RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 043662
(330 letters)
>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 = 312 bits (803), Expect = e-107
Identities = 109/248 (43%), Positives = 151/248 (60%), Gaps = 9/248 (3%)
Query: 53 LVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVA 112
L I YDGT ++GWQ Q + T+Q +EKAL ++ E +R++GA RTD GVHA GQVA
Sbjct: 1 LTIEYDGTNFSGWQRQPNGRTVQGELEKALSKIAG---EPVRVIGAGRTDAGVHALGQVA 57
Query: 113 HFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMD 172
HF TP LE + ALN LLPPDIRV +FHARFSAKS+ Y Y+I N V
Sbjct: 58 HFDTPSEIP-LEKLIKALNSLLPPDIRVLSAEEVPDDFHARFSAKSRTYRYRILNRPVPS 116
Query: 173 PFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMG 232
PF R Y +H L+ M++AA+ +G HDFS+F + + V++++R DV G
Sbjct: 117 PFLRRYVWHVPRPLDIEAMQEAAKLLLGTHDFSSFRAAGCQSK--STVRTIYRADVYREG 174
Query: 233 ALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHG 292
L+ E+ +GFLY VRN+V LL++G+ + P+ + +IL +DR +AP HG
Sbjct: 175 DLIVFEIRANGFLYHMVRNIVGTLLEVGRGKLSPEDIKEILEAKDRTAAGP---TAPAHG 231
Query: 293 LCLVEVKY 300
L LV+V+Y
Sbjct: 232 LYLVKVEY 239
>gnl|CDD|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated.
Length = 244
Score = 308 bits (791), Expect = e-105
Identities = 104/251 (41%), Positives = 146/251 (58%), Gaps = 9/251 (3%)
Query: 50 KWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWG 109
+ L I YDGT + GWQ Q + T+Q +EKAL ++ E +R++GA RTD GVHA G
Sbjct: 3 RIALTIEYDGTNFHGWQRQPNGRTVQGELEKALSKLAG---EPVRVIGAGRTDAGVHALG 59
Query: 110 QVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDA 169
QVAHF TP E ALN LLP DI V +FHARFSAK++ Y Y+IYN
Sbjct: 60 QVAHFDTPAPRP-PEKWRRALNALLPDDIAVLWAEEVPDDFHARFSAKARRYRYRIYNRP 118
Query: 170 VMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVI 229
PF R Y +H Y L+ M +AA+Y +G+HDF++F + +PV++++ DV
Sbjct: 119 ARPPFLRGYVWHYPYPLDVDAMNEAAQYLLGEHDFTSFRASGCQSK--SPVRTIYEADVT 176
Query: 230 EMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAP 289
G + ++ +GFL+ VRN+V LL++GK PP+ + ++L +DR +AP
Sbjct: 177 REGDFIVFDISANGFLHNMVRNIVGTLLEVGKGKRPPEDIKELLEAKDRT---LAGPTAP 233
Query: 290 PHGLCLVEVKY 300
GL LVEV Y
Sbjct: 234 AEGLYLVEVDY 244
>gnl|CDD|223179 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal
structure and biogenesis].
Length = 266
Score = 272 bits (699), Expect = 2e-91
Identities = 111/259 (42%), Positives = 158/259 (61%), Gaps = 10/259 (3%)
Query: 50 KWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWG 109
+ L IAYDGTR+ GWQ Q + T+Q +EKAL ++ E +R++GA RTD GVHA G
Sbjct: 3 RIALKIAYDGTRFHGWQRQPNVRTVQGELEKALSKIGG---ESVRVIGAGRTDAGVHALG 59
Query: 110 QVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDA 169
QV HF TP + LE + ALN LLPPDIRV +++ +FHARFSAKS+ Y Y IYN
Sbjct: 60 QVVHFDTP-ADRPLEKLVRALNALLPPDIRVLDVAEVPDDFHARFSAKSRTYRYIIYNAP 118
Query: 170 VMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVI 229
+ PF +Y +H Y L+ MR+AA+ +G HDF++F + +PV++++R DV
Sbjct: 119 LRPPFLANYVWHVPYPLDLDAMREAAKLLLGTHDFTSFRKAG--CQSKSPVRTIYRIDVS 176
Query: 230 EMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAP 289
G L+ +++ G+ FL+ VRN+V LL +G+ P + + ++L +DRK +AP
Sbjct: 177 RDGDLIVIDISGNSFLWHMVRNIVGALLLVGRGKRPVEWIKELLEAKDRK---LAGPTAP 233
Query: 290 PHGLCLVEVKYNEEHLRLP 308
GL LV V Y E LP
Sbjct: 234 AEGLYLVRVDY-PEDFELP 251
>gnl|CDD|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed.
