RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 045140
(468 letters)
>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 = 191 bits (487), Expect = 5e-58
Identities = 65/119 (54%), Positives = 83/119 (69%), Gaps = 1/119 (0%)
Query: 338 YGEEEKKRFNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSV-VNVEGIDFLKC 396
+ E +RFN ILK YVG+HNFHNFT + K EDPSA R+I SF V EG++++
Sbjct: 127 FALETLQRFNEILKEYVGTHNFHNFTVKKKFEDPSANRFIKSFYVSEPFVIEEGLEWISI 186
Query: 397 EVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETALQKDVNINVPTAPEVGLYLDECIF 455
++ GQSFMLHQIRKMIGLA+A+VR AP+SLIE + KD I +P AP +GL L+ F
Sbjct: 187 KIHGQSFMLHQIRKMIGLAIAIVRGGAPESLIELSFNKDKIIIIPLAPGLGLLLERPHF 245
Score = 190 bits (484), Expect = 2e-57
Identities = 75/130 (57%), Positives = 93/130 (71%), Gaps = 8/130 (6%)
Query: 64 IFFAYCGVGYQGMQKNPGA-KTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDKGV 122
+ F YCG GY GMQ NPGA KTIEG+LE ALF +GA+SE + G+P++ ++R+ARTDKGV
Sbjct: 1 LLFGYCGTGYHGMQYNPGAYKTIEGELERALFKAGAISESNAGDPKKIGFSRAARTDKGV 60
Query: 123 SAVGQVVSGRFCIDPPG-------LVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRY 175
A VVS + ID P LVE+LNS+LP+ IR+FG RVT SFNA+K CD R Y
Sbjct: 61 HAARNVVSLKVIIDDPEGLGILEDLVEKLNSHLPSDIRVFGITRVTKSFNARKACDSRTY 120
Query: 176 VYLLPVFALD 185
YLLP FAL+
Sbjct: 121 EYLLPTFALE 130
>gnl|CDD|215562 PLN03078, PLN03078, Putative tRNA pseudouridine synthase;
Provisional.
Length = 513
Score = 148 bits (374), Expect = 3e-39
Identities = 116/446 (26%), Positives = 182/446 (40%), Gaps = 75/446 (16%)
Query: 30 SATSTSDDERDLIPAAAGADST---TKRQLCKRRKIAIFFAYCGVGYQGMQKN---PGAK 83
S +STS P K + +++K+ + Y G Y+G+QK
Sbjct: 38 SPSSTSLSPPSSDPPLTDNSDQGGGMKWESARKKKVVLRVGYVGTDYRGLQKQRDLSSLS 97
Query: 84 TIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDKGVSAVGQVVSGRFCI-------D 136
TIEG+LE A+F +G + E + GN + WARS+RTDKGV ++ ++S + I D
Sbjct: 98 TIEGELETAIFKAGGIRESNYGNLHKIGWARSSRTDKGVHSLATMISLKMEIPENAWKDD 157
Query: 137 PPG--LVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYLLPVFALDSSSHRDRES 194
P G L + +NS+LP IR+F SF+ ++ CD R+Y YLLP + S E
Sbjct: 158 PDGIALAKFINSHLPDNIRVFSILPAQRSFDPRRECDLRKYSYLLPAEVIGIKSGFSSEE 217
Query: 195 VMASLGSGNELVKCLECSERGRKVIGVMGKRTYQLGLPSNDENASLNSQVKVDTVVSTCN 254
+ + N ++ E P ++ A + K+ N
Sbjct: 218 IDEHISEFNSILNGFEGEH------------------PFHNYTARSKYRKKLPGKHKQRN 259
Query: 255 GDRHNTNLESVESNKTISESVMVENANSESVNETLVESRTSETVQNENTDLSLDLDSKND 314
G S E + + SE E + + + + + + +NE+ L ++
Sbjct: 260 GAVSRRAKSSKEMSSSESEENHGEISEEDEEDLSFSSIPSGSSDENEDI-----LKFQS- 313
Query: 315 SKVMAEERSVNGEEKLLKGSGFCYGEEEKKRFNRILKHYVGSHNFHNFTTRTKAEDPSAR 374
S+V R + + +E R + SH
Sbjct: 314 SQVQIRAR-------------WLHEPDETDRIS-------ASH----------------F 337
Query: 375 RYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETALQK 434
R I + G DF++ + G+SFMLHQIRKM+G AVAV R P+ +I +L K
Sbjct: 338 RKIFRCSCGKLEKSLGFDFVELSIWGESFMLHQIRKMVGTAVAVKRELLPRDIIRLSLTK 397
Query: 435 DVNINVPTAPEVGLYLDECIFASYNK 460
I +P AP L L F+ K
Sbjct: 398 FSRIVLPLAPSEVLILRGNSFSVRKK 423
>gnl|CDD|223179 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal
structure and biogenesis].
