RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13081
(335 letters)
>gnl|CDD|211336 cd02569, PseudoU_synth_ScPus3, Pseudouridine synthase,
Saccharomyces cerevisiae Pus3 like. This group consists
of eukaryotic pseudouridine synthases similar to S.
cerevisiae Pus3p, mouse Pus3p and, human PUS2.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required. S.
cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse
Pus3p has been shown to makes psi38 and, possibly also
psi 39, in tRNAs. Psi38 and psi39 are highly conserved
in tRNAs from eubacteria, archea and eukarya.
Length = 256
Score = 357 bits (919), Expect = e-124
Identities = 125/260 (48%), Positives = 168/260 (64%), Gaps = 13/260 (5%)
Query: 6 LKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGVSAFCQ 65
L+ Y G+NY+GF +Q + NT+ L +AL+KT LIED++ S+++ CGRTD GVSAF Q
Sbjct: 1 LRFAYLGWNYNGFAVQEETTNTVEETLFEALEKTRLIEDRQTSNYSRCGRTDKGVSAFGQ 60
Query: 66 VVTLKIRSKLTSPGEES---------DDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSAR 116
V++L +RS L D+ ELPY K+LN LP DI+++AW+PVP +SAR
Sbjct: 61 VISLDVRSNLKPEDGLDPSTDVKSTADEEELPYCKILNRVLPPDIRILAWAPVPPDFSAR 120
Query: 117 FDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFRRLVTHAGVT 176
F C+ R Y+Y+FP+ LDI+ M KAA+ L+G HDFRN CKM+V N V N+ R V A V
Sbjct: 121 FSCVSRTYRYFFPKGDLDIELMRKAAKLLLGEHDFRNFCKMDVANQVTNYVRRVLSAEV- 179
Query: 177 SAWQNVQFNDSHHNICEFNIRSQGFLWHQIRCIMSVLFLVGQGNEKPEIIQQLVDIEKYP 236
+ V + + F +R FLWHQ+RC+M+VLFL+GQG E P +I QL+D+EK P
Sbjct: 180 ---EPVDQHPDGDGLYYFEVRGSAFLWHQVRCMMAVLFLIGQGLEPPSVISQLLDVEKNP 236
Query: 237 RKPVYPMVRGEPLNLYHTEF 256
RKP Y M PL LY F
Sbjct: 237 RKPQYTMASEVPLVLYDCGF 256
>gnl|CDD|223179 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal
structure and biogenesis].
Length = 266
Score = 203 bits (518), Expect = 6e-64
Identities = 85/278 (30%), Positives = 119/278 (42%), Gaps = 44/278 (15%)
Query: 1 MRPIALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGV 60
M+ IALKI Y G +HG+Q Q + T+ L KAL K E GRTD+GV
Sbjct: 1 MKRIALKIAYDGTRFHGWQRQPN-VRTVQGELEKALSKIG----GESVRVIGAGRTDAGV 55
Query: 61 SAFCQVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCL 120
A QVV +D ++ LN LP DI+V+ + VP+ + ARF
Sbjct: 56 HALGQVVHFDT---------PADRPLEKLVRALNALLPPDIRVLDVAEVPDDFHARFSAK 106
Query: 121 FRNYKYWFPQAG----------------LDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVV 164
R Y+Y A LD+DAM +AA+ L+GTHDF + K G
Sbjct: 107 SRTYRYIIYNAPLRPPFLANYVWHVPYPLDLDAMREAAKLLLGTHDFTSFRK--AGCQSK 164
Query: 165 NFRRLVTHAGVTSAWQNVQFNDSHHNICEFNIRSQGFLWHQIRCIMSVLFLVGQGNEKPE 224
+ R + V+ ++ +I FLWH +R I+ L LVG+G E
Sbjct: 165 SPVRTIYRIDVS----------RDGDLIVIDISGNSFLWHMVRNIVGALLLVGRGKRPVE 214
Query: 225 IIQQLVDIEKYPRKPVYPMVRGEPLNLYHTEFDNLTWH 262
I++L +E RK P E L L ++
Sbjct: 215 WIKEL--LEAKDRKLAGPTAPAEGLYLVRVDYPEDFEL 250
>gnl|CDD|232810 TIGR00071, hisT_truA, tRNA pseudouridine(38-40) synthase. Members
of this family are the tRNA modification enzyme TruA,
tRNA pseudouridine(38-40) synthase. In a few species
(e.g. Bacillus anthracis), TruA is represented by two
paralogs [Protein synthesis, tRNA and rRNA base
modification].