Length = 245
Score = 227 bits (580), Expect = 1e-73
Identities = 91/250 (36%), Positives = 141/250 (56%), Gaps = 10/250 (4%)
Query: 52 RLVIAYDGTRYAGWQFQTSPP-TIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQ 110
+L I YDG+RY GWQ + TIQ +E L +++ E++ ++G RTD GVHA Q
Sbjct: 5 KLTIQYDGSRYKGWQKLGNNDNTIQGKIESVL---SEMTGEEIEIIGCGRTDAGVHALNQ 61
Query: 111 VAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAV 170
VA+F T + I LN LP DI V + FHAR++ KSK Y YKI+N+
Sbjct: 62 VANFQTDEK-LSEDKIKKYLNEYLPNDIVVTNVEEVDERFHARYNVKSKTYLYKIWNEKF 120
Query: 171 MDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIE 230
+ F R Y+ H KL+ M++AA+Y VG HDF++F N + + + V+ ++ D++E
Sbjct: 121 HNVFMRKYSMHVNEKLDVKAMKEAAKYLVGSHDFTSFTNAKSKKK--STVREIYSIDIME 178
Query: 231 MGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPP 290
+Q+ V G+GFL+ VR +V L+++G + + + +IL +DR + +AP
Sbjct: 179 EDGFVQIRVSGNGFLHNMVRIIVGALIEVGLGQLKAEDIKQILEAKDR---NQANCTAPA 235
Query: 291 HGLCLVEVKY 300
GL L V+Y
Sbjct: 236 SGLYLENVEY 245
>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 = 206 bits (527), Expect = 5e-66
Identities = 94/246 (38%), Positives = 133/246 (54%), Gaps = 20/246 (8%)
Query: 50 KWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWG 109
K L IAYDG+ Y GWQ Q + T+Q +EKAL + K + + ++ A RTD GVHA G
Sbjct: 2 KIALKIAYDGSNYHGWQRQPNKRTVQGELEKALEAIGK---KKITIMSAGRTDKGVHAMG 58
Query: 110 QVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDA 169
QV F TP ++A LN LLPPDIRV+ ++ FHARFSA + Y Y +YN
Sbjct: 59 QVISFDTP-KEIPDNKLNAKLNALLPPDIRVKALAPVNDNFHARFSASKRHYRYILYN-- 115
Query: 170 VMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVI 229
RHY L+ MR AA+ +GKHDFS F + R +P++++ V
Sbjct: 116 -----HRHY----YSPLDLEKMRAAAKQLLGKHDFSNFSKAKSKSR--SPIRTISDIKVS 164
Query: 230 EMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAP 289
E G + ++ G+ FL+ VR +V L+ +G+ +PP+ V K+L + R AP
Sbjct: 165 ESGEYIIFDIIGNSFLWHMVRKIVGALVLVGRGKLPPEWVAKLLDAKKRNLAPTT---AP 221
Query: 290 PHGLCL 295
+GL L
Sbjct: 222 ANGLYL 227
>gnl|CDD|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional.