Length = 266
Score = 119 bits (300), Expect = 1e-30
Identities = 44/131 (33%), Positives = 62/131 (47%), Gaps = 15/131 (11%)
Query: 60 RKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTD 119
++IA+ AY G + G Q+ P +T++G+LE+AL G S R G + RTD
Sbjct: 2 KRIALKIAYDGTRFHGWQRQPNVRTVQGELEKALSKIGGESVRVIG---------AGRTD 52
Query: 120 KGVSAVGQVVSGRFC----IDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRY 175
GV A+GQVV F LV LN+ LP IR+ V F+A+ R Y
Sbjct: 53 AGVHALGQVVH--FDTPADRPLEKLVRALNALLPPDIRVLDVAEVPDDFHARFSAKSRTY 110
Query: 176 VYLLPVFALDS 186
Y++ L
Sbjct: 111 RYIIYNAPLRP 121
Score = 94.3 bits (235), Expect = 8e-22
Identities = 30/117 (25%), Positives = 49/117 (41%), Gaps = 7/117 (5%)
Query: 345 RFNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSFM 404
K +G+H+F +F + + S R I + D + ++ G SF+
Sbjct: 139 AMREAAKLLLGTHDFTSFR-KAGCQSKSPVRTI-----YRIDVSRDGDLIVIDISGNSFL 192
Query: 405 LHQIRKMIGLAVAVVRNCAPQSLIETAL-QKDVNINVPTAPEVGLYLDECIFASYNK 460
H +R ++G + V R P I+ L KD + PTAP GLYL + +
Sbjct: 193 WHMVRNIVGALLLVGRGKRPVEWIKELLEAKDRKLAGPTAPAEGLYLVRVDYPEDFE 249
>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 = 100 bits (250), Expect = 3e-24
Identities = 44/123 (35%), Positives = 65/123 (52%), Gaps = 11/123 (8%)
Query: 60 RKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTD 119
RKIA+ AY G Y G Q+ P +T++G+LE+AL G ++ + RTD
Sbjct: 1 RKIALKIAYDGSNYHGWQRQPNKRTVQGELEKALEAIGK---------KKITIMSAGRTD 51
Query: 120 KGVSAVGQVVSGRFCIDPP--GLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVY 177
KGV A+GQV+S + P L +LN+ LP IR+ V +F+A+ +R Y Y
Sbjct: 52 KGVHAMGQVISFDTPKEIPDNKLNAKLNALLPPDIRVKALAPVNDNFHARFSASKRHYRY 111
Query: 178 LLP 180
+L
Sbjct: 112 ILY 114
Score = 80.8 bits (200), Expect = 2e-17
Identities = 35/123 (28%), Positives = 57/123 (46%), Gaps = 9/123 (7%)
Query: 330 LLKGSGFCYGEEEKKRFNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNV- 388
+L Y + ++ K +G H+F NF+ K++ S R I + V
Sbjct: 112 ILYNHRHYYSPLDLEKMRAAAKQLLGKHDFSNFSKA-KSKSRSPIRTISD------IKVS 164
Query: 389 EGIDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETAL-QKDVNINVPTAPEVG 447
E +++ +++G SF+ H +RK++G V V R P + L K N+ TAP G
Sbjct: 165 ESGEYIIFDIIGNSFLWHMVRKIVGALVLVGRGKLPPEWVAKLLDAKKRNLAPTTAPANG 224
Query: 448 LYL 450
LYL
Sbjct: 225 LYL 227
>gnl|CDD|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated.
