions and duplex DNA targets. The second group
(MATA) includes fungal mating type gene products MC,
MATA1 and Ste11. Class II and III proteins (HMGB-UBF)
bind DNA in a non-sequence specific fashion and contain
two or more tandem HMG boxes. Class II members include
non-histone chromosomal proteins, HMG1 and HMG2, which
bind to bent or distorted DNA such as four-way DNA
junctions, synthetic DNA cruciforms, kinked
cisplatin-modified DNA, DNA bulges, cross-overs in
supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 44.5 bits (106), Expect = 2e-06
Identities = 17/37 (45%), Positives = 26/37 (70%)
Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 90
+++K+LG W LS EKK Y ++AE DK+RY +E+
Sbjct: 30 EISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEMP 66
Score = 44.1 bits (105), Expect = 3e-06
Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 36
++K+LG W LS EKK Y ++AE DK+RY +E+
Sbjct: 31 ISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEMP 66
>gnl|CDD|197700 smart00398, HMG, high mobility group.
Length = 70
Score = 41.1 bits (97), Expect = 3e-05
Identities = 17/40 (42%), Positives = 26/40 (65%)
Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 93
+++K LG W LS EK Y ++A+ DK+RY EE+ Y+
Sbjct: 31 EISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70
Score = 41.1 bits (97), Expect = 3e-05
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 39
++K LG W LS EK Y ++A+ DK+RY EE+ Y+
Sbjct: 32 ISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 38.4 bits (90), Expect = 3e-04
Identities = 16/40 (40%), Positives = 26/40 (65%)
Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 93
+++K+LG +W LS EKK Y ++AE +K RY + Y+
Sbjct: 30 EISKILGEKWKNLSEEEKKPYEEKAEKEKARYEKAYPAYK 69
Score = 37.6 bits (88), Expect = 5e-04
Identities = 16/39 (41%), Positives = 25/39 (64%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 39
++K+LG +W LS EKK Y ++AE +K RY + Y+
Sbjct: 31 ISKILGEKWKNLSEEEKKPYEEKAEKEKARYEKAYPAYK 69
>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional.
Length = 94
Score = 37.1 bits (86), Expect = 0.002
Identities = 18/41 (43%), Positives = 24/41 (58%)
Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 94
V K++G W+KLS EK Y +A+ DK RY +E Y K
Sbjct: 54 AVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYAK 94
Score = 36.0 bits (83), Expect = 0.004
Identities = 18/40 (45%), Positives = 24/40 (60%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 40
V K++G W+KLS EK Y +A+ DK RY +E Y K
Sbjct: 55 VGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYAK 94
>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 = 34.4 bits (80), Expect = 0.003
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 166 LYCRVCDQWFTTLHNKREHLNGRQH 190
YC +C+ FT+ + HL G++H
Sbjct: 1 FYCELCNVTFTSESQLKSHLRGKKH 25
>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898). This
domain is predominantly found in Maelstrom homolog
proteins. It has no known function.
Length = 69
Score = 33.2 bits (76), Expect = 0.021
Identities = 14/44 (31%), Positives = 23/44 (52%)
Query: 45 QSYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 88
+ + + +KL +W +S EK+ Y ++A DKKRY E
Sbjct: 25 EGPQVPGVAEFSKLCSEKWKAMSEEEKEKYEEKAREDKKRYDRE 68
Score = 32.0 bits (73), Expect = 0.063
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 34
+KL +W +S EK+ Y ++A DKKRY E
Sbjct: 35 FSKLCSEKWKAMSEEEKEKYEEKAREDKKRYDRE 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 = 31.4 bits (72), Expect = 0.034
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 165 ELYCRVCDQWFTTLHNKREHLNGRQH 190
+ YC CD++F + + HL ++H
Sbjct: 1 QFYCVACDKYFKSENALENHLKSKKH 26
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG
domain [Chromatin structure and dynamics].
