RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 013857
(435 letters)
>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 = 186 bits (475), Expect = 5e-57
Identities = 59/118 (50%), Positives = 78/118 (66%)
Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
+L++KP G TS V K+RRL+ KKVGH GTLDP+ATG+L + +G+ATKL K
Sbjct: 3 LLLDKPAGLTSHDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEATKLSQYLLDADK 62
Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKV 429
Y RLGEAT T DA+ +I+ P + +E+I A +F GEI QVPPM+SA+KV
Sbjct: 63 TYRATVRLGEATDTDDAEGEIIETSPPPRLTEEEIEAALKAFTGEIEQVPPMYSAVKV 120
>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 = 166 bits (422), Expect = 5e-50
Identities = 54/100 (54%), Positives = 69/100 (69%)
Query: 330 RRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDAD 389
+R++ KKVGH GTLDP+ATG+L VCVGKATKL+ K Y RLG AT T DA+
Sbjct: 1 KRILGAKKVGHTGTLDPLATGVLPVCVGKATKLLQYLLDADKEYRATIRLGVATDTLDAE 60
Query: 390 SPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKV 429
+++ P +HI +E I + ASF GEI QVPPM+SA+KV
Sbjct: 61 GEIVEEPPVDHITEEKIEEVLASFTGEIEQVPPMYSAVKV 100
>gnl|CDD|235113 PRK03287, truB, tRNA pseudouridine synthase B; Provisional.
Length = 298
Score = 162 bits (412), Expect = 1e-46
Identities = 61/133 (45%), Positives = 79/133 (59%), Gaps = 4/133 (3%)
Query: 297 STELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCV 356
+P T G +V+V+KP G TS V + RRL +KVGHAGTLDPMATG+L++ V
Sbjct: 1 MMAMPLTGSG----LVVVDKPAGMTSHDVVARCRRLFGTRKVGHAGTLDPMATGVLVLGV 56
Query: 357 GKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGE 416
+ATKL+ K Y+ RLG+AT+T DA+ V+ + DE I A A+ GE
Sbjct: 57 ERATKLLGHLTLTDKSYTATIRLGQATTTDDAEGEVLASADASAVTDEAIAAAVAALTGE 116
Query: 417 IWQVPPMFSAIKV 429
I QVP SAIKV
Sbjct: 117 IMQVPSAVSAIKV 129
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal
structure and biogenesis].
Length = 271
Score = 140 bits (354), Expect = 1e-38
Identities = 49/121 (40%), Positives = 72/121 (59%), Gaps = 17/121 (14%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
++ ++KP G TS V ++R++ V+K GH GTLDP+ATG+L +C+G+ATKLV
Sbjct: 17 VINLDKPPGPTSHEVVAWVKRILGVEKAGHGGTLDPLATGVLPICLGEATKLVQYLLDAD 76
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVR 430
K Y RLG+ T + +E++R A +F GEI+Q+PPMFSA+K
Sbjct: 77 KEYVATVRLGDQTDS-----------------EEEVRAALEAFTGEIYQIPPMFSAVKRE 119
Query: 431 V 431
V
Sbjct: 120 V 120
>gnl|CDD|178886 PRK00130, truB, tRNA pseudouridine synthase B; Provisional.
Length = 290
Score = 138 bits (351), Expect = 6e-38
Identities = 57/117 (48%), Positives = 82/117 (70%)
Query: 314 VNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGY 373
+ KP G TSF V K+R++ K+KKVGH GTLDP+A+G+L VC+GKATK+VD K Y
Sbjct: 7 ILKPPGMTSFDVVRKIRKIAKIKKVGHTGTLDPLASGVLPVCLGKATKIVDYLMEGKKTY 66
Query: 374 SGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVR 430
+LG T T+D + +++ + H+ +E+IR+A SF+GEI QVPPM+SA+K+
Sbjct: 67 RAEIKLGVETDTYDREGEILKEKEVSHLTEEEIREAILSFQGEIDQVPPMYSALKIN 123
>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 = 135 bits (342), Expect = 1e-37
Identities = 58/118 (49%), Positives = 76/118 (64%), Gaps = 1/118 (0%)
Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
+L++KP+G TSF K+RRL+ VKKVGH GTLDP ATG+L + VGKATKL + K
Sbjct: 5 LLLDKPQGMTSFDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKATKLSPYLTDLDK 64
Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKV 429
Y RLG T T D D +++ P + D+ A +FRGEI Q+PPM+SA+KV
Sbjct: 65 EYRAEIRLGVRTDTLDPDGQIVETRPVNPTTE-DVEAALPTFRGEIEQIPPMYSALKV 121
>gnl|CDD|179469 PRK02755, truB, tRNA pseudouridine synthase B; Provisional.