Length = 244
Score = 89.8 bits (224), Expect = 2e-20
Identities = 39/125 (31%), Positives = 56/125 (44%), Gaps = 15/125 (12%)
Query: 60 RKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTD 119
+IA+ Y G + G Q+ P +T++G+LE+AL G P R + RTD
Sbjct: 2 MRIALTIEYDGTNFHGWQRQPNGRTVQGELEKALSKLA-------GEPVRV--IGAGRTD 52
Query: 120 KGVSAVGQVVSGRF----CIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRY 175
GV A+GQV F P LN+ LP I + + V F+A+ RRY
Sbjct: 53 AGVHALGQVAH--FDTPAPRPPEKWRRALNALLPDDIAVLWAEEVPDDFHARFSAKARRY 110
Query: 176 VYLLP 180
Y +
Sbjct: 111 RYRIY 115
Score = 57.5 bits (140), Expect = 2e-09
Identities = 27/108 (25%), Positives = 49/108 (45%), Gaps = 9/108 (8%)
Query: 345 RFNRILKHYVGSHNFHNF-TTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSF 403
N ++ +G H+F +F + +++ P R I DF+ ++ F
Sbjct: 139 AMNEAAQYLLGEHDFTSFRASGCQSKSP--VRTI-----YEADVTREGDFIVFDISANGF 191
Query: 404 MLHQIRKMIGLAVAVVRNCAPQSLIETALQ-KDVNINVPTAPEVGLYL 450
+ + +R ++G + V + P I+ L+ KD + PTAP GLYL
Sbjct: 192 LHNMVRNIVGTLLEVGKGKRPPEDIKELLEAKDRTLAGPTAPAEGLYL 239
>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 = 87.8 bits (218), Expect = 5e-20
Identities = 47/125 (37%), Positives = 62/125 (49%), Gaps = 15/125 (12%)
Query: 66 FAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDKGVSAV 125
F Y G Y G Q+ T+EG+L AL +G + Y +ARTD+GVSA+
Sbjct: 1 FGYDGTKYHGFQRQNDVPTVEGELIIALLKAGNIP---------YFIKAAARTDRGVSAL 51
Query: 126 GQVVSGRFCIDPPGL--VERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYLLPVFA 183
GQVV+ I+ E LN LP IR+F V F+A ++CD R Y Y +P F
Sbjct: 52 GQVVA----IETERRLTPEALNGILPGDIRVFAVHSVPPDFHAPRYCDHRTYRYYIPSFP 107
Query: 184 LDSSS 188
LD
Sbjct: 108 LDDER 112
Score = 65.1 bits (159), Expect = 4e-12
Identities = 29/122 (23%), Positives = 51/122 (41%), Gaps = 10/122 (8%)
Query: 336 FCYG-EEEKKRFNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVEGIDFL 394
+ + +R ++G+H+F NF+ K + + R IIS + F+
Sbjct: 102 YIPSFPLDDERLKSAASRFLGTHDFTNFS---KKDTRNTVRTIISIECK-----DLNPFV 153
Query: 395 KCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETALQ-KDVNINVPTAPEVGLYLDEC 453
E +SF+ HQ+R+M+G + V S + L I + AP GL L +
Sbjct: 154 VVEFKAKSFLWHQVRRMVGFLMLVGEGLHSPSSVSRLLAGPAPPIPMVPAPAEGLLLVDV 213
Query: 454 IF 455
+
Sbjct: 214 KY 215
>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 = 76.7 bits (189), Expect = 3e-17
Identities = 31/108 (28%), Positives = 46/108 (42%), Gaps = 7/108 (6%)
Query: 349 ILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQI 408
K Y G+H+F F + + S R I S G + L E+ G F+ HQ+
Sbjct: 1 AAKLYDGTHDFSGFQ-KQRTVQKSLIRTIESIG-----IERDGELLVFEIKGNGFLYHQV 54
Query: 409 RKMIGLAVAVVRN-CAPQSLIETALQKDVNINVPTAPEVGLYLDECIF 455
R M+G + + A + ++ K PTAP VGLYL +
Sbjct: 55 RIMVGALLRTGKGVHALEQVVSLLNSKLRPRAPPTAPAVGLYLFHVRY 102
Score = 44.0 bits (104), Expect = 1e-05
Identities = 22/102 (21%), Positives = 32/102 (31%), Gaps = 27/102 (26%)
Query: 64 IFFAYCG-VGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRG-----------NPRRYD 111
Y G + G QK +T++ L + G + + + R
Sbjct: 1 AAKLYDGTHDFSGFQKQ---RTVQKSLIRTIESIGIERDGELLVFEIKGNGFLYHQVRIM 57
Query: 112 WARSARTDKGVSAVGQVVSGRFCIDPPGLVERLNSNLPTQIR 153
RT KGV A+ QV V LNS L +
Sbjct: 58 VGALLRTGKGVHALEQV------------VSLLNSKLRPRAP 87
>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 = 80.0 bits (198), Expect = 6e-17