Length = 211
Score = 34.8 bits (80), Expect = 0.045
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 50 LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY 98
L F +V KLL +W +L+ EK+ Y A D++RY+ E + Y K
Sbjct: 96 LTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPN 144
Score = 32.9 bits (75), Expect = 0.20
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY 44
V KLL +W +L+ EK+ Y A D++RY+ E + Y K
Sbjct: 101 VGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPN 144
>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 = 31.1 bits (71), Expect = 0.058
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 166 LYCRVCDQWFTTLHNKREHLNGRQHFQAVEQ 196
YC++C+ FT + HL G++H + V++
Sbjct: 4 FYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 30.2 bits (68), Expect = 1.7
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 6/53 (11%)
Query: 292 APLQNEKSARETAQAEKGIRSAQATGIEPVSKSSEDFALN--RGDRKVHPVHL 342
A LQ E +ARE+ E IR+A+ P KS E+F + R ++ HL
Sbjct: 41 ACLQREVAARESHGGEGRIRAARF----PARKSLEEFDFDHQRSLKRDTIAHL 89
>gnl|CDD|222683 pfam14327, CSTF2_hinge, Hinge domain of cleavage stimulation factor
subunit 2. The hinge domain of cleavage stimulation
factor subunit 2 proteins, CSTF2, is necessary for
binding to the subunit CstF-77 within the
polyadenylation complex and subsequent nuclear
localisation. This suggests that nuclear import of a
pre-formed CSTF complex is an essential step in
polyadenylation. Accurate and efficient polyadenylation
is essential for transcriptional termination, nuclear
export, translation, and stability of eukaryotic mRNAs.
CSTF2 is an important regulatory subunit of the
polyadenylation complex.
Length = 84
Score = 27.6 bits (62), Expect = 2.6
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 224 LPNQLPPSPPPLTMEDNIASVVRTMIDQNKEIQLLRSKMKSL 265
LP +P PLT D I+ + + + ++L+ S+MK+L
Sbjct: 3 LPAP-YGNPLPLTAPDAISQTLSKL-PPEQLLELI-SQMKTL 41
>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the
HMG-box superfamily of DNA-binding proteins. These
proteins contain a single HMG box, and bind the minor
groove of DNA in a highly sequence-specific manner.
Members include SRY and its homologs in insects and
vertebrates, and transcription factor-like proteins,
TCF-1, -3, -4, and LEF-1. They appear to bind the minor
groove of the A/T C A A A G/C-motif.
Length = 72
Score = 27.3 bits (61), Expect = 3.2
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 34
++K+LG+ W LS EK+ Y + A+ K+ + +
Sbjct: 32 ISKILGDRWKALSNEEKQPYYEEAKKLKELHMKL 65
Score = 27.3 bits (61), Expect = 3.2
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 55 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 88
++K+LG+ W LS EK+ Y + A+ K+ + +
Sbjct: 32 ISKILGDRWKALSNEEKQPYYEEAKKLKELHMKL 65
>gnl|CDD|221712 pfam12687, DUF3801, Protein of unknown function (DUF3801). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 158 and 187 amino
acids in length. This family includes the PcfB protein.
Length = 137
Score = 28.0 bits (63), Expect = 4.4
Identities = 9/39 (23%), Positives = 21/39 (53%)
Query: 74 YLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQH 112
L + + +K R++LK +++ A + R+ +VK +
Sbjct: 99 KLKKEQDEKPSVRKKLKKFKEEQAAKKKERKDKVKNKKK 137
>gnl|CDD|109884 pfam00846, Hanta_nucleocap, Hantavirus nucleocapsid protein.
Length = 428
Score = 28.4 bits (63), Expect = 6.7
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 88 ELKVYRKSDAYQSYLRRKRVKKIQ 111
E K+ +KS YQSYLRR + IQ
Sbjct: 351 EEKLKKKSAFYQSYLRRTQSMGIQ 374
>gnl|CDD|227515 COG5188, PRP9, Splicing factor 3a, subunit 3 [RNA processing and
modification].
