RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1090
(169 letters)
>gnl|CDD|215770 pfam00176, SNF2_N, SNF2 family N-terminal domain. This domain is
found in proteins involved in a variety of processes
including transcription regulation (e.g., SNF2, STH1,
brahma, MOT1), DNA repair (e.g. ERCC6, RAD16, RAD5), DNA
recombination (e.g. RAD54), and chromatin unwinding
(e.g. ISWI) as well as a variety of other proteins with
little functional information (e.g. lodestar, ETL1).
Length = 301
Score = 91.3 bits (227), Expect = 1e-22
Identities = 49/150 (32%), Positives = 73/150 (48%), Gaps = 25/150 (16%)
Query: 15 GK---VIAFFCKIIEEQALE--PNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERK 69
GK IA ++E P L+VCPLS L+NW EF K+AP +R V Y+G+ ER
Sbjct: 28 GKTLQTIALLATYLKEGKDRRGPTLVVCPLSTLHNWLNEFEKWAPALRVVVYHGDGRERS 87
Query: 70 ALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF---GFLKKITWNCIIV 126
L+ K +++TT +++ D L K+ W+ +++
Sbjct: 88 KLRQS-----MAKRLDTYD------------VVITTYEVLRKDKKLLSLLNKVEWDRVVL 130
Query: 127 DEGHSVKNKKSKLSIKLTALRATFKVLLTG 156
DE H +KN KSKL L L+ ++LLTG
Sbjct: 131 DEAHRLKNSKSKLYKALKKLKTRNRLLLTG 160
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 82.2 bits (203), Expect = 9e-19
Identities = 40/125 (32%), Positives = 63/125 (50%), Gaps = 18/125 (14%)
Query: 32 PNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTIKVPAKKGKTK 91
P+++V P S L NW E R+F P +R VK++GN ER + E L V K
Sbjct: 221 PHMVVAPKSTLGNWMNEIRRFCPVLRAVKFHGNPEERAHQREELL------VAGKFD--- 271
Query: 92 KQISLKLPLILVTTPQIIENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTALRATFK 151
+ VT+ ++ + LK+ +W II+DE H +KN+ S LS + ++
Sbjct: 272 ---------VCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNENSLLSKTMRLFSTNYR 322
Query: 152 VLLTG 156
+L+TG
Sbjct: 323 LLITG 327
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 78.2 bits (192), Expect = 2e-17
Identities = 47/145 (32%), Positives = 71/145 (48%), Gaps = 16/145 (11%)
Query: 17 VIAFFCKIIE--EQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTV-KYYGNAIERKALQS 73
IA ++E + L P LIV P S+L+NW+ EF KFAP +R V Y+G
Sbjct: 375 TIALLLSLLESIKVYLGPALIVVPASLLSNWKREFEKFAPDLRLVLVYHGEK-------- 426
Query: 74 EALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIEN--DFGFLKKITWNCIIVDEGHS 131
S K A + K + + +++ T + D G LKKI W+ +++DE H
Sbjct: 427 ---SELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHR 483
Query: 132 VKNKKSKLSIKLTALRATFKVLLTG 156
+KN +S L L+A ++ LTG
Sbjct: 484 IKNDQSSEGKALQFLKALNRLDLTG 508
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 57.1 bits (138), Expect = 1e-10
Identities = 37/164 (22%), Positives = 62/164 (37%), Gaps = 33/164 (20%)
Query: 1 MDTVIPDPTRYRKSGK---VIAFFCKIIEEQALEPNLIVCPLSVL-NNWEAEFRKFAPF- 55
D ++ PT SGK + + ++ L++ P L W E +K P
Sbjct: 25 RDVILAAPT---GSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSL 81
Query: 56 -VRTVKYYGNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF- 113
++ V YG +R+ L+ + GKT ILVTTP + +
Sbjct: 82 GLKVVGLYGGDSKREQLRKL-----------ESGKTD---------ILVTTPGRLLDLLE 121
Query: 114 -GFLKKITWNCIIVDEGHSVKNK--KSKLSIKLTALRATFKVLL 154
L + +I+DE H + + +L L L ++LL
Sbjct: 122 NDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLL 165
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 49.3 bits (118), Expect = 5e-08
Identities = 30/141 (21%), Positives = 47/141 (33%), Gaps = 26/141 (18%)
Query: 14 SGKVIAFFCKIIEEQALEPN---LIVCPLSVLNNWEAE-FRKFAPFVRTVKYYGNAIERK 69
SGK +A I+E L++ P L N AE ++ V Y
Sbjct: 11 SGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGT--- 67
Query: 70 ALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIENDF--GFLKKITWNCIIVD 127
+IK K K I +V TP + ++ L + +I+D
