RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4559
(336 letters)
>gnl|CDD|211345 cd02868, PseudoU_synth_hTruB2_like, Pseudouridine synthase,
humanTRUB2_like. This group consists of eukaryotic
pseudouridine synthases similar to human TruB
pseudouridine synthase homolog 2 (TRUB2). Pseudouridine
synthases catalyze the isomerization of specific
uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi).
Length = 226
Score = 132 bits (335), Expect = 3e-37
Identities = 45/106 (42%), Positives = 74/106 (69%)
Query: 188 RQAGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIR 247
V SQ+A ++A +G IRPA P++YG++ + F+PP+FT+EV CI E +E+L +
Sbjct: 121 ELCSVDDQSQQAAELAARGLIRPADKSPPIIYGIRLLEFRPPEFTLEVQCINETQEYLRK 180
Query: 248 LIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENI 293
LI+++G +LRS+A+CT ++ R F ++ +LLRK W +Q++I NI
Sbjct: 181 LIHEIGLELRSSAVCTQVRRTRDGPFTVDDALLRKQWNLQNIISNI 226
Score = 58.2 bits (141), Expect = 6e-10
Identities = 21/65 (32%), Positives = 39/65 (60%), Gaps = 4/65 (6%)
Query: 95 LQKVLKIIDN--NNCLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKP 152
++++L +I + F V SQ+A ++A +G IRPA P++YG++ + F+P
Sbjct: 104 IERLLAVIQSGHQQKAFEL--CSVDDQSQQAAELAARGLIRPADKSPPIIYGIRLLEFRP 161
Query: 153 PDFTI 157
P+FT+
Sbjct: 162 PEFTL 166
>gnl|CDD|211323 cd00506, PseudoU_synth_TruB_like, Pseudouridine synthase, TruB
family. This group consists of eukaryotic, bacterial
and archeal pseudouridine synthases similar to
Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M.
tuberculosis TruB, S. cerevisiae Cbf5 and human
dyskerin. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. E. coli TruB, M. tuberculosis TruB and S.
cerevisiae Pus4, make psi55 in the T loop of tRNAs.
Pus4 catalyses the formation of psi55 in both
cytoplasmic and mitochondrial tRNAs. Psi55 is almost
universally conserved. 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.
Mutations in human dyskerin cause X-linked dyskeratosis
congenitas.
Length = 210
Score = 67.9 bits (166), Expect = 2e-13
Identities = 31/95 (32%), Positives = 52/95 (54%)
Query: 190 AGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIRLI 249
+ V+ Q AY++AR+G + P + P +Y L C+ F PP F +EV + E ++ LI
Sbjct: 116 SAVKRQGQRAYELARRGLLVPDEARPPTIYELLCIRFNPPHFLLEVEVVCETGTYIRTLI 175
Query: 250 YDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHW 284
+DLG +L A T ++ R F +E+++ H
Sbjct: 176 HDLGLELGVGAHVTELRRTRVGPFKVENAVTLHHL 210
Score = 37.5 bits (87), Expect = 0.004
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 114 AGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKPPDFTI 157
+ V+ Q AY++A +G + P + P +Y L C+ F PP F +
Sbjct: 116 SAVKRQGQRAYELARRGLLVPDEARPPTIYELLCIRFNPPHFLL 159
>gnl|CDD|216540 pfam01509, TruB_N, TruB family pseudouridylate synthase (N terminal
domain). Members of this family are involved in
modifying bases in RNA molecules. They carry out the
conversion of uracil bases to pseudouridine. This family
includes TruB, a pseudouridylate synthase that
specifically converts uracil 55 to pseudouridine in most
tRNAs. This family also includes Cbf5p that modifies
rRNA.
Length = 149
Score = 46.7 bits (112), Expect = 2e-06
Identities = 14/46 (30%), Positives = 25/46 (54%)
Query: 192 VRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHC 237
V++N + Y++AR+G + +Y L+ + F P+ T EV C
Sbjct: 98 VKVNGKRLYELAREGIEVERPPRPVTIYSLELLEFDLPEVTFEVSC 143
Score = 31.3 bits (72), Expect = 0.31
Identities = 10/42 (23%), Positives = 21/42 (50%)
Query: 116 VRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKPPDFTI 157
V++N + Y++A +G + +Y L+ + F P+ T
Sbjct: 98 VKVNGKRLYELAREGIEVERPPRPVTIYSLELLEFDLPEVTF 139
>gnl|CDD|211339 cd02573, PseudoU_synth_EcTruB, Pseudouridine synthase, Escherichia
coli TruB like. This group consists of bacterial
pseudouridine synthases similar to E. coli TruB and
Mycobacterium tuberculosis TruB. Pseudouridine synthases
catalyze the isomerization of specific uridines in an
RNA molecule to pseudouridines (5-ribosyluracil, psi).
