RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 009253
(539 letters)
>gnl|CDD|215562 PLN03078, PLN03078, Putative tRNA pseudouridine synthase;
Provisional.
Length = 513
Score = 711 bits (1837), Expect = 0.0
Identities = 329/522 (63%), Positives = 381/522 (72%), Gaps = 36/522 (6%)
Query: 9 LHSPWSARSITSTLSTVGFSNKISAVNLLPL-SCYRCPASSSSKSSPSVSHTLTRPTPNS 67
L +PW S+ S + N +L S SS+S S PS LT +
Sbjct: 5 LRAPWPLWRFWSSTSLLRRVNP----RILRTSSSASSSPSSTSLSPPSSDPPLTDNSDQG 60
Query: 68 SDDKWEPVRKKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGN 127
KWE RKKKV LRVGYVGTDYRGLQ QRD SLSTIEGELETA+FKAGGIRESNYGN
Sbjct: 61 GGMKWESARKKKVVLRVGYVGTDYRGLQKQRDLSSLSTIEGELETAIFKAGGIRESNYGN 120
Query: 128 LQKIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSI 187
L KI WARSSRTDKGVHSLATMI LKMEIP +AWKDDP GI LAK +N+HLP NI+VFSI
Sbjct: 121 LHKIGWARSSRTDKGVHSLATMISLKMEIPENAWKDDPDGIALAKFINSHLPDNIRVFSI 180
Query: 188 LPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHN 247
LP+QRSFDPRREC+LRKYSYLLPAEVIGI S ++ EID HIS+FN+ILN FEGEHPFHN
Sbjct: 181 LPAQRSFDPRRECDLRKYSYLLPAEVIGIKSGFSSEEIDEHISEFNSILNGFEGEHPFHN 240
Query: 248 YTERSKYRRK-----PHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLG 302
YT RSKYR+K + G VS+RAK+SK+ S EE+ GE
Sbjct: 241 YTARSKYRKKLPGKHKQRNGAVSRRAKSSKEMSSSESEENHGEIS--------------- 285
Query: 303 IGGEISSDDEKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSAS 362
D+E + +S+ SG +++ + LK Q+S IRARWL+E DE D++SAS
Sbjct: 286 -----EEDEEDLSFSSIPSGS-----SDENEDILKFQSSQVQIRARWLHEPDETDRISAS 335
Query: 363 HFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSL 422
HFRKIF CSCGKLEKSLGF +VE+SI GESFMLHQIRKMVGTAVAVKR+LLPRDI+ LSL
Sbjct: 336 HFRKIFRCSCGKLEKSLGFDFVELSIWGESFMLHQIRKMVGTAVAVKRELLPRDIIRLSL 395
Query: 423 AKHSRIVLPLAPSEVLFLRANSFSVRTRPG-VTRPEMQTMVESEEILKMVDEFYTSVTLP 481
K SRIVLPLAPSEVL LR NSFSVR +PG + RP M+TM ESEEILK V+EFY +V LP
Sbjct: 396 TKFSRIVLPLAPSEVLILRGNSFSVRKKPGNIKRPGMETMNESEEILKGVEEFYRAVMLP 455
Query: 482 EVSKFLDATKSPWTEWIENLEKFTSIPNEQLDEVRNAWQLWK 523
+VSKFLD +K PW EW+ENL++FTSIP+ QLDEVR AW++WK
Sbjct: 456 QVSKFLDPSKPPWKEWVENLDRFTSIPDAQLDEVRKAWKVWK 497
>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 = 204 bits (522), Expect = 2e-62
Identities = 71/176 (40%), Positives = 99/176 (56%), Gaps = 16/176 (9%)
Query: 82 LRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDK 141
L GY GT Y G+Q + TIEGELE ALFKAG I ESN G+ +KI ++R++RTDK
Sbjct: 1 LLFGYCGTGYHGMQYNPGAYK--TIEGELERALFKAGAISESNAGDPKKIGFSRAARTDK 58
Query: 142 GVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECN 201
GVH+ ++ LK+ I DL +++N+HLP +I+VF I +SF+ R+ C+
Sbjct: 59 GVHAARNVVSLKVIIDDPEGLGIL--EDLVEKLNSHLPSDIRVFGITRVTKSFNARKACD 116
Query: 202 LRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHNYTERSKYRRK 257
R Y YLLP + + FN IL E+ G H FHN+T + K+
Sbjct: 117 SRTYEYLLPTFAL------------ETLQRFNEILKEYVGTHNFHNFTVKKKFEDP 160