Length = 295
Score = 136 bits (345), Expect = 5e-37
Identities = 57/124 (45%), Positives = 77/124 (62%), Gaps = 2/124 (1%)
Query: 306 GPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDR 365
G FG + L +KP G TS +LRRL+++K+VGH GTLDP ATG+L + +GKAT+L+
Sbjct: 1 GMFGFLNL-DKPAGLTSHDCVARLRRLLRLKRVGHGGTLDPAATGVLPIALGKATRLL-P 58
Query: 366 YQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFS 425
Y K Y G R G TST D ++ +PW H+ +I A FRG+I Q PP +S
Sbjct: 59 YLPGEKTYRGTIRFGVRTSTDDLQGEILSSQPWPHLSLAEIETALPQFRGKIEQRPPQYS 118
Query: 426 AIKV 429
AI+V
Sbjct: 119 AIQV 122
>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 = 132 bits (334), Expect = 2e-36
Identities = 54/119 (45%), Positives = 79/119 (66%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
+ V+KP+G +S V +RR+ +KVGH GTLDP ATG+L+V +GKATKL+
Sbjct: 2 LFAVDKPQGPSSHDVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKATKLLKHLLAAT 61
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKV 429
K Y+ + RLG+AT T+DA VI+ P++HI E + +A + G+I QVPP++SA+K
Sbjct: 62 KDYTAIGRLGQATDTFDATGQVIEETPYDHITHEQLERALETLTGDIQQVPPLYSAVKR 120
>gnl|CDD|234959 PRK01550, truB, tRNA pseudouridine synthase B; Provisional.
Length = 304
Score = 132 bits (333), Expect = 3e-35
Identities = 55/119 (46%), Positives = 78/119 (65%), Gaps = 1/119 (0%)
Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
+L++KP+G TS KLR++++ KKVGH GTLDP +G+L +CVG+ATK+ + K
Sbjct: 5 LLLHKPRGMTSHDCVFKLRKILRTKKVGHTGTLDPEVSGVLPICVGRATKIAEYLTDEGK 64
Query: 372 GYSGVFRLGEATSTWDADSPVIQREPW-EHIKDEDIRKAAASFRGEIWQVPPMFSAIKV 429
Y G LG +T+T DAD V++ +P I E+I A AS G I Q+PPM+SA+KV
Sbjct: 65 TYEGEVTLGFSTTTEDADGEVVETKPVDRPITREEIEAALASLTGTIEQIPPMYSAVKV 123
>gnl|CDD|235333 PRK05033, truB, tRNA pseudouridine synthase B; Provisional.
Length = 312
Score = 126 bits (319), Expect = 4e-33
Identities = 51/122 (41%), Positives = 73/122 (59%), Gaps = 9/122 (7%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATK----LVDRY 366
++L++KP+G +S K++RL K GH G LDP+ATG+L +C+G+ATK L+D
Sbjct: 12 VLLLDKPQGMSSNDALQKVKRLFNANKAGHTGALDPLATGMLPICLGEATKFSQYLLDSD 71
Query: 367 QGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSA 426
K Y RLG+ T T DAD V++ P + E + A FRG+I QVP M+SA
Sbjct: 72 ----KRYRVTARLGQRTDTSDADGEVVEERPVT-LSAEQLEAALEKFRGDIEQVPSMYSA 126
Query: 427 IK 428
+K
Sbjct: 127 LK 128
>gnl|CDD|234986 PRK01851, truB, tRNA pseudouridine synthase B; Provisional.
Length = 303
Score = 125 bits (316), Expect = 9e-33
Identities = 52/118 (44%), Positives = 69/118 (58%), Gaps = 1/118 (0%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
++L++KP G +S + +RL++ KK GH GTLDP+ATGLL +C G+ATK
Sbjct: 18 VLLLDKPLGLSSNDALQRAKRLLRAKKAGHTGTLDPLATGLLPLCFGEATKFSQDLLDAD 77
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIK 428
K Y RLG TST DA+ V+ P + A A F GEI QVPPM+SA+K
Sbjct: 78 KTYEATLRLGVRTSTGDAEGEVLATRP-VDCDPAALEAALARFTGEIRQVPPMYSALK 134
>gnl|CDD|235442 PRK05389, truB, tRNA pseudouridine synthase B; Provisional.
