RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8191
(257 letters)
>gnl|CDD|223638 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific
[Translation, ribosomal structure and biogenesis].
Length = 289
Score = 243 bits (622), Expect = 2e-80
Identities = 107/241 (44%), Positives = 145/241 (60%), Gaps = 8/241 (3%)
Query: 5 GYELIIIKPKKNFFLNKTEKKVIKLDIIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNL 64
G + I P++ + I LDI+YED +++++NK AGLVVHP G+ GTL + L
Sbjct: 55 GDVVRIPLPEEPEEEKLVPED-IPLDILYEDEDLLVVNKPAGLVVHPGGGHHEGTLVNAL 113
Query: 65 LEIYPFLINVPRAGIVHRLDKNSSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWG-I 123
L V R GIVHRLDK++SGL++VAK+ ++ L Q K V++ YLA+V G +
Sbjct: 114 L--RHCQDGVERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKKTYLALVRGHL 171
Query: 124 PKLNGMINAAIMRNPHNRIKMTVSKNFNAKPALTYYERLATGIINKKHISLIRCNLKTGR 183
P+ G I+A I R+P NR KM V K + KPA+T+YE L + +L+ +TGR
Sbjct: 172 PEDEGTIDAPIGRDPKNRKKMAVVKEGSGKPAITHYEVLE---RFGDNYTLVELKPETGR 228
Query: 184 THQIRVHMQWLGHGIVGDNLYG-KKYSKSLIFNRQALHAYKLGLIHPKNNLKLKWRINLP 242
THQIRVH+ LGH IVGD LYG K S RQALHAYKL HP +L++ LP
Sbjct: 229 THQIRVHLAHLGHPIVGDPLYGGKDKSAGAGLKRQALHAYKLSFTHPLTGEELEFEAPLP 288
Query: 243 D 243
+
Sbjct: 289 E 289
>gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family. In E.
coli, RluD (SfhB) modifies uridine to pseudouridine at
23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504
and 2580, and RluA modifies U746 and tRNA U32. An
additional homolog from E. coli outside this family,
TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to
pseudouridine [Protein synthesis, tRNA and rRNA base
modification].
Length = 299
Score = 236 bits (603), Expect = 2e-77
Identities = 105/231 (45%), Positives = 144/231 (62%), Gaps = 11/231 (4%)
Query: 26 VIKLDIIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHRLDK 85
I LDI++ED +II++NK +GLVVHP GN GT+ + LL P + V R GIVHRLD+
Sbjct: 69 DIPLDILFEDEDIIVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGIVHRLDR 128
Query: 86 NSSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIPK-LNGMINAAIMRNPHNRIKM 144
++SGLMVVAK+ + L QLK V ++Y+A+V G G ++A + R P+NR M
Sbjct: 129 DTSGLMVVAKTPLALRELQRQLKNRTVTKEYVALVHGQFDSGGGTVDAPLGRVPNNRGLM 188
Query: 145 TVSKNFNAKPALTYYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDNLY 204
V + KPA+T++ L + SL+ C L+TGRTHQIRVH+Q+LGH + GD LY
Sbjct: 189 AVHPSSEGKPAVTHFRVLE----RFGNASLVECELETGRTHQIRVHLQYLGHPLAGDPLY 244
Query: 205 GKK------YSKSLIFNRQALHAYKLGLIHPKNNLKLKWRINLPDDISKLI 249
G K + L F+RQALHAY+LG IHP L++ LP D+ L+
Sbjct: 245 GNKPVPGNNLNGLLNFDRQALHAYELGFIHPATGEILEFEAPLPADLVLLL 295
>gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional.
