RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1178
(144 letters)
>gnl|CDD|232971 TIGR00425, CBF5, rRNA pseudouridine synthase, putative. This
family, found in archaea and eukaryotes, includes the
only archaeal proteins markedly similar to bacterial
TruB, the tRNA pseudouridine 55 synthase. However, among
two related yeast proteins, the archaeal set matches
yeast YLR175w far better than YNL292w. The first, termed
centromere/microtubule binding protein 5 (CBF5), is an
apparent rRNA pseudouridine synthase, while the second
is the exclusive tRNA pseudouridine 55 synthase for both
cytosolic and mitochondrial compartments. It is unclear
whether archaeal proteins found by this model modify
tRNA, rRNA, or both [Protein synthesis, tRNA and rRNA
base modification].
Length = 322
Score = 203 bits (517), Expect = 5e-66
Identities = 73/139 (52%), Positives = 100/139 (71%), Gaps = 1/139 (0%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
M ELRR RSG ED +VTLHD+ DA + + DES LRR+I+P+E LL KR+++K
Sbjct: 185 MQELRRTRSGC-FGEDDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRHLKRVVVK 243
Query: 61 DSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGV 120
DSAV+A+C+GA +M+ G+ R E GIE + +V+++ KGEAVA+ +A M+T +A D GV
Sbjct: 244 DSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIANADKGV 303
Query: 121 VAKIKRVIMDRDTYPRKWG 139
VA +KRVIM+R TYPR W
Sbjct: 304 VADVKRVIMERGTYPRMWK 322
>gnl|CDD|179806 PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p;
Reviewed.
Length = 300
Score = 140 bits (355), Expect = 7e-42
Identities = 56/129 (43%), Positives = 81/129 (62%), Gaps = 1/129 (0%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
M ELRR R+G +EED LVTL D+ DA Y + + DE LRRVI P+E L +II+K
Sbjct: 173 MQELRRTRTGPFTEED-LVTLQDLADAYYFWKEDGDEEELRRVILPMEYALSHLPKIIIK 231
Query: 61 DSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGV 120
DSAV+A+ +GA + PG+ + E GI+ + + + + KGE VAL A M + + + G+
Sbjct: 232 DSAVDAIAHGAPLYAPGIAKLEKGIKKGDLVAVFTLKGELVALGKALMDSDEILKAEKGI 291
Query: 121 VAKIKRVIM 129
V ++RV M
Sbjct: 292 VVDLERVFM 300
>gnl|CDD|201816 pfam01472, PUA, PUA domain. The PUA domain named after
Pseudouridine synthase and Archaeosine transglycosylase,
was detected in archaeal and eukaryotic pseudouridine
synthases, archaeal archaeosine synthases, a family of
predicted ATPases that may be involved in RNA
modification, a family of predicted archaeal and
bacterial rRNA methylases. Additionally, the PUA domain
was detected in a family of eukaryotic proteins that
also contain a domain homologous to the translation
initiation factor eIF1/SUI1; these proteins may comprise
a novel type of translation factors. Unexpectedly, the
PUA domain was detected also in bacterial and yeast
glutamate kinases; this is compatible with the
demonstrated role of these enzymes in the regulation of
the expression of other genes. It is predicted that the
PUA domain is an RNA binding domain.
Length = 74
Score = 81.0 bits (201), Expect = 3e-21
Identities = 26/74 (35%), Positives = 44/74 (59%)
Query: 55 KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMA 114
R+++ D AV A+ GA ++ PGV+ + +E+V+V+ KGE VA+ LA ++ MA
Sbjct: 1 GRVVVDDGAVEAILNGASLLAPGVVEVDGDFRRGDEVVVVTEKGELVAVGLANYSSEEMA 60
Query: 115 TCDHGVVAKIKRVI 128
G K++RV+
Sbjct: 61 KIKGGKAVKVRRVL 74
>gnl|CDD|214635 smart00359, PUA, Putative RNA-binding Domain in PseudoUridine
synthase and Archaeosine transglycosylase.