Length = 305
Score = 125 bits (315), Expect = 1e-32
Identities = 49/118 (41%), Positives = 66/118 (55%), Gaps = 1/118 (0%)
Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
++++KP G TS K++ L +K GHAGTLDP+A+G+L + +G+ATK V K
Sbjct: 16 LILDKPAGMTSTEAVSKVKWLFDAQKAGHAGTLDPLASGVLPIALGEATKTVPYVMDGTK 75
Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKV 429
Y GE T D + V DE+IR A +F GEI QVPP FSAIK+
Sbjct: 76 RYRFTVAWGEERDTDDLEGEVTATSD-VRPTDEEIRAALPAFTGEIMQVPPQFSAIKI 132
>gnl|CDD|235042 PRK02484, truB, tRNA pseudouridine synthase B; Provisional.
Length = 294
Score = 123 bits (311), Expect = 3e-32
Identities = 49/117 (41%), Positives = 70/117 (59%), Gaps = 1/117 (0%)
Query: 314 VNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGY 373
+ K G TS KLR++++ KK+GH GTLDP G+L + VGKAT+L++ K Y
Sbjct: 8 LKKEAGMTSHDAVFKLRKILQTKKIGHGGTLDPDVVGVLPIAVGKATRLIEYMTEAGKVY 67
Query: 374 SGVFRLGEATSTWDADSPVIQREPWEHIKDED-IRKAAASFRGEIWQVPPMFSAIKV 429
G LG +T+T DA V+ P E+ + +A SF G+I Q+PPM+SA+KV
Sbjct: 68 EGEITLGYSTTTEDASGEVVAETPLTQPLTEEEVDQAMTSFTGKITQIPPMYSAVKV 124
>gnl|CDD|179199 PRK00989, truB, tRNA pseudouridine synthase B; Provisional.
Length = 230
Score = 118 bits (296), Expect = 8e-31
Identities = 56/121 (46%), Positives = 81/121 (66%), Gaps = 4/121 (3%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVG-KATKLVDRYQGM 369
++LV+KP+G TSF++ L +L+ VKK+GHAGTLDP ATG++++ +G K T+L D
Sbjct: 11 ILLVDKPQGRTSFSLIRSLTKLIGVKKIGHAGTLDPFATGVMVMLIGRKFTRLSDILLFE 70
Query: 370 IKGYSGVFRLGEATSTWDADSPVIQREPWEHIKD-EDIRKAAASFRGEIWQVPPMFSAIK 428
K Y+ V LG T ++D D ++ R + I E++ AA+ F+GEI QVPPMFSA K
Sbjct: 71 DKEYAAVAHLGTTTDSYDCDGKIVGRS--KKIPTLEEVLSAASYFQGEIQQVPPMFSAKK 128
Query: 429 V 429
V
Sbjct: 129 V 129
>gnl|CDD|172614 PRK14124, PRK14124, tRNA pseudouridine synthase B; Provisional.
Length = 308
Score = 112 bits (281), Expect = 7e-28
Identities = 54/118 (45%), Positives = 75/118 (63%), Gaps = 1/118 (0%)
Query: 313 LVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKG 372
+ KPKG TS V ++R+ +K +KVGHAGTLDP ATG+LIV V KAT+L++ + K
Sbjct: 7 VAYKPKGPTSHDVVDEVRKKLKTRKVGHAGTLDPFATGVLIVGVNKATRLLEYLKNEKKV 66
Query: 373 YSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVR 430
Y RLG T T+D V++ ++ +E+IR+A SF GE QVPP +SA K +
Sbjct: 67 YYVKMRLGLITETFDITGEVVEERE-CNVTEEEIREAIFSFVGEYKQVPPAYSAKKYK 123
>gnl|CDD|211344 cd02867, PseudoU_synth_TruB_4, Pseudouridine synthase homolog 4.
This group consists of Eukaryotic TruB proteins similar
to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4,
makes psi55 in the T loop of both cytoplasmic and
mitochondrial tRNAs. Psi55 is almost universally
conserved. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi).
