RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12530
(189 letters)
>gnl|CDD|198121 smart01053, CaMBD, Calmodulin binding domain. Small-conductance
Ca2+-activated K+ channels (SK channels) are independent
of voltage and gated solely by intracellular Ca2+. These
membrane channels are heteromeric complexes that
comprise pore-forming alpha-subunits and the
Ca2+-binding protein calmodulin (CaM). CaM binds to the
SK channel through this the CaM-binding domain (CaMBD),
which is located in an intracellular region of the
alpha-subunit immediately carboxy-terminal to the pore.
Channel opening is triggered when Ca2+ binds the EF
hands in the N-lobe of CaM. The structure of this domain
complexed with CaM is known. This domain forms an
elongated dimer with a CaM molecule bound at each end;
each CaM wraps around three alpha-helices, two from one
CaMBD subunit and one from the other.
Length = 76
Score = 69.0 bits (169), Expect = 4e-16
Identities = 33/43 (76%), Positives = 39/43 (90%)
Query: 147 RLKNAAANVLRETWLIYKHTRLVKRVNAGRVRTHQRKFLLAIY 189
R+KNAAANVLRETWLIYKHT+LVK+ + GR+R HQRKFL AI+
Sbjct: 7 RVKNAAANVLRETWLIYKHTKLVKKGDQGRLRKHQRKFLQAIH 49
>gnl|CDD|111742 pfam02888, CaMBD, Calmodulin binding domain. Small-conductance
Ca2+-activated K+ channels (SK channels) are independent
of voltage and gated solely by intracellular Ca2+. These
membrane channels are heteromeric complexes that
comprise pore-forming alpha-subunits and the
Ca2+-binding protein calmodulin (CaM). CaM binds to the
SK channel through this the CaM-binding domain (CaMBD),
which is located in an intracellular region of the
alpha-subunit immediately carboxy-terminal to the pore.
Channel opening is triggered when Ca2+ binds the EF
hands in the N-lobe of CaM. The structure of this domain
complexed with CaM is known. This domain forms an
elongated dimer with a CaM molecule bound at each end;
each CaM wraps around three alpha-helices, two from one
CaMBD subunit and one from the other.
Length = 76
Score = 64.8 bits (158), Expect = 2e-14
Identities = 29/43 (67%), Positives = 35/43 (81%)
Query: 147 RLKNAAANVLRETWLIYKHTRLVKRVNAGRVRTHQRKFLLAIY 189
KNAAANVL+ETWLIYKHT+LV + + R+R HQRKFL AI+
Sbjct: 7 EHKNAAANVLQETWLIYKHTKLVSKGDQQRLRKHQRKFLQAIH 49
>gnl|CDD|221586 pfam12457, TIP_N, Tuftelin interacting protein N terminal. This
domain family is found in eukaryotes, and is typically
between 99 and 114 amino acids in length. The family is
found in association with pfam08697, pfam01585. There
are two completely conserved residues (G and F) that
may be functionally important. TIP is involved in
enamel assembly by interacting with one of the major
proteins responsible for biomineralisation of enamel -
tuftelin.
Length = 106
Score = 34.3 bits (79), Expect = 0.007
Identities = 12/47 (25%), Positives = 24/47 (51%), Gaps = 11/47 (23%)
Query: 42 NKRRRKE----------GEEDKEEGGGGGGKRKKKKKKKKEKSWIRP 78
N+RRR++ ++D ++ G R +++ KKK K + +P
Sbjct: 23 NRRRRRQTKEQAIYGIFADDDDDDEGERRRGRGRRRSKKK-KDYSKP 68
>gnl|CDD|178307 PLN02705, PLN02705, beta-amylase.
Length = 681
Score = 31.8 bits (72), Expect = 0.22
Identities = 12/22 (54%), Positives = 20/22 (90%)
Query: 56 GGGGGGKRKKKKKKKKEKSWIR 77
GGGGGGK K++++K+KE++ +R
Sbjct: 70 GGGGGGKGKREREKEKERTKLR 91
>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein
complex aNOP56 subunit; Provisional.