Length = 76
Score = 72.7 bits (179), Expect = 5e-18
Identities = 24/76 (31%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 55 KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMA 114
++++ D A A+ GA ++ PGV+R + I+ + +VIV KGE + + LA M++ +A
Sbjct: 1 GKVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIVDEKGEPLGIGLANMSSEEIA 60
Query: 115 TCD-HGVVAKIKRVIM 129
G+ K++R +M
Sbjct: 61 RIKGKGLAVKVRRAVM 76
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal
structure and biogenesis].
Length = 271
Score = 58.8 bits (143), Expect = 4e-11
Identities = 46/129 (35%), Positives = 61/129 (47%), Gaps = 27/129 (20%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
M ELRR R G SEED VTL + + ESLLR ++ PLE L R++LK
Sbjct: 169 MSELRRTRVGPFSEED-AVTLELLDELDA-------ESLLRLLL-PLESALSDLPRLVLK 219
Query: 61 DSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGV 120
DSA NA+ YGA+ IE+ + + + KG +AL + G+
Sbjct: 220 DSAANAIKYGAK-------PGLLDIELGGLVRVYTAKGLGIAL---------GEIDEEGL 263
Query: 121 VAKIKRVIM 129
K KRV M
Sbjct: 264 --KPKRVFM 270
>gnl|CDD|237510 PRK13795, PRK13795, hypothetical protein; Provisional.
Length = 636
Score = 54.6 bits (132), Expect = 2e-09
Identities = 27/108 (25%), Positives = 47/108 (43%), Gaps = 6/108 (5%)
Query: 36 DESLLRRVIRP-LEG--LLVGHKR---IILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDE 89
D LR P LEG L+ + +I+ A+ + G ++ PGV+ + I+ +
Sbjct: 102 DLLELRWRFEPRLEGAKRLLKKRLKKWVIVDKGALEPIKNGKNVLAPGVVEADLDIKKGD 161
Query: 90 EIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRK 137
E+V+V+ GE V + A+M M G K+++ P
Sbjct: 162 EVVVVTEDGEVVGVGRAKMDGDDMIKRFRGRAVKVRKSGRGSPRLPPG 209
>gnl|CDD|211338 cd02572, PseudoU_synth_hDyskerin, Pseudouridine synthase, human
dyskerin like. This group consists of eukaryotic and
archeal pseudouridine synthases similar to human
dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila
melanogaster Mfl (minifly protein). Pseudouridine
synthases catalyze the isomerization of specific
uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactor is required. S.
cerevisiae Cbf5 and human dyskerin are nucleolar
proteins that, with the help of guide RNAs, make the
hundreds of psueudouridnes present in rRNA and small
nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic
subunit of eukaryotic box H/ACA small nucleolar
ribonucleoprotein (snoRNP) particles. D. melanogaster
mfl hosts in its fourth intron, a box H/AC snoRNA gene.
In addition dyskerin is likely to have a structural role
in the telomerase complex. Mutations in human dyskerin
cause X-linked dyskeratosis congenitas. Mutations in
Drosophila Mfl results in miniflies that suffer
abnormalities.
Length = 182
Score = 51.5 bits (124), Expect = 6e-09
Identities = 19/28 (67%), Positives = 21/28 (75%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAM 28
M ELRR RSG SEED +VTLHD+ DA
Sbjct: 155 MQELRRTRSGPFSEEDNMVTLHDVLDAQ 182
>gnl|CDD|224927 COG2016, COG2016, Predicted RNA-binding protein (contains PUA
domain) [Translation, ribosomal structure and
biogenesis].
Length = 161
Score = 43.8 bits (104), Expect = 3e-06
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 1/82 (1%)
Query: 44 IRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTK-GEAVA 102
+R L L G +++ + AV V GA +M PG++ + I+ + +V+V K G +A
Sbjct: 66 LRLLLKLPPGKYVVVVDEGAVKFVLNGADVMAPGIVSADGEIKEGDIVVVVDEKKGRPLA 125
Query: 103 LALAQMTTSTMATCDHGVVAKI 124
+ +A M+ M G K
Sbjct: 126 VGIALMSGKEMEEKKKGKAVKN 147
>gnl|CDD|237509 PRK13794, PRK13794, hypothetical protein; Provisional.
