RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4929
(633 letters)
>gnl|CDD|191925 pfam08005, PHR, PHR domain. This domain is called PHR as it was
original found in the proteins PAM, highwire and RPM.
This domain can be duplicated in the highwire, PFAM and
PRM sequence. The C-terminal region of the protein BTBD1
includes the PHR domain and is known to interact with
Topoisomerase I, an enzyme which relaxes DNA supercoils.
Length = 147
Score = 146 bits (371), Expect = 2e-41
Identities = 64/99 (64%), Positives = 78/99 (78%), Gaps = 1/99 (1%)
Query: 88 HRFQHIESRWGYSGTS-DRIRFSVDRRIFVVGFGLYGCIHGPTEYDVQMQLVRTANGKVI 146
+RFQ + SRWGYSGTS D IRFSVDRRIF+VGFGLYG HGP EY V+++L+ G+V+
Sbjct: 1 NRFQSVGSRWGYSGTSVDAIRFSVDRRIFIVGFGLYGGSHGPGEYQVKLELLHEHTGEVL 60
Query: 147 AGNRTSFACDGSTFTSRVMFKEPVEVMPNISYTACATLK 185
A N T+F+ DGS+ T RVMF EPVE+ PN+ YTA ATLK
Sbjct: 61 AENDTTFSSDGSSSTFRVMFDEPVEIKPNVWYTARATLK 99
Score = 37.7 bits (88), Expect = 0.005
Identities = 15/21 (71%), Positives = 17/21 (80%), Gaps = 1/21 (4%)
Query: 589 HRFQHIESRWGYSGTS-DRIR 608
+RFQ + SRWGYSGTS D IR
Sbjct: 1 NRFQSVGSRWGYSGTSVDAIR 21
>gnl|CDD|224986 COG2075, RPL24A, Ribosomal protein L24E [Translation, ribosomal
structure and biogenesis].
Length = 66
Score = 68.9 bits (169), Expect = 8e-15
Identities = 22/40 (55%), Positives = 28/40 (70%)
Query: 185 KIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRGKDLAVD 224
K+ RFC SKC KLFK +NPRK WTK YRK+ K++ +
Sbjct: 27 KVLRFCSSKCEKLFKLGRNPRKLKWTKKYRKMHKKEIKEE 66
>gnl|CDD|197943 smart00875, BACK, BTB And C-terminal Kelch. The BACK domain is
found juxtaposed to the BTB domain; they are separated
by as little as two residues.
Length = 101
Score = 65.1 bits (159), Expect = 4e-13
Identities = 27/101 (26%), Positives = 47/101 (46%), Gaps = 10/101 (9%)
Query: 416 ARLFDEPQLAALCLDTIDKNTPDALAADGFTDVDRDTLCAVLERDTLRIR-EAKLFQAVI 474
A +LA L I +N + +++ F ++ + L +L D L + E ++F+AV+
Sbjct: 8 ADAHGLEELAEKALRFILQNFSEVSSSEEFLELPLEQLLELLSSDDLNVSSEEEVFEAVL 67
Query: 475 RWSEAECTRQSLPITPENQRAVLGPSLTLVRFPLMSVEEFA 515
RW + + PE +R L L VR PL+S +
Sbjct: 68 RWVKHD---------PEKRREHLPELLEHVRLPLLSPDYLL 99
>gnl|CDD|216043 pfam00651, BTB, BTB/POZ domain. The BTB (for BR-C, ttk and bab)
or POZ (for Pox virus and Zinc finger) domain is
present near the N-terminus of a fraction of zinc
finger (pfam00096) proteins and in proteins that
contain the pfam01344 motif such as Kelch and a family
of pox virus proteins. The BTB/POZ domain mediates
homomeric dimerisation and in some instances
heteromeric dimerisation. The structure of the
dimerised PLZF BTB/POZ domain has been solved and
consists of a tightly intertwined homodimer. The
central scaffolding of the protein is made up of a
cluster of alpha-helices flanked by short beta-sheets
at both the top and bottom of the molecule. POZ domains
from several zinc finger proteins have been shown to
mediate transcriptional repression and to interact with
components of histone deacetylase co-repressor
complexes including N-CoR and SMRT. The POZ or BTB
domain is also known as BR-C/Ttk or ZiN.
Length = 101
Score = 64.9 bits (159), Expect = 6e-13
Identities = 29/73 (39%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 11 MFNNEILCDVHFIVGRETELQRIPAHRFVLSVGSVVFDAMFNGTLATRSDEIELPDVEPA 70
+ N LCDV +VG + AH+ VL+ S F A+F G EI L DV P
Sbjct: 4 LRENGELCDVTLVVGD----KEFHAHKAVLAACSPYFKALFTGNKEV---EITLEDVSPE 56
Query: 71 AFLALLRCSMTGK 83
F ALL TGK
Sbjct: 57 DFEALLEFIYTGK 69
>gnl|CDD|110260 pfam01246, Ribosomal_L24e, Ribosomal protein L24e.
