RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3344
(1282 letters)
>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and
modification].
Length = 2365
Score = 335 bits (861), Expect = 2e-94
Identities = 140/282 (49%), Positives = 182/282 (64%), Gaps = 5/282 (1%)
Query: 420 AFSRLILILRALHVNTERTKVILKPDKSTITEPHHIWPSLSDDEWIKVEVQLKDLILADY 479
AFSRL+L+LRAL VN ER K IL+PDKS IT+ +H+WP SD +WIK E+QL+DLIL Y
Sbjct: 1961 AFSRLLLVLRALDVNEERVKEILRPDKSIITKINHLWPGFSDSQWIKKEIQLRDLILDRY 2020
Query: 480 GKKNNVNVASLTQSEIRDIILGMEISAPSAQRQQIAEIEKQTKE--QSQLTATTTRTVNK 537
K+N+N + LTQSE+RDIILG ISAPS RQ+ AE EKQ E S+ T +T+T+N
Sbjct: 2021 CSKHNINPSGLTQSEVRDIILGFRISAPSGARQETAETEKQNSEKALSRPTNVSTKTING 2080
Query: 538 HGDEIITSTTSNYETATFGSKTEWRVRAISATNLHLRTNHIYVSSDDIKETG-YTYILPK 596
G E + YE F SK EWR AI L LRT +IYV++D+ +E+ Y LP
Sbjct: 2081 WGREYVVLDGMIYEGEKFSSKEEWRSEAIRTGPLELRTKNIYVTADENEESIQQMYRLPL 2140
Query: 597 NVLKKFVTISDLRAQIAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPASLPGH-P 655
N+L+KF+ ISD Q+AG +YG S +DNPQ+KEI + PQ G+ V + +P P
Sbjct: 2141 NLLEKFMRISDPHVQVAGLVYGKSGSDNPQIKEILSFGLVPQLGSLSGVQSSSFVPHDLP 2200
Query: 656 YLKEMEPLGWIHTQPNELPQLSPQDVTSHAKIMADNASWDGV 697
+++E LGWIHTQ +ELP L V +H K + D WD V
Sbjct: 2201 GDEDLEILGWIHTQDDELPYLEVAGVLTHRKKIVDP-EWDAV 2241
Score = 220 bits (561), Expect = 9e-58
Identities = 112/365 (30%), Positives = 166/365 (45%), Gaps = 27/365 (7%)
Query: 874 PQVRELFKYNWGFIYTVSLDFYDN--MSHYVNSMEISAPSAQRQQIAEIEKQTKE--QSQ 929
Q+R+L + + ++ + + ISAPS RQ+ AE EKQ E S+
Sbjct: 2010 IQLRDLILDRYCSKHNINPSGLTQSEVRDIILGFRISAPSGARQETAETEKQNSEKALSR 2069
Query: 930 LTATTTRTVNKHGDEIITSTTSNYETATFGSKTEWRVRAISATNLHLRTNHIYVSSDDIK 989
T +T+T+N G E + YE F SK EWR AI L LRT +IYV++D+ +
Sbjct: 2070 PTNVSTKTINGWGREYVVLDGMIYEGEKFSSKEEWRSEAIRTGPLELRTKNIYVTADENE 2129
Query: 990 ETG-YTYILPKNVLKKFVTISDLRAQIAGYLYDHLVCGRHERVSSDHTQDIRRQSDHQTF 1048
E+ Y LP N+L+KF+ ISD Q+AG +Y + SD+ Q + +F
Sbjct: 2130 ESIQQMYRLPLNLLEKFMRISDPHVQVAGLVYG--------KSGSDNPQ----IKEILSF 2177
Query: 1049 IFHSQIIWFVDDTNVYRVTIHKTFEGNL-TTKPINGAIFIFNPRTGQLFLKIIHTSVWAG 1107
Q+ ++ V +L + + +I +L++
Sbjct: 2178 GLVPQL------GSLSGVQSSSFVPHDLPGDEDLEILGWIHTQDDELPYLEVAGVLTHR- 2230
Query: 1108 QKRLGQLGEKTVVITCSFTPGSCSLTAYKLTPSGFEWGRQNTDKGNN-PKGYLPSHYERV 1166
K++ V +T S+ PGS SL AY + G WG +N D ++ G P +
Sbjct: 2231 -KKIVDPEWDAVTLTVSYLPGSISLRAYVVKKEGCNWGSKNMDINSDEAIGVEPVLGKDC 2289
Query: 1167 QMLLSDRFLGFFMVPAQSSWNYNFMGVRHDPNMKYDLQLANPKEFYHEIHRPAHFLNFSS 1226
Q+LLSDR G F VP + WNYNF G D ++Y ++ P FY HRP HF F
Sbjct: 2290 QLLLSDRIQGVFYVPEEEVWNYNFAGPFFDDRLEYTWKIGMPLGFYDGFHRPGHFSRFYE 2349
Query: 1227 LEDGD 1231
L G
Sbjct: 2350 LRAGG 2354
Score = 218 bits (557), Expect = 3e-57
Identities = 100/124 (80%), Positives = 107/124 (86%)