Identities = 45/141 (31%), Positives = 57/141 (40%), Gaps = 26/141 (18%)
Query: 66 FAYCGVGYQGMQKNPGAK-TIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDKGVSA 124
FAY G Y G T+E L EAL + + +R +++R RTDKGVSA
Sbjct: 3 FAYLGWNYNGFAVQEETTNTVEETLFEALEKTRLIEDRQT-----SNYSRCGRTDKGVSA 57
Query: 125 VGQVVSGRF---CIDPPGL-----------------VERLNSNLPTQIRIFGYKRVTASF 164
GQV+S GL + LN LP IRI + V F
Sbjct: 58 FGQVISLDVRSNLKPEDGLDPSTDVKSTADEEELPYCKILNRVLPPDIRILAWAPVPPDF 117
Query: 165 NAKKFCDQRRYVYLLPVFALD 185
+A+ C R Y Y P LD
Sbjct: 118 SARFSCVSRTYRYFFPKGDLD 138
Score = 46.9 bits (112), Expect = 7e-06
Identities = 33/114 (28%), Positives = 49/114 (42%), Gaps = 13/114 (11%)
Query: 351 KHYVGSHNFHNFTTRTKAEDPSA-----RRYIISFGADSVVNVEGIDFLKC-EVVGQSFM 404
K +G H+F NF D + R ++S + V D L EV G +F+
Sbjct: 147 KLLLGEHDFRNFCKM----DVANQVTNYVRRVLSAEVEPVDQHPDGDGLYYFEVRGSAFL 202
Query: 405 LHQIRKMIGLAVAVVRNCAPQSLIETALQKDVNINVPT---APEVGLYLDECIF 455
HQ+R M+ + + + P S+I L + N P A EV L L +C F
Sbjct: 203 WHQVRCMMAVLFLIGQGLEPPSVISQLLDVEKNPRKPQYTMASEVPLVLYDCGF 256
>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 = 77.1 bits (191), Expect = 4e-16
Identities = 39/122 (31%), Positives = 56/122 (45%), Gaps = 19/122 (15%)
Query: 64 IFFAYCGVGYQGMQKNPGAKTIEGDLEEAL--FHSGAVSERDRGNPRRYDWARSARTDKG 121
+ Y G + G Q+ P +T++G+LE+AL V R G + RTD G
Sbjct: 1 LTIEYDGTNFSGWQRQPNGRTVQGELEKALSKIAGEPV--RVIG---------AGRTDAG 49
Query: 122 VSAVGQVVSGRFC----IDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVY 177
V A+GQV F I L++ LNS LP IR+ + V F+A+ R Y Y
Sbjct: 50 VHALGQVAH--FDTPSEIPLEKLIKALNSLLPPDIRVLSAEEVPDDFHARFSAKSRTYRY 107
Query: 178 LL 179
+
Sbjct: 108 RI 109
Score = 55.2 bits (134), Expect = 1e-08
Identities = 33/108 (30%), Positives = 49/108 (45%), Gaps = 7/108 (6%)
Query: 344 KRFNRILKHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSF 403
+ K +G+H+F +F + S R I + AD V EG D + E+ F
Sbjct: 133 EAMQEAAKLLLGTHDFSSFR-AAGCQSKSTVRTI--YRAD--VYREG-DLIVFEIRANGF 186
Query: 404 MLHQIRKMIGLAVAVVRNCAPQSLIETALQ-KDVNINVPTAPEVGLYL 450
+ H +R ++G + V R I+ L+ KD PTAP GLYL
Sbjct: 187 LYHMVRNIVGTLLEVGRGKLSPEDIKEILEAKDRTAAGPTAPAHGLYL 234
>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 = 64.3 bits (157), Expect = 9e-12
Identities = 36/115 (31%), Positives = 57/115 (49%), Gaps = 11/115 (9%)
Query: 67 AYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSA-RTDKGVSAV 125
AY G + G Q+ P +T+EG+L +AL G + R R SA RTD+GV A+
Sbjct: 4 AYDGTNFHGFQRQPDVRTVEGELIKALEELGIIESRAR--------LYSAGRTDRGVHAL 55
Query: 126 GQVVSGRFCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYLLP 180
G VV F + + +N+ LP I + +V F+ +++ ++ Y Y L
Sbjct: 56 GNVVV--FETEKEPIPPMINAKLPKDIWVLAGAKVPEDFDPRRWAHRKYYRYNLG 108
Score = 44.3 bits (105), Expect = 4e-05
Identities = 26/105 (24%), Positives = 47/105 (44%), Gaps = 16/105 (15%)
Query: 351 KHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQIRK 410
K +G+H+F NF+ R +DP I + +F+ +VVG+SF+ + +R+
Sbjct: 121 KKLIGTHDFSNFSKRDGRKDPVRTIERIEISENG-------EFITIDVVGESFLWNMVRR 173
Query: 411 MIGLAVAVVRNCAPQSLIETALQKDVNIN-----VPTAPEVGLYL 450
++G + ++K ++ VP AP GL L
Sbjct: 174 IVGA----LSEVGKGKRENEWVEKLLDGEFRPEGVPPAPPEGLIL 214
>gnl|CDD|237759 PRK14589, PRK14589, tRNA pseudouridine synthase ACD; Provisional.