E. coli TruB and M. tuberculosis TruB make psi55 in the
T loop of tRNAs. Psi55 is nearly universally conserved.
E. coli TruB is not inhibited by RNA containing
5-fluorouridine.
Length = 213
Score = 42.4 bits (101), Expect = 1e-04
Identities = 29/97 (29%), Positives = 46/97 (47%), Gaps = 18/97 (18%)
Query: 192 VRLNSQEAYDIARQG-----PIRPALLKEPVVYGLKCVHF--KPPDFTIEVHC-IGEYEE 243
V+++ + Y++AR G P R +Y L+ + F + P+ EVHC G Y
Sbjct: 118 VKVDGKRLYELARAGEEVERPPRKV-----TIYSLELLSFDPENPEADFEVHCSKGTY-- 170
Query: 244 FLIR-LIYDLGTKLRSAAICTSIQCIRFAQFGLEHSL 279
IR L DLG L A ++++ R F LE ++
Sbjct: 171 --IRSLARDLGKALGCGAHLSALRRTRSGPFTLEQAI 205
>gnl|CDD|235333 PRK05033, truB, tRNA pseudouridine synthase B; Provisional.
Length = 312
Score = 40.6 bits (96), Expect = 8e-04
Identities = 24/64 (37%), Positives = 32/64 (50%), Gaps = 16/64 (25%)
Query: 200 YDIARQG-----PIRPALLKEPVVYGLKCVHFKPPDFTIEVHCI-GEYEEFLIR-LIYDL 252
Y+ ARQG RP +Y L+ + F+ + +EVHC G Y IR L+ DL
Sbjct: 135 YEYARQGIEVEREARPI-----TIYELELIRFEGDELELEVHCSKGTY----IRTLVDDL 185
Query: 253 GTKL 256
G KL
Sbjct: 186 GEKL 189
>gnl|CDD|178886 PRK00130, truB, tRNA pseudouridine synthase B; Provisional.
Length = 290
Score = 39.9 bits (94), Expect = 0.001
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 15/93 (16%)
Query: 191 GVRLNSQEAYDIARQGPI--RPALLKEPVVYGLKCVHFKPPDFTIEVHCI-GEYEEFLIR 247
G +L Y++ARQG R A ++ +Y ++ + P +V C G Y IR
Sbjct: 124 GKKL-----YELARQGIEVEREA--RKITIYDIEILEIDLPYVIFDVKCSKGTY----IR 172
Query: 248 -LIYDLGTKLRSAAICTSIQCIRFAQFGLEHSL 279
L +D+G KL A ++ F +E+S+
Sbjct: 173 SLCFDIGEKLNCGAYMWNLIRTETGPFNIENSI 205
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal
structure and biogenesis].
Length = 271
Score = 38.4 bits (90), Expect = 0.003
Identities = 29/135 (21%), Positives = 50/135 (37%), Gaps = 24/135 (17%)
Query: 207 PIRPALLKEPV------VYGLKCVHFKPPDFTIEVHC-IGEYEEFLIR-LIYDLGTKLRS 258
P+ A+ K V +Y L + F T+ V C G Y IR L DLG L
Sbjct: 111 PMFSAV-KREVERRKITIYDLLELDFDRNLVTLRVECSKGTY----IRTLARDLGEALGC 165
Query: 259 AAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIENI--AHNETLVDKMDPMRPQLQSVNMT 316
A + ++ R F E ++ +E + E+L+ + P+ L +
Sbjct: 166 GAHMSELRRTRVGPFSEEDAVT---------LELLDELDAESLLRLLLPLESALSDLPRL 216
Query: 317 DSDSTDGSNVSDGNR 331
+ + + G +
Sbjct: 217 VLKDSAANAIKYGAK 231
>gnl|CDD|129523 TIGR00431, TruB, tRNA pseudouridine(55) synthase. TruB, the tRNA
pseudouridine 55 synthase, converts uracil to
pseudouridine in the T loop of most tRNAs in all three
domains of life. This model is built on a seed alignment
of bacterial proteins only. Saccharomyces cerevisiae
protein YNL292w (Pus4) has been shown to be the
pseudouridine 55 synthase of both cytosolic and
mitochondrial compartments, active at no other position
on tRNA and the only enzyme active at that position in
the species. A distinct yeast protein YLR175w,
(centromere/microtubule-binding protein CBF5) is an rRNA
pseudouridine synthase, and the archaeal set is much
more similar to CBF5 than to Pus4. It is unclear whether
the archaeal proteins found by this model are tRNA
pseudouridine 55 synthases like TruB, rRNA pseudouridine
synthases like CBF5, or (as suggested by the absence of
paralogs in the Archaea) both. CBF5 likely has
additional, eukaryotic-specific functions. The trusted
cutoff is set above the scores for the archaeal homologs
of unknown function, so yeast Pus4p scores between
trusted and noise [Protein synthesis, tRNA and rRNA base
modification].