Query: 297 AYGNWFPGSKPLIQQALAKIMKANPALYVLRERIRKALQLYSSEPTEPYLSSQNYGELFS 356
AYGNW G KPLIQ ++ +IMKANPALYVLRERIRK LQLY+SEP E YLSS NY ELFS
Sbjct: 1743 AYGNWNEGLKPLIQSSMERIMKANPALYVLRERIRKGLQLYTSEPQEQYLSSSNYAELFS 1802
Query: 357 NQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRL 416
N I FVDDTNVYRVT+HKTFEGNLTTKPINGAIF+ NP TG LFLK+IHTSVWAGQKRL
Sbjct: 1803 NSIDLFVDDTNVYRVTLHKTFEGNLTTKPINGAIFVLNPATGNLFLKVIHTSVWAGQKRL 1862
Query: 417 GQLA 420
QLA
Sbjct: 1863 IQLA 1866
Score = 209 bits (533), Expect = 2e-54
Identities = 84/114 (73%), Positives = 95/114 (83%)
Query: 27 LRALHSDLRWSKQTDVGITHFRSGMSHDEDQLIPNLYRYIQPWESEFIDSQRVWAEYALK 86
+ HSDL WSKQTD GITHFRSGM+ + ++LIP RYI WE EF DSQRVWAEYA K
Sbjct: 1362 ILIPHSDLEWSKQTDTGITHFRSGMTTNGERLIPAAMRYISRWEYEFEDSQRVWAEYARK 1421
Query: 87 RQEANAQNRRLTLEDLEDSWDRGIPRINTLFQKDRHTLAYDKGWRIRTEFKQYQ 140
RQEA QNRRLTLEDLE SWDRGIPRI+TLFQ+DRHTLAYD+G+R+R+EFKQY
Sbjct: 1422 RQEAGQQNRRLTLEDLEMSWDRGIPRISTLFQRDRHTLAYDRGFRMRSEFKQYS 1475
Score = 154 bits (391), Expect = 1e-37
Identities = 56/76 (73%), Positives = 65/76 (85%)
Query: 220 RHTLAYDKGWRIRTEFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMIQALGGVEGILE 279
RHTLAYD+G+R+R+EFKQY + NPFWWT +HDGKLW+LN YR D+IQALGGVEGILE
Sbjct: 1456 RHTLAYDRGFRMRSEFKQYSLKPNNPFWWTDAKHDGKLWSLNRYRLDVIQALGGVEGILE 1515
Query: 280 HTLFKGTYFPTWEGLF 295
HTLFK T F +WEGLF
Sbjct: 1516 HTLFKATGFRSWEGLF 1531
Score = 125 bits (314), Expect = 1e-28
Identities = 53/84 (63%), Positives = 68/84 (80%)
Query: 139 YQDMNHTNSYGIIRGLQFASFIVQYYGLVLDLLVLGLQRASEMAGPPQMPNDFLTFQDTA 198
Y+DM+HTN YG+IRGLQF+SFI Q+YGLV+DLLVLGLQRA+E+AGP PN F+ F+ A
Sbjct: 1047 YKDMSHTNHYGLIRGLQFSSFIYQFYGLVVDLLVLGLQRATEIAGPADAPNVFMDFKSRA 1106
Query: 199 TELAHPIRLYCRYVDKVHLFLRHT 222
TE +HPIRLY RY+D +++ R
Sbjct: 1107 TETSHPIRLYTRYMDDIYIVFRFQ 1130
Score = 116 bits (292), Expect = 5e-26
Identities = 53/66 (80%), Positives = 58/66 (87%)
Query: 1049 IFHSQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQ 1108
+F + I FVDDTNVYRVT+HKTFEGNLTTKPINGAIF+ NP TG LFLK+IHTSVWAGQ
Sbjct: 1800 LFSNSIDLFVDDTNVYRVTLHKTFEGNLTTKPINGAIFVLNPATGNLFLKVIHTSVWAGQ 1859
Query: 1109 KRLGQL 1114
KRL QL
Sbjct: 1860 KRLIQL 1865
Score = 103 bits (259), Expect = 4e-22
Identities = 37/58 (63%), Positives = 45/58 (77%)
Query: 737 IVNKWNTALIGLMTYFRESVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPAVF 794
+ KWNT LI L+TY+RE++ +T+ LLD LVK E IQ R+K GLNSKMP RFPPAVF
Sbjct: 1288 VATKWNTQLIALVTYYREAICDTKGLLDKLVKAERLIQNRVKKGLNSKMPVRFPPAVF 1345
Score = 92.7 bits (230), Expect = 9e-19
Identities = 40/61 (65%), Positives = 46/61 (75%)
Query: 793 VFDQELDALEIETVQKETIHPRKSYKMNSSCADVLLFAAYKWNVSRPSLLADSKGKFPPV 852
V D+ELD L+IETVQKET+HPRKSYKMNSSCAD+LL AY W VS PSLL + + V