Length = 312
Score = 109 bits (273), Expect = 7e-27
Identities = 45/102 (44%), Positives = 68/102 (66%), Gaps = 1/102 (0%)
Query: 328 KLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWD 387
K R+ K+K +GH GTLDP+ATG+L+V VG TK + Y K Y G +T+T+D
Sbjct: 49 KGRKRSKLK-IGHGGTLDPLATGVLVVGVGAGTKQLQDYLSCSKTYEATGLFGASTTTYD 107
Query: 388 ADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKV 429
+ +++++P+ HI EDI + A FRG+I QVPP++SA+K+
Sbjct: 108 REGKILKKKPYSHITREDIEEVLAKFRGDIKQVPPLYSALKM 149
>gnl|CDD|184521 PRK14122, PRK14122, tRNA pseudouridine synthase B; Provisional.
Length = 312
Score = 104 bits (261), Expect = 3e-25
Identities = 48/116 (41%), Positives = 66/116 (56%)
Query: 314 VNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGY 373
V+KP G TS V + RR + ++VGH GTLDP+ATG+L++C +TKLV K Y
Sbjct: 6 VDKPLGLTSHDVVNRARRALGTRRVGHTGTLDPLATGVLVLCTDDSTKLVPFLSAEDKEY 65
Query: 374 SGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKV 429
G T T DA+ P+ + P + ++D+ A F G QVPP +SAIKV
Sbjct: 66 LAWVSFGATTPTLDAEGPISEEAPVSPLDEKDLEAALPGFLGLTEQVPPQYSAIKV 121
>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 = 98.9 bits (247), Expect = 2e-24
Identities = 41/118 (34%), Positives = 62/118 (52%), Gaps = 18/118 (15%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
++ ++KP G +S V ++R++ V+K GH+GTLDP TG L VC+ +AT+LV Q
Sbjct: 4 VINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAG 63
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIK 428
K Y V RL + +E +R+ F G I+Q PP+ SA+K
Sbjct: 64 KEYVCVMRLHDDVD------------------EEKVRRVLEEFTGAIFQRPPLISAVK 103
>gnl|CDD|184522 PRK14123, PRK14123, tRNA pseudouridine synthase B; Provisional.
Length = 305
Score = 100 bits (251), Expect = 8e-24
Identities = 46/118 (38%), Positives = 68/118 (57%), Gaps = 2/118 (1%)
Query: 314 VNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGY 373
V K +G TS V KLR+++K KK+GH GTLDP G+L VC+G AT++ D M K Y
Sbjct: 8 VYKERGLTSHDVVFKLRKILKTKKIGHTGTLDPEVAGVLPVCIGNATRVSDYVMDMGKAY 67
Query: 374 SGVFRLGEATSTWDADSPVIQREPWE--HIKDEDIRKAAASFRGEIWQVPPMFSAIKV 429
+G +T+T D ++ + +DI + F+G I Q+PPM+S++KV
Sbjct: 68 EATVSIGRSTTTEDQTGDTLETKGVHSADFNKDDIDRLLEQFKGIIEQIPPMYSSVKV 125
>gnl|CDD|179870 PRK04642, truB, tRNA pseudouridine synthase B; Provisional.
Length = 300
Score = 100 bits (250), Expect = 9e-24
Identities = 46/122 (37%), Positives = 67/122 (54%)
Query: 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRY 366
++L++KP G +S RRL++ +K GH G+LDP+ATGLL +C G+ATK+
Sbjct: 8 RLDGILLLDKPAGLSSNNALQAARRLLRAEKGGHTGSLDPLATGLLPLCFGEATKIAGLL 67
Query: 367 QGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSA 426
G K Y LG T T DAD V++ P + ++ A A G I Q P++SA
Sbjct: 68 LGSAKAYDAEIVLGVTTDTDDADGQVLRERPVPDLSAAALQAALAPLIGRIRQRAPIYSA 127
Query: 427 IK 428
+K
Sbjct: 128 LK 129
>gnl|CDD|134035 PRK00020, truB, tRNA pseudouridine synthase B; Provisional.