Length = 325
Score = 219 bits (560), Expect = 1e-70
Identities = 102/237 (43%), Positives = 142/237 (59%), Gaps = 23/237 (9%)
Query: 27 IKLDIIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHRLDKN 86
I LDI+YED++I+++NK LVVHP GN GT+ + LL YP + +VPRAGIVHRLDK+
Sbjct: 82 IPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKD 141
Query: 87 SSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIPKLNGMINAAIMRNPHNRIKMTV 146
++GLMVVAK++ + LV L+ + R+Y A+ G G ++ I R+P R M V
Sbjct: 142 TTGLMVVAKTVPAQTRLVEALQKREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAV 201
Query: 147 SKNFNAKPALTYY---ERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDNL 203
KPA+T+Y E + H + +R L+TGRTHQIRVHM + H +VGD +
Sbjct: 202 HP--MGKPAVTHYRIMEHF------RVH-TRLRLRLETGRTHQIRVHMAHITHPLVGDQV 252
Query: 204 YG------KKYSKSLI-----FNRQALHAYKLGLIHPKNNLKLKWRINLPDDISKLI 249
YG K S+ I F+RQALHA L L HP ++++W LP D+ +LI
Sbjct: 253 YGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPLPQDMVELI 309
>gnl|CDD|211346 cd02869, PseudoU_synth_RluCD_like, Pseudouridine synthase,
RsuA/RluD family. This group is comprised of
eukaryotic, bacterial and archeal proteins similar to
eight site specific Escherichia coli pseudouridine
synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and
TruA. Pseudouridine synthases catalyze the
isomerization of specific uridines in a n RNA molecule
to pseudouridines (5-ribosyluracil, psi) requiring no
cofactors. E. coli RluC for example makes psi955, 2504
and 2580 in 23S RNA. Some psi sites such as psi1917 in
23S RNA made by RluD are universally conserved. Other
psi sites occur in a more restricted fashion, for
example psi2819 in 21S mitochondrial ribosomal RNA made
by S. cerevisiae Pus5p is only found in mitochondrial
large subunit rRNAs from some other species and in gram
negative bacteria. The E. coli counterpart of this psi
residue is psi2580 in 23S rRNA. psi2604in 23S RNA made
by RluF has only been detected in E.coli.
Length = 185
Score = 204 bits (522), Expect = 7e-67
Identities = 79/189 (41%), Positives = 115/189 (60%), Gaps = 4/189 (2%)
Query: 38 IIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHRLDKNSSGLMVVAKSI 97
++++NK AGL VHP G+L+GTL + LL++ L R G+VHRLDK++SGL++VAK+
Sbjct: 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNK 60
Query: 98 KSYIHLVNQLKMHIVQRKYLAMVWGIPKLNGMINAAIMRNPHNRIKMTVSKNFNAKPALT 157
K+ L Q K V++ YLA+V G P + A + + + V + + KPA+T
Sbjct: 61 KAAAKLSKQFKERKVKKTYLALVDGKPPEDEGTIDAPLGRKKRKKRARVVVSEDGKPAIT 120
Query: 158 YYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDNLYGKKYSKSLIFNRQ 217
+Y+ L +++L+ L+TGRTHQIRVH+ +GH IVGD YG K S S R
Sbjct: 121 HYKVLERF----GNVTLVELQLETGRTHQIRVHLASIGHPIVGDPKYGGKASDSPGLKRL 176
Query: 218 ALHAYKLGL 226
ALHAY+L
Sbjct: 177 ALHAYRLSF 185
>gnl|CDD|211331 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synthases similar to
Saccharomyces cerevisiae RIB2. Pseudouridine synthase,
Saccharomyces cerevisiae RIB2_like. This group is
comprised of eukaryotic and bacterial proteins similar
to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p
and human hRPUDSD2. S. cerevisiae RIB2 displays two
distinct catalytic activities. The N-terminal domain of
RIB2 is RNA:psi-synthase which makes psi32 on
cytoplasmic tRNAs. Psi32 is highly phylogenetically
conserved. The C-terminal domain of RIB2 has a DRAP
deaminase activity which catalyses the formation of
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione
5'-phosphate from
2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone
5'-phosphate during riboflavin biosynthesis. S.
cerevisiae Pus6p makes the psi31 of cytoplasmic and
mitochondrial tRNAs.