Length = 245
Score = 198 bits (506), Expect = 2e-62
Identities = 92/246 (37%), Positives = 138/246 (56%), Gaps = 10/246 (4%)
Query: 54 VIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAH 113
V++YDG+ + G+Q Q T+Q + E AL R+ K + + A RTDTGVHA GQV
Sbjct: 7 VVSYDGSNFFGYQGQPDVRTVQGVFEDALERIFK---QRIYTQAAGRTDTGVHANGQVIA 63
Query: 114 FITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDP 173
F P E I A+N LP DI V+++ FH RF AK +IYHY I +
Sbjct: 64 FNCPNDRMTEEDIKNAMNANLPDDIYVKKVFEVPKNFHPRFDAKKRIYHYFILTSKEKNV 123
Query: 174 FQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEM-G 232
F R Y + Y+L+ MR+AA+Y G+HDF++F + NPV++++R ++ +
Sbjct: 124 FLRKYVWWFPYELDLEAMRKAAKYLEGEHDFTSF---KTGSDERNPVRTIYRIRILRLKK 180
Query: 233 ALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHG 292
L+ + VEG FL R VRN+V L+++G P+ + ++L +DR + A +AP HG
Sbjct: 181 DLILIRVEGRSFLRRMVRNIVGALVKVGLGQWEPEKIKEVLEARDRSKAAG---TAPAHG 237
Query: 293 LCLVEV 298
L L +V
Sbjct: 238 LYLYKV 243
>gnl|CDD|173052 PRK14588, PRK14588, tRNA pseudouridine synthase ACD; Provisional.
Length = 272
Score = 161 bits (409), Expect = 9e-48
Identities = 98/278 (35%), Positives = 135/278 (48%), Gaps = 15/278 (5%)
Query: 53 LVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVA 112
L++ YDGT +AG Q+QT T+Q +E A +T+ R R+V A RTD GVHA GQVA
Sbjct: 6 LLLEYDGTDFAGSQWQTDGRTVQGALEAAWQALTQERR---RIVLAGRTDAGVHARGQVA 62
Query: 113 HFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMD 172
H T + L +I LN LP DI V+ A P+FHARFSA + Y Y I
Sbjct: 63 HVQTDTRHS-LATIWRGLNAHLPEDIGVQNAWEAPPDFHARFSAIQREYRYVIDCAPAPS 121
Query: 173 PFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNV--QRNDRLLNPVKSVFRFDVIE 230
P RH H L+ M A + +G HDF+AF + + +
Sbjct: 122 PQLRHQVLHYAGTLDVAAMDAALKLLIGTHDFAAFTTAPQEGSTVRTCYWARCTDTEWFG 181
Query: 231 MGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPP 290
LL +EV + FL VRN+V LL +G+ + D +LA++DR+ LA +AP
Sbjct: 182 R-PLLAIEVAANAFLQHMVRNIVGTLLLVGRGRMTVDQFGAVLASRDRR-LAG--PTAPA 237
Query: 291 HGLCLVEVKYNEEHLRLPAACPLSSFGRHHSVRKCKLP 328
HGL L V+Y +R + R + K + P
Sbjct: 238 HGLYLTAVRYPPGLIR-----WVEPSKRQNGTTKVRQP 270
>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 = 156 bits (396), Expect = 2e-46
Identities = 75/246 (30%), Positives = 113/246 (45%), Gaps = 31/246 (12%)
Query: 55 IAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHF 114
YDGT+Y G+Q Q PT++ + +I + K + A+RTD GV A GQV
Sbjct: 1 FGYDGTKYHGFQRQNDVPTVE---GELIIALLKAGNIPYFIKAAARTDRGVSALGQVVAI 57
Query: 115 ITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPF 174
T E ALNG+LP DIRV + + P+FHA + Y Y I +
Sbjct: 58 ETE-RRLTPE----ALNGILPGDIRVFAVHSVPPDFHAPRYCDHRTYRYYIPS------- 105
Query: 175 QRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGAL 234
+ L+ ++ AA F+G HDF+ F N V+++ + ++
Sbjct: 106 ---------FPLDDERLKSAASRFLGTHDFTNFSKKDTR----NTVRTIISIECKDLNPF 152