Sbjct: 1625 VLDKELDVLQIETVQKETVHPRKSYKMNSSCADILLSGAYDWCVSSPSLLLEERDGGSNV 1684
Query: 853 V 853
Sbjct: 1685 R 1685
Score = 64.2 bits (156), Expect = 5e-10
Identities = 24/41 (58%), Positives = 31/41 (75%)
Query: 1234 ILKPDKSTITEPHHIWPSLSDDEWIKVEVQLKDLILADYGK 1274
IL+PDKS IT+ +H+WP SD +WIK E+QL+DLIL Y
Sbjct: 1982 ILRPDKSIITKINHLWPGFSDSQWIKKEIQLRDLILDRYCS 2022
Score = 62.7 bits (152), Expect = 1e-09
Identities = 24/41 (58%), Positives = 29/41 (70%)
Query: 835 NVSRPSLLADSKGKFPPVVFYTPKELGGLGMLSMGHVLIPQ 875
N + L + +FPP VFY PKELGGLGMLS+GH+LIP
Sbjct: 1326 NRVKKGLNSKMPVRFPPAVFYAPKELGGLGMLSVGHILIPH 1366
Score = 59.6 bits (144), Expect = 1e-08
Identities = 32/62 (51%), Positives = 37/62 (59%), Gaps = 7/62 (11%)
Query: 1 MVLFNLYDDWLKTISSYTAFSRLILILRALHSD-------LRWSKQTDVGITHFRSGMSH 53
MVLFNLYDDWL+ SSYTAFSRL+L+LRAL + LR K I H G S
Sbjct: 1943 MVLFNLYDDWLQETSSYTAFSRLLLVLRALDVNEERVKEILRPDKSIITKINHLWPGFSD 2002
Query: 54 DE 55
+
Sbjct: 2003 SQ 2004
Score = 45.0 bits (106), Expect = 3e-04
Identities = 15/45 (33%), Positives = 21/45 (46%)
Query: 691 NASWDGVRHDPNMKYDLQLANPKEFYHEIHRPAHFLNFSSLEDGD 735
N ++ G D ++Y ++ P FY HRP HF F L G
Sbjct: 2310 NYNFAGPFFDDRLEYTWKIGMPLGFYDGFHRPGHFSRFYELRAGG 2354
>gnl|CDD|163687 cd08056, MPN_PRP8, Mpr1p, Pad1p N-terminal (MPN) domains without
isopeptidase activity found in splicing factor Prp8.
Members of this family are found in pre-mRNA-processing
factor 8 (Prp8) which is a critical splicing factor,
interacting with several other spliceosomal proteins,
snRNAs, and the pre-mRNA, thus organizing and
stabilizing the spliceosome catalytic core. Prp8 is one
of the largest and most highly conserved of nuclear
proteins, occupying a central position in the catalytic
core of the spliceosome. Its C-terminal domain exhibits
a JAB1/MPN-like core similar to deubiquitinating
enzymes, but does not show catalytic isopeptidase
activity, possibly because the putative isopeptidase
center is covered by insertions and terminal appendices
that are grafted onto this core, thus impairing the
metal binding site. It is proposed that this domain is a
protein interaction domain instead of a Zn(2+)-dependent
metalloenzyme as proposed for some MPN proteins. The
DEAD-box protein Brr2 and the GTPase Snu114 bind to the
Prp8 C-terminus, a region where mutations in human Prp8
(hPrp8) cause a severe form of the genetic disorder
retinitis pigmentosa, RP13, which leads to progressive
photoreceptor degeneration in the retina and eventual
blindness. At the N-terminus of Prp8, there are several
domains, including a highly variable nuclear
localization signal (NLS) motif rich in prolines, a
conserved RNA recognition motif (RRM), and U5 and U6
snRNA binding sites.