Length = 265
Score = 64.4 bits (157), Expect = 1e-11
Identities = 42/132 (31%), Positives = 60/132 (45%), Gaps = 8/132 (6%)
Query: 61 KIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTDK 120
++A +Y G + G Q P +T+EG+ A G S+ R +A + RTD+
Sbjct: 2 RLAFRISYIGTRFFGSQYQPDQRTVEGEFIAACRRLGLFSD-----WREAGFALAGRTDR 56
Query: 121 GVSAVGQVVSGRFCIDPPGL-VERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYVYLL 179
GV A GQV++ F P VE LN LP I G+ V SF+ + R Y Y
Sbjct: 57 GVHARGQVLA--FSTHKPERAVEALNGQLPPDIWCTGWAEVPESFHPRYDAISRTYRYYF 114
Query: 180 PVFALDSSSHRD 191
D ++ RD
Sbjct: 115 SRPPSDINAMRD 126
Score = 44.8 bits (106), Expect = 4e-05
Identities = 28/98 (28%), Positives = 39/98 (39%), Gaps = 8/98 (8%)
Query: 353 YVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQIRKMI 412
++G+H+F F + E S R I+ V + G EV QSF+ H +R M
Sbjct: 131 FIGTHDFSCFA---RVEGKSPVRTILRI---RVFSDGGFPVF--EVTAQSFLWHMVRCMA 182
Query: 413 GLAVAVVRNCAPQSLIETALQKDVNINVPTAPEVGLYL 450
G + + IE L V AP GL L
Sbjct: 183 GALLQIGEGEMEPDDIERLLSGPCKRKVKPAPAEGLVL 220
>gnl|CDD|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional.
Length = 245
Score = 57.9 bits (140), Expect = 2e-09
Identities = 33/123 (26%), Positives = 56/123 (45%), Gaps = 12/123 (9%)
Query: 60 RKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTD 119
+++A +Y G + G Q P +T++G E+AL +R +R + RTD
Sbjct: 2 KRVAAVVSYDGSNFFGYQGQPDVRTVQGVFEDAL---------ERIFKQRIYTQAAGRTD 52
Query: 120 KGVSAVGQVVSGRFCID---PPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRYV 176
GV A GQV++ D + +N+NLP I + V +F+ + +R Y
Sbjct: 53 TGVHANGQVIAFNCPNDRMTEEDIKNAMNANLPDDIYVKKVFEVPKNFHPRFDAKKRIYH 112
Query: 177 YLL 179
Y +
Sbjct: 113 YFI 115
Score = 38.6 bits (90), Expect = 0.004
Identities = 30/110 (27%), Positives = 49/110 (44%), Gaps = 15/110 (13%)
Query: 351 KHYVGSHNFHNFTTRTKAEDPSARRY---IISFGADSV-VNVEGIDFLKCEVVGQSFMLH 406
K+ G H+F +F T + +P Y I+ D + + VEG FL+
Sbjct: 146 KYLEGEHDFTSFKTGSDERNPVRTIYRIRILRLKKDLILIRVEGRSFLR----------R 195
Query: 407 QIRKMIGLAVAV-VRNCAPQSLIETALQKDVNINVPTAPEVGLYLDECIF 455
+R ++G V V + P+ + E +D + TAP GLYL + +F
Sbjct: 196 MVRNIVGALVKVGLGQWEPEKIKEVLEARDRSKAAGTAPAHGLYLYKVLF 245
>gnl|CDD|173052 PRK14588, PRK14588, tRNA pseudouridine synthase ACD; Provisional.