Query: 235 LQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHGLC 294
+ +E + FL+ QVR MV L+ +G+ P V ++LA + AP GL
Sbjct: 153 VVVEFKAKSFLWHQVRRMVGFLMLVGEGLHSPSSVSRLLAGPAPPIP---MVPAPAEGLL 209
Query: 295 LVEVKY 300
LV+VKY
Sbjct: 210 LVDVKY 215
>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 = 155 bits (394), Expect = 4e-46
Identities = 79/249 (31%), Positives = 116/249 (46%), Gaps = 31/249 (12%)
Query: 53 LVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVA 112
L IAYDGT + G+Q Q T++ + KAL + RL A RTD GVHA G V
Sbjct: 1 LKIAYDGTNFHGFQRQPDVRTVEGELIKAL-EELGIIESRARLYSAGRTDRGVHALGNVV 59
Query: 113 HFITPFSYDGLESIH-AALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVM 171
++ + +N LP DI V + +F R A K Y Y + +D
Sbjct: 60 ------VFETEKEPIPPMINAKLPKDIWVLAGAKVPEDFDPRRWAHRKYYRYNLGSD--- 110
Query: 172 DPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEM 231
+ M++AA+ +G HDFS F + D +PV+++ R ++ E
Sbjct: 111 --------------YDVEAMKEAAKKLIGTHDFSNF---SKRDGRKDPVRTIERIEISEN 153
Query: 232 GALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPH 291
G + ++V G FL+ VR +V L ++GK + V K+L + R E APP
Sbjct: 154 GEFITIDVVGESFLWNMVRRIVGALSEVGKGKRENEWVEKLLDGEFRPEGVP---PAPPE 210
Query: 292 GLCLVEVKY 300
GL LV+VKY
Sbjct: 211 GLILVDVKY 219
>gnl|CDD|237759 PRK14589, PRK14589, tRNA pseudouridine synthase ACD; Provisional.
Length = 265
Score = 138 bits (349), Expect = 5e-39
Identities = 81/247 (32%), Positives = 113/247 (45%), Gaps = 29/247 (11%)
Query: 55 IAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKL-EREDLRLVGASRTDTGVHAWGQVAH 113
I+Y GTR+ G Q+Q T++ A R+ + + A RTD GVHA GQV
Sbjct: 7 ISYIGTRFFGSQYQPDQRTVEGEFIAACRRLGLFSDWREAGFALAGRTDRGVHARGQVLA 66
Query: 114 FITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDP 173
F T +E ALNG LPPDI + FH R+ A S+ Y Y
Sbjct: 67 FSTHKPERAVE----ALNGQLPPDIWCTGWAEVPESFHPRYDAISRTYRY---------- 112
Query: 174 FQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGA 233
Y S + MR AA F+G HDFS F V+ + +PV+++ R V G
Sbjct: 113 ------YFSRPPSDINAMRDAAGEFIGTHDFSCFARVE--GK--SPVRTILRIRVFSDGG 162
Query: 234 LLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHGL 293
EV FL+ VR M LLQIG+ + PD + ++L+ ++++ AP GL
Sbjct: 163 FPVFEVTAQSFLWHMVRCMAGALLQIGEGEMEPDDIERLLSGPCKRKVK----PAPAEGL 218
Query: 294 CLVEVKY 300
L +V
Sbjct: 219 VLWDVDC 225
>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 = 135 bits (343), Expect = 4e-38
Identities = 78/275 (28%), Positives = 119/275 (43%), Gaps = 46/275 (16%)
Query: 53 LVIAYDGTRYAGWQFQ-TSPPTIQCIVEKALIRVTKL--EREDLRLVGASRTDTGVHAWG 109
L AY G Y G+ Q + T++ + +AL + T+L +R+ RTD GV A+G
Sbjct: 1 LRFAYLGWNYNGFAVQEETTNTVEETLFEALEK-TRLIEDRQTSNYSRCGRTDKGVSAFG 59
Query: 110 QVAHF--------------ITPFSYDGLES----IHAALNGLLPPDIRVREISAAVPEFH 151
QV T E LN +LPPDIR+ + P+F