Length = 479
Score = 44.7 bits (106), Expect = 4e-06
Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 55 KRII-LKDSAVNAV-CYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTST 112
K+ I +KD + GA ++ PGV + IE ++++I+ G+ V + A+M+
Sbjct: 124 KKFIVVKDDVPKFIRNKGASVLRPGVAEASEDIEEGDDVIILDENGDVVGVGRARMSYEE 183
Query: 113 MATCDHGVVAKIKR 126
+ + G+V K+++
Sbjct: 184 IVNMEKGMVVKVRK 197
>gnl|CDD|227595 COG5270, COG5270, PUA domain (predicted RNA-binding domain)
[Translation, ribosomal structure and biogenesis].
Length = 202
Score = 40.9 bits (96), Expect = 6e-05
Identities = 32/127 (25%), Positives = 51/127 (40%), Gaps = 15/127 (11%)
Query: 15 EDGLVTLHDIKDAMYLYD----------QHKDESLLRRVIRP-LEG----LLVGHKRIIL 59
E +V L+ I + D LR LEG L G K +
Sbjct: 74 EGEIVLLNKIPGEDDADEIVVDGFIFGIIRFDLRKLRWRFGLKLEGAKLLLEKGKKGRKI 133
Query: 60 KDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHG 119
AV V G ++ PGV+ ED IE +E+++VS G V + +A+ + + + G
Sbjct: 134 DRGAVEPVKNGKNVLPPGVIEAEDSIERGDEVIVVSENGRVVGVGIAKKSYEELINPERG 193
Query: 120 VVAKIKR 126
K ++
Sbjct: 194 TGVKPRK 200
>gnl|CDD|234310 TIGR03684, arCOG00985, arCOG04150 universal archaeal PUA-domain
protein. This universal archaeal protein contains a
domain possibly associated with RNA binding (pfam01472,
TIGR00451).
Length = 150
Score = 38.0 bits (89), Expect = 4e-04
Identities = 36/131 (27%), Positives = 56/131 (42%), Gaps = 11/131 (8%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLL----RRVIRPLEGLL---VG 53
++E + GI E+ L K +YL D + LL R+ L GLL
Sbjct: 12 LLEELKEYYGIDIEKAKLEVAETDKFEIYLVD---GKPLLFEVDGRLFPTLYGLLELNPD 68
Query: 54 HKRIILKDSAVNAVCYGAQIMLPGVLRYEDGI-EMDEEIVIVSTKGEAVALALAQMTTST 112
+++ + AV + GA IM PG++ + I E D V+ T G+ +A+ +A M
Sbjct: 69 KNVVVVDEGAVKFIINGADIMAPGIVEADPSIKEGDIVFVVDETHGKPLAVGIALMDAEE 128
Query: 113 MATCDHGVVAK 123
M G K
Sbjct: 129 MVEEKKGKAVK 139
>gnl|CDD|129543 TIGR00451, unchar_dom_2, uncharacterized domain 2. This
uncharacterized domain is found a number of enzymes and
uncharacterized proteins, often at the C-terminus. It is
found in some but not all members of a family of related
tRNA-guanine transglycosylases (tgt), which exchange a
guanine base for some modified base without breaking the
phosphodiester backbone of the tRNA. It is also found in
rRNA pseudouridine synthase, another enzyme of RNA base
modification not otherwise homologous to tgt. It is
found, again at the C-terminus, in two putative
glutamate 5-kinases. It is also found in a family of
small, uncharacterized archaeal proteins consisting
mostly of this domain.
Length = 107
Score = 34.7 bits (80), Expect = 0.003
Identities = 27/93 (29%), Positives = 47/93 (50%), Gaps = 4/93 (4%)
Query: 42 RVIRPLEG---LLVGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGI-EMDEEIVIVSTK 97
+VI L+G L+ K +++ + AV + GA +M PG++ ++ I E D+ +V+ K
Sbjct: 15 KVIPSLKGALKLMEDKKIVVVDNGAVKFLKNGADVMRPGIVDADEDIKEGDDVVVVDENK 74
Query: 98 GEAVALALAQMTTSTMATCDHGVVAKIKRVIMD 130
+A+ +A M+ M D G K I D
Sbjct: 75 DRPLAVGIALMSGEEMKEMDKGKAVKNIHHIGD 107
>gnl|CDD|237757 PRK14560, PRK14560, putative RNA-binding protein; Provisional.