Length = 71
Score = 62.5 bits (152), Expect = 2e-12
Identities = 24/38 (63%), Positives = 26/38 (68%)
Query: 185 KIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRGKDLA 222
K+FRFC SKC K F K+NPRK AWTK YRK K A
Sbjct: 27 KVFRFCSSKCEKNFHMKRNPRKLAWTKLYRKQHKKGEA 64
>gnl|CDD|100103 cd00472, Ribosomal_L24e_L24, Ribosomal protein L24e/L24 is a
ribosomal protein found in eukaryotes (L24) and in
archaea (L24e, distinct from archaeal L24). L24e/L24 is
located on the surface of the large subunit, adjacent to
proteins L14 and L3, and near the translation factor
binding site. L24e/L24 appears to play a role in the
kinetics of peptide synthesis, and may be involved in
interactions between the large and small subunits,
either directly or through other factors. In mouse, a
deletion mutation in L24 has been identified as the
cause for the belly spot and tail (Bst) mutation that
results in disrupted pigmentation, somitogenesis and
retinal cell fate determination. L24 may be an
important protein in eukaryotic reproduction: in
shrimp, L24 expression is elevated in the ovary,
suggesting a role in oogenesis, and in Arabidopsis, L24
has been proposed to have a specific function in
gynoecium development. No protein with sequence or
structural homology to L24e/L24 has been identified in
bacteria, but a functionally equivalent protein may
exist. Bacterial L19 forms an interprotein beta sheet
with L14 that is similar to the L24e/L14 interprotein
beta sheet observed in the archaeal L24e structures.
Some eukaryotic L24 proteins were initially identified
as L30, and this alignment model contains several
sequences called L30.
Length = 54
Score = 61.8 bits (151), Expect = 2e-12
Identities = 19/28 (67%), Positives = 21/28 (75%)
Query: 185 KIFRFCRSKCHKLFKRKKNPRKTAWTKA 212
K+FRFC SKC K F RK+NPRK WT A
Sbjct: 27 KVFRFCSSKCEKNFLRKRNPRKLKWTVA 54
>gnl|CDD|149006 pfam07707, BACK, BTB And C-terminal Kelch. This domain is found
associated with pfam00651 and pfam01344. The BACK domain
is found juxtaposed to the BTB domain; they are
separated by as little as two residues. This family
appears to be closely related to the BTB domain (Finn
RD, personal observation).
Length = 101
Score = 51.4 bits (124), Expect = 3e-08
Identities = 28/102 (27%), Positives = 49/102 (48%), Gaps = 14/102 (13%)
Query: 416 ARLFDEPQLAALCLDTIDKNTPDALAADGFTDVDRDTLCAVLERDTLRIR-EAKLFQAVI 474
A + +LA + L I KN + ++ F ++ ++ L +L D L + E ++F+AVI
Sbjct: 8 ADTYGCEELAEVALRFILKNFLEVSKSEEFLELSKEQLLELLSSDELNVPSEEEVFEAVI 67
Query: 475 RW--SEAECTRQSLPITPENQRAVLGPSLTLVRFPLMSVEEF 514
+W + E ++ LP L+ VR PL+S E
Sbjct: 68 KWVKHDVENRKKHLPEL-----------LSAVRLPLLSPEYL 98
>gnl|CDD|197585 smart00225, BTB, Broad-Complex, Tramtrack and Bric a brac.
Domain in Broad-Complex, Tramtrack and Bric a brac.
Also known as POZ (poxvirus and zinc finger) domain.
Known to be a protein-protein interaction motif found
at the N-termini of several C2H2-type transcription
factors as well as Shaw-type potassium channels. Known
structure reveals a tightly intertwined dimer formed
via interactions between N-terminal strand and helix
structures. However in a subset of BTB/POZ domains,
these two secondary structures appear to be missing. Be
aware SMART predicts BTB/POZ domains without the beta1-
and alpha1-secondary structures.
Length = 97
Score = 47.3 bits (113), Expect = 8e-07
Identities = 25/66 (37%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 19 DVHFIVGRETELQRIPAHRFVLSVGSVVFDAMFNGTLA-TRSDEIELPDVEPAAFLALLR 77
DV +VG ++ AH+ VL+ S F A+F+ + EI L DV P F ALL
Sbjct: 1 DVTLVVGG----KKFHAHKAVLAAHSPYFKALFSSDFKESDKSEIYLDDVSPEDFRALLN 56
Query: 78 CSMTGK 83
TGK
Sbjct: 57 FLYTGK 62
>gnl|CDD|179131 PRK00807, PRK00807, 50S ribosomal protein L24e; Validated.