Length = 252
Score = 292 bits (749), Expect = 1e-90
Identities = 117/144 (81%), Positives = 130/144 (90%)
Query: 555 FGSKTEWRVRAISATNLHLRTNHIYVSSDDIKETGYTYILPKNVLKKFVTISDLRAQIAG 614
F SKT+WRVRAI+ATNLHLRT +IYVSSDDIKETGYTYILPKN+LKKF++ISDLR QIAG
Sbjct: 1 FSSKTDWRVRAIAATNLHLRTKNIYVSSDDIKETGYTYILPKNLLKKFISISDLRTQIAG 60
Query: 615 YLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPASLPGHPYLKEMEPLGWIHTQPNELP 674
YLYG SP DNPQVKEIRCIV+ PQ GTHQTV LP LP H YL+++EPLGWIHTQPNELP
Sbjct: 61 YLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQLPQHEYLEDLEPLGWIHTQPNELP 120
Query: 675 QLSPQDVTSHAKIMADNASWDGVR 698
QLSPQDVT+HAKI+ADN SWDG +
Sbjct: 121 QLSPQDVTTHAKILADNPSWDGEK 144
Score = 227 bits (582), Expect = 1e-67
Identities = 85/111 (76%), Positives = 95/111 (85%), Gaps = 1/111 (0%)
Query: 1115 GEKTVVITCSFTPGSCSLTAYKLTPSGFEWGRQNTDKGNN-PKGYLPSHYERVQMLLSDR 1173
GEKTV++TCSFTPGSCSLTAYKLTP G+EWG+QN D GNN PKGY PS YE+VQ+LLSDR
Sbjct: 142 GEKTVILTCSFTPGSCSLTAYKLTPEGYEWGKQNKDLGNNTPKGYSPSFYEKVQLLLSDR 201
Query: 1174 FLGFFMVPAQSSWNYNFMGVRHDPNMKYDLQLANPKEFYHEIHRPAHFLNF 1224
FLGFF+VP WNYNFMG +H PNMKYDL+L PKEFYHE+HRP HFL F
Sbjct: 202 FLGFFLVPEDGVWNYNFMGAKHSPNMKYDLKLDIPKEFYHELHRPTHFLQF 252
Score = 134 bits (340), Expect = 4e-35
Identities = 54/63 (85%), Positives = 60/63 (95%)
Query: 958 FGSKTEWRVRAISATNLHLRTNHIYVSSDDIKETGYTYILPKNVLKKFVTISDLRAQIAG 1017
F SKT+WRVRAI+ATNLHLRT +IYVSSDDIKETGYTYILPKN+LKKF++ISDLR QIAG
Sbjct: 1 FSSKTDWRVRAIAATNLHLRTKNIYVSSDDIKETGYTYILPKNLLKKFISISDLRTQIAG 60
Query: 1018 YLY 1020
YLY
Sbjct: 61 YLY 63
Score = 75.0 bits (185), Expect = 1e-14
Identities = 25/43 (58%), Positives = 31/43 (72%), Gaps = 4/43 (9%)
Query: 690 DNASWD----GVRHDPNMKYDLQLANPKEFYHEIHRPAHFLNF 728
++ W+ G +H PNMKYDL+L PKEFYHE+HRP HFL F
Sbjct: 210 EDGVWNYNFMGAKHSPNMKYDLKLDIPKEFYHELHRPTHFLQF 252
>gnl|CDD|219717 pfam08084, PROCT, PROCT (NUC072) domain. The PROCT domain is the
C-terminal domain in pre-mRNA splicing factors of PRO8
family.