Length = 160
Score = 32.5 bits (75), Expect = 0.031
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 55 KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVS-TKGEAVALALAQMTTSTM 113
+R+++ AV V GA +M PG++ ++ I+ + + +V T G+ +A+ A M M
Sbjct: 77 RRVVVDAGAVKFVSNGADVMAPGIVEADEDIKEGDIVFVVEETHGKPLAVGRALMDGDEM 136
Query: 114 ATCDHGVVAK 123
G K
Sbjct: 137 VEEKKGKAVK 146
>gnl|CDD|224466 COG1549, COG1549, Queuine tRNA-ribosyltransferases, contain PUA
domain [Translation, ribosomal structure and
biogenesis].
Length = 519
Score = 32.4 bits (74), Expect = 0.058
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 76 PGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRV 127
PGV+ ++ I ++E+V+V GE + A M+ M G+ +++R
Sbjct: 467 PGVVDADEDIRPNDEVVVVHG-GEVRGVGRAVMSGREMVEAKKGIAVRVRRR 517
>gnl|CDD|224289 COG1370, COG1370, tRNA modification protein, contains pre-PUA and
PUA domains [Translation, ribosomal structure and
biogenesis].
Length = 155
Score = 27.7 bits (62), Expect = 1.8
Identities = 15/71 (21%), Positives = 36/71 (50%)
Query: 56 RIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMAT 115
R+++ D A V G + V+ ++ I +E+++V+ E +A+ A ++ + M
Sbjct: 82 RVVVSDEAEEFVRKGKSVFAKFVIDVDEEIRAGDEVLVVNEDDELLAVGRALLSGAEMRE 141
Query: 116 CDHGVVAKIKR 126
+ G+ K++
Sbjct: 142 FERGMAVKVRE 152
>gnl|CDD|238183 cd00295, RNA_Cyclase, RNA 3' phosphate cyclase domain - RNA
phosphate cyclases are enzymes that catalyze the
ATP-dependent conversion of 3'-phosphate at the end of
RNA into 2', 3'-cyclic phosphodiester bond. The enzymes
are conserved in eucaryotes, bacteria and archaea. The
exact biological role of this enzyme is unknown, but it
has been proposed that it is likely to function in
cellular RNA metabolism and processing. RNA phosphate
cyclase has been characterized in human (with at least
three isozymes), and E. coli, and it seems to be
taxonomically widespread. The crystal structure of RNA
phospate cyclase shows that it consists of two domains.
The larger domain contains three repeats of a fold
originally identified in the bacterial translation
initiation factor IF3.
Length = 338
Score = 26.2 bits (57), Expect = 6.8
Identities = 15/65 (23%), Positives = 21/65 (32%), Gaps = 9/65 (13%)
Query: 33 QHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIV 92
H DE LR R G N +C + +L G E G + E +
Sbjct: 142 IHGDELELRHGFRGAAGGGGA---------EENFLCASFKELLLGERGSEFGRQFRGEGI 192
Query: 93 IVSTK 97
T+
Sbjct: 193 AAGTR 197
>gnl|CDD|236532 PRK09470, cpxA, two-component sensor protein; Provisional.
Length = 461
Score = 26.0 bits (58), Expect = 8.3
Identities = 12/58 (20%), Positives = 24/58 (41%)
Query: 5 RRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDS 62
R+ + SE+ + + +A D D RR+ R ++ +R++L S
Sbjct: 37 RQMTELLDSEQRQGLMIEQHIEAELANDPPNDLMWWRRLFRAIDKWAPPGQRLLLVTS 94
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 0.137 0.392
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,414,463
Number of extensions: 679790
Number of successful extensions: 578
Number of sequences better than 10.0: 1
Number of HSP's gapped: 572
Number of HSP's successfully gapped: 24
Length of query: 144
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 56
Effective length of database: 7,034,450
Effective search space: 393929200
Effective search space used: 393929200
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: 54 (24.5 bits)