Length = 52
Score = 45.4 bits (108), Expect = 1e-06
Identities = 15/27 (55%), Positives = 17/27 (62%)
Query: 186 IFRFCRSKCHKLFKRKKNPRKTAWTKA 212
I FC SKC K +K + PRK WTKA
Sbjct: 26 ILYFCSSKCEKNYKLGRVPRKLKWTKA 52
>gnl|CDD|140068 PTZ00033, PTZ00033, 60S ribosomal protein L24; Provisional.
Length = 125
Score = 42.7 bits (100), Expect = 7e-05
Identities = 17/44 (38%), Positives = 25/44 (56%)
Query: 176 ISYTACATLKIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRGK 219
+ + +T + F R KC L+ RKKNPR WT+ YR++ K
Sbjct: 22 VPFAFLSTKPVLTFLRPKCFALYMRKKNPRFLPWTRTYRRINRK 65
>gnl|CDD|214799 smart00746, TRASH, metallochaperone-like domain.
Length = 39
Score = 31.6 bits (72), Expect = 0.068
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 185 KIFRFCRSKCHKLFKRKK 202
K++ FC SKC FK+K+
Sbjct: 22 KVYYFCSSKCLSKFKKKR 39
>gnl|CDD|165086 PHA02713, PHA02713, hypothetical protein; Provisional.
Length = 557
Score = 35.8 bits (82), Expect = 0.074
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 11 MFNNEILCDVHFIVGRETELQRIPAHRFVLSVGSVVFDAMFNGTLATR 58
+ +++ILCDV +G E I AH+ +L+ GS F +F + R
Sbjct: 19 LLDDDILCDVIITIGDGEE---IKAHKTILAAGSKYFRTLFTTPMIIR 63
>gnl|CDD|227533 COG5208, HAP5, CCAAT-binding factor, subunit C [Transcription].
Length = 286
Score = 30.4 bits (68), Expect = 3.1
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 242 EFWNKTVEAIKKVEHIKTKRHNLYLAQRLRKAREVETARDIKAVQRDIAIL 292
+W +T++A ++ I K HNL LA R++K ++T D+K + + +L
Sbjct: 88 RYWQQTIKAAEEERQILLKDHNLPLA-RIKKV--MKTDEDVKMISAEAPVL 135
>gnl|CDD|129361 TIGR00259, thylakoid_BtpA, membrane complex biogenesis protein,
BtpA family. Members of this family are found in C.
elegans, Synechocystis sp., E. coli, and several of the
Archaea. Members in Cyanobacteria have been shown to
play a role in protein complex biogenesis, and
designated BtpA (biogenesis of thylakoid protein).
Homologs in non-photosynthetic species, where thylakoid
intracytoplasmic membranes are lacking, are likely to
act elsewhere in membrane protein biogenesis [Protein
fate, Protein folding and stabilization].
Length = 257
Score = 30.2 bits (68), Expect = 3.3
Identities = 27/126 (21%), Positives = 45/126 (35%), Gaps = 28/126 (22%)
Query: 268 QRLRKAREVETARDIKAVQRDIAI-------LNDP-----------TEVIRAKKKKMVEA 309
+ + A ++ D++I ND + IR V A
Sbjct: 57 KEVDPETVAAMAVIAGQLKSDVSIPLGINVLRNDAVAALAIAMAVGAKFIRVNVLTGVYA 116
Query: 310 ---GIVE-EIHEMQIRESNLLHGK-----QILLTTARLFDEPQLAALCLDTIDKNTPDAL 360
GI+E E+ IR LL + I++ A L ++ LDT+++ DA+
Sbjct: 117 SDQGIIEGNAGEL-IRYKKLLGSEVKILADIVVKHAVHLGNRDLESIALDTVERGLADAV 175
Query: 361 AADGFT 366
G T
Sbjct: 176 ILSGKT 181
>gnl|CDD|236278 PRK08506, PRK08506, replicative DNA helicase; Provisional.