Score = 95.8 bits (239), Expect = 2e-22
Identities = 36/86 (41%), Positives = 49/86 (56%), Gaps = 1/86 (1%)
Query: 360 SASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILT 419
SA+ F K F S + + G ++ I I G+SFMLHQIRKM+G A+A+ R P ++
Sbjct: 161 SANRFIKSFYVSEPFVIE-EGLEWISIKIHGQSFMLHQIRKMIGLAIAIVRGGAPESLIE 219
Query: 420 LSLAKHSRIVLPLAPSEVLFLRANSF 445
LS K I++PLAP L L F
Sbjct: 220 LSFNKDKIIIIPLAPGLGLLLERPHF 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 = 112 bits (281), Expect = 3e-28
Identities = 55/199 (27%), Positives = 90/199 (45%), Gaps = 38/199 (19%)
Query: 78 KKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSS 137
+K+AL++ Y G++Y G Q Q ++ T++GELE AL G +KI +
Sbjct: 1 RKIALKIAYDGSNYHGWQRQPNKR---TVQGELEKALEAIGK---------KKITIMSAG 48
Query: 138 RTDKGVHSLATMICLKM--EIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFD 195
RTDKGVH++ +I EIP + ++NA LP +I+V ++ P +F
Sbjct: 49 RTDKGVHAMGQVISFDTPKEIPDNKLN---------AKLNALLPPDIRVKALAPVNDNFH 99
Query: 196 PRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHNYT-----E 250
R + R Y Y+L N + + +D + A + G+H F N++
Sbjct: 100 ARFSASKRHYRYILY------NHRHYYSPLD--LEKMRAAAKQLLGKHDFSNFSKAKSKS 151
Query: 251 RSKYRRKPHKTGRVSKRAK 269
RS R VS+ +
Sbjct: 152 RSPIRTISDIK--VSESGE 168
Score = 48.8 bits (117), Expect = 2e-06
Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 382 GYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRD-ILTLSLAKHSRIVLPLAPSEVLFL 440
Y+ I G SF+ H +RK+VG V V R LP + + L AK + AP+ L+L
Sbjct: 168 EYIIFDIIGNSFLWHMVRKIVGALVLVGRGKLPPEWVAKLLDAKKRNLAPTTAPANGLYL 227
>gnl|CDD|223179 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal
structure and biogenesis].
Length = 266
Score = 109 bits (275), Expect = 5e-27
Identities = 42/177 (23%), Positives = 66/177 (37%), Gaps = 26/177 (14%)
Query: 78 KKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSS 137
K++AL++ Y GT + G Q Q + T++GELE AL K GG + +
Sbjct: 2 KRIALKIAYDGTRFHGWQRQPNVR---TVQGELEKALSKIGGE---------SVRVIGAG 49
Query: 138 RTDKGVHSLA--TMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFD 195
RTD GVH+L + P + + +NA LP +I+V + F
Sbjct: 50 RTDAGVHALGQVVHFDTPADRPLEKLV---------RALNALLPPDIRVLDVAEVPDDFH 100
Query: 196 PRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISD---FNAILNEFEGEHPFHNYT 249
R R Y Y++ + + D G H F ++
Sbjct: 101 ARFSAKSRTYRYIIYNAPLRPPFLANYVWHVPYPLDLDAMREAAKLLLGTHDFTSFR 157
Score = 61.9 bits (151), Expect = 1e-10
Identities = 25/82 (30%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 360 SASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILT 419
S S R I+ + + I ISG SF+ H +R +VG + V R P + +
Sbjct: 163 SKSPVRTIYRIDVSRDG-----DLIVIDISGNSFLWHMVRNIVGALLLVGRGKRPVEWIK 217
Query: 420 LSLAKHSR-IVLPLAPSEVLFL 440
L R + P AP+E L+L
Sbjct: 218 ELLEAKDRKLAGPTAPAEGLYL 239
>gnl|CDD|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated.