Length = 227
Score = 179 bits (455), Expect = 5e-55
Identities = 85/256 (33%), Positives = 120/256 (46%), Gaps = 37/256 (14%)
Query: 2 RPIALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGVS 61
R IALKI Y G NYHG+Q Q + T+ L KAL+ K+K + GRTD GV
Sbjct: 1 RKIALKIAYDGSNYHGWQRQPNK-RTVQGELEKALEAI----GKKKITIMSAGRTDKGVH 55
Query: 62 AFCQVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLF 121
A QV++ ++ DN+L LN LP DI+V A +PV + + ARF
Sbjct: 56 AMGQVISFDTPKEIP-------DNKLNA--KLNALLPPDIRVKALAPVNDNFHARFSASK 106
Query: 122 RNYKYWFP-----QAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFRRLVTHAGVT 176
R+Y+Y + LD++ M AA+ L+G HDF N K +
Sbjct: 107 RHYRYILYNHRHYYSPLDLEKMRAAAKQLLGKHDFSNFSKAK--------------SKSR 152
Query: 177 SAWQNVQ---FNDSHHNICEFNIRSQGFLWHQIRCIMSVLFLVGQGNEKPEIIQQLVDIE 233
S + + ++S I F+I FLWH +R I+ L LVG+G PE + +L+D +
Sbjct: 153 SPIRTISDIKVSESGEYII-FDIIGNSFLWHMVRKIVGALVLVGRGKLPPEWVAKLLDAK 211
Query: 234 KYPRKPVYPMVRGEPL 249
K P G L
Sbjct: 212 KRNLAPTTAPANGLYL 227
>gnl|CDD|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated.
Length = 244
Score = 178 bits (454), Expect = 1e-54
Identities = 84/270 (31%), Positives = 114/270 (42%), Gaps = 46/270 (17%)
Query: 1 MRPIALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGV 60
M IAL I Y G N+HG+Q Q + T+ L KAL K E GRTD+GV
Sbjct: 1 MMRIALTIEYDGTNFHGWQRQPN-GRTVQGELEKALSKLA----GEPVRVIGAGRTDAGV 55
Query: 61 SAFCQVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCL 120
A QV + + + LN LP DI V+ VP+ + ARF
Sbjct: 56 HALGQVAHFDT---------PAPRPPEKWRRALNALLPDDIAVLWAEEVPDDFHARFSAK 106
Query: 121 FRNYKY-----------------WFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGV 163
R Y+Y +P LD+DAM++AAQYL+G HDF + G
Sbjct: 107 ARRYRYRIYNRPARPPFLRGYVWHYPYP-LDVDAMNEAAQYLLGEHDFTSFRA--SGCQS 163
Query: 164 VNFRRLVTHAGVTSAWQNVQFNDSHHNICEFNIRSQGFLWHQIRCIMSVLFLVGQGNEKP 223
+ R + A VT + F+I + GFL + +R I+ L VG+G P
Sbjct: 164 KSPVRTIYEADVT----------REGDFIVFDISANGFLHNMVRNIVGTLLEVGKGKRPP 213
Query: 224 EIIQQLVDIEKYPRKPVYPMVRGEPLNLYH 253
E I++L +E R P E L L
Sbjct: 214 EDIKEL--LEAKDRTLAGPTAPAEGLYLVE 241
>gnl|CDD|211322 cd00497, PseudoU_synth_TruA_like, Pseudouridine synthase, TruA
family. This group consists of eukaryotic, bacterial
and archeal pseudouridine synthases similar to
Escherichia coli TruA, Saccharomyces cerevisiae Pus1p,
S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and
human PUS1. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. S. cerevisiae PUS1 catalyzes the formation of
psi34 and psi36 in the intron containing tRNAIle, psi35
in the intron containing tRNATyr, psi27 and/or psi28 in
several yeast cytoplasmic tRNAs and, psi44 in U2 small
nuclear RNA (U2 snRNA). The presence of the intron is
required for the formation of psi 34, 35 and 36. In
addition S. cerevisiae PUS1 makes psi 26, 65 and 67. C.