Length = 110
Score = 205 bits (524), Expect = 7e-62
Identities = 65/110 (59%), Positives = 80/110 (72%), Gaps = 1/110 (0%)
Query: 1118 TVVITCSFTPGSCSLTAYKLTPSGFEWGRQNTD-KGNNPKGYLPSHYERVQMLLSDRFLG 1176
T+ +T SFTPGS SL+AY LTP G+EWG +N D +NP+G+ PS E+VQ+LLSDR G
Sbjct: 1 TITLTVSFTPGSVSLSAYTLTPEGYEWGLENKDLLSDNPQGFSPSFSEKVQLLLSDRIQG 60
Query: 1177 FFMVPAQSSWNYNFMGVRHDPNMKYDLQLANPKEFYHEIHRPAHFLNFSS 1226
FF+VP WNYNFMG + NMKYDL+L P FY E+HRP HFLNF+
Sbjct: 61 FFLVPDDGIWNYNFMGAKFSENMKYDLKLDIPLPFYDELHRPTHFLNFAE 110
Score = 70.4 bits (173), Expect = 2e-14
Identities = 22/45 (48%), Positives = 28/45 (62%), Gaps = 4/45 (8%)
Query: 690 DNASWD----GVRHDPNMKYDLQLANPKEFYHEIHRPAHFLNFSS 730
D+ W+ G + NMKYDL+L P FY E+HRP HFLNF+
Sbjct: 66 DDGIWNYNFMGAKFSENMKYDLKLDIPLPFYDELHRPTHFLNFAE 110
>gnl|CDD|152569 pfam12134, PRP8_domainIV, PRP8 domain IV core. This domain is
found in eukaryotes, and is about 20 amino acids in
length. It is found associated with pfam10597,
pfam10596, pfam10598, pfam08083, pfam08082, pfam01398,
pfam08084. There is a conserved LILR sequence motif. The
domain is a selenomethionine domain in a subunit of the
spliceosome. The function of PRP8 domain IV is believed
to be interaction with the splicosomal core.
Length = 231
Score = 180 bits (458), Expect = 3e-51
Identities = 67/78 (85%), Positives = 73/78 (93%)
Query: 343 EPYLSSQNYGELFSNQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFL 402
EP+L+SQNY ELFSN+ WFVDDTNVYRVTIHKTFEGNLTTKPINGA+FI NP+TGQLFL
Sbjct: 1 EPFLNSQNYAELFSNETTWFVDDTNVYRVTIHKTFEGNLTTKPINGAVFILNPKTGQLFL 60
Query: 403 KIIHTSVWAGQKRLGQLA 420
K+IHTSVWAGQKRL QLA
Sbjct: 61 KVIHTSVWAGQKRLSQLA 78
Score = 149 bits (378), Expect = 1e-40
Identities = 55/66 (83%), Positives = 61/66 (92%)
Query: 1049 IFHSQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQ 1108
+F ++ WFVDDTNVYRVTIHKTFEGNLTTKPINGA+FI NP+TGQLFLK+IHTSVWAGQ
Sbjct: 12 LFSNETTWFVDDTNVYRVTIHKTFEGNLTTKPINGAVFILNPKTGQLFLKVIHTSVWAGQ 71
Query: 1109 KRLGQL 1114
KRL QL
Sbjct: 72 KRLSQL 77
Score = 113 bits (285), Expect = 4e-28
Identities = 43/59 (72%), Positives = 55/59 (93%)
Query: 420 AFSRLILILRALHVNTERTKVILKPDKSTITEPHHIWPSLSDDEWIKVEVQLKDLILAD 478
AFSRLILILRALH+N E+TK+IL+PD + +T+PHH+WP+L+D EWI+VE+QLKDLILAD
Sbjct: 173 AFSRLILILRALHINEEKTKIILRPDPNVVTQPHHLWPTLTDQEWIEVEIQLKDLILAD 231
Score = 75.9 bits (187), Expect = 4e-15
Identities = 26/39 (66%), Positives = 36/39 (92%)
Query: 1233 VILKPDKSTITEPHHIWPSLSDDEWIKVEVQLKDLILAD 1271
+IL+PD + +T+PHH+WP+L+D EWI+VE+QLKDLILAD
Sbjct: 193 IILRPDPNVVTQPHHLWPTLTDQEWIEVEIQLKDLILAD 231
Score = 73.6 bits (181), Expect = 2e-14
Identities = 31/39 (79%), Positives = 34/39 (87%)
Query: 1 MVLFNLYDDWLKTISSYTAFSRLILILRALHSDLRWSKQ 39
MVLFNLYDDWLK+ISSYTAFSRLILILRALH + +K
Sbjct: 155 MVLFNLYDDWLKSISSYTAFSRLILILRALHINEEKTKI 193
>gnl|CDD|119117 pfam10597, U5_2-snRNA_bdg, U5-snRNA binding site 2 of PrP8. The
essential spliceosomal protein Prp8 interacts with U5
and U6 snRNAs and with specific pre-mRNA sequences that
participate in catalysis. This close association with
crucial RNA sequences, together with extensive genetic
evidence, suggests that Prp8 could directly affect the
function of the catalytic core, perhaps acting as a
splicing cofactor.