Length = 244
Score = 86.7 bits (216), Expect = 3e-19
Identities = 44/179 (24%), Positives = 68/179 (37%), Gaps = 32/179 (17%)
Query: 78 KKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSS 137
++AL + Y GT++ G Q Q + T++GELE AL K G + + +
Sbjct: 2 MRIALTIEYDGTNFHGWQRQPN---GRTVQGELEKALSKLAG---------EPVRVIGAG 49
Query: 138 RTDKGVHSLATMIC---LKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSF 194
RTD GVH+L + PP+ W+ + +NA LP +I V F
Sbjct: 50 RTDAGVHALG-QVAHFDTPAPRPPEKWR---------RALNALLPDDIAVLWAEEVPDDF 99
Query: 195 DPRRECNLRKYSYLLPAE--VIGINSQLTAA---EIDSHISDFNAILNEFEGEHPFHNY 248
R R+Y Y + +D + N GEH F ++
Sbjct: 100 HARFSAKARRYRYRIYNRPARPPFLRGYVWHYPYPLD--VDAMNEAAQYLLGEHDFTSF 156
Score = 48.2 bits (116), Expect = 4e-06
Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 360 SASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAV-KRKLLPRDIL 418
S S R I+ + ++ IS F+ + +R +VGT + V K K P DI
Sbjct: 163 SKSPVRTIYEADVTREG-----DFIVFDISANGFLHNMVRNIVGTLLEVGKGKRPPEDIK 217
Query: 419 TLSLAKHSRIVLPLAPSEVLFL 440
L AK + P AP+E L+L
Sbjct: 218 ELLEAKDRTLAGPTAPAEGLYL 239
>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 = 82.1 bits (204), Expect = 1e-17
Identities = 44/178 (24%), Positives = 65/178 (36%), Gaps = 44/178 (24%)
Query: 82 LRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDK 141
L + Y GT++ G Q Q + T++GELE AL K G + + + RTD
Sbjct: 1 LTIEYDGTNFSGWQRQPN---GRTVQGELEKALSKIAG---------EPVRVIGAGRTDA 48
Query: 142 GVHSLATMIC---LKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRR 198
GVH+L + EIP + K +N+ LP +I+V S F R
Sbjct: 49 GVHALG-QVAHFDTPSEIPLEKLI---------KALNSLLPPDIRVLSAEEVPDDFHARF 98
Query: 199 ECNLRKYSYLLPAEVIGINSQLTAA-----------EIDSHISDFNAILNEFEGEHPF 245
R Y Y + +N + + +D I G H F
Sbjct: 99 SAKSRTYRYRI------LNRPVPSPFLRRYVWHVPRPLD--IEAMQEAAKLLLGTHDF 148
Score = 52.1 bits (126), Expect = 2e-07
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 6/82 (7%)
Query: 360 SASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAV-KRKLLPRDIL 418
S S R I+ + + I F+ H +R +VGT + V + KL P DI
Sbjct: 158 SKSTVRTIYRADVYREG-----DLIVFEIRANGFLYHMVRNIVGTLLEVGRGKLSPEDIK 212
Query: 419 TLSLAKHSRIVLPLAPSEVLFL 440
+ AK P AP+ L+L
Sbjct: 213 EILEAKDRTAAGPTAPAHGLYL 234
>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 = 81.3 bits (201), Expect = 1e-17
Identities = 49/168 (29%), Positives = 73/168 (43%), Gaps = 40/168 (23%)
Query: 84 VGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGV 143
GY GT Y G Q Q D + T+EGEL AL KAG I ++RTD+GV
Sbjct: 1 FGYDGTKYHGFQRQND---VPTVEGELIIALLKAGNI---------PYFIKAAARTDRGV 48
Query: 144 HSLATMICLKME--IPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECN 201
+L ++ ++ E + P+A +N LP +I+VF++ F R C+
Sbjct: 49 SALGQVVAIETERRLTPEA-------------LNGILPGDIRVFAVHSVPPDFHAPRYCD 95