Length = 209
Score = 37.3 bits (87), Expect = 0.005
Identities = 32/92 (34%), Positives = 48/92 (52%), Gaps = 8/92 (8%)
Query: 192 VRLNSQEAYDIARQGPIRPALLKEPV-VYGLKCVHFKPPDFTIEVHC-IGEYEEFLIR-L 248
+++N + Y+ ARQG I PV VY L+ + ++ P+ T+EVHC G Y IR L
Sbjct: 119 LKVNGKRLYEYARQG-IEVERKARPVTVYDLQFLKYEGPELTLEVHCSKGTY----IRTL 173
Query: 249 IYDLGTKLRSAAICTSIQCIRFAQFGLEHSLL 280
DLG KL A + ++ F L+ S+
Sbjct: 174 ARDLGEKLGCGAYVSHLRRTAVGDFPLDQSVT 205
>gnl|CDD|179469 PRK02755, truB, tRNA pseudouridine synthase B; Provisional.
Length = 295
Score = 36.9 bits (86), Expect = 0.009
Identities = 24/98 (24%), Positives = 45/98 (45%), Gaps = 19/98 (19%)
Query: 192 VRLNSQEAYDIARQG-----PIRPALLKEPVVYGLKCVHFKPPDF---TIEVHC-IGEYE 242
++++ + Y +AR+G P R ++ L+ + ++P D +E+HC G Y
Sbjct: 120 IQVDGERLYALARRGETMELPARTV-----TIFRLQLLDWRPGDQPELDLEIHCGAGTY- 173
Query: 243 EFLIRLI-YDLGTKLRSAAICTSIQCIRFAQFGLEHSL 279
IR + DLG L + +++ + F L SL
Sbjct: 174 ---IRSLARDLGAVLGTGGTLAALRRTQSLGFHLAQSL 208
>gnl|CDD|179381 PRK02193, truB, tRNA pseudouridine synthase B; Provisional.
Length = 279
Score = 33.2 bits (76), Expect = 0.16
Identities = 25/106 (23%), Positives = 50/106 (47%), Gaps = 16/106 (15%)
Query: 193 RLNSQEAYDIARQG---PIRPALLKEPVVYGLKCVHFKPPDFTIEVHCI---GEYEEFLI 246
++N + AYD+ARQG ++P +K + ++ ++F + G Y I
Sbjct: 119 KVNGKRAYDLARQGKQIELKPIEIK---ISKIELLNFDEKLQNCVFMWVVSRGTY----I 171
Query: 247 R-LIYDLGTKLRSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIE 291
R LI+DLG L++ A + ++ + L+ + L + +I+
Sbjct: 172 RSLIHDLGKMLKTGAYMSDLERTKIG--NLDKNFLNQSLNPLDLID 215
>gnl|CDD|172614 PRK14124, PRK14124, tRNA pseudouridine synthase B; Provisional.
Length = 308
Score = 32.4 bits (74), Expect = 0.33
Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 6/83 (7%)
Query: 200 YDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHC-IGEYEEFLIR-LIYDLGTKLR 257
Y +AR+G I KE +Y + + + PD + V G Y IR L D+G KL
Sbjct: 128 YKLAREGKIINLPPKEVKIYEIWDISIEGPDVSFRVEVSPGTY----IRSLCMDIGYKLG 183
Query: 258 SAAICTSIQCIRFAQFGLEHSLL 280
A + + +F +E S+
Sbjct: 184 CGATAVELVRLSVGKFSIEDSIN 206
>gnl|CDD|184804 PRK14720, PRK14720, transcript cleavage factor/unknown domain
fusion protein; Provisional.