Length = 136
Score = 129 bits (327), Expect = 6e-35
Identities = 46/58 (79%), Positives = 55/58 (94%)
Query: 737 IVNKWNTALIGLMTYFRESVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPAVF 794
I NKWNTALIGL+TY+RE++V+T+ELLD+LVKCENKIQ R+K+GLNSKMPSRFPP VF
Sbjct: 52 IANKWNTALIGLVTYYREAIVSTEELLDILVKCENKIQNRVKMGLNSKMPSRFPPVVF 109
Score = 72.0 bits (177), Expect = 9e-15
Identities = 25/28 (89%), Positives = 27/28 (96%)
Query: 848 KFPPVVFYTPKELGGLGMLSMGHVLIPQ 875
+FPPVVFYTPKELGGLGMLSMGH+LIP
Sbjct: 103 RFPPVVFYTPKELGGLGMLSMGHILIPA 130
>gnl|CDD|151125 pfam10596, U6-snRNA_bdg, U6-snRNA interacting domain of PrP8. This
domain incorporates the interacting site for the
U6-snRNA as part of the U4/U6.U5 tri-snRNPs complex of
the spliceosome, and is the prime candidate for the role
of cofactor for the spliceosome's RNA core. The
essential spliceosomal protein Prp8 interacts with U5
and U6 snRNAs and with specific pre-mRNA sequences that
participate in catalysis. This close association with
crucial RNA sequences, together with extensive genetic
evidence, suggests that Prp8 could directly affect the
function of the catalytic core, perhaps acting as a
splicing cofactor.
Length = 160
Score = 127 bits (320), Expect = 9e-34
Identities = 51/61 (83%), Positives = 55/61 (90%)
Query: 235 FKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMIQALGGVEGILEHTLFKGTYFPTWEGL 294
FK+YQ+ K NPFWWTHQRHDGKLWNLN YRTD+IQALGGVE ILEHTLFK T FP+WEGL
Sbjct: 1 FKKYQLSKSNPFWWTHQRHDGKLWNLNRYRTDVIQALGGVETILEHTLFKATGFPSWEGL 60
Query: 295 F 295
F
Sbjct: 61 F 61
>gnl|CDD|192639 pfam10598, RRM_4, RNA recognition motif of the spliceosomal PrP8.
The large RNA-protein complex of the spliceosome
catalyzes pre-mRNA splicing. One of the most conserved
core proteins is PrP8 which occupies a central position
in the catalytic core of the spliceosome, and has been
implicated in several crucial molecular rearrangements
that occur there, and has recently come under the
spotlight for its role in the inherited human disease,
Retinitis Pigmentosa. The RNA-recognition motif of PrP8
is highly conserved and provides a possible RNA binding
centre for the 5-prime SS, BP, or 3-prime SS of pre-mRNA
which are known to contact with Prp8. The most conserved
regions of an RRM are defined as the RNP1 and RNP2
sequences. Recognition of RNA targets can also be
modulated by a number of other factors, most notably the
two loops beta1-alpha1, beta2-beta3 and the amino acid
residues C-terminal to the RNP2 domain.
Length = 94
Score = 121 bits (306), Expect = 1e-32
Identities = 44/61 (72%), Positives = 54/61 (88%)
Query: 139 YQDMNHTNSYGIIRGLQFASFIVQYYGLVLDLLVLGLQRASEMAGPPQMPNDFLTFQDTA 198
Y+DM+HTNSYG+IRGLQF+SFI QYYGLVLDLL+LGLQRA+E+AGPP PN+F+ F+
Sbjct: 34 YKDMSHTNSYGLIRGLQFSSFIYQYYGLVLDLLILGLQRANEIAGPPNAPNEFMQFKSKE 93
Query: 199 T 199
T
Sbjct: 94 T 94
>gnl|CDD|214573 smart00232, JAB_MPN, JAB/MPN domain. Domain in Jun kinase
activation domain binding protein and proteasomal
subunits. Domain at Mpr1p and Pad1p N-termini. Domain of
unknown function.
Length = 135
Score = 85.9 bits (213), Expect = 1e-19
Identities = 33/119 (27%), Positives = 49/119 (41%), Gaps = 12/119 (10%)
Query: 590 YTYILPKNVLKKFVTISDLRAQIAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPA 649
++P N+LK I D ++ G L G S D P+VKE+ + P +V
Sbjct: 4 VHPLVPLNILKHA--IRDGPEEVCGVLLGKSNKDRPEVKEVFAV---PNEPQDDSVQEYD 58
Query: 650 SLPGHPYL-------KEMEPLGWIHTQPNELPQLSPQDVTSHAKIMADNASWDGVRHDP 701
H K++E +GW H+ P+E P S DV +H A + DP
Sbjct: 59 EDYSHLMDEELKKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDP 117
>gnl|CDD|163686 cd07767, MPN, Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also
known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are
found in the N-terminal termini of proteins with a
variety of functions; they are components of the
proteasome regulatory subunits, the signalosome (CSN),
eukaryotic translation initiation factor 3 (eIF3)
complexes, and regulators of transcription factors.