Length = 414
Score = 31.5 bits (72), Expect = 0.25
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 43 KRRRKEGEEDKEEGGGGGGKRKKKKKKKKEK 73
K++R+E + K + K+ KK+KKK K
Sbjct: 384 KKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414
Score = 27.6 bits (62), Expect = 4.4
Identities = 8/28 (28%), Positives = 16/28 (57%)
Query: 40 KENKRRRKEGEEDKEEGGGGGGKRKKKK 67
+E K+ +K ++ K + G K+K +K
Sbjct: 387 REEKKPQKRKKKKKRKKKGKKRKKKGRK 414
Score = 27.6 bits (62), Expect = 4.5
Identities = 9/31 (29%), Positives = 18/31 (58%)
Query: 40 KENKRRRKEGEEDKEEGGGGGGKRKKKKKKK 70
K+ + +K + K++ GK++KKK +K
Sbjct: 384 KKKREEKKPQKRKKKKKRKKKGKKRKKKGRK 414
>gnl|CDD|218747 pfam05786, Cnd2, Condensin complex subunit 2. This family consists
of several Barren protein homologues from several
eukaryotic organisms. In Drosophila Barren (barr) is
required for sister-chromatid segregation in mitosis.
barr encodes a novel protein that is present in
proliferating cells and has homologues in yeast and
human. Mitotic defects in barr embryos become apparent
during cycle 16, resulting in a loss of PNS and CNS
neurons. Centromeres move apart at the
metaphase-anaphase transition and Cyclin B is degraded,
but sister chromatids remain connected, resulting in
chromatin bridging. Barren protein localises to
chromatin throughout mitosis. Colocalisation and
biochemical experiments indicate that Barren associates
with Topoisomerase II throughout mitosis and alters the
activity of Topoisomerase II. It has been suggested that
this association is required for proper chromosomal
segregation by facilitating the decatenation of
chromatids at anaphase. This family forms one of the
three non-structural maintenance of chromosomes (SMC)
subunits of the mitotic condensation complex along with
Cnd1 and Cnd3.
Length = 719
Score = 30.5 bits (69), Expect = 0.49
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 48 EGEEDKEEGGGGGGKRKKKKKKKK 71
+GE+D EEG G KKK KKK
Sbjct: 166 DGEDDDEEGSDGEEDGAKKKAKKK 189
>gnl|CDD|149438 pfam08374, Protocadherin, Protocadherin. The structure of
protocadherins is similar to that of classic cadherins
(pfam00028), but particularly on the cytoplasmic domains
they also have some unique features. They are expressed
in a variety of organisms and are found in high
concentrations in the brain where they seem to be
localised mainly at cell-cell contact sites. Their
expression seems to be developmentally regulated.
Length = 223
Score = 29.0 bits (65), Expect = 1.1
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 6/53 (11%)
Query: 24 ISTALILKQCHLVLIQKENKRRRKEGEEDKEE--GGGGGGKRKKKKKKKKEKS 74
I ++++ C Q E K+ + G+++ E+ K+KKKKK KK+KS
Sbjct: 54 ILVVVLVRYC----RQAERKKGYQAGKKETEDWFSPNQENKQKKKKKDKKKKS 102
>gnl|CDD|150884 pfam10278, Med19, Mediator of RNA pol II transcription subunit 19.
Med19 represents a family of conserved proteins which
are members of the multi-protein co-activator Mediator
complex. Mediator is required for activation of RNA
polymerase II transcription by DNA binding
transactivators.
Length = 178
Score = 29.0 bits (65), Expect = 1.1
Identities = 16/33 (48%), Positives = 23/33 (69%), Gaps = 6/33 (18%)
Query: 41 ENKRRRKEGEEDKEEGGGGGGKRKKKKKKKKEK 73
E K ++K+ E+DKE K+KKK+KKKK+K
Sbjct: 141 EKKHKKKKHEDDKER------KKKKKEKKKKKK 167
Score = 26.3 bits (58), Expect = 9.6
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 10/62 (16%)
Query: 22 FHISTALILKQCHLVLIQ--------KENKRRRKE--GEEDKEEGGGGGGKRKKKKKKKK 71
F + + +Q L+ IQ K K R ++ EE + G G KK KKKK
Sbjct: 90 FRLHPGPLPEQYRLMHIQPPKKKHKHKHKKHRTQDPLPEETPSDSEGLKGHEKKHKKKKH 149
Query: 72 EK 73
E
Sbjct: 150 ED 151
>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit
RPA34.5. This is a family of proteins conserved from
yeasts to human. Subunit A34.5 of RNA polymerase I is a
non-essential subunit which is thought to help Pol I
overcome topological constraints imposed on ribosomal
DNA during the process of transcription.
