RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 044732
(250 letters)
>gnl|CDD|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated.
Length = 244
Score = 92.1 bits (230), Expect = 2e-22
Identities = 57/232 (24%), Positives = 82/232 (35%), Gaps = 56/232 (24%)
Query: 9 KDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSID 68
P A+N+ P I V+ +V FH FSAK RRY Y + + R
Sbjct: 68 APRPPEKWRRALNALLPDDIAVLWAEEVPDDFHARFSAKARRYRYR--IYNRPAR----- 120
Query: 69 SEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGK 128
V Y P + +N Q L G+
Sbjct: 121 ------PPFLRGYVW-----HY-------------------PYPLDVDAMNEAAQYLLGE 150
Query: 129 LLSYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLR 188
+ +F S++ IY A V G+ + ++ AN FL
Sbjct: 151 H-DFTSFRASGCQSKS----PVRTIYEAD---------VTREGD---FIVFDISANGFLH 193
Query: 189 KMVRVLVATLVREAAAGA-DEDALLKLMDATCRRATAPPAPPEGLCLVDVGY 239
MVR +V TL+ E G + + +L++A R P AP EGL LV+V Y
Sbjct: 194 NMVRNIVGTLL-EVGKGKRPPEDIKELLEAKDRTLAGPTAPAEGLYLVEVDY 244
>gnl|CDD|223179 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal
structure and biogenesis].
Length = 266
Score = 85.4 bits (212), Expect = 7e-20
Identities = 51/242 (21%), Positives = 79/242 (32%), Gaps = 57/242 (23%)
Query: 4 LDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENR 63
DT D + A+N+ P IRV+ V++V FH FSAK R Y YI N
Sbjct: 64 FDT-PADRPLEKLVRALNALLPPDIRVLDVAEVPDDFHARFSAKSRTYRYIIY-----NA 117
Query: 64 EQSIDSEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQ 123
P + + +
Sbjct: 118 PLRPPFLANYVWHV--------------------------------PYPLDLDAMREAAK 145
Query: 124 RLEGKLLSYKTFAR-DTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELV 182
L G + +F + ++ + IY V+ G+ + ++
Sbjct: 146 LLLGTH-DFTSFRKAGCQSKSPVR-----TIYRID---------VSRDGDLIVI---DIS 187
Query: 183 ANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGYTNF 242
N FL MVR +V L+ + + +L++A R+ P AP EGL LV V Y
Sbjct: 188 GNSFLWHMVRNIVGALLLVGRGKRPVEWIKELLEAKDRKLAGPTAPAEGLYLVRVDYPED 247
Query: 243 DP 244
Sbjct: 248 FE 249
>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 = 69.4 bits (171), Expect = 3e-14
Identities = 31/92 (33%), Positives = 41/92 (44%), Gaps = 14/92 (15%)
Query: 149 TECFIYHARATEAILPCPVNDHGEGRKVMCVELVANRFLRKMVRVLVATLVREAAAGA-D 207
T IY A EG + E+ AN FL MVR +V TL+ E G
Sbjct: 161 TVRTIYRADVYR-----------EGDLI-VFEIRANGFLYHMVRNIVGTLL-EVGRGKLS 207
Query: 208 EDALLKLMDATCRRATAPPAPPEGLCLVDVGY 239
+ + ++++A R A P AP GL LV V Y
Sbjct: 208 PEDIKEILEAKDRTAAGPTAPAHGLYLVKVEY 239
Score = 49.8 bits (120), Expect = 2e-07
Identities = 18/47 (38%), Positives = 24/47 (51%)
Query: 9 KDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIF 55
++ + A+NS P IRV+S +V FH FSAK R Y Y
Sbjct: 63 SEIPLEKLIKALNSLLPPDIRVLSAEEVPDDFHARFSAKSRTYRYRI 109
>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 = 54.0 bits (130), Expect = 1e-09
Identities = 19/68 (27%), Positives = 32/68 (47%)
Query: 172 EGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEG 231
+++ E+ N FL VR++V L+R + ++ L+++ R P AP G
Sbjct: 35 RDGELLVFEIKGNGFLYHQVRIMVGALLRTGKGVHALEQVVSLLNSKLRPRAPPTAPAVG 94
Query: 232 LCLVDVGY 239
L L V Y
Sbjct: 95 LYLFHVRY 102
>gnl|CDD|173052 PRK14588, PRK14588, tRNA pseudouridine synthase ACD; Provisional.
Length = 272
Score = 55.3 bits (133), Expect = 4e-09
Identities = 24/67 (35%), Positives = 34/67 (50%)
Query: 173 GRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGL 232
GR ++ +E+ AN FL+ MVR +V TL+ D ++ + RR P AP GL
Sbjct: 181 GRPLLAIEVAANAFLQHMVRNIVGTLLLVGRGRMTVDQFGAVLASRDRRLAGPTAPAHGL 240
Query: 233 CLVDVGY 239
L V Y
Sbjct: 241 YLTAVRY 247
Score = 31.8 bits (72), Expect = 0.26
Identities = 13/42 (30%), Positives = 19/42 (45%)
Query: 14 SDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIF 55
+ I +N+ P I V + + FH FSA R Y Y+
Sbjct: 73 ATIWRGLNAHLPEDIGVQNAWEAPPDFHARFSAIQREYRYVI 114
>gnl|CDD|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional.
Length = 245
Score = 49.0 bits (117), Expect = 5e-07
Identities = 55/228 (24%), Positives = 88/228 (38%), Gaps = 60/228 (26%)
Query: 13 PSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDGENREQSIDSEVE 72
DI++A+N+ P I V V +V + FHP F AK +R + F L ++E+++
Sbjct: 73 EEDIKNAMNANLPDDIYVKKVFEVPKNFHPRFDAK-KRIYHYFILT---SKEKNVFLRKY 128
Query: 73 VENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHEKPRNFTICRVNLLLQRLEGK--LL 130
V F P + + + LEG+
Sbjct: 129 VWWF---------------------------------PYELDLEAMRKAAKYLEGEHDFT 155
Query: 131 SYKTFARDTKASRNIGPPTECFIYHARATEAILPCPVNDHGEGRKVMCVELVANR-FLRK 189
S+KT + + R I Y R IL +K + + V R FLR+
Sbjct: 156 SFKTGSDERNPVRTI--------YRIR----IL--------RLKKDLILIRVEGRSFLRR 195
Query: 190 MVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDV 237
MVR +V LV+ + + + ++++A R A AP GL L V
Sbjct: 196 MVRNIVGALVKVGLGQWEPEKIKEVLEARDRSKAAGTAPAHGLYLYKV 243
>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 = 47.8 bits (114), Expect = 1e-06
Identities = 27/69 (39%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 172 EGRKVMCVELVANRFLRKMVRVLVATLVREAAAGA-DEDALLKLMDATCRRATAPPAPPE 230
E + + +++V FL MVR +V + E G + + + KL+D R PPAPPE
Sbjct: 152 ENGEFITIDVVGESFLWNMVRRIV-GALSEVGKGKRENEWVEKLLDGEFRPEGVPPAPPE 210
Query: 231 GLCLVDVGY 239
GL LVDV