Length = 472
Score = 30.4 bits (69), Expect = 3.6
Identities = 28/122 (22%), Positives = 49/122 (40%), Gaps = 13/122 (10%)
Query: 219 KDLAVDPSFEFAKRRNVPLKYDRE-----FWNKTVEAIKK-VEHIK---TKRHNLYLAQR 269
+D +D F K+ K D E ++ I+ VE IK KR L LA
Sbjct: 54 EDEPIDEEF-IRKKLPKDKKIDEEILLEILATNPIDNIEAYVEEIKEKSIKRELLSLANT 112
Query: 270 LRKAR--EVETARDI-KAVQRDIAILNDPTEVIRAKKKKMVEAGIVEEIHEMQIRESNLL 326
+ + E + + DI V+R++ + + + K K V +E I + + + +
Sbjct: 113 IPEQAVEEDQKSSDILDEVERELYSITNGSNSEDFKDSKEVIESTMEHIKKQKRLGNKDI 172
Query: 327 HG 328
G
Sbjct: 173 IG 174
>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain
fusion protein; Provisional.
Length = 131
Score = 28.8 bits (64), Expect = 4.6
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 189 FCRSKCHKLFKRKKNPRKTAWTKAYRKVRG 218
F SKC K + + R WT+A R +G
Sbjct: 32 FVDSKCEKNYDLGREARDLEWTEAGRAEKG 61
>gnl|CDD|153332 cd07648, F-BAR_FCHO, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of FCH domain Only proteins.
F-BAR domains are dimerization modules that bind and
bend membranes and are found in proteins involved in
membrane dynamics and actin reorganization. Proteins in
this group have been named FCH domain Only (FCHO)
proteins. Vertebrates have two members, FCHO1 and FCHO2.
These proteins contain an F-BAR domain and a C-terminal
domain of unknown function named SAFF which is also
present in endophilin interacting protein 1. 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 = 261
Score = 29.2 bits (66), Expect = 5.6
Identities = 26/105 (24%), Positives = 42/105 (40%), Gaps = 15/105 (14%)
Query: 248 VEAIKKVEHIKTKRHNLYLAQ---RLRKAREVETARDI-------KAVQRDIAILNDPTE 297
V+AI+ K Y A+ R RE + ++I K Q + L +
Sbjct: 115 VQAIQTTTAALQKAKEAYHARCLELERLRRENASPKEIEKAEAKLKKAQDEYKALVEKYN 174
Query: 298 VIRAK-KKKMVEAGIVEEIHEMQIRESNLLHGKQILLTTARLFDE 341
IRA + KM ++ + E ES+L K+ L + A + E
Sbjct: 175 NIRADFETKMTDSCKRFQEIE----ESHLRQMKEFLASYAEVLSE 215
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.7 bits (66), Expect = 5.7
Identities = 24/105 (22%), Positives = 39/105 (37%), Gaps = 9/105 (8%)
Query: 231 KRRNVPLKYDREFWNKTVEAIKKVEHIKTKRHNLYLAQRLRKAREVETARDIKAVQ---- 286
++ K E K + KK K K A+ +KA E + A + K
Sbjct: 1482 AKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKK 1541
Query: 287 ----RDIAILNDPTEVIRAKKKKMVE-AGIVEEIHEMQIRESNLL 326
+ L E+ +A++KK E A EE M +R++
Sbjct: 1542 AEEKKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEA 1586
>gnl|CDD|216525 pfam01486, K-box, K-box region. The K-box region is commonly found
associated with SRF-type transcription factors see
pfam00319. The K-box is a possible coiled-coil
structure. Possible role in multimer formation.
Length = 100
Score = 27.5 bits (62), Expect = 6.3
Identities = 8/27 (29%), Positives = 17/27 (62%), Gaps = 4/27 (14%)
Query: 299 IRAKKKKMVEAGIVEEIHEMQIRESNL 325
IR++K ++ ++ +I E+Q +E L
Sbjct: 65 IRSRKNEL----LLNQIEELQKKEREL 87
>gnl|CDD|151968 pfam11531, CARM1, Coactivator-associated arginine
methyltransferase 1 N terminal. CARM1 is an arginine
methyltransferase which methylates a variety of
different proteins and plays a role in gene expression.
This is the N terminal domain of the protein which has
a PH domain, normally present to regulate
protein-protein interactions.A molecular switch is also
present on the N terminal domain.
Length = 112
Score = 28.0 bits (62), Expect = 6.9
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 11 MFNNEILCDVHFIVGRETELQRIPAHRFVLSVG 43
++N+E +C V RETE R+ F++++G
Sbjct: 44 LYNHEDVCVFKCTVSRETECSRVGKQSFIITLG 76
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 0.137 0.408
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 33,036,573
Number of extensions: 3312774
Number of successful extensions: 2713
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2702
Number of HSP's successfully gapped: 30
Length of query: 633
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 530
Effective length of database: 6,369,140
Effective search space: 3375644200
Effective search space used: 3375644200
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: 41 (22.0 bits)
S2: 62 (27.7 bits)