Length = 213
Score = 121 bits (305), Expect = 7e-34
Identities = 63/207 (30%), Positives = 108/207 (52%), Gaps = 36/207 (17%)
Query: 28 KLDIIYEDNEIIILNKSAGLVVHPAIGN-----LSGTLFD--NLLEIYPFLINVPRAGIV 80
+ I++ED+++++++K +G+ VHP G ++ L L E+ P
Sbjct: 15 PIKIVHEDDDLLVVDKPSGIPVHPT-GRYRYNTVTEILKSEYGLTELRP----------C 63
Query: 81 HRLDKNSSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWG-IPKLNGMINAAIMRNPH 139
HRLD+ +SGL++ AK+ ++ L Q++ V+++YLA V G P +++ I
Sbjct: 64 HRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKEYLARVKGEFPDGEVVVDQPIG---L 120
Query: 140 NRIKMTVSKNFNA--KPALTYYERLATGIINK-KHISLIRCNLKTGRTHQIRVHMQWLGH 196
K + + + K A T ++RL+ N + S++ C TGRTHQIRVH+Q+LGH
Sbjct: 121 VSPKGGLRNDVDEKGKDARTIFKRLSY---NGDLNTSVVLCKPITGRTHQIRVHLQYLGH 177
Query: 197 GIVGDNLYGKKYSKSLIFNRQALHAYK 223
IV D + Y+ I+ LHA +
Sbjct: 178 PIVNDPI----YNNLGIY----LHALR 196
>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 = 113 bits (284), Expect = 2e-31
Identities = 49/156 (31%), Positives = 75/156 (48%), Gaps = 7/156 (4%)
Query: 38 IIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHRLDKNSSGLMVVAKSI 97
I++NK AG+ VHP + L + + R VHRLD+N+SGL+++AK
Sbjct: 1 YIVVNKPAGVPVHPTDPS---DLLSLTALLLVAELGKFRLYPVHRLDRNTSGLLLLAKDG 57
Query: 98 KSYIHLVNQLKMHIVQRKYLAMVWGIPKLNGMINAAIMRNPHNRIKMTVSKNFNAKPALT 157
++ L V+++YLA+V G + G I A I + + + K A+T
Sbjct: 58 EAANKLNKLFPERKVEKEYLALVDGPEEEEGTIKAPI--KKDKAVGFRKKEELDGKLAVT 115
Query: 158 YYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQW 193
+ L +G K SL+ L TGR HQIR H+
Sbjct: 116 HLRVLRSGSKEKY--SLVELELVTGRKHQIRAHLAA 149
>gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C;
Provisional.
Length = 317
Score = 116 bits (292), Expect = 6e-31
Identities = 80/233 (34%), Positives = 116/233 (49%), Gaps = 29/233 (12%)
Query: 25 KVIKLD--IIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYP---FLINVPRAGI 79
KV L I+YED+ I++LNK +G VH G LS + + L + P FL +
Sbjct: 87 KVAALADVILYEDDHILVLNKPSGTAVHGGSG-LSFGVIEGLRALRPEARFL------EL 139
Query: 80 VHRLDKNSSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWG-IPKLNGMINAAIMRNP 138
VHRLD+++SG+++VAK + L QL+ +Q+ YLA+V G ++ A +++N
Sbjct: 140 VHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKVVQAPLLKNI 199
Query: 139 HNRIKMTVSKNFNAKPALTYY---ERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLG 195
+ V + KP+ T + ER A +L+R + TGRTHQIRVH Q+ G
Sbjct: 200 LQSGERIVRVSQEGKPSETRFKVEERYA-------FATLVRASPVTGRTHQIRVHTQYAG 252
Query: 196 HGIVGDNLYGKK----YSKSLIFNRQALHAYKLGLIHPKNNLKLKWRINLPDD 244
H I D+ YG + NR LHA L HP + RI P D
Sbjct: 253 HPIAFDDRYGDREFDQQLTGTGLNRLFLHAAALKFTHPGTGEVM--RIEAPLD 303
>gnl|CDD|211333 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an tRNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required. TruC
makes psi65 in tRNAs. This psi residue is not
universally conserved.
Length = 223
Score = 113 bits (284), Expect = 1e-30
Identities = 63/227 (27%), Positives = 103/227 (45%), Gaps = 29/227 (12%)
Query: 29 LDIIYEDNEIIILNKSAGLVVHPAIGNLSGTLF-----DNLL--EIYPFLINVPRAGIVH 81
L+I+Y+D ++ +NK +GL+VH + + T F + L +YP VH
Sbjct: 1 LEILYQDEHLVAINKPSGLLVHRSELDRHETRFALQTLRDQLGQHVYP----------VH 50
Query: 82 RLDKNSSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIPKLNGMINAAIMRNPHNR 141
RLD+ +SG+++ A S + L Q H V + YLA+V G +G I+ +
Sbjct: 51 RLDRPTSGVLLFALSSEVARKLGEQFTEHRVHKTYLAVVRGYVPESGTIDYPLSEELDKL 110
Query: 142 IKMTVSKNFNAKPALTYYERLATG---IINKKH----ISLIRCNLKTGRTHQIRVHMQWL 194
S + + A T+Y LA ++ K+ SL+ TGR HQ+R H+ +
Sbjct: 111 ADKFASDDKAPQAATTHYRLLAVEELPVVVGKYPTSRYSLVELTPHTGRKHQLRRHLAHI 170
Query: 195 GHGIVGDNLYGKK-----YSKSLIFNRQALHAYKLGLIHPKNNLKLK 236
H I+GD +G + + +R L A +L HP +L
Sbjct: 171 RHPIIGDTTHGDGRHNRFFREHFGCHRLLLAATRLEFTHPVTGERLL 217
>gnl|CDD|236659 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A;
Provisional.