elegans Pus1p does not modify psi44 in U2 snRNA. S.
cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Psi44
in U2 snRNA and, psi38 and psi39 in tRNAs are highly
phylogenetically conserved. Psi 26,27,28,34,35,36,65
and 67 in tRNAs are less highly conserved. Mouse Pus1p
regulates nuclear receptor activity through
pseudouridylation of Steroid Receptor RNA Activator.
Missense mutation in human PUS1 causes mitochondrial
myopathy and sideroblastic anemia (MLASA).
Length = 215
Score = 169 bits (431), Expect = 1e-51
Identities = 71/247 (28%), Positives = 97/247 (39%), Gaps = 34/247 (13%)
Query: 10 YQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGVSAFCQVVTL 69
Y G YHGFQ Q + T+ L+ AL K RTD GVSA QVV +
Sbjct: 3 YDGTKYHGFQRQ-NDVPTVEGELIIALLK-AGNIPYF---IKAAARTDRGVSALGQVVAI 57
Query: 70 KIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFP 129
+ +LT LN LP DI+V A VP + A C R Y+Y+ P
Sbjct: 58 ETERRLTPE-------------ALNGILPGDIRVFAVHSVPPDFHAPRYCDHRTYRYYIP 104
Query: 130 QAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFRRLVTHAGVTSAWQNVQFNDSHH 189
LD + + AA +GTHDF N K N R + V
Sbjct: 105 SFPLDDERLKSAASRFLGTHDFTNFSK----KDTRNTVRTIISIECKDLNPFVV------ 154
Query: 190 NICEFNIRSQGFLWHQIRCIMSVLFLVGQGNEKPEIIQQLVDIEKYPRKPVYPMVRGEPL 249
+++ FLWHQ+R ++ L LVG+G P + +L+ E L
Sbjct: 155 ----VEFKAKSFLWHQVRRMVGFLMLVGEGLHSPSSVSRLLAGP--APPIPMVPAPAEGL 208
Query: 250 NLYHTEF 256
L ++
Sbjct: 209 LLVDVKY 215
>gnl|CDD|211337 cd02570, PseudoU_synth_EcTruA, Eukaryotic and bacterial
pseudouridine synthases similar to E. coli TruA. This
group consists of eukaryotic and bacterial pseudouridine
synthases similar to E. coli TruA, Pseudomonas
aeruginosa truA and human pseudouridine synthase-like 1
(PUSL1). Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. E. coli TruA makes psi38/39 and/or 40 in tRNA.
psi38 and psi39 in tRNAs are highly phylogenetically
conserved. P. aeruginosa truA is required for induction
of type III secretory genes and may act through
modifying tRNAs critical for the expression of type III
genes or their regulators.
Length = 239
Score = 151 bits (385), Expect = 2e-44
Identities = 81/269 (30%), Positives = 114/269 (42%), Gaps = 48/269 (17%)
Query: 6 LKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGVSAFCQ 65
L I Y G N+ G+Q Q + T+ L KAL K E GRTD+GV A Q
Sbjct: 1 LTIEYDGTNFSGWQRQPN-GRTVQGELEKALSKIA----GEPVRVIGAGRTDAGVHALGQ 55
Query: 66 VVTLKIRSKLTSPGEESDDNELPYLKM-LNNNLPRDIKVVAWSPVPEKYSARFDC----- 119
V S++ L L LN+ LP DI+V++ VP+ + ARF
Sbjct: 56 VAHFDTPSEIP----------LEKLIKALNSLLPPDIRVLSAEEVPDDFHARFSAKSRTY 105
Query: 120 ------------LFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFR 167
R Y + P+ LDI+AM +AA+ L+GTHDF + G +
Sbjct: 106 RYRILNRPVPSPFLRRYVWHVPRP-LDIEAMQEAAKLLLGTHDFSSFRA--AGCQSKSTV 162
Query: 168 RLVTHAGVTSAWQNVQFNDSHHNICEFNIRSQGFLWHQIRCIMSVLFLVGQGNEKPEIIQ 227
R + A +V F IR+ GFL+H +R I+ L VG+G PE I+
Sbjct: 163 RTIYRA-------DVYREGDLI---VFEIRANGFLYHMVRNIVGTLLEVGRGKLSPEDIK 212
Query: 228 QLVDIEKYPRKPVYPMVRGEPLNLYHTEF 256
++ +E R P L L E+
Sbjct: 213 EI--LEAKDRTAAGPTAPAHGLYLVKVEY 239
>gnl|CDD|237759 PRK14589, PRK14589, tRNA pseudouridine synthase ACD; Provisional.