Query: 202 LRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHNYT 249
R Y Y +P+ L + S + F G H F N++
Sbjct: 96 HRTYRYYIPSF------PLDDERLKS-------AASRFLGTHDFTNFS 130
Score = 40.4 bits (95), Expect = 9e-04
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 380 GFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHSRIVLPL-APSEVL 438
+V + +SF+ HQ+R+MVG + V L ++ LA + + + AP+E L
Sbjct: 149 LNPFVVVEFKAKSFLWHQVRRMVGFLMLVGEGLHSPSSVSRLLAGPAPPIPMVPAPAEGL 208
Query: 439 FL 440
L
Sbjct: 209 LL 210
>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 = 71.5 bits (176), Expect = 6e-14
Identities = 49/181 (27%), Positives = 69/181 (38%), Gaps = 37/181 (20%)
Query: 82 LRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRE---SNYGNLQKIAWARSSR 138
LR Y+G +Y G +Q E + +T+E L AL K I + SNY R R
Sbjct: 1 LRFAYLGWNYNGFAVQ--EETTNTVEETLFEALEKTRLIEDRQTSNYS--------RCGR 50
Query: 139 TDKGVHSLATMICLKM-----------EIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSI 187
TDKGV + +I L + D + K +N LP +I++ +
Sbjct: 51 TDKGVSAFGQVISLDVRSNLKPEDGLDPSTDVKSTADEEELPYCKILNRVLPPDIRILAW 110
Query: 188 LPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHN 247
P F R C R Y Y P + I AA++ GEH F N
Sbjct: 111 APVPPDFSARFSCVSRTYRYFFPKGDLDIELMRKAAKL-------------LLGEHDFRN 157
Query: 248 Y 248
+
Sbjct: 158 F 158
Score = 31.5 bits (72), Expect = 0.97
Identities = 13/62 (20%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 362 SHFRKIFSCSCGKLEKSL-GFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTL 420
++ R++ S +++ G G + G +F+ HQ+R M+ + + L P +++
Sbjct: 169 NYVRRVLSAEVEPVDQHPDGDGLYYFEVRGSAFLWHQVRCMMAVLFLIGQGLEPPSVISQ 228
Query: 421 SL 422
L
Sbjct: 229 LL 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 = 67.8 bits (166), Expect = 7e-13
Identities = 51/180 (28%), Positives = 79/180 (43%), Gaps = 36/180 (20%)
Query: 82 LRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDK 141
L++ Y GT++ G Q Q D + T+EGEL AL + G I A RTD+
Sbjct: 1 LKIAYDGTNFHGFQRQPD---VRTVEGELIKALEELGIIESRA---RLYSA----GRTDR 50
Query: 142 GVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECN 201
GVH+L ++ + E P + +NA LP++I V + FDPRR +
Sbjct: 51 GVHALGNVVVFETEKEP-----------IPPMINAKLPKDIWVLAGAKVPEDFDPRRWAH 99
Query: 202 LRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHNYTERSKYRRKPHKT 261
+ Y Y L + + AA+ + G H F N+++R R+ P +T
Sbjct: 100 RKYYRYNLG-SDYDVEAMKEAAK-------------KLIGTHDFSNFSKRDG-RKDPVRT 144
Score = 29.3 bits (66), Expect = 4.2
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 382 GYVEISISGESFMLHQIRKMVGTAVAV-KRKLLPRDILTLSLAKHSRIVLPLAPSEVLFL 440
++ I + GESF+ + +R++VG V K K + L + +P AP E L L
Sbjct: 155 EFITIDVVGESFLWNMVRRIVGALSEVGKGKRENEWVEKLLDGEFRPEGVPPAPPEGLIL 214
>gnl|CDD|237759 PRK14589, PRK14589, tRNA pseudouridine synthase ACD; Provisional.