Sbjct: 60 QVISLDVRSNLKPEDGLDPSTDVKSTADEEELPYCKI-LNRVLPPDIRILAWAPVPPDFS 118
Query: 152 ARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQ 211
ARFS S+ Y Y + L+ LMR+AA+ +G+HDF F +
Sbjct: 119 ARFSCVSRTYRY----------------FFPKGDLDIELMRKAAKLLLGEHDFRNFCKMD 162
Query: 212 RNDRLLNPVKSVFRFDVIE------MGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIP 265
+++ N V+ V +V L EV GS FL+ QVR M+A+L IG+ P
Sbjct: 163 VANQVTNYVRRVLSAEVEPVDQHPDGDGLYYFEVRGSAFLWHQVRCMMAVLFLIGQGLEP 222
Query: 266 PDIVPKILATQDRKELAKYALSAPPHGLCLVEVKY 300
P ++ ++L + +Y + A L L + +
Sbjct: 223 PSVISQLLDVEKNPRKPQYTM-ASEVPLVLYDCGF 256
>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 = 106 bits (268), Expect = 3e-27
Identities = 67/268 (25%), Positives = 111/268 (41%), Gaps = 43/268 (16%)
Query: 53 LVIAYDGTRYAGWQFQT-SPPTIQCIVEKALIR---VTKLEREDLRLVG---ASRTDTGV 105
L+ Y GT Y G Q+ + TI+ +E+AL + +++ D + +G A+RTD GV
Sbjct: 1 LLFGYCGTGYHGMQYNPGAYKTIEGELERALFKAGAISESNAGDPKKIGFSRAARTDKGV 60
Query: 106 HAWGQV--AHFIT--PFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIY 161
HA V I P LE + LN LP DIRV I+ F+AR + S+ Y
Sbjct: 61 HAARNVVSLKVIIDDPEGLGILEDLVEKLNSHLPSDIRVFGITRVTKSFNARKACDSRTY 120
Query: 162 HYKIYNDAVMDPFQRHYAYHSVYKLNTT-LMRQAAEYFVGKHDFSAFVNVQRNDRLLNP- 219
Y + + L T + + +VG H+F F V++ +P
Sbjct: 121 EYLL----------------PTFALETLQRFNEILKEYVGTHNFHNF-TVKKKFE--DPS 161
Query: 220 ----VKSVFRFDVIEMGALLQ---LEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKI 272
+KS + + + L+ +++ G F+ Q+R M+ L + I + P ++
Sbjct: 162 ANRFIKSFYVSEPFVIEEGLEWISIKIHGQSFMLHQIRKMIGLAIAIVRGGAPESLIELS 221
Query: 273 LATQDRKELAKYALSAPPHGLCLVEVKY 300
+ AP GL L +
Sbjct: 222 FNKDKIIIIPL----APGLGLLLERPHF 245
>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 = 88.6 bits (220), Expect = 5e-22
Identities = 36/108 (33%), Positives = 56/108 (51%), Gaps = 5/108 (4%)
Query: 194 AAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMV 253
AA+ + G HDFS F + + + ++++ + G LL E++G+GFLY QVR MV
Sbjct: 1 AAKLYDGTHDFSGFQKQRTVQK--SLIRTIESIGIERDGELLVFEIKGNGFLYHQVRIMV 58
Query: 254 ALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHGLCLVEVKYN 301
LL+ GK + V +L ++ R AP GL L V+Y+
Sbjct: 59 GALLRTGKGVHALEQVVSLLNSKLRPRAPPT---APAVGLYLFHVRYD 103
Score = 44.0 bits (104), Expect = 6e-06
Identities = 27/121 (22%), Positives = 40/121 (33%), Gaps = 36/121 (29%)
Query: 53 LVIAYDGT-RYAGWQFQTSPPTIQCIVEKALIRVTKLEREDL----------------RL 95
YDGT ++G+Q Q T+Q + + + + +L +
Sbjct: 1 AAKLYDGTHDFSGFQKQ---RTVQKSLIRTIESIGIERDGELLVFEIKGNGFLYHQVRIM 57
Query: 96 VG-ASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARF 154
VG RT GVHA QV LN L P + + FH R+
Sbjct: 58 VGALLRTGKGVHALEQVVSL---------------LNSKLRPRAPPTAPAVGLYLFHVRY 102
Query: 155 S 155
Sbjct: 103 D 103
>gnl|CDD|173051 PRK14587, PRK14587, tRNA pseudouridine synthase ACD; Provisional.