Length = 244
Score = 96.6 bits (240), Expect = 6e-23
Identities = 45/124 (36%), Positives = 69/124 (55%), Gaps = 2/124 (1%)
Query: 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRY 366
++L++KP G +S + +R V K GH GTLDP ATGLL+ C+G+ATK+ R
Sbjct: 8 ALDGVLLLDKPVGLSSNHALQRAKRTVDAAKAGHTGTLDPFATGLLVCCMGRATKISGRM 67
Query: 367 QGMIKGYSGVFRLGEATSTWDADSPVIQREP--WEHIKDEDIRKAAASFRGEIWQVPPMF 424
K Y + GE T + D ++ R P + +++ +R + F G I Q+PPM+
Sbjct: 68 LEADKTYQATLQFGEETDSGDLTGHIVARAPDGFAGVEEAALRDVLSRFVGTIEQIPPMY 127
Query: 425 SAIK 428
SA+K
Sbjct: 128 SALK 131
>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 = 91.0 bits (226), Expect = 2e-20
Identities = 44/118 (37%), Positives = 62/118 (52%), Gaps = 18/118 (15%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
+V ++KP G +S V +RR++ V+K GH GTLDP TG+L VC+ +AT+LV Q
Sbjct: 36 VVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVCIERATRLVKSQQEAP 95
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIK 428
K Y + RL K+EDI + F G I+Q PP+ SA+K
Sbjct: 96 KEYVCLMRLHRD------------------AKEEDILRVLKEFTGRIFQRPPLKSAVK 135
>gnl|CDD|179806 PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p;
Reviewed.
Length = 300
Score = 87.6 bits (218), Expect = 2e-19
Identities = 48/123 (39%), Positives = 64/123 (52%), Gaps = 22/123 (17%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
+V ++KP G TS V +R ++ V+K GH GTLDP TG+L V +GKATK+V
Sbjct: 24 VVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQALLESG 83
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEH--IKDEDIRKAAASFRGEIWQVPPMFSAIK 428
K Y V L H + +EDIRK F GEI+Q PP+ SA+K
Sbjct: 84 KEYVCVMHL--------------------HGDVPEEDIRKVFKEFTGEIYQKPPLKSAVK 123
Query: 429 VRV 431
R+
Sbjct: 124 RRL 126
>gnl|CDD|179381 PRK02193, truB, tRNA pseudouridine synthase B; Provisional.
Length = 279
Score = 81.7 bits (202), Expect = 2e-17
Identities = 43/117 (36%), Positives = 66/117 (56%)
Query: 313 LVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKG 372
L+ KPKG +SF + +KK+GH GTLDP+A+GLL+V + TKL+D K
Sbjct: 4 LLYKPKGISSFKFIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDEDTKLIDYLDQKDKT 63
Query: 373 YSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKV 429
Y + G ++T+D++ +I + E++ +A + G QVPP+FSA KV
Sbjct: 64 YIAKIKFGFISTTYDSEGQIINVSQNIKVTKENLEEALNNLVGSQKQVPPVFSAKKV 120
>gnl|CDD|179739 PRK04099, truB, tRNA pseudouridine synthase B; Provisional.
Length = 273
Score = 78.8 bits (195), Expect = 2e-16
Identities = 47/125 (37%), Positives = 61/125 (48%), Gaps = 13/125 (10%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
+ + NKP G +S +L+R VKK G +GTLDP A G+LIV G+ TKL +
Sbjct: 4 LFVANKPAGMSSNAFLSRLKRKYGVKKAGFSGTLDPFAKGVLIVAFGQYTKLFRFLKKTP 63
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKD------EDIRKAAASFRGEIWQVPPMF 424
K Y LG A SP + E E I+ + I K S +GEI PP F
Sbjct: 64 KTYRATLWLG-------ASSPSLDIENIESIQIIKPFDKDLIEKILKSLQGEISYTPPKF 116
Query: 425 SAIKV 429
SA K+
Sbjct: 117 SAKKI 121
>gnl|CDD|179300 PRK01528, truB, tRNA pseudouridine synthase B; Provisional.
Length = 292
Score = 69.6 bits (170), Expect = 3e-13
Identities = 42/116 (36%), Positives = 64/116 (55%), Gaps = 1/116 (0%)
Query: 314 VNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGY 373
+ KP+G +S + +++++ K+GHAGTLD A G+L + VG+ATKLV K Y
Sbjct: 8 IYKPRGISSAKLVSIVKKILGKVKIGHAGTLDVEAEGVLPLAVGEATKLVQLLIDAKKTY 67
Query: 374 SGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKV 429
+ G+ T + D VI + + K E+ + F G I Q+PP FSA+KV
Sbjct: 68 IFTVKFGKQTDSGDYAGKVIATKDYIPSK-EEAYAVCSKFIGNITQIPPAFSALKV 122
>gnl|CDD|237834 PRK14846, truB, tRNA pseudouridine synthase B; Provisional.