Length = 265
Score = 148 bits (376), Expect = 8e-43
Identities = 78/262 (29%), Positives = 120/262 (45%), Gaps = 32/262 (12%)
Query: 1 MRPIALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGV 60
MR +A +I Y G + G Q Q T+ + A ++ L D ++ FA GRTD GV
Sbjct: 1 MR-LAFRISYIGTRFFGSQYQPDQ-RTVEGEFIAACRRLGLFSDWREAGFALAGRTDRGV 58
Query: 61 SAFCQVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCL 120
A QV+ S ++ LN LP DI W+ VPE + R+D +
Sbjct: 59 HARGQVLAF------------STHKPERAVEALNGQLPPDIWCTGWAEVPESFHPRYDAI 106
Query: 121 FRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFRRLVTHAGVTSAWQ 180
R Y+Y+F + DI+AM AA +GTHDF ++ + V R + V
Sbjct: 107 SRTYRYYFSRPPSDINAMRDAAGEFIGTHDFSCFARVEGKSPV----RTILRIRV----- 157
Query: 181 NVQFNDSHHNICEFNIRSQGFLWHQIRCIMSVLFLVGQGNEKPEIIQQLVDIEKYPRKPV 240
F+D F + +Q FLWH +RC+ L +G+G +P+ I++L+ ++ V
Sbjct: 158 ---FSDG--GFPVFEVTAQSFLWHMVRCMAGALLQIGEGEMEPDDIERLLSGPC--KRKV 210
Query: 241 YPMVRGEPLNLYHTEFDNLTWH 262
P E L L+ + LT+
Sbjct: 211 KP-APAEGLVLWDVDCG-LTFT 230
>gnl|CDD|211343 cd02866, PseudoU_synth_TruA_Archea, Archeal pseudouridine
synthases. This group consists of archeal pseudouridine
synthases.Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. This group of proteins make Psedouridine in
tRNAs.
Length = 219
Score = 133 bits (336), Expect = 1e-37
Identities = 76/251 (30%), Positives = 117/251 (46%), Gaps = 32/251 (12%)
Query: 6 LKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGVSAFCQ 65
LKI Y G N+HGFQ Q T+ L+KAL++ +IE + + GRTD GV A
Sbjct: 1 LKIAYDGTNFHGFQRQPDVR-TVEGELIKALEELGIIESRAR--LYSAGRTDRGVHALGN 57
Query: 66 VVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYK 125
VV E++ P M+N LP+DI V+A + VPE + R + Y+
Sbjct: 58 VVVF-----------ETEKE--PIPPMINAKLPKDIWVLAGAKVPEDFDPRRWAHRKYYR 104
Query: 126 YWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFRRLVTHAGVTSAWQNVQFN 185
Y D++AM +AA+ L+GTHDF N K + V R + ++
Sbjct: 105 YNLGS-DYDVEAMKEAAKKLIGTHDFSNFSKRDGRKDPV---RTIERIEIS--------- 151
Query: 186 DSHHNICEFNIRSQGFLWHQIRCIMSVLFLVGQGNEKPEIIQQLVDIEKYPRKPVYPMVR 245
+ ++ + FLW+ +R I+ L VG+G + E +++L+D E P P
Sbjct: 152 -ENGEFITIDVVGESFLWNMVRRIVGALSEVGKGKRENEWVEKLLDGEFRPEG--VPPAP 208
Query: 246 GEPLNLYHTEF 256
E L L ++
Sbjct: 209 PEGLILVDVKY 219
>gnl|CDD|211335 cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine synthase, PUS1/
PUS2 like. This group consists of eukaryotic
pseudouridine synthases similar to Saccharomyces
cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis
elegans Pus1p and human PUS1. Pseudouridine synthases
catalyze the isomerization of specific uridines in an
RNA molecule to pseudouridines (5-ribosyluracil, psi).