Length = 265
Score = 67.9 bits (166), Expect = 1e-12
Identities = 46/182 (25%), Positives = 69/182 (37%), Gaps = 36/182 (19%)
Query: 79 KVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSR 138
++A R+ Y+GT + G Q Q D T+EGE A R + + ++ +A + R
Sbjct: 2 RLAFRISYIGTRFFGSQYQPD---QRTVEGEFIAA-----CRRLGLFSDWREAGFALAGR 53
Query: 139 TDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKR-VNAHLPRNIKVFSILPSQRSFDPR 197
TD+GVH+ ++ P + A +N LP +I SF PR
Sbjct: 54 TDRGVHARGQVLAFSTHKP-----------ERAVEALNGQLPPDIWCTGWAEVPESFHPR 102
Query: 198 RECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHNYT---ERSKY 254
+ R Y Y IN+ AA EF G H F + +S
Sbjct: 103 YDAISRTYRYYFSRPPSDINAMRDAAG-------------EFIGTHDFSCFARVEGKSPV 149
Query: 255 RR 256
R
Sbjct: 150 RT 151
Score = 31.3 bits (71), Expect = 1.1
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 380 GFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHSRIVLPLAPSEVLF 439
GF E++ +SF+ H +R M G + + + D + L+ + + AP+E L
Sbjct: 162 GFPVFEVT--AQSFLWHMVRCMAGALLQIGEGEMEPDDIERLLSGPCKRKVKPAPAEGLV 219
Query: 440 L 440
L
Sbjct: 220 L 220
>gnl|CDD|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional.
Length = 245
Score = 61.7 bits (150), Expect = 1e-10
Identities = 56/215 (26%), Positives = 89/215 (41%), Gaps = 40/215 (18%)
Query: 78 KKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETAL---FKAGGIRESNYGNLQKIAWA 134
K+VA V Y G+++ G Q Q D + T++G E AL FK Q+I
Sbjct: 2 KRVAAVVSYDGSNFFGYQGQPD---VRTVQGVFEDALERIFK------------QRIYTQ 46
Query: 135 RSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSF 194
+ RTD GVH+ +I D D+ +NA+LP +I V + ++F
Sbjct: 47 AAGRTDTGVHANGQVIAFNCPN------DRMTEEDIKNAMNANLPDDIYVKKVFEVPKNF 100
Query: 195 DPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILN---------EFEGEHPF 245
PR + R Y Y + + S+ + ++ F L+ EGEH F
Sbjct: 101 HPRFDAKKRIYHYFI------LTSKEKNVFLRKYVWWFPYELDLEAMRKAAKYLEGEHDF 154
Query: 246 HNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVE 280
++ + R P +T + + KD + RVE
Sbjct: 155 TSF-KTGSDERNPVRTIYRIRILRLKKDLILIRVE 188
>gnl|CDD|173052 PRK14588, PRK14588, tRNA pseudouridine synthase ACD; Provisional.