Length = 193
Score = 28.9 bits (65), Expect = 1.3
Identities = 16/33 (48%), Positives = 23/33 (69%)
Query: 39 QKENKRRRKEGEEDKEEGGGGGGKRKKKKKKKK 71
+KE K+ +KE ++ KE+ G +KKKKKKKK
Sbjct: 160 KKEVKKEKKEKKDKKEKMVEPKGSKKKKKKKKK 192
Score = 27.0 bits (60), Expect = 4.7
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 40 KENKRRRKEGEEDKEEGGGGGGKRKKKKKKKKEKS 74
+E K ++K+ E KE K++KK KK+K
Sbjct: 152 EEKKEKKKKKEVKKE-------KKEKKDKKEKMVE 179
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 29.2 bits (65), Expect = 1.4
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 47 KEGEEDKEEGGGGGGKRKKKKKKKKEK 73
+E EE+K E GG K+ KK KK K K
Sbjct: 321 EESEEEKNEEEGGLSKKGKKLKKLKGK 347
Score = 28.0 bits (62), Expect = 3.2
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 40 KENKRRRKEGEEDKEEGGGGGGKRKKKKKKKKEKS 74
E ++ E ++E+ GG KK KK KK K
Sbjct: 312 PEIEQDEDSEESEEEKNEEEGGLSKKGKKLKKLKG 346
Score = 27.6 bits (61), Expect = 4.0
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 37 LIQKENKRRRKEGEEDKEEGGGGGGKRKKKKKKKKEKS 74
I+++ E EE EE GG K KK KK K +K+
Sbjct: 313 EIEQDEDSEESE-EEKNEEEGGLSKKGKKLKKLKGKKN 349
>gnl|CDD|217553 pfam03430, TATR, Trans-activating transcriptional regulator. This
family of trans-activating transcriptional regulator
(TATR), also known as intermediate early protein 1, are
common to the Nucleopolyhedroviruses.
Length = 571
Score = 29.1 bits (65), Expect = 1.5
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 43 KRRRKEGEEDKEEGGGGGGKRKKKKKKKKEK 73
KR+ E + D + GK+ K KK++K
Sbjct: 126 KRKGSELDSDSDSSDSSKGKKLVNKPKKRQK 156
>gnl|CDD|219547 pfam07741, BRF1, Brf1-like TBP-binding domain. This region
covers both the Brf homology II and III regions. This
region is involved in binding TATA binding protein.
Length = 95
Score = 27.6 bits (62), Expect = 1.6
Identities = 9/35 (25%), Positives = 18/35 (51%)
Query: 40 KENKRRRKEGEEDKEEGGGGGGKRKKKKKKKKEKS 74
+E + + + + D+ G K++K KKK+ E
Sbjct: 30 EEQEEKELKQKADEGNNSGKKKKKRKAKKKRDEAG 64
>gnl|CDD|240411 PTZ00419, PTZ00419, valyl-tRNA synthetase-like protein;
Provisional.