These domains are isopeptidases that release ubiquitin
from ubiquitinated proteins (thus having
deubiquitinating (DUB) activity) that are tagged for
degradation. Catalytically active MPN domains contain a
metalloprotease signature known as the JAB1/MPN/Mov34
metalloenzyme (JAMM) motif. For example, Rpn11 (also
known as POH1 or PSMD14), a subunit of the 19S
proteasome lid is involved in the ATP-dependent
degradation of ubiquitinated proteins, contains the
conserved JAMM motif involved in zinc ion coordination.
Poh1 is a regulator of c-Jun, an important regulator of
cell proliferation, differentiation, survival and death.
JAB1 is a component of the COP9 signalosome (CSN), a
regulatory particle of the ubiquitin (Ub)/26S proteasome
system occurring in all eukaryotic cells; it cleaves the
ubiquitin-like protein NEDD8 from the cullin subunit of
the SCF (Skp1, Cullins, F-box proteins) family of E3
ubiquitin ligases. AMSH (associated molecule with the
SH3 domain of STAM, also known as STAMBP), a member of
JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves
Lys 63-linked polyubiquitin (poly-Ub) chains, thus
facilitating the recycling and subsequent trafficking of
receptors to the cell surface. Similarly, BRCC36, part
of the nuclear complex that includes BRCA1 protein and
is targeted to DNA damage foci after irradiation,
specifically disassembles K63-linked polyUb. BRCC36 is
aberrantly expressed in sporadic breast tumors,
indicative of a potential role in the pathogenesis of
the disease. Some variants of the JAB1/MPN domains lack
key residues in their JAMM motif and are unable to
coordinate a metal ion. Comparisons of key catalytic and
metal binding residues explain why the MPN-containing
proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the
translation initiation factor 3 subunits f (p47) and h
(p40) do not show catalytic isopeptidase activity. It
has been proposed that the MPN domain in these proteins
has a primarily structural function.
Length = 116
Score = 77.6 bits (191), Expect = 7e-17
Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 7/92 (7%)
Query: 599 LKKFVTISDL--RAQIAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQTVHLPASLPGHPY 656
LK F+ + ++ G LYG +V ++ ++ P + ++ +
Sbjct: 1 LKMFLDAAKSINGKEVIGLLYGSKT---KKVLDVDEVIAVPFDEGDKDDNVWFLMYLDFK 57
Query: 657 LKE--MEPLGWIHTQPNELPQLSPQDVTSHAK 686
+ +GW HT P LSP D+ +H
Sbjct: 58 KLNAGLRIVGWYHTHPKPSCFLSPNDLATHEL 89
>gnl|CDD|216478 pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin protease. Members
of this family are found in proteasome regulatory
subunits, eukaryotic initiation factor 3 (eIF3) subunits
and regulators of transcription factors. This family is
also known as the MPN domain and PAD-1-like domain,
JABP1 domain or JAMM domain. These are metalloenzymes
that function as the ubiquitin isopeptidase/
deubiquitinase in the ubiquitin-based signaling and
protein turnover pathways in eukaryotes. Versions of the
domain in prokaryotic cognates of the
ubiquitin-modification pathway are predicted to have a
similar role.