Length = 219
Score = 101 bits (254), Expect = 2e-26
Identities = 69/211 (32%), Positives = 108/211 (51%), Gaps = 11/211 (5%)
Query: 29 LDIIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHRLDKNSS 88
L I+Y+D I+++NK +GL+ P G L + I + P+A VHRLD +S
Sbjct: 14 LVILYQDEHIMVVNKPSGLLSVP--GRLEEHKDSVMTRIQR---DYPQAESVHRLDMATS 68
Query: 89 GLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIP-KLNGMINAAIMRNPHNRIKMTVS 147
G++VVA + + L Q + +++Y+A VWG P G+++ ++ + NR K V
Sbjct: 69 GVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVC 128
Query: 148 KNFNAKPALTYYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDNLYGKK 207
KPA T YE + N + L TGR+HQ+RVHM LGH I+GD Y
Sbjct: 129 YE-TGKPAQTEYEVVEYAADNTARVVL---KPITGRSHQLRVHMLALGHPILGDRFYASP 184
Query: 208 YSKSLIFNRQALHAYKLGLIHPKNNLKLKWR 238
++++ R LHA L + HP + ++
Sbjct: 185 EARAMA-PRLLLHAEMLTITHPAYGNSMTFK 214
>gnl|CDD|211325 cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine synthase,
Rsu/Rlu family. This group is comprised of eukaryotic,
bacterial and archeal proteins similar to eight site
specific Escherichia coli pseudouridine synthases: RsuA,
RluA, RluB, RluC, RluD, RluE, RluF and TruA.
Pseudouridine synthases catalyze the isomerization of
specific uridines in a n RNA molecule to pseudouridines
(5-ribosyluracil, psi) requiring no cofactors. E. coli
RluC for example makes psi955, 2504 and 2580 in 23S RNA.
Some psi sites such as psi1917 in 23S RNA made by RluD
are universally conserved. Other psi sites occur in a
more restricted fashion, for example psi2819 in 21S
mitochondrial ribosomal RNA made by S. cerevisiae Pus5p
is only found in mitochondrial large subunit rRNAs from
some other species and in gram negative bacteria. The E.
coli counterpart of this psi residue is psi2580 in 23S
rRNA. psi2604in 23S RNA made by RluF has only been
detected in E.coli.
Length = 154
Score = 99.4 bits (248), Expect = 4e-26
Identities = 41/163 (25%), Positives = 65/163 (39%), Gaps = 17/163 (10%)
Query: 38 IIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHRLDKNSSGLMVVAKSI 97
I++LNK +GLV HP + T+ ++ PR RLDK++SGL+++
Sbjct: 1 ILVLNKPSGLVCHPTDRDRDPTVVV-----RLDKLHGPRVHAAGRLDKDTSGLLLLTNDG 55
Query: 98 KSYIHLVNQLKMHIVQRKYLAMVWGIPKLNGMINAAIMRNPHNRIKMTVS-KNFNAKPAL 156
+ L ++++YL V G I R + A+
Sbjct: 56 RLQRRLTEP--RREIEKEYLVTVRGELD-----EEGIEDLATVRRGRLSGLVDEGVPLAV 108
Query: 157 TYYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIV 199
T + +R LKTGRTHQIR H +G ++
Sbjct: 109 TKVRVIGEHGGT----GRLRLTLKTGRTHQIRRHCAAVGFPVL 147
>gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional.