Length = 995
Score = 28.0 bits (63), Expect = 3.7
Identities = 16/32 (50%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 109 FMMDTQLTKRLKNAAANVLRETWLIYKHTRLV 140
F MD Q +K +K A L E LIY+ TRLV
Sbjct: 170 FTMDEQRSKAVKEAFVR-LYEDGLIYRDTRLV 200
>gnl|CDD|153340 cd07656, F-BAR_srGAP, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase
Activating Proteins. F-BAR domains are dimerization
modules that bind and bend membranes and are found in
proteins involved in membrane dynamics and actin
reorganization. Slit-Robo GTPase Activating Proteins
(srGAPs) are Rho GAPs that interact with Robo1, the
transmembrane receptor of Slit proteins. Slit proteins
are secreted proteins that control axon guidance and the
migration of neurons and leukocytes. Vertebrates contain
three isoforms of srGAPs, all of which are expressed
during embryonic and early development in the nervous
system but with different localization and timing.
srGAPs contain an N-terminal F-BAR domain, a Rho GAP
domain, and a C-terminal SH3 domain. F-BAR domains form
banana-shaped dimers with a positively-charged concave
surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 241
Score = 27.7 bits (62), Expect = 4.0
Identities = 11/42 (26%), Positives = 17/42 (40%)
Query: 32 QCHLVLIQKENKRRRKEGEEDKEEGGGGGGKRKKKKKKKKEK 73
H E K + E +E+K+E + + KK EK
Sbjct: 142 TYHAESKSAERKLKEAEKQEEKQEQSPEKKLERSRSSKKIEK 183
>gnl|CDD|240341 PTZ00272, PTZ00272, heat shock protein 83 kDa (Hsp83); Provisional.
Length = 701
Score = 27.7 bits (61), Expect = 4.3
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 39 QKENKRRRKEGEEDKEEGGGGGGKRKKKKKKK 70
+++ K+ ++GEE K E G + KKKK KK
Sbjct: 220 EEDTKKADEDGEEPKVEEVKEGDEGKKKKTKK 251
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 27.7 bits (62), Expect = 4.7
Identities = 11/41 (26%), Positives = 22/41 (53%)
Query: 38 IQKENKRRRKEGEEDKEEGGGGGGKRKKKKKKKKEKSWIRP 78
+Q+E + + E+ + ++KKK+ +K EK+ I P
Sbjct: 553 LQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLEKAKIPP 593
>gnl|CDD|233294 TIGR01159, DRP1, density-regulated protein DRP1. This protein
family shows weak but suggestive similarity to
translation initiation factor SUI1 and its prokaryotic
homologs.
Length = 173
Score = 27.2 bits (60), Expect = 4.7
Identities = 8/34 (23%), Positives = 14/34 (41%)
Query: 40 KENKRRRKEGEEDKEEGGGGGGKRKKKKKKKKEK 73
E + + E + + + KKKKK +K
Sbjct: 57 GEAQEEKGEKDLLGIQKAQEAREGGKKKKKLPQK 90
Score = 26.8 bits (59), Expect = 5.7
Identities = 9/39 (23%), Positives = 15/39 (38%)
Query: 36 VLIQKENKRRRKEGEEDKEEGGGGGGKRKKKKKKKKEKS 74
+ + ++GE+D R+ KKKKK
Sbjct: 51 AEAVTIGEAQEEKGEKDLLGIQKAQEAREGGKKKKKLPQ 89
>gnl|CDD|215822 pfam00257, Dehydrin, Dehydrin.
Length = 137
Score = 26.7 bits (59), Expect = 5.1
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 54 EEGGGGGGKRKKKKKKKKEKSW 75
G G ++K K K KEK
Sbjct: 111 GYGQHGHEEKKGKMDKIKEKLP 132
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 27.0 bits (60), Expect = 6.2
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 40 KENKRRRKEGEEDKEEGGGGGGKRKKKKKKKKEKSW 75
+E K KE E D+EE ++KKK KK KE +
Sbjct: 50 EEEKTTDKEEEVDEEEEKE---EKKKKTKKVKETTT 82
>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional.
Length = 413
Score = 27.0 bits (60), Expect = 6.7
Identities = 12/40 (30%), Positives = 24/40 (60%)
Query: 39 QKENKRRRKEGEEDKEEGGGGGGKRKKKKKKKKEKSWIRP 78
+K++++++K+ +E KE G K K KK +K+ +P
Sbjct: 67 KKKSEKKKKKKKEKKEPKSEGETKLGFKTPKKSKKTKKKP 106
>gnl|CDD|219555 pfam07753, DUF1609, Protein of unknown function (DUF1609). This
region is found in a number of hypothetical proteins
thought to be expressed by the eukaryote
Encephalitozoon cuniculi, an obligate intracellular
microsporidial parasite. It is approximately 200
residues long.