Length = 272
Score = 56.4 bits (136), Expect = 6e-09
Identities = 35/124 (28%), Positives = 51/124 (41%), Gaps = 15/124 (12%)
Query: 60 RKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSARTD 119
R IA+ Y G + G Q +T++G LE A + RR + RTD
Sbjct: 2 RTIALLLEYDGTDFAGSQWQTDGRTVQGALEAAW-------QALTQERRR--IVLAGRTD 52
Query: 120 KGVSAVGQVV----SGRFCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCDQRRY 175
GV A GQV R + + LN++LP I + F+A+ QR Y
Sbjct: 53 AGVHARGQVAHVQTDTRHSLAT--IWRGLNAHLPEDIGVQNAWEAPPDFHARFSAIQREY 110
Query: 176 VYLL 179
Y++
Sbjct: 111 RYVI 114
>gnl|CDD|173051 PRK14587, PRK14587, tRNA pseudouridine synthase ACD; Provisional.
Length = 256
Score = 49.8 bits (119), Expect = 8e-07
Identities = 31/86 (36%), Positives = 45/86 (52%), Gaps = 9/86 (10%)
Query: 114 RSARTDKGVSAVGQVV--SGRFCIDPPGLVERLNSNLPTQIRIFGYKRVTASFNAKKFCD 171
R +RTD GVSAVG VV S + P G V NS LP + + V FN ++
Sbjct: 38 RGSRTDPGVSAVGNVVMTSQKL---PLGYV---NSKLPRGVWAWAVAEVPEGFNPRR-AK 90
Query: 172 QRRYVYLLPVFALDSSSHRDRESVMA 197
+RRY+Y+ P + D + R+ ++A
Sbjct: 91 RRRYLYVAPHWGEDVEAMREAAELLA 116
Score = 32.5 bits (74), Expect = 0.35
Identities = 29/99 (29%), Positives = 41/99 (41%), Gaps = 9/99 (9%)
Query: 354 VGSHNFHNFTTR--TKAEDPSARRYIISFGADSVVNVEGIDFLKCEVVGQSFMLHQIRKM 411
G+H++ +F R KA Y I V + G D + VG+ F IRKM
Sbjct: 116 AGTHDYSSFIQRRGEKATPTVTTVYEIG------VELRG-DLIYLYFVGRGFRNKMIRKM 168
Query: 412 IGLAVAVVRNCAPQSLIETALQKDVNINVPTAPEVGLYL 450
+A R + I L++ VP+AP GL L
Sbjct: 169 AWAILAAGRGVLSRRDIAELLERPRPGAVPSAPAEGLVL 207
>gnl|CDD|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed.
Length = 245
Score = 45.5 bits (108), Expect = 2e-05
Identities = 31/104 (29%), Positives = 52/104 (50%), Gaps = 9/104 (8%)
Query: 351 KHYVGSHNFHNFTTRTKAEDPSARRYIISFGADSVVNV-EGIDFLKCEVVGQSFMLHQIR 409
K+ VGSH+F +FT K++ S R I S +++ E F++ V G F+ + +R
Sbjct: 146 KYLVGSHDFTSFT-NAKSKKKSTVREIYS------IDIMEEDGFVQIRVSGNGFLHNMVR 198
Query: 410 KMIGLAVAV-VRNCAPQSLIETALQKDVNINVPTAPEVGLYLDE 452
++G + V + + + + KD N TAP GLYL+
Sbjct: 199 IIVGALIEVGLGQLKAEDIKQILEAKDRNQANCTAPASGLYLEN 242
Score = 35.1 bits (81), Expect = 0.053
Identities = 35/123 (28%), Positives = 50/123 (40%), Gaps = 16/123 (13%)
Query: 60 RKIAIFFAYCGVGYQGMQK-NPGAKTIEGDLEEALFHSGAVSERDRGNPRRYDWARSART 118
R I + Y G Y+G QK TI+G +E L S E + RT
Sbjct: 2 RNIKLTIQYDGSRYKGWQKLGNNDNTIQGKIESVL--SEMTGEE-------IEIIGCGRT 52
Query: 119 DKGVSAVGQVVSGRFCIDPPGLVER----LNSNLPTQIRIFGYKRVTASFNAKKFCDQRR 174
D GV A+ QV + F D ++ LN LP I + + V F+A+ +
Sbjct: 53 DAGVHALNQVAN--FQTDEKLSEDKIKKYLNEYLPNDIVVTNVEEVDERFHARYNVKSKT 110
Query: 175 YVY 177
Y+Y
Sbjct: 111 YLY 113
>gnl|CDD|233185 TIGR00918, 2A060602, The Eukaryotic (Putative) Sterol Transporter
(EST) Family.