No cofactors are required. S. cerevisiae Pus1p catalyzes
the formation of psi34 and psi36 in the
intron-containing tRNAIle, psi35 in the
intron-containing tRNATyr, psi27 and/or psi28 in several
yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear
RNA (U2 snRNA). The presence of the intron is required
for the formation of psi 34, 35 and 36. In addition S.
cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans
Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p
makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle,
psi 34/36 in tRNAIle and, psi 32 and potentially 67 in
tRNAVal. Psi44 in U2 snRNA and psi32 in tRNAs are
highly phylogenetically conserved. Psi
26,27,28,34,35,36,65 and 67 in tRNAs are less highly
conserved. Mouse Pus1p regulates nuclear receptor
activity through pseudouridylation of Steroid Receptor
RNA Activator. Missense mutation in human PUS1 causes
mitochondrial myopathy and sideroblastic anemia (MLASA).
Length = 245
Score = 113 bits (285), Expect = 1e-29
Identities = 66/258 (25%), Positives = 106/258 (41%), Gaps = 28/258 (10%)
Query: 10 YQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLI-----EDKEKSSFACCGRTDSGVSAFC 64
Y G YHG Q + TI L +AL K I D +K F+ RTD GV A
Sbjct: 5 YCGTGYHGMQYNPGAYKTIEGELERALFKAGAISESNAGDPKKIGFSRAARTDKGVHAAR 64
Query: 65 QVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNY 124
VV+LK+ + E E ++ LN++LP DI+V + V + ++AR C R Y
Sbjct: 65 NVVSLKV---IIDDPEGLGILED-LVEKLNSHLPSDIRVFGITRVTKSFNARKACDSRTY 120
Query: 125 KYWFPQAGLD-IDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFRRLVTHAGVTSAWQNVQ 183
+Y P L+ + ++ + VGTH+F N R + ++
Sbjct: 121 EYLLPTFALETLQRFNEILKEYVGTHNFHNFTVKKKFEDPSANRFI----------KSFY 170
Query: 184 FNDSH-----HNICEFNIRSQGFLWHQIRCIMSVLFLVGQGNEKPEIIQQLVDIEKYPRK 238
++ I Q F+ HQIR ++ + + +G +I+ + +K
Sbjct: 171 VSEPFVIEEGLEWISIKIHGQSFMLHQIRKMIGLAIAIVRGGAPESLIELSFNKDKI--- 227
Query: 239 PVYPMVRGEPLNLYHTEF 256
+ P+ G L L F
Sbjct: 228 IIIPLAPGLGLLLERPHF 245
>gnl|CDD|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed.
Length = 245
Score = 100 bits (251), Expect = 6e-25
Identities = 71/251 (28%), Positives = 104/251 (41%), Gaps = 43/251 (17%)
Query: 1 MRPIALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGV 60
MR I L I Y G Y G+Q ++DNTI + L + E+ CGRTD+GV
Sbjct: 1 MRNIKLTIQYDGSRYKGWQKLGNNDNTIQGKIESVLSEMT----GEEIEIIGCGRTDAGV 56
Query: 61 SAFCQVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARF--- 117
A QV + KL+ E K LN LP DI V V E++ AR+
Sbjct: 57 HALNQVANFQTDEKLS---------EDKIKKYLNEYLPNDIVVTNVEEVDERFHARYNVK 107
Query: 118 --------------DCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGV 163
+ R Y + LD+ AM +AA+YLVG+HDF +
Sbjct: 108 SKTYLYKIWNEKFHNVFMRKYSMHVNEK-LDVKAMKEAAKYLVGSHDFTSFTNAK-SKKK 165
Query: 164 VNFRRLVTHAGVTSAWQNVQFNDSHHNICEFNIRSQGFLWHQIRCIMSVLFLVGQGNEKP 223
R + + ++ D + + GFL + +R I+ L VG G K
Sbjct: 166 STVREIYS--------IDIMEED---GFVQIRVSGNGFLHNMVRIIVGALIEVGLGQLKA 214
Query: 224 EIIQQLVDIEK 234
E I+Q+++ +
Sbjct: 215 EDIKQILEAKD 225
>gnl|CDD|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional.