Length = 272
Score = 56.4 bits (136), Expect = 9e-09
Identities = 49/193 (25%), Positives = 74/193 (38%), Gaps = 42/193 (21%)
Query: 78 KKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSS 137
+ +AL + Y GTD+ G Q Q D T++G LE A R +
Sbjct: 2 RTIALLLEYDGTDFAGSQWQTD---GRTVQGALEAAWQALTQERRR---------IVLAG 49
Query: 138 RTDKGVHSLATMICLKMEIPPDAWKDDPYGID-LAKRVNAHLPRNIKVFSILPSQRSFDP 196
RTD GVH+ + ++ D + + + + +NAHLP +I V + + F
Sbjct: 50 RTDAGVHARGQVAHVQ--------TDTRHSLATIWRGLNAHLPEDIGVQNAWEAPPDFHA 101
Query: 197 RRECNLRKYSYL----------LPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEHPFH 246
R R+Y Y+ L +V+ L A +D A L G H F
Sbjct: 102 RFSAIQREYRYVIDCAPAPSPQLRHQVLHYAGTLDVAAMD-------AALKLLIGTHDFA 154
Query: 247 NYT----ERSKYR 255
+T E S R
Sbjct: 155 AFTTAPQEGSTVR 167
Score = 37.2 bits (86), Expect = 0.017
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 384 VEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLA-KHSRIVLPLAPSEVLFLRA 442
+ I ++ +F+ H +R +VGT + V R + D LA + R+ P AP+ L+L A
Sbjct: 185 LAIEVAANAFLQHMVRNIVGTLLLVGRGRMTVDQFGAVLASRDRRLAGPTAPAHGLYLTA 244
Query: 443 NSFSVRTRPGVTRP 456
VR PG+ R
Sbjct: 245 ----VRYPPGLIRW 254
>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 = 50.9 bits (122), Expect = 4e-08
Identities = 21/83 (25%), Positives = 31/83 (37%), Gaps = 18/83 (21%)
Query: 82 LRVGYVGT-DYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYG-----------NLQ 129
Y GT D+ G Q QR T++ L + G R+ +
Sbjct: 1 AAKLYDGTHDFSGFQKQR------TVQKSLIRTIESIGIERDGELLVFEIKGNGFLYHQV 54
Query: 130 KIAWARSSRTDKGVHSLATMICL 152
+I RT KGVH+L ++ L
Sbjct: 55 RIMVGALLRTGKGVHALEQVVSL 77
Score = 41.7 bits (98), Expect = 7e-05
Identities = 25/88 (28%), Positives = 36/88 (40%), Gaps = 10/88 (11%)
Query: 362 SHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLS 421
S R I S +E+ EI G F+ HQ+R MVG + + + + +
Sbjct: 23 SLIRTIESI---GIERDGELLVFEIK--GNGFLYHQVRIMVGALLRTGKGVHALEQVVSL 77
Query: 422 LAKHSRI-VLPLAPSEVLFLRANSFSVR 448
L R P AP+ L+L F VR
Sbjct: 78 LNSKLRPRAPPTAPAVGLYL----FHVR 101
>gnl|CDD|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed.
Length = 245
Score = 44.0 bits (104), Expect = 8e-05
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 382 GYVEISISGESFMLHQIRKMVGTAVAV-KRKLLPRDILTLSLAKHSRIVLPLAPSEVLFL 440
G+V+I +SG F+ + +R +VG + V +L DI + AK AP+ L+L
Sbjct: 181 GFVQIRVSGNGFLHNMVRIIVGALIEVGLGQLKAEDIKQILEAKDRNQANCTAPASGLYL 240
Score = 40.5 bits (95), Expect = 0.001
Identities = 44/194 (22%), Positives = 79/194 (40%), Gaps = 52/194 (26%)
Query: 82 LRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDK 141
L + Y G+ Y+G Q + + +TI+G++E+ L + G ++I RTD
Sbjct: 6 LTIQYDGSRYKGWQKLGN--NDNTIQGKIESVLSEMTG---------EEIEIIGCGRTDA 54
Query: 142 GVHSLATMICLKMEIPPDAWKDDPYGID-LAKRVNAHLPRNIKVFSILPSQRSFDPR--- 197
GVH+L + + D+ D + K +N +LP +I V ++ F R
Sbjct: 55 GVHALNQVANFQT--------DEKLSEDKIKKYLNEYLPNDIVVTNVEEVDERFHARYNV 106
Query: 198 -------RECN-------LRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEH 243
+ N +RKYS + E + + + AA+ G H
Sbjct: 107 KSKTYLYKIWNEKFHNVFMRKYSMHVN-EKLDVKAMKEAAKY-------------LVGSH 152
Query: 244 PFHNYTERSKYRRK 257
F ++T +K ++K
Sbjct: 153 DFTSFT-NAKSKKK 165
>gnl|CDD|173051 PRK14587, PRK14587, tRNA pseudouridine synthase ACD; Provisional.