Length = 117
Score = 72.4 bits (178), Expect = 4e-15
Identities = 27/119 (22%), Positives = 41/119 (34%), Gaps = 19/119 (15%)
Query: 588 TGYTYILPKNVLKKFVTISDLRAQ----IAGYLYGVSPADNPQVKEIRCIVMPPQWGTHQ 643
+ T ++ VL K V + + + G L G D +V E+ PQ T
Sbjct: 1 SVRTVVIHPLVLLKIVDHARRGGKSGEEVMGVLLGTLEGD--RVIEVTNSFALPQSETED 58
Query: 644 TVHLPASLPGHPYLKEM-----------EPLGWIHTQPNELPQLSPQDVTSHAKIMADN 691
V H Y+++M E +GW H+ P LS DV +
Sbjct: 59 DVEAVE--LDHEYMEKMLEMLKKVNRDEEVVGWYHSHPGYGCWLSSVDVHTQELYQRMI 115
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 34.4 bits (80), Expect = 0.46
Identities = 21/104 (20%), Positives = 41/104 (39%), Gaps = 30/104 (28%)
Query: 486 NVASLTQSEIRDIIL-GMEISAPSAQRQQIAEIEKQTKEQSQLTATTTRTVNKHGDEIIT 544
++ LT E ++I+L +E A R + A + K+ +E+++ A +K EI+
Sbjct: 146 RISGLTAEEAKEILLEKVEEEA----RHEAAVLIKEIEEEAKEEA------DKKAKEILA 195
Query: 545 STTSNY--ETATFGSKTEWRVRAISATNLHLRTNHIYVSSDDIK 586
+ E +S NL +D++K
Sbjct: 196 QAIQRCAADHV-----AE---TTVSVVNL---------PNDEMK 222
>gnl|CDD|163689 cd08058, MPN_euk_mb, Mpr1p, Pad1p N-terminal (MPN) domains with
catalytic isopeptidase activity (metal-binding);
eukaryotic. This family contains eukaryotic MPN (also
known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in
proteins with a variety of functions, including AMSH
(associated molecule with the Src homology 3 domain
(SH3) of STAM), H2A-DUB (histone H2A deubiquitinase),
BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as
well as Rpn11 (regulatory particle number 11) and CSN5
(COP9 signalosome complex subunit 5). These domains
contain the signature JAB1/MPN/Mov34 metalloenzyme
(JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc
ion coordination and provides the active site for
isopeptidase activity. Rpn11 is responsible for
substrate deubiquitination during proteasomal
degradation. It is essential for maintaining a correct
cell cycle and normal mitochondrial morphology and
physiology. CSN5 is critical for nuclear export and the
degradation of several tumor suppressor proteins,
including p53, p27, and Smad4. Over-expression of CSN5
has been implicated in cancer initiation and
progression. AMSH specifically cleaves Lys 63 and not
Lys48-linked polyubiquitin (poly-Ub) chains, thus
facilitating the recycling and subsequent trafficking of
receptors to the cell surface. It is involved in the
degradation of EGF receptor (EGFR) and possibly other
ubiquitinated endocytosed proteins. BRCC36 is part of
the BRCA1/BRCA2/BARD1-containing nuclear complex that
displays an E3 ubiquitin ligase activity; it is targeted
to DNA damage foci after irradiation. 2A-DUB is specific
for monoubiquitinated H2A (uH2A), regulating
transcription by coordinating histone acetylation and
deubiquitination, and destabilizing the association of
linker histone H1 with nucleosomes. It is a positive
regulator of androgen receptor (AR) transactivation
activity on a reporter gene and serves as a marker in
prostate tumors.
Length = 119
Score = 31.8 bits (72), Expect = 0.73
Identities = 15/74 (20%), Positives = 21/74 (28%), Gaps = 6/74 (8%)
Query: 630 IRCIVMP-PQWGTH-QTVHLPASLPGHPYLKEMEPLGWIHTQPNELPQLSPQDVTSHAKI 687
I P T L G P + +GW H+ P LS D+ + A
Sbjct: 37 IVPKQSAGPDSCTGENVEELFNVQTGRP----LLVVGWYHSHPTFTAWLSSVDIHTQASY 92
Query: 688 MADNASWDGVRHDP 701
+ P
Sbjct: 93 QLMLPEAIAIVVSP 106
>gnl|CDD|227403 COG5071, RPN5, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 439
Score = 31.8 bits (72), Expect = 2.7
Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 15/82 (18%)
Query: 704 KYDLQLANPKEFYHEIHRPAHFLNFSSLEDGDGIVNKWNTALIGLMTYFRESVVNTQELL 763
++ L N FY +I+RPA ++F ++ +N+W + N ELL
Sbjct: 372 QFISDLVNKGHFYAKINRPAQIISFEKSQNVQEQLNEWGS--------------NVTELL 417
Query: 764 DLLVKCENKI-QTRIKIGLNSK 784
L K + I + + + +K
Sbjct: 418 GKLEKVRHLIIKEEMMNSIQAK 439
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 0.135 0.414
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 65,877,568
Number of extensions: 6508393
Number of successful extensions: 5512
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5497
Number of HSP's successfully gapped: 47
Length of query: 1282
Length of database: 10,937,602
Length adjustment: 108
Effective length of query: 1174
Effective length of database: 6,147,370
Effective search space: 7217012380
Effective search space used: 7217012380
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: 65 (28.9 bits)