Length = 230
Score = 26.7 bits (59), Expect = 6.8
Identities = 16/33 (48%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 48 EGEEDKEEGGGGGGKRKKKKKKKKEKSWIRPCY 80
E E EE GG + KKK KKK K R CY
Sbjct: 7 EAEVPLEEMAVGGARAKKKGGKKKSKGG-RHCY 38
>gnl|CDD|219901 pfam08555, DUF1754, Eukaryotic family of unknown function
(DUF1754). This is a eukaryotic protein family of
unknown function.
Length = 90
Score = 25.5 bits (56), Expect = 7.7
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 58 GGGGKRKKKKKKKKEKSW 75
G KKKKKKKK+K+
Sbjct: 14 GKKIDVKKKKKKKKKKNK 31
Score = 25.5 bits (56), Expect = 9.9
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 56 GGGGGGKRKKKKKKKKEKS 74
G K+KKKKKKKK KS
Sbjct: 14 GKKIDVKKKKKKKKKKNKS 32
>gnl|CDD|220129 pfam09159, Ydc2-catalyt, Mitochondrial resolvase Ydc2 / RNA
splicing MRS1. Members of this family adopt a secondary
structure consisting of two beta sheets and one alpha
helix, arranged as a beta-alpha-beta motif. Each beta
sheet has five strands, arranged in a 32145 order, with
the second strand being antiparallel to the rest.
Mitochondrial resolvase Ydc2 is capable of resolving
Holliday junctions and cleaves DNA after 5'-CT-3' and
5'-TT-3' sequences. This family also contains the
mitochondrial RNA-splicing protein MRS1 which is
involved in the excision of group I introns.
Length = 254
Score = 26.6 bits (59), Expect = 7.8
Identities = 8/29 (27%), Positives = 11/29 (37%)
Query: 48 EGEEDKEEGGGGGGKRKKKKKKKKEKSWI 76
E E E K+K K KK + +
Sbjct: 147 ERTEILAEKKKPRSKKKSSKNSKKLRIDL 175
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 26.8 bits (60), Expect = 8.0
Identities = 11/39 (28%), Positives = 23/39 (58%)
Query: 36 VLIQKENKRRRKEGEEDKEEGGGGGGKRKKKKKKKKEKS 74
I+K ++ K+ EE+K+E KKK+++++E+
Sbjct: 410 KKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEK 448
Score = 26.4 bits (59), Expect = 9.7
Identities = 9/36 (25%), Positives = 28/36 (77%)
Query: 38 IQKENKRRRKEGEEDKEEGGGGGGKRKKKKKKKKEK 73
I ++ +++R+E +++K++ G K++++++++KEK
Sbjct: 415 IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEK 450
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This
protein, which interacts with both microtubules and
TRAF3 (tumour necrosis factor receptor-associated factor
3), is conserved from worms to humans. The N-terminal
region is the microtubule binding domain and is
well-conserved; the C-terminal 100 residues, also
well-conserved, constitute the coiled-coil region which
binds to TRAF3. The central region of the protein is
rich in lysine and glutamic acid and carries KKE motifs
which may also be necessary for tubulin-binding, but
this region is the least well-conserved.
Length = 506
Score = 26.8 bits (59), Expect = 9.8
Identities = 10/35 (28%), Positives = 22/35 (62%)
Query: 39 QKENKRRRKEGEEDKEEGGGGGGKRKKKKKKKKEK 73
+ + KR KE E++KE+ R+++KK+++ +
Sbjct: 136 EAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVR 170
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
0.322 0.133 0.392
Gapped
Lambda K H
0.267 0.0679 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,490,051
Number of extensions: 873163
Number of successful extensions: 1851
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1666
Number of HSP's successfully gapped: 105
Length of query: 189
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 98
Effective length of database: 6,901,388
Effective search space: 676336024
Effective search space used: 676336024
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 (22.0 bits)
S2: 56 (25.5 bits)