Length = 345
Score = 65.1 bits (158), Expect = 1e-11
Identities = 39/116 (33%), Positives = 61/116 (52%), Gaps = 1/116 (0%)
Query: 314 VNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGY 373
+ KP+G +S + +++++ K+GHAGTLD A G+L VG+ATKL+ K Y
Sbjct: 8 IYKPRGISSAQLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEATKLIHLLIDARKTY 67
Query: 374 SGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKV 429
+ G T++ D VI + E+ + F G + Q+PP FSA+KV
Sbjct: 68 IFTVKFGMQTNSGDCAGKVIATKDCIP-SQEEAYAVCSKFIGNVTQIPPAFSALKV 122
>gnl|CDD|211324 cd01291, PseudoU_synth, Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). Pseudouridine
synthases contains the RsuA/RluD, TruA, TruB and TruD
families. This group consists of eukaryotic, bacterial
and archeal pseudouridine synthases. Some psi sites such
as psi55,13,38 and 39 in tRNA are highly conserved,
being in the same position in eubacteria, archeabacteria
and eukaryotes. Other psi sites occur in a more
restricted fashion, for example psi2604in 23S RNA made
by E.coli RluF has only been detected in E.coli. Human
dyskerin with the help of guide RNAs makes the hundreds
of psueudouridnes present in rRNA and small nuclear RNAs
(snRNAs). Mutations in human dyskerin cause X-linked
dyskeratosis congenitas. Missense mutation in human PUS1
causes mitochondrial myopathy and sideroblastic anemia
(MLASA).
Length = 87
Score = 41.4 bits (98), Expect = 5e-05
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 314 VNKPKGWTSFTVCGKLRRL-VKVKKVGHAGTLDPMATGLLIVC 355
+ KP G T + L + K+VG+AG D A +V
Sbjct: 1 LYKPGGDTMEAARQLAKLLGIPPKRVGYAGRKDKRAVTTQLVS 43
>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 = 34.7 bits (80), Expect = 0.060
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 344 LDPMATGLLIVCVGKATKLVDR-YQGM-IKGYSGVFRLGEATSTWDADSPVIQREPWEHI 401
LD ++G+L++ V KL+ Y + Y+ LG+AT + VI++ ++HI
Sbjct: 40 LDAFSSGVLVLGVNHGNKLLSHLYSNHPTRVYTIRGLLGKATENFFHTGRVIEKTTYDHI 99
Query: 402 KDEDIRKAAASFRGE 416
E I + A +
Sbjct: 100 TREKIERLLAVIQSG 114
>gnl|CDD|216150 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase. 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 RluD, a
pseudouridylate synthase that converts specific uracils
to pseudouridine in 23S rRNA. RluA from E. coli converts
bases in both rRNA and tRNA.
Length = 149
Score = 32.4 bits (74), Expect = 0.23
Identities = 12/71 (16%), Positives = 24/71 (33%), Gaps = 11/71 (15%)
Query: 312 VLVNKPKGWTS---------FTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKL 362
++VNKP G L + ++ LD +GLL+ + K +
Sbjct: 2 IVVNKPAGVPVHPTDPSDLLSLTALLLVAELGKFRLYPVHRLDRNTSGLLL--LAKDGEA 59
Query: 363 VDRYQGMIKGY 373
++ +
Sbjct: 60 ANKLNKLFPER 70
>gnl|CDD|187793 cd09662, Csm5_III-A, CRISPR/Cas system-associated RAMP superfamily
protein Csm5. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
RAMP superfamily protein.
Length = 365
Score = 30.1 bits (68), Expect = 2.3
Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 2/67 (2%)
Query: 220 KAGGKSEEKKYNKEDDKRLVFFDDQEKKSEKDSILGEDVNVKGEVSEKKVEEFFKCLKKV 279
K G E ++Y + D E+ + +K EEF K K+V
Sbjct: 233 KRGLDRENERYLPCLPFNK--LIIIKINDASDHTKNEEAETELSDVQKAYEEFRKLEKEV 290
Query: 280 PNKENEV 286
NK E+
Sbjct: 291 NNKVGEI 297
>gnl|CDD|217233 pfam02794, HlyC, RTX toxin acyltransferase family. Members of this
family are enzymes EC:2.3.1.-. involved in fatty
acylation of the protoxins (HlyA) at lysine residues,
thereby converting them to the active toxin. Acyl-acyl
carrier protein (ACP) is the essential acyl donor. This
family show a number of conserved residues that are
possible candidates for participation in acyl transfer.