Length = 906
Score = 30.1 bits (68), Expect = 2.2
Identities = 26/88 (29%), Positives = 39/88 (44%), Gaps = 11/88 (12%)
Query: 42 KDHKKINMTLLIKGWLSYMKNKKNITVLVSLIDLFVPALLPWQ--ETVTVPSIKPLQKVL 99
K+HKK L I G LS + N + L++LID F L W E + K+L
Sbjct: 59 KEHKKSISALYISGILSLSRRPLNDSNLLNLIDSFSQN-LKWAIVEHIC-------DKIL 110
Query: 100 KIIDNNNCLFVHRQAGVRLN-SQEAYDV 126
+N L +A +LN +++ V
Sbjct: 111 LYGENKLALRTLAEAYAKLNENKKLKGV 138
>gnl|CDD|237834 PRK14846, truB, tRNA pseudouridine synthase B; Provisional.
Length = 345
Score = 29.6 bits (66), Expect = 2.2
Identities = 19/90 (21%), Positives = 40/90 (44%)
Query: 190 AGVRLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVHCIGEYEEFLIRLI 249
+ +++N AY +AR+G + +Y LKC++F + T + ++ L
Sbjct: 118 SALKVNGVRAYKLAREGKKVELKPRNITIYDLKCLNFDEKNATATYYTECSKGTYIRTLA 177
Query: 250 YDLGTKLRSAAICTSIQCIRFAQFGLEHSL 279
DL L+S ++ + F E+++
Sbjct: 178 EDLALSLQSLGFVIELRRTQVGIFKEENAI 207
>gnl|CDD|218856 pfam06022, Cir_Bir_Yir, Plasmodium variant antigen protein
Cir/Yir/Bir. This family consists of several Cir, Yir
and Bir proteins from the Plasmodium species
P.chabaudi, P.yoelii and P.berghei.
Length = 279
Score = 28.3 bits (64), Expect = 4.7
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 31 FSKDSWLKSQRKDHKKINMTLLIKGWLSYMKNKKN 65
F S K+ K+ IN+ I WLSY N K+
Sbjct: 62 FGDSSSFKNSAKN--NINIVEYIIIWLSYKLNLKS 94
>gnl|CDD|129752 TIGR00669, asnA, aspartate--ammonia ligase, AsnA-type. This model
represents one of two non-homologous forms of
aspartate--ammonia ligase (asparagine synthetase) found
in E. coli. This type is also found in Haemophilus
influenzae, Treponema pallidum and Lactobacillus
delbrueckii, but appears to have a very limited
distribution. The fact that the protein from the H.
influenzae is more than 70 % identical to that from the
spirochete Treponema pallidum, but less than 65 %
identical to that from the closely related E. coli,
strongly suggests lateral transfer [Amino acid
biosynthesis, Aspartate family].
Length = 330
Score = 28.7 bits (64), Expect = 4.9
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 3/67 (4%)
Query: 257 RSAAICTSIQCIRFAQFGLEHSLLRKHWRVQHVIE-NIAHNETLVDKMDPMRPQLQSVNM 315
R A+ ++ I AQF + HSL + W+ + + + E L M +RP ++
Sbjct: 51 REKAVQVKVKAIPDAQFEVVHSLAK--WKRHTLARHDFSAGEGLFVHMKALRPDEDRLDP 108
Query: 316 TDSDSTD 322
S D
Sbjct: 109 LHSVYVD 115
>gnl|CDD|177477 PHA02695, PHA02695, hypothetical protein; Provisional.
Length = 725
Score = 28.8 bits (64), Expect = 5.3
Identities = 14/29 (48%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 178 NCLFVCLFVHRQAGVRLNSQ-EAYDIARQ 205
+ LF CLFVH GVRL Q + + RQ
Sbjct: 628 DALFRCLFVHIAMGVRLVEQVDVVVLVRQ 656
>gnl|CDD|234986 PRK01851, truB, tRNA pseudouridine synthase B; Provisional.
Length = 303
Score = 28.4 bits (64), Expect = 5.9
Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 10/83 (12%)
Query: 200 YDIARQGPI--RPALLKEPVVYGLKCVHFKPPDFTIEVHCI-GEYEEFLIR-LIYDLGTK 255
Y+ AR G R A ++ ++ L + PD TI V C G Y IR L D+G
Sbjct: 141 YEYARAGITVEREA--RDVTIHALDLLACDLPDVTIRVTCSKGTY----IRTLAEDIGEA 194
Query: 256 LRSAAICTSIQCIRFAQFGLEHS 278
L A T+++ LE +
Sbjct: 195 LGCGAHLTALRRTGVGGLTLEQA 217
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 0.138 0.429
Gapped
Lambda K H
0.267 0.0779 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,963,301
Number of extensions: 1611067
Number of successful extensions: 1068
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1067
Number of HSP's successfully gapped: 20
Length of query: 336
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 239
Effective length of database: 6,635,264
Effective search space: 1585828096
Effective search space used: 1585828096
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: 59 (26.4 bits)