Length = 256
Score = 43.3 bits (102), Expect = 2e-04
Identities = 27/108 (25%), Positives = 50/108 (46%), Gaps = 15/108 (13%)
Query: 135 RSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSF 194
R SRTD GV ++ ++ ++P VN+ LPR + +++ F
Sbjct: 38 RGSRTDPGVSAVGNVVMTSQKLPLGY-------------VNSKLPRGVWAWAVAEVPEGF 84
Query: 195 DPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGE 242
+PRR R+Y Y+ P + + AAE+ + D+++ + + GE
Sbjct: 85 NPRR-AKRRRYLYVAPHWGEDVEAMREAAELLAGTHDYSSFI-QRRGE 130
>gnl|CDD|203428 pfam06350, HSL_N, Hormone-sensitive lipase (HSL) N-terminus. This
family consists of several mammalian hormone-sensitive
lipase (HSL) proteins (EC:3.1.1.-). Hormone-sensitive
lipase, a key enzyme in fatty acid mobilisation, overall
energy homeostasis, and possibly steroidogenesis, is
acutely controlled through reversible phosphorylation by
catecholamines and insulin.
Length = 315
Score = 30.1 bits (68), Expect = 2.8
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 391 ESFMLHQIRKMVGTAVAVKRKL-LPRDILTLSLAKHSRIVLPLAP 434
ES ML + +V + V V R L LP + L L LA + + + P
Sbjct: 246 ESEMLSSLPSIVSSKVKVNRLLTLPPEPLQLPLASDPELSVTIPP 290
>gnl|CDD|181231 PRK08114, PRK08114, cystathionine beta-lyase; Provisional.
Length = 395
Score = 29.3 bits (66), Expect = 5.6
Identities = 17/41 (41%), Positives = 26/41 (63%), Gaps = 2/41 (4%)
Query: 371 SCGKLEKSLGFGYVEISI-SGESFMLHQIRKMVGTAVAVKR 410
+ G L K+L FG ++ISI +G +++ M+GTAVA R
Sbjct: 189 AAGVLFKALDFG-IDISIQAGTKYLVGHSDAMIGTAVANAR 228
>gnl|CDD|238858 cd01820, PAF_acetylesterase_like, PAF_acetylhydrolase (PAF-AH)_like
subfamily of SGNH-hydrolases. Platelet-activating factor
(PAF) and PAF-AH are key players in inflammation and in
atherosclerosis. PAF-AH is a calcium independent
phospholipase A2 which exhibits strong substrate
specificity towards PAF, hydrolyzing an acetyl ester at
the sn-2 position. PAF-AH also degrades a family of
oxidized PAF-like phospholipids with short sn-2
residues. In addition, PAF and PAF-AH are associated
with neural migration and mammalian reproduction.
Length = 214
Score = 28.8 bits (65), Expect = 5.8
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 167 GID-LAKRVNAHLPR-NIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGIN 217
GI + + + LP I + +LP ++ +P RE N + + LL G+
Sbjct: 114 GILAIVEEIREKLPNAKILLLGLLPRGQNPNPLRERN-AQVNRLLAVRYDGLP 165
>gnl|CDD|223602 COG0528, PyrH, Uridylate kinase [Nucleotide transport and
metabolism].
Length = 238
Score = 28.3 bits (64), Expect = 9.3
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 12/61 (19%)
Query: 195 DPRRECNLRKYSYLLPAEVIGINSQ---LTAAEI--DSHI-------SDFNAILNEFEGE 242
DP+++ + +KY L EV+ I + TA + D+ I + + +GE
Sbjct: 171 DPKKDPDAKKYDTLTYDEVLKIGLKVMDPTAFSLARDNGIPIIVFNINKPGNLKRALKGE 230
Query: 243 H 243
Sbjct: 231 E 231
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 0.130 0.377
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,780,718
Number of extensions: 2544443
Number of successful extensions: 2300
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2247
Number of HSP's successfully gapped: 45
Length of query: 539
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 437
Effective length of database: 6,413,494
Effective search space: 2802696878
Effective search space used: 2802696878
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: 41 (21.6 bits)
S2: 61 (27.3 bits)