Length = 256
Score = 67.2 bits (164), Expect = 8e-13
Identities = 70/256 (27%), Positives = 111/256 (43%), Gaps = 54/256 (21%)
Query: 55 IAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHF 114
IAYDGT + G F P +++ + + + L SRTD GV A G V
Sbjct: 7 IAYDGTLFYG--FTGHPNSLEPALRRVFGEI---------LGRGSRTDPGVSAVGNVV-- 53
Query: 115 ITPFSYDGLESIH-AALNGLLPPDIRVREISAAVPE-FHARFSAKSKIYHYKIYNDAVMD 172
+T + + +N LP + + A VPE F+ R AK + Y Y
Sbjct: 54 MTS------QKLPLGYVNSKLPRGVWAWAV-AEVPEGFNPR-RAKRRRYLY--------- 96
Query: 173 PFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMG 232
A H + + MR+AAE G HD+S+F+ +R ++ V +V+ V G
Sbjct: 97 -----VAPH--WGEDVEAMREAAELLAGTHDYSSFIQ-RRGEKATPTVTTVYEIGVELRG 148
Query: 233 ALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAK-----YALS 287
L+ L G GF + +R M +L G+ +L+ +D EL + S
Sbjct: 149 DLIYLYFVGRGFRNKMIRKMAWAILAAGR---------GVLSRRDIAELLERPRPGAVPS 199
Query: 288 APPHGLCLVEVKYNEE 303
AP GL L++++Y+ +
Sbjct: 200 APAEGLVLLDIEYDVK 215
>gnl|CDD|215562 PLN03078, PLN03078, Putative tRNA pseudouridine synthase;
Provisional.
Length = 513
Score = 34.9 bits (80), Expect = 0.048
Identities = 48/166 (28%), Positives = 71/166 (42%), Gaps = 39/166 (23%)
Query: 33 GTNNTVKPPTDDSF--------PGFKWR--------LVIAYDGTRYAGWQFQ---TSPPT 73
++ ++ PP+ D G KW L + Y GT Y G Q Q +S T
Sbjct: 39 PSSTSLSPPSSDPPLTDNSDQGGGMKWESARKKKVVLRVGYVGTDYRGLQKQRDLSSLST 98
Query: 74 IQCIVEKALIRVTKLERE----DLRLVG---ASRTDTGVHAWGQVAHFIT-----PFSY- 120
I+ +E A+ + + RE +L +G +SRTD GVH+ +A I+ P +
Sbjct: 99 IEGELETAIFKAGGI-RESNYGNLHKIGWARSSRTDKGVHS---LATMISLKMEIPENAW 154
Query: 121 -DGLESIHAA--LNGLLPPDIRVREISAAVPEFHARFSAKSKIYHY 163
D + I A +N LP +IRV I A F R + Y Y
Sbjct: 155 KDDPDGIALAKFINSHLPDNIRVFSILPAQRSFDPRRECDLRKYSY 200
>gnl|CDD|215937 pfam00479, G6PD_N, Glucose-6-phosphate dehydrogenase, NAD binding
domain.