Length = 1145
Score = 34.5 bits (79), Expect = 0.14
Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 12/68 (17%)
Query: 405 LHQIRKMIGLAVAVVRNCAPQSLIETALQKDVNINVPTAPEVGLYLDECIFAS------Y 458
L R+ IG PQ LI+T Q+ N+ P A + +LD + AS Y
Sbjct: 100 LAYTRQKIGEEAMF----TPQLLIQTPHQEGANVLTPEA--LLQHLDSALKASRVHVYLY 153
Query: 459 NKKWKDSH 466
N++W H
Sbjct: 154 NRQWGLEH 161
>gnl|CDD|116942 pfam08361, TetR_C_2, MAATS-type transcriptional repressor,
C-terminal region. This family is named after the
various transcriptional regulatory proteins that it
contains, including MtrR, AcrR, ArpR, TtgR and SmeT.
These are members of the TetR family of transcriptional
repressors, that are involved in the control of
expression of multidrug resistance proteins.
Length = 119
Score = 29.6 bits (67), Expect = 1.1
Identities = 17/43 (39%), Positives = 21/43 (48%), Gaps = 8/43 (18%)
Query: 391 IDFLKCEVVGQSFMLHQIRKMIGLAVAVVRNCAPQSLIETALQ 433
I F KCE VG+ + QIR+ +GL S IE LQ
Sbjct: 29 IIFHKCEFVGEMSPVQQIRQELGL--------ESYSRIEEVLQ 63
>gnl|CDD|238655 cd01345, OM_channels, Porin superfamily. These outer membrane
channels share a beta-barrel structure that differ in
strand and shear number. Classical (gram-negative )
porins are non-specific channels for small hydrophillic
molecules and form 16 beta-stranded barrels (16,20),
which associate as trimers. Maltoporin-like channels
have specificities for various sugars and form 18
beta-stranded barrels (18,22), which associate as
trimers. Ligand-gated protein channels cooperate with a
TonB associated inner membrane complex to actively
transport ligands via the proton motive force and they
form monomeric, (22,24) barrels. The 150-200 N-terminal
residues form a plug that blocks the channel from the
periplasmic end.
Length = 253
Score = 30.1 bits (67), Expect = 2.3
Identities = 13/58 (22%), Positives = 19/58 (32%), Gaps = 6/58 (10%)
Query: 70 GVGYQGMQKNPGAKTIEGDLEEAL------FHSGAVSERDRGNPRRYDWARSARTDKG 121
GY K P ++A G +RD G +AR+ T+K
Sbjct: 28 KXGYARANKAPSLYQTNPGNDDAKAETSDGKEIGLEFKRDGGWLAGVTYARNDYTNKI 85
>gnl|CDD|223147 COG0069, GltB, Glutamate synthase domain 2 [Amino acid transport
and metabolism].
Length = 485
Score = 29.5 bits (67), Expect = 3.7
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 12/48 (25%)
Query: 107 PRRYDWARSARTDKGVSAVGQVVSGRFCIDPPGLVERLNSNLPTQIRI 154
P RY+ RSA + QV SGRF + P E L + +I+I
Sbjct: 207 PERYEDGRSA--------IKQVASGRFGVTP----EYLANADAIEIKI 242
>gnl|CDD|241465 cd13311, PH_Slm1, Slm1 Pleckstrin homology (PH) domain. Slm1 is a
component of the target of rapamycin complex 2 (TORC2)
signaling pathway. It plays a role in the regulation of
actin organization and is a target of sphingolipid
signaling during the heat shock response. Slm1 contains
a single PH domain that binds PtdIns(4,5)P2, PtdIns(4)P,
and dihydrosphingosine 1-phosphate (DHS-1P). Slm1
possesses two binding sites for anionic lipids. The
non-canonical binding site of the PH domain of Slm1 is
used for ligand binding, and it is proposed that
beta-spectrin, Tiam1 and ArhGAP9 also have this type of
phosphoinositide binding site. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold, which
is electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 110
Score = 28.1 bits (63), Expect = 4.1
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 443 APEVGLYLDECIFASYNKKWKDSH 466
APE+ LYL EC+ + + + SH
Sbjct: 45 APEMSLYLPECVLGAPSDEGGKSH 68
>gnl|CDD|172418 PRK13898, PRK13898, type IV secretion system ATPase VirB4;
Provisional.