Length = 245
Score = 96.0 bits (239), Expect = 3e-23
Identities = 70/250 (28%), Positives = 110/250 (44%), Gaps = 47/250 (18%)
Query: 1 MRPIALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGV 60
M+ +A + Y G N+ G+Q Q T+ AL++ K++ GRTD+GV
Sbjct: 1 MKRVAAVVSYDGSNFFGYQGQPDV-RTVQGVFEDALERIF----KQRIYTQAAGRTDTGV 55
Query: 61 SAFCQVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDC- 119
A QV+ P + + ++ +N NLP DI V VP+ + RFD
Sbjct: 56 HANGQVIAFN------CPNDRMTEEDIK--NAMNANLPDDIYVKKVFEVPKNFHPRFDAK 107
Query: 120 ---------------LF-RNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGV 163
+F R Y +WFP LD++AM KAA+YL G HDF + G+
Sbjct: 108 KRIYHYFILTSKEKNVFLRKYVWWFPYE-LDLEAMRKAAKYLEGEHDFTSFKT---GSDE 163
Query: 164 VNFRRLVTHAGVTSAWQNVQFNDSHHNICEFNIRSQG--FLWHQIRCIMSVLFLVGQGNE 221
N R + + +++ IR +G FL +R I+ L VG G
Sbjct: 164 RNPVRTIYRIRILRLKKDLIL-----------IRVEGRSFLRRMVRNIVGALVKVGLGQW 212
Query: 222 KPEIIQQLVD 231
+PE I+++++
Sbjct: 213 EPEKIKEVLE 222
>gnl|CDD|216487 pfam01416, PseudoU_synth_1, tRNA pseudouridine synthase. Involved
in the formation of pseudouridine at the anticodon stem
and loop of transfer-RNAs Pseudouridine is an isomer of
uridine (5-(beta-D-ribofuranosyl) uracil, and id the
most abundant modified nucleoside found in all cellular
RNAs. The TruA-like proteins also exhibit a conserved
sequence with a strictly conserved aspartic acid, likely
involved in catalysis.
Length = 103
Score = 78.6 bits (194), Expect = 3e-18
Identities = 29/117 (24%), Positives = 45/117 (38%), Gaps = 14/117 (11%)
Query: 141 AAQYLVGTHDFRNLCKMNVGNGVVNFRRLVTHAGVTSAWQNVQFNDSHHNICEFNIRSQG 200
AA+ GTHDF K + R + G+ + + F I+ G
Sbjct: 1 AAKLYDGTHDFSGFQKQRTVQK--SLIRTIESIGI----------ERDGELLVFEIKGNG 48
Query: 201 FLWHQIRCIMSVLFLVGQGNEKPEIIQQLVDIEKYPRKPVYPMVRGEPLNLYHTEFD 257
FL+HQ+R ++ L G+G E + L + R P L L+H +D
Sbjct: 49 FLYHQVRIMVGALLRTGKGVHALEQVVSL--LNSKLRPRAPPTAPAVGLYLFHVRYD 103
Score = 37.4 bits (87), Expect = 0.001
Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 13/77 (16%)
Query: 6 LKILYQGF-NYHGFQIQTSSDNTIAHHLLKA---LQKTCLIEDKEKSSF---------AC 52
LY G ++ GFQ Q + ++ + L+ + + + F
Sbjct: 1 AAKLYDGTHDFSGFQKQRTVQKSLIRTIESIGIERDGELLVFEIKGNGFLYHQVRIMVGA 60
Query: 53 CGRTDSGVSAFCQVVTL 69
RT GV A QVV+L
Sbjct: 61 LLRTGKGVHALEQVVSL 77
>gnl|CDD|173052 PRK14588, PRK14588, tRNA pseudouridine synthase ACD; Provisional.