Site-directed mutagenesis of the single conserved
histidine residue in E. coli hlyC resulted in complete
inactivation of the enzyme.
Length = 134
Score = 28.0 bits (63), Expect = 4.9
Identities = 10/41 (24%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 184 HYKMVY-QLEKKYFPDQCLDKAFLDPSADQNVKKMRKKAGG 223
H + +Y L ++ FP Q + D + K M + G
Sbjct: 92 HARAIYRDLRRRIFPGQKVRALRYDKGGQKRGKIMEFRGGA 132
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.0 bits (64), Expect = 7.3
Identities = 26/111 (23%), Positives = 46/111 (41%), Gaps = 3/111 (2%)
Query: 180 EKDKHYKMVYQLEKKYFPDQCLDKAFLDPSADQNVKKMRKKAGGKSEEKKYNKEDDKRLV 239
K K ++ E+K +Q K + + +KK ++ K+ E+ E+DK+
Sbjct: 1618 AKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKA 1677
Query: 240 FFDDQEKKSEKDSILGEDVNVKGEVSEKKVEEFFKCLKKVPNKENEVGSGE 290
++ KK+E+D + K KK EE K + K E+ E
Sbjct: 1678 ---EEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAE 1725
>gnl|CDD|215124 PLN02195, PLN02195, cellulose synthase A.
Length = 977
Score = 28.8 bits (64), Expect = 7.9
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 9/66 (13%)
Query: 77 VNSTNSDENQNPDGELGFDSWVDKKLEKEAKTRQPGSDNAEMTKSMRKYYNKRRQRMYGT 136
V+S +DE NP + +SW DKK +K+ ++ + A++ Q+M
Sbjct: 101 VDSELNDEYGNPIWKNRVESWKDKKNKKKKSAKKKEAHKAQIPP---------EQQMEEK 151
Query: 137 DSEDEY 142
S D Y
Sbjct: 152 PSADAY 157
>gnl|CDD|148609 pfam07100, ASRT, Anabaena sensory rhodopsin transducer. The family
of bacterial Anabaena sensory rhodopsin transducers are
likely to bind sugars or related metabolites. The entire
protein is comprised of a single globular domain with an
eight-stranded beta-sandwich fold. There are a few
characteristics which define this beta-sandwich fold as
being distinct from other so-named folds, and these are:
1) a well conserved tryptophan, usually following a
polar residue, present at the start of the first strand;
this tryptophan appears to be central to a hydrophobic
interaction required to hold the two beta-sheets of the
sandwich together, and 2) a nearly absolutely conserved
asparagine located at the end of the second beta-strand,
that hydrogen bonds with the backbone carbonyls of the
residues 2 and 4 positions downstream from it, thereby
stabilising the characteristic tight turn between
strands 2 and 3 of the structure.
Length = 120
Score = 27.3 bits (61), Expect = 8.5
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 154 PEVVEFNRLHKREEELYFYDTFAYP 178
P VV+ +RL R+ E T AYP
Sbjct: 96 PVVVQHSRLDSRQAENALMSTIAYP 120
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 28.3 bits (64), Expect = 9.6
Identities = 19/65 (29%), Positives = 32/65 (49%)
Query: 207 DPSADQNVKKMRKKAGGKSEEKKYNKEDDKRLVFFDDQEKKSEKDSILGEDVNVKGEVSE 266
A + +KK+ +KA K EE+K K+ ++E++ EK+ E + E E
Sbjct: 405 SKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEE 464
Query: 267 KKVEE 271
+K EE
Sbjct: 465 EKEEE 469
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
0.315 0.133 0.394
Gapped
Lambda K H
0.267 0.0629 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,302,258
Number of extensions: 2165640
Number of successful extensions: 1584
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1547
Number of HSP's successfully gapped: 74
Length of query: 435
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 335
Effective length of database: 6,502,202
Effective search space: 2178237670
Effective search space used: 2178237670
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 60 (27.1 bits)