Sbjct: 68 ----------SIKQQEKLLSGKTDI-------VVGTPGRLLDELERLKLSLKKLDLLILD 110
Query: 128 EGHSVKNKKSKLSIKLTALRA 148
E H + N+ L L+
Sbjct: 111 EAHRLLNQGFGLLGLKILLKL 131
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 41.0 bits (97), Expect = 1e-04
Identities = 51/160 (31%), Positives = 68/160 (42%), Gaps = 40/160 (25%)
Query: 14 SGKVIAFFCKII-------EEQALEPNLIVC----PLSVLNNWEAEFRK--FAPFVRTVK 60
SGK +A F II E LE + + C PL LNN + + P
Sbjct: 58 SGKTLAAFLAIIDELFRLGREGELE-DKVYCLYVSPLRALNN---DIHRNLEEPL----- 108
Query: 61 YYGNAIERKALQSEALSLPTIKVPAKKGKT---KKQISL-KLPLILVTTPQ---IIENDF 113
I A + LP I+V + G T +KQ L K P IL+TTP+ I+ N
Sbjct: 109 ---TEIREIA-KERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSP 164
Query: 114 GF---LKKITWNCIIVDEGHSVKNKK--SKLSIKLTALRA 148
F L+ + W +IVDE HS+ K LS+ L L
Sbjct: 165 KFREKLRTVKW--VIVDEIHSLAENKRGVHLSLSLERLEE 202
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 33.5 bits (77), Expect = 0.044
Identities = 27/146 (18%), Positives = 54/146 (36%), Gaps = 40/146 (27%)
Query: 1 MDTVIPDPTRYRKSGKVIAFFCKIIEEQALEPN---LIVCPLSVL-NNWEAEFRKF-APF 55
+ V+ T SGK +F I++ +P+ L++ P + L N+ R+ +
Sbjct: 86 RNVVVTTGT---GSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQAERLRELISDL 142
Query: 56 VRTVK---YYGNAIERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQIIE-- 110
V Y G+ + ++ I P IL+T P ++
Sbjct: 143 PGKVTFGRYTGDT---------------------PPEERRAIIRNPPDILLTNPDMLHYL 181
Query: 111 -----NDFGFLKKITWNCIIVDEGHS 131
+ + +L + ++VDE H+
Sbjct: 182 LLRNHDAWLWLLR-NLKYLVVDELHT 206
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 32.1 bits (74), Expect = 0.12
Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 22/80 (27%)
Query: 66 IERKALQS--EALSLPTIKVPAKKGKT----KKQISLKLPLILVTTPQII---------E 110
I R LQ+ E L LP I+V + G T + + K P IL+TTP+ +
Sbjct: 78 IAR-NLQAPIEELGLP-IRVETRTGDTSSSERARQRKKPPDILLTTPESLALLLSYPDAA 135
Query: 111 NDFGFLKKITWNCIIVDEGH 130
F L+ C++VDE H
Sbjct: 136 RLFKDLR-----CVVVDEWH 150
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 30.7 bits (70), Expect = 0.34
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 10/66 (15%)
Query: 91 KKQISLKLPLILVTTPQIIENDFG------FLKKITWNCIIVDEGHSVKNKK--SKLSIK 142
K+++ P IL+TTP+ + L+ + + +IVDE H++ K +L++
Sbjct: 116 KQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRY--VIVDEIHALAESKRGVQLALS 173
Query: 143 LTALRA 148
L LR
Sbjct: 174 LERLRE 179
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 30.0 bits (68), Expect = 0.60
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 16/61 (26%)
Query: 101 ILVTTPQIIENDF--GFLKKITWNCIIVDEGHS--------------VKNKKSKLSIKLT 144
+ V TPQ++END G + + +I DE H +++ K+ L + LT
Sbjct: 110 VFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYAYVFVAKEYLRSAKNPLILGLT 169
Query: 145 A 145
A
Sbjct: 170 A 170
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 29.1 bits (66), Expect = 0.64
Identities = 27/155 (17%), Positives = 51/155 (32%), Gaps = 36/155 (23%)
Query: 14 SGKVIAFFCKIIEEQALEPN----LIVCPLSVL-NNWEAEFRKFAPF--VRTVKYYGNAI 66
SGK +AF I++ + L++ P L E +K +R G
Sbjct: 25 SGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQIYEELKKLFKILGLRVALLTGGT- 83
Query: 67 ERKALQSEALSLPTIKVPAKKGKTKKQISLKLPLILVTTPQII-----ENDFGFLKKITW 121
+ +++ ILV TP + LK +
Sbjct: 84 -------------------SLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLKNLKL 124
Query: 122 NCIIVDEGHSVKNKKSKLSIK--LTALRATFKVLL 154
+++DE H + + ++ L+ L ++LL
Sbjct: 125 --LVLDEAHRLLDMGFGDDLEEILSRLPPDRQILL 157
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 28.2 bits (63), Expect = 2.4
Identities = 19/88 (21%), Positives = 32/88 (36%), Gaps = 32/88 (36%)
Query: 22 CKIIEEQALEPNLIVCPLSVLNNWEAEFRKFAPFVRTVKYYGNAIERKALQSEALSLPTI 81
C++I E P F +AP + V +YG K + ++AL+