Length = 272
Score = 74.9 bits (184), Expect = 2e-15
Identities = 70/238 (29%), Positives = 94/238 (39%), Gaps = 45/238 (18%)
Query: 1 MRPIALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGV 60
MR IAL + Y G ++ G Q QT T+ L A Q L +++ + A GRTD+GV
Sbjct: 1 MRTIALLLEYDGTDFAGSQWQTDG-RTVQGALEAAWQA--LTQERRRIVLA--GRTDAGV 55
Query: 61 SAFCQV--VTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFD 118
A QV V R L + + LN +LP DI V P + ARF
Sbjct: 56 HARGQVAHVQTDTRHSLAT-----------IWRGLNAHLPEDIGVQNAWEAPPDFHARFS 104
Query: 119 CLFRNYKYWFPQAG----------------LDIDAMHKAAQYLVGTHDFRNLCKMNVGNG 162
+ R Y+Y A LD+ AM A + L+GTHDF
Sbjct: 105 AIQREYRYVIDCAPAPSPQLRHQVLHYAGTLDVAAMDAALKLLIGTHDFAAFTTAPQEGS 164
Query: 163 VVNFRRLVTHAGVTSA-WQNVQFNDSHHNICEFNIRSQGFLWHQIRCIMSVLFLVGQG 219
V R A T W + + + FL H +R I+ L LVG+G
Sbjct: 165 TV---RTCYWARCTDTEWFG-------RPLLAIEVAANAFLQHMVRNIVGTLLLVGRG 212
>gnl|CDD|173051 PRK14587, PRK14587, tRNA pseudouridine synthase ACD; Provisional.
Length = 256
Score = 65.6 bits (160), Expect = 3e-12
Identities = 49/149 (32%), Positives = 69/149 (46%), Gaps = 29/149 (19%)
Query: 3 PIALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIEDKEKSSFACCGRTDSGVSA 62
P +I Y G ++GF T N++ L + E + S RTD GVSA
Sbjct: 2 PYLYRIAYDGTLFYGF---TGHPNSLEPALRRVFG-----EILGRGS-----RTDPGVSA 48
Query: 63 FCQVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFR 122
VV +TS +LP L +N+ LPR + A + VPE ++ R R
Sbjct: 49 VGNVV-------MTS-------QKLP-LGYVNSKLPRGVWAWAVAEVPEGFNPR-RAKRR 92
Query: 123 NYKYWFPQAGLDIDAMHKAAQYLVGTHDF 151
Y Y P G D++AM +AA+ L GTHD+
Sbjct: 93 RYLYVAPHWGEDVEAMREAAELLAGTHDY 121
>gnl|CDD|215562 PLN03078, PLN03078, Putative tRNA pseudouridine synthase;
Provisional.
Length = 513
Score = 65.3 bits (159), Expect = 1e-11
Identities = 41/165 (24%), Positives = 74/165 (44%), Gaps = 9/165 (5%)
Query: 4 IALKILYQGFNYHGFQIQ--TSSDNTIAHHLLKALQKTCLIEDK-----EKSSFACCGRT 56
+ L++ Y G +Y G Q Q SS +TI L A+ K I + K +A RT
Sbjct: 73 VVLRVGYVGTDYRGLQKQRDLSSLSTIEGELETAIFKAGGIRESNYGNLHKIGWARSSRT 132
Query: 57 DSGVSAFCQVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSAR 116
D GV + +++LK+ ++ + D + + K +N++LP +I+V + P + R
Sbjct: 133 DKGVHSLATMISLKM--EIPENAWKDDPDGIALAKFINSHLPDNIRVFSILPAQRSFDPR 190
Query: 117 FDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGN 161
+C R Y Y P + I + + + +F ++ G
Sbjct: 191 RECDLRKYSYLLPAEVIGIKSGFSSEEIDEHISEFNSILNGFEGE 235
>gnl|CDD|220446 pfam09860, DUF2087, Uncharacterized protein conserved in bacteria
(DUF2087). This domain, found in various hypothetical
prokaryotic proteins and transcriptional activators, has
no known function. Structural modelling suggests this
domain may bind nucleic acids.