Length = 257
Score = 95.5 bits (238), Expect = 1e-23
Identities = 65/241 (26%), Positives = 112/241 (46%), Gaps = 29/241 (12%)
Query: 29 LDIIYEDNEIIILNKSAGLVVHPAIGNLSGTLF------DNLLE-IYPFLINVPRAGIVH 81
L+I+Y+D ++ +NK AG +VH + + T+F D + + ++ H
Sbjct: 2 LEILYQDEWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQIGQHVFT----------AH 51
Query: 82 RLDKNSSGLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIPKLNGMINAAIMRNPHNR 141
RLD+ +SG++++A S + L Q + H +Q+ Y A+V G +++ +
Sbjct: 52 RLDRPTSGVLLMALSSEVARLLAQQFEQHQIQKTYHAIVRGWLMEEAVLDYPLKEELDKI 111
Query: 142 IKMTVSKNFNAKPALTYYERLAT-------GIINKKHISLIRCNLKTGRTHQIRVHMQWL 194
++ +PA+T+Y LAT G SL+ KTGR HQ+R HM L
Sbjct: 112 ADKFAREDKAPQPAVTHYRGLATVEMPVATGRYPTTRYSLVELEPKTGRKHQLRRHMAHL 171
Query: 195 GHGIVGDNLYG-----KKYSKSLIFNRQALHAYKLGLIHPKNNLKLKWRINLPDDISKLI 249
H I+GD +G + ++ +R LHA +L L HP L L + +L+
Sbjct: 172 RHPIIGDTKHGDLRQNRSLAEHFGCSRLMLHASELSLTHPFTGEPLTITAGLDETWQQLL 231
Query: 250 T 250
+
Sbjct: 232 S 232
>gnl|CDD|130682 TIGR01621, RluA-like, pseudouridine synthase Rlu family protein,
TIGR01621. This model represents a clade of sequences
within the pseudouridine synthase superfamily
(pfam00849). The superfamily includes E. coli proteins:
RluA, RluB, RluC, RluD, and RsuA. The sequences modeled
here are most closely related to RluA. Neisseria, among
those species hitting this model, does not appear to
have an RluA homolog. It is presumed that these
sequences function as pseudouridine synthases, although
perhaps with different specificity [Protein synthesis,
tRNA and rRNA base modification].
Length = 217
Score = 92.7 bits (230), Expect = 8e-23
Identities = 55/197 (27%), Positives = 94/197 (47%), Gaps = 18/197 (9%)
Query: 29 LDIIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHRLDKNSS 88
+I++ + +++NK G+ VH G LL+ + V + +VHRLDK +S
Sbjct: 2 FEILFTHPDFLLINKHPGISVHKDDGE------TGLLQEVATQLGVGQVWLVHRLDKMTS 55
Query: 89 GLMVVAKSIKSYIHLVNQLKMHIVQRKYLAMVWGIP-KLNGMINAAIMRNPHNRIKMTVS 147
G++++A + +S L +++ YLA+ P K G+I + ++ K+ S
Sbjct: 56 GILLLALNAESASELSQGFAKRKIEKTYLALSSKKPKKKQGLICGDMEKSRRGSWKLVNS 115
Query: 148 KNFNAKPALTYYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHGIVGDNLYGKK 207
+ PA+T + + + L TG+THQ+RV M+ LG I+GD LYG
Sbjct: 116 QE---NPAITRFFSASA----ATGLRLFILKPHTGKTHQLRVAMKSLGSPILGDPLYGTT 168
Query: 208 YSKSLIFNRQALHAYKL 224
+R LHA+ L
Sbjct: 169 DES----DRGYLHAFAL 181
>gnl|CDD|211332 cd02558, PSRA_1, Pseudouridine synthase, a subgroup of the RluA
family. This group is comprised of bacterial proteins
assigned to the RluA family of pseudouridine synthases.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required. The
RluA family is comprised of proteins related to
Escherichia coli RluA.
Length = 246
Score = 55.7 bits (135), Expect = 3e-09
Identities = 50/187 (26%), Positives = 82/187 (43%), Gaps = 35/187 (18%)
Query: 31 IIYEDNEIIILNKSAGLVVHPAIGNLSGTLFDNL---LEIYPFLINVPRAGIVHRLDKNS 87
I+++D +++ +K L V P ++ TL L P L P HRLD+ +
Sbjct: 41 ILHQDEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTGN-PDL--TP----AHRLDRLT 93
Query: 88 SGLMVVAKSIKS---YIHLVNQLKMHIVQRKYLAMVWGIPKLNGMINAAIMRNPHNRIKM 144
+GL++ +K ++ Y L + V + Y A+ +P L +R+ ++
Sbjct: 94 AGLVLFSKRPETRGAYQTLFAR---REVSKTYEAVAPYVPALTF---PLTVRS-----RI 142
Query: 145 TVSKNF------NAKP-ALTYYERLATGIINKKHISLIRCNLKTGRTHQIRVHMQWLGHG 197
+ F +P A T E LA + L R + TG+THQ+RVHM LG
Sbjct: 143 VKGRGFFQAREVEGEPNAETRIELLA----RRGGWGLYRLSPHTGKTHQLRVHMAALGVP 198
Query: 198 IVGDNLY 204
I+ D Y
Sbjct: 199 ILNDPFY 205
>gnl|CDD|224108 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and
related pseudouridylate synthases [Translation,
ribosomal structure and biogenesis].