Sbjct: 133 CRLIMEYLENPE--------------RFGDWAP--KNVLFYGPPGTGKTMMAKALANEA- 175
Query: 82 KVPAKKGKTKKQISLKLPLILVTTPQII 109
K+PL+LV ++I
Sbjct: 176 ---------------KVPLLLVKATELI 188
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 28.3 bits (64), Expect = 2.5
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 101 ILVTTPQIIENDFGFLKKITWN---CIIVDEGH 130
++V TPQ+IEND +I+ +I DE H
Sbjct: 110 VIVATPQVIENDL-IAGRISLEDVSLLIFDEAH 141
>gnl|CDD|239741 cd03772, MATH_HAUSP, Herpesvirus-associated ubiquitin-specific
protease (HAUSP, also known as USP7) family, N-terminal
MATH (TRAF-like) domain; composed of proteins similar to
human HAUSP, an enzyme that specifically catalyzes the
deubiquitylation of p53 and MDM2, hence playing an
important role in the p53-MDM2 pathway. It contains an
N-terminal TRAF-like domain and a C-terminal catalytic
protease (C19 family) domain. The tumor suppressor p53
protein is a transcription factor that responds to many
cellular stress signals and is regulated primarily
through ubiquitylation and subsequent degradation. MDM2
is a RING-finger E3 ubiquitin ligase that promotes p53
ubiquitinylation. p53 and MDM2 bind to the same site in
the N-terminal TRAF-like domain of HAUSP in a mutually
exclusive manner. HAUSP also interacts with the
Epstein-Barr nuclear antigen 1 (EBNA1) protein of the
Epstein-Barr virus (EBV), which efficiently immortalizes
infected cells predisposing the host to a variety of
cancers. EBNA1 plays several important roles in EBV
latent infection and cellular transformation. It binds
the same pocket as p53 in the HAUSP TRAF-like domain.
Through interactions with p53, MDM2 and EBNA1, HAUSP
plays a role in cell proliferation, apoptosis and
EBV-mediated immortalization.
Length = 137
Score = 26.6 bits (59), Expect = 4.4
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 110 ENDFGFLKKITWNCIIVDEGHSVKNKKSKLSIKLTA 145
END+GF +TW+ + E +++ L + + A
Sbjct: 97 ENDWGFSNFMTWSEVTDPEKGFIEDDTITLEVYVQA 132
>gnl|CDD|233452 TIGR01533, lipo_e_P4, 5'-nucleotidase, lipoprotein e(P4) family.
This model represents a set of bacterial lipoproteins
belonging to a larger acid phosphatase family
(pfam03767), which in turn belongs to the haloacid
dehalogenase (HAD) superfamily of aspartate-dependent
hydrolases. Members are found on the outer membrane of
Gram-negative bacteria and the cytoplasmic membrane of
Gram-positive bacteria. Most members have classic
lipoprotein signal sequences. A critical role of this
5'-nucleotidase in Haemophilus influenzae is the
degradation of external riboside in order to allow
transport into the cell. An earlier suggested role in
hemin transport is no longer current. This enzyme may
also have other physiologically significant roles
[Transport and binding proteins, Other, Biosynthesis of
cofactors, prosthetic groups, and carriers, Pyridine
nucleotides].
Length = 266
Score = 26.3 bits (58), Expect = 7.5
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 56 VRTVKYYGNAIERKALQSEALSLPTIKVPA--KKGKTKK 92
+V + + E KAL +A +L +++ KK K KK
Sbjct: 37 TMSVAWMQRSAEYKALYLQAYNLAKMRLDNNLKKVKDKK 75
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
0.321 0.136 0.413
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,552,003
Number of extensions: 758029
Number of successful extensions: 587
Number of sequences better than 10.0: 1
Number of HSP's gapped: 578
Number of HSP's successfully gapped: 26
Length of query: 169
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 79
Effective length of database: 6,945,742
Effective search space: 548713618
Effective search space used: 548713618
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: 55 (25.1 bits)