Length = 71
Score = 29.0 bits (66), Expect = 0.59
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 262 HYDEIEVSHVLRDLHEDWSLL 282
Y E EV+ +L+ HED++LL
Sbjct: 29 EYSEKEVNAILKRFHEDYALL 49
>gnl|CDD|227402 COG5070, VRG4, Nucleotide-sugar transporter [Carbohydrate transport
and metabolism / Posttranslational modification, protein
turnover, chaperones / Intracellular trafficking and
secretion].
Length = 309
Score = 28.3 bits (63), Expect = 6.3
Identities = 29/114 (25%), Positives = 45/114 (39%), Gaps = 24/114 (21%)
Query: 121 FRNYKYWFPQAGLDIDAM----HKAAQYL-VGTHD-FRNLCKMNVGNGVVNFRR------ 168
K WFP + L + M K+ QYL V + F+NL + + G V F
Sbjct: 65 LTKAKKWFPISFL-LVVMIYTSSKSLQYLAVPIYTIFKNLTIILIAYGEVLFFGGRVTSL 123
Query: 169 ------LVTHAGVTSAWQNVQFNDSHHNICEFNIRSQGFLWHQIRCIMSVLFLV 216
L+ + V + W + Q + I N G+LW C+ S F++
Sbjct: 124 ELLSFILMVLSSVVATWGDQQASAFKAQI--LNP---GYLWMFTNCLSSAAFVL 172
>gnl|CDD|136048 PRK06781, PRK06781, amidophosphoribosyltransferase; Provisional.
Length = 471
Score = 28.4 bits (63), Expect = 6.3
Identities = 20/54 (37%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 4 IALKILYQGFNYHGFQIQTSSDNTIAHHLLKALQKTCLIED------KEKSSFA 51
I K+L + G QTSSD + HL+K K LIE K K +FA
Sbjct: 116 INAKMLRRELEAEGSIFQTSSDTEVLLHLIKRSTKDSLIESVKEALNKVKGAFA 169
>gnl|CDD|226533 COG4047, COG4047, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 243
Score = 27.9 bits (62), Expect = 7.3
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 135 IDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFR 167
+D +KA YL ++ + N +V+++
Sbjct: 22 VDPQYKAVSYLSKGIGSTKFVRLAIANALVSYQ 54
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 28.5 bits (63), Expect = 7.8
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 6/81 (7%)
Query: 244 VRGEPLNLYHTEFDNLTWHYDEIEVSHVLRDL------HEDWSLLSIKATMLGEMIKDTV 297
+GE N + +L + + ++ + DL ED + I + G D V
Sbjct: 1263 NKGEDKNKFLMSSLDLHLSHKKNQIKEIFHDLDAKKPADEDANPEQIFEELAGNESNDDV 1322
Query: 298 RESKCTMGDLDINHLIEGEFS 318
+ C MGD+D H+I ++
Sbjct: 1323 TGAPCPMGDIDAEHIIGDDYD 1343
>gnl|CDD|217795 pfam03923, Lipoprotein_16, Uncharacterized lipoprotein. The
function of this presumed lipoprotein is unknown. The
family includes E. coli YajG.
Length = 159
Score = 26.8 bits (60), Expect = 9.9
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 8 ILYQGFNYHGFQIQTSSDNTIAHHLLKAL 36
L Q G++I +S+N + + + L
Sbjct: 55 ALQQQLTSQGYRIDPNSNNNLQLQVNELL 83
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
0.322 0.137 0.427
Gapped
Lambda K H
0.267 0.0813 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,927,166
Number of extensions: 1586478
Number of successful extensions: 1225
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1175
Number of HSP's successfully gapped: 28
Length of query: 335
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 238
Effective length of database: 6,635,264
Effective search space: 1579192832
Effective search space used: 1579192832
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 (21.9 bits)
S2: 59 (26.3 bits)