Length = 800
Score = 29.4 bits (66), Expect = 4.7
Identities = 17/53 (32%), Positives = 31/53 (58%), Gaps = 6/53 (11%)
Query: 367 KAEDPSARRYIISFGADSVV---NVEGIDFLKCEVVGQS---FMLHQIRKMIG 413
K DP+ R ++I G +VV N++G+D + + G++ +L QIR+ +G
Sbjct: 731 KHTDPTTRFFLIKQGVSAVVARINLDGMDDIISVLSGRAETVLLLDQIREEVG 783
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 28.8 bits (64), Expect = 7.5
Identities = 25/114 (21%), Positives = 44/114 (38%), Gaps = 6/114 (5%)
Query: 235 DENASLNSQVKVDTVVSTCNGDRHNTNLESVESNKTISESVMVENANSESVNETLVESRT 294
+EN +L+ ++ D D N + E N +E + S+ E
Sbjct: 4038 EENNTLDEDIQQDDFSDLAE-DDEKMNEDGFEENVQENEESTEDGVKSDEELEQGEVPED 4096
Query: 295 S-----ETVQNENTDLSLDLDSKNDSKVMAEERSVNGEEKLLKGSGFCYGEEEK 343
+ ++T S + D +N K + E GEE ++G+G GE E+
Sbjct: 4097 QAIDNHPKMDAKSTFASAEADEENTDKGIVGENEELGEEDGVRGNGTADGEFEQ 4150
>gnl|CDD|220585 pfam10123, Mu-like_Pro, Mu-like prophage I protein. Members of
this family of proteins comprise various viral Mu-like
prophage I proteins.
Length = 326
Score = 28.5 bits (64), Expect = 7.7
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 154 IFGYKRVTASFNAKKFCDQRRYVYLLPVFALDSSSHRDRESVMASL 199
++ TA A+++ + Y YL PVF D ++ R E + A+L
Sbjct: 78 LWADVEWTA--RAREYIAAKEYRYLSPVFLYDKTTGRVLELLSAAL 121
>gnl|CDD|224635 COG1721, COG1721, Uncharacterized conserved protein (some members
contain a von Willebrand factor type A (vWA) domain)
[General function prediction only].
Length = 416
Score = 28.6 bits (64), Expect = 7.8
Identities = 9/14 (64%), Positives = 9/14 (64%)
Query: 107 PRRYDWARSARTDK 120
RR DW SART K
Sbjct: 200 LRRIDWKASARTGK 213
>gnl|CDD|176235 cd08274, MDR9, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 350
Score = 28.4 bits (64), Expect = 8.2
Identities = 29/99 (29%), Positives = 35/99 (35%), Gaps = 19/99 (19%)
Query: 38 ERDLIPAAAGADSTTKRQLCKRRKIAIFFAYCGVGYQGMQKNPGAKTIEGDLEEALFHSG 97
E L+ A+G + QL KRR AI A G AK EEA+ G
Sbjct: 179 ETVLVTGASGGVGSALVQLAKRRG-AIVIAVAG----------AAK------EEAVRALG 221
Query: 98 AVSERDRGNPRRYDWARSARTDKGVSAVGQVVSGRFCID 136
A + R P A + V V VV G D
Sbjct: 222 ADTVILRDAPL--LADAKALGGEPVDVVADVVGGPLFPD 258
>gnl|CDD|217551 pfam03428, RP-C, Replication protein C N-terminal domain.
Replication protein C is involved in the early stages of
viral DNA replication.
Length = 177
Score = 27.9 bits (63), Expect = 8.8
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 92 ALFHSGAVSERDRGNPRRYDWARSARTDKGVSAVG 126
AL +G + RD N +RY AR + A G
Sbjct: 94 ALVDAGLIIRRDSPNGKRY--ARRGGDGEIEEAFG 126
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
0.314 0.130 0.369
Gapped
Lambda K H
0.267 0.0688 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,750,280
Number of extensions: 2148304
Number of successful extensions: 1241
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1197
Number of HSP's successfully gapped: 48
Length of query: 468
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 368
Effective length of database: 6,502,202
Effective search space: 2392810336
Effective search space used: 2392810336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 61 (27.4 bits)