Length = 248
Score = 40.3 bits (95), Expect = 4e-04
Identities = 39/158 (24%), Positives = 65/158 (41%), Gaps = 24/158 (15%)
Query: 34 EDNEIIILNKSAGLVVHPAIGNLSGTLFDNLLEIYPFLINVPRAGIVHRLDKNSSGLMVV 93
E+ ++LNK G V T+FD L E P + G RLDK++ GL+++
Sbjct: 61 EERVYLLLNKPRGYVSSTEDDEGRPTVFDLLPERLPRKKRLFPVG---RLDKDTEGLLLL 117
Query: 94 AKSIKSYIHLVNQLKMHI---VQRKYLAMVWGIPKLNGMINAAIMRNPHNRIKMTVSKNF 150
+ L ++L MH V+++YL ++ G + + + + +
Sbjct: 118 TNDGE----LAHRL-MHPSSEVEKEYLV------RVEGPVTEEDLEKLRKGVTL---DDG 163
Query: 151 NAKPALTYYERLATGIINKKHISLIRCNLKTGRTHQIR 188
KPA L K+ S +R L GR Q+R
Sbjct: 164 ETKPAK--PASL--EKEPGKNNSWLRITLTEGRNRQVR 197
>gnl|CDD|211329 cd02555, PSSA_1, Pseudouridine synthase, a subgroup of the RsuA
family. This group is comprised of bacterial proteins
assigned to the RsuA family of pseudouridine synthases.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required. The
TruA family is comprised of proteins related to
Escherichia coli RsuA.
Length = 177
Score = 28.9 bits (65), Expect = 2.1
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 39 IILNKSAGLVVHPAIGNLS-GTLF-DNLLEIYPFLINVPRAGIVHRLDKNSSGLMV 92
++L+K AG+V A+ L G + P + R + LDK++SGL+V
Sbjct: 7 LLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGHFARLAPIGPLDKDASGLLV 62
>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 = 27.5 bits (62), Expect = 2.4
Identities = 7/24 (29%), Positives = 10/24 (41%)
Query: 72 INVPRAGIVHRLDKNSSGLMVVAK 95
I R G R DK + +V+
Sbjct: 21 IPPKRVGYAGRKDKRAVTTQLVSN 44
>gnl|CDD|148235 pfam06504, RepC, Replication protein C (RepC). This family
consists of several bacterial replication protein C
(RepC) sequences.
Length = 283
Score = 28.3 bits (63), Expect = 3.4
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 126 LNGMINAAIM-RNPHNRIKMTVSKNFNAKPALTYYERL 162
LN I AIM PH RI+M + PA ++RL
Sbjct: 177 LNPRIAEAIMGGRPHTRIEMAEVRALQTDPARLLHQRL 214
>gnl|CDD|232821 TIGR00093, TIGR00093, pseudouridine synthase. This model
identifies panels of pseudouridine synthase enzymes that
RNA modifications involved in maturing the protein
translation apparatus. Counts per genome vary: two in
Staphylococcus aureus, three in Pseudomonas putida, four
in E. coli, etc [Protein synthesis, tRNA and rRNA base
modification].
Length = 128
Score = 26.9 bits (60), Expect = 5.5
Identities = 22/119 (18%), Positives = 41/119 (34%), Gaps = 37/119 (31%)
Query: 80 VHRLDKNSSGLMVVAKSIKSYIHLVNQLKMH---IVQRKYLAMVWGIP---KLNGMINAA 133
RLD++S GL+++ + LV++L H ++ YL V G L +
Sbjct: 1 AGRLDRDSEGLLLLTNDGE----LVHRL-THPGHHCEKTYLVTVEGPVTDEDLEALRKGV 55
Query: 134 IMRN----PHNRIKMTVSKNFNAKPALTYYERLATGIINKKHISLIRCNLKTGRTHQIR 188
+ + P ++++ +T E GR Q+R
Sbjct: 56 QLEDGPTKPA-KLEVITEPGIPTWLRITLSE---------------------GRNRQVR 92
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
0.324 0.141 0.419
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,368,693
Number of extensions: 1297636
Number of successful extensions: 969
Number of sequences better than 10.0: 1
Number of HSP's gapped: 935
Number of HSP's successfully gapped: 37
Length of query: 257
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 162
Effective length of database: 6,723,972
Effective search space: 1089283464
Effective search space used: 1089283464
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (26.1 bits)