Length = 470
Score = 28.4 bits (63), Expect = 6.7
Identities = 11/47 (23%), Positives = 20/47 (42%)
Query: 158 EEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSGHLAVNE 204
E E ++YC C + F+ HL G++H + + +E
Sbjct: 231 EGAEWFPKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQGKEEFVYSE 277
>gnl|CDD|187693 cd07180, RNase_HII_Archaea_like, Archaeal ribonuclease HII.
Ribonuclease (RNase) H is classified into two families,
type I (prokaryotic RNase HI, eukaryotic RNase H1 and
viral RNase H) and type II (prokaryotic RNase HII and
HIII, archaeal RNase HII and eukaryotic RNase H2/HII).
RNase H endonucleolytically hydrolyzes an RNA strand
when it is annealed to a complementary DNA strand in the
presence of divalent cations, in DNA replication or
repair. Some archaeal RNase HII show broad divalent
cation specificity. It is proposed that three of the
four acidic residues at the active site are involved in
metal binding and the fourth one involved in the
catalytic process in archaea. Most archaeal genomes
contain multiple RNase H genes. Despite a lack of
evidence for homology from sequence comparisons, type I
and type II RNase H share a common fold and similar
steric configurations of the four acidic active-site
residues, suggesting identical or very similar catalytic
mechanisms. It appears that type I and type II RNases H
also have overlapping functions in cells, as
over-expression of Escherichia coli RNase HII can
complement an RNase HI deletion phenotype in E. coli.
Length = 204
Score = 28.0 bits (63), Expect = 7.3
Identities = 9/33 (27%), Positives = 20/33 (60%)
Query: 10 SKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD 42
++L L + VY+D +V+++R+ E L+ +
Sbjct: 92 NRLKLKPEIVYVDACDVNEERFAERLRERLNTG 124
Score = 28.0 bits (63), Expect = 7.3
Identities = 9/33 (27%), Positives = 20/33 (60%)
Query: 64 SKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD 96
++L L + VY+D +V+++R+ E L+ +
Sbjct: 92 NRLKLKPEIVYVDACDVNEERFAERLRERLNTG 124
>gnl|CDD|239146 cd02683, MIT_1, MIT: domain contained within Microtubule
Interacting and Trafficking molecules. This sub-family
of MIT domains is found in proteins with unknown
function, co-occuring with an as yet undescribed
domain. The molecular function of the MIT domain is
unclear.
Length = 77
Score = 26.2 bits (58), Expect = 8.8
Identities = 28/75 (37%), Positives = 40/75 (53%), Gaps = 10/75 (13%)
Query: 18 KVYLDRA-EVDKK-RYREELKVYRKSDAYQSYLILLFFQVTKLLGNEWSKLSLPEK-KVY 74
K L RA E+D++ R++E L Y++ I L QV K +E K +L +K Y
Sbjct: 7 KEVLKRAVELDQEGRFQEALVCYQEG-------IDLLMQVLKGTKDEAKKKNLRQKISEY 59
Query: 75 LDRAEVDKKRYREEL 89
+DRAE KKR +E
Sbjct: 60 MDRAEAIKKRLDQEK 74
>gnl|CDD|224273 COG1354, scpA, Rec8/ScpA/Scc1-like protein (kleisin family)
[Replication, recombination, and repair].
Length = 248
Score = 27.7 bits (62), Expect = 9.6
Identities = 10/42 (23%), Positives = 20/42 (47%)
Query: 72 KVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQHH 113
K+ + ++R EE+ + AYQ LRR + +++
Sbjct: 124 KIKPEIKIKKERRPVEEISLIDLFRAYQKILRRVKQEELVEI 165
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 0.129 0.366
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: 18,964,198
Number of extensions: 1773974
Number of successful extensions: 1732
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1731
Number of HSP's successfully gapped: 41
Length of query: 382
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 283
Effective length of database: 6,546,556
Effective search space: 1852675348
Effective search space used: 1852675348
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)