Length = 183
Score = 30.2 bits (69), Expect = 1.0
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 7/58 (12%)
Query: 131 NGLLPPDIRV-----REISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSV 183
GLLP D R+ E S +F R K + ++ V + F +Y S
Sbjct: 24 EGLLPEDFRIVGVARSEWSDE--DFRERVREALKKFVRTELDEEVWEEFLSRLSYVSG 79
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 29.4 bits (67), Expect = 2.6
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 120 YDGLESIHAALNGLLPPDIRVREISAAVP 148
Y +E + AA+ G+L P+ + R I A
Sbjct: 390 YKLIEDVEAAMKGMLEPEKKERVIGLAEV 418
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 28.9 bits (65), Expect = 3.4
Identities = 13/47 (27%), Positives = 16/47 (34%)
Query: 111 VAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAK 157
V D E+I AAL P +RV + A V E
Sbjct: 59 VEKLPDALGEDEAEAIAAALLRPPPRSLRVNTLKADVEELLEALEEA 105
>gnl|CDD|223441 COG0364, Zwf, Glucose-6-phosphate 1-dehydrogenase [Carbohydrate
transport and metabolism].
Length = 483
Score = 29.1 bits (66), Expect = 3.9
Identities = 15/62 (24%), Positives = 23/62 (37%), Gaps = 7/62 (11%)
Query: 127 HAALNGLLPPDIRV-----REISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYH 181
GLLP D R+ + S EF A + + ++AV + F +Y
Sbjct: 30 RLYKEGLLPEDFRIIGVARSKWSNE--EFRALVREAIEFAKTEEIDEAVWEEFASRLSYV 87
Query: 182 SV 183
S
Sbjct: 88 SG 89
>gnl|CDD|234405 TIGR03936, sam_1_link_chp, radical SAM-linked protein. This model
describes an uncharacterized protein encoded adjacent
to, or as a fusion protein with, an uncharacterized
radical SAM protein.
Length = 209
Score = 28.3 bits (64), Expect = 4.5
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 123 LESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKI 165
E + LN +LP I V E+ VP+ A Y+I
Sbjct: 74 PEEVLERLNAVLPEGIEVLEV-EEVPDKAPSLMALIDAADYRI 115
>gnl|CDD|236202 PRK08249, PRK08249, cystathionine gamma-synthase; Provisional.
Length = 398
Score = 28.6 bits (64), Expect = 4.9
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 158 SKIYHYKIYNDAVMDPF 174
++YHY+ N A MDP
Sbjct: 231 EQVYHYREINGATMDPM 247
>gnl|CDD|234515 TIGR04234, seadorna_RNAP, seadornavirus RNA-directed RNA
polymerase. Members of this protein family are the
seadornavirus VP1 protein, the RNA-directed RNA
polymerase.
Length = 1144
Score = 28.6 bits (64), Expect = 5.3
Identities = 22/85 (25%), Positives = 32/85 (37%), Gaps = 12/85 (14%)
Query: 131 NGLLPPD-IRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYK---- 185
NG+ PD IR +IS +PEF + I PF Y + +
Sbjct: 96 NGIDDPDVIRAWDIST-IPEFVELGGEIFNLRKEMIRRIKDEAPF---YFFCRIIPYAVT 151
Query: 186 ---LNTTLMRQAAEYFVGKHDFSAF 207
+ + R+ YF+G DF F
Sbjct: 152 NIDKDDPMWREWLSYFIGGEDFFKF 176
>gnl|CDD|187877 cd09746, Csm6_III-A, CRISPR/Cas system-associated protein Csm6.
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;
Protein of this family often fused to HTH domain;
loosely associated with CRISPR/Cas systems.
Length = 382
Score = 28.3 bits (63), Expect = 5.5
Identities = 28/134 (20%), Positives = 48/134 (35%), Gaps = 28/134 (20%)
Query: 185 KLNTTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGF 244
L L+R+AA + D+SA + + + P + + MGA +
Sbjct: 119 NLRYLLLREAAISLINAFDYSAALAILASVAEFVPEDVIH----LLMGAQHR-------- 166
Query: 245 LYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHGLCLVEVKYNEEH 304
+ + + + PDI P K+L +Y L L+++ N E
Sbjct: 167 -----KKLDLREAKKKSHLVNPDIFPVKSD-DAAKKLLEYYL--------LLDLLQNREQ 212
Query: 305 LR--LPAACPLSSF 316
L L A P + F
Sbjct: 213 LADFLRGAKPAAEF 226
>gnl|CDD|226504 COG4017, COG4017, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 254
Score = 27.9 bits (62), Expect = 6.3
Identities = 19/112 (16%), Positives = 35/112 (31%), Gaps = 18/112 (16%)
Query: 67 FQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQ-VAHFITPFSYDGLES 125
+ + + E A + + GV+ G A ++ +
Sbjct: 15 IDSKTRVVDVVNEIAKKKYQAIRDFLEGEEFKEVLIFGVYLTGNYTAQMLSKADKVTVVD 74
Query: 126 IHAALNGLLPPDIRVRE-----------------ISAAVPEFHARFSAKSKI 160
IH + G LP +++ R + PEF A+F+ K I
Sbjct: 75 IHPFMRGFLPNNVKFRNLLKFIRGEVDLIVDLTGLGGIEPEFLAKFNPKVFI 126
>gnl|CDD|220403 pfam09788, Tmemb_55A, Transmembrane protein 55A. Members of this
family catalyze the hydrolysis of the 4-position
phosphate of phosphatidylinositol 4,5-bisphosphate, in
the reaction: 1-phosphatidyl-myo-inositol
4,5-bisphosphate + H(2)O =
1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Length = 258
Score = 27.5 bits (61), Expect = 8.4
Identities = 23/82 (28%), Positives = 29/82 (35%), Gaps = 4/82 (4%)
Query: 10 SPLYSNGLLPSTNKQGVGVVGLEGTNNTVKPPTDDSFPGFKWRLVIAYDGTRYAGWQFQT 69
SPL S + G EG KPP D +F F L A
Sbjct: 8 SPLLSED----IDGGTGVSPGDEGAGPPSKPPYDQNFAPFPVLLSELPPPYSPAQSPDSG 63
Query: 70 SPPTIQCIVEKALIRVTKLERE 91
S P + C V ++LI V E +
Sbjct: 64 SAPVVNCRVCQSLISVEGKEHQ 85
>gnl|CDD|218263 pfam04784, DUF547, Protein of unknown function, DUF547. Family of
uncharacterized proteins from C. elegans and A.
thaliana.
Length = 112
Score = 26.7 bits (60), Expect = 8.9
Identities = 9/42 (21%), Positives = 15/42 (35%), Gaps = 1/42 (2%)
Query: 165 IYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSA 206
+YN + +Y S+ + +A Y VG S
Sbjct: 19 LYNALTIHLILDNYPVPSIRDIGFGPWNKAF-YTVGGQALSL 59
>gnl|CDD|215222 PLN02397, PLN02397, aspartate transaminase.
Length = 423
Score = 27.6 bits (62), Expect = 9.0
Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 10/40 (25%)
Query: 149 EFHARFSAKSKIY--------HYKIYNDAVMDPFQRHYAY 180
EF ARF S IY H+ I+ DA + R Y Y
Sbjct: 134 EFLARFYPGSTIYIPNPTWGNHHNIFRDAGVP--VRTYRY 171
>gnl|CDD|216871 pfam02092, tRNA_synt_2f, Glycyl-tRNA synthetase beta subunit.
Length = 549
Score = 27.8 bits (63), Expect = 9.8
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 255 LLLQIGKEAIPPDIVPKI---LATQDRKELAKYALS 287
LLL+IG E +P + K LA K L + LS
Sbjct: 1 LLLEIGTEELPAKFLKKALEQLAELITKGLKEARLS 36
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 0.138 0.421
Gapped
Lambda K H
0.267 0.0726 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,314,372
Number of extensions: 1688249
Number of successful extensions: 1323
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1267
Number of HSP's successfully gapped: 46
Length of query: 330
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 233
Effective length of database: 6,635,264
Effective search space: 1546016512
Effective search space used: 1546016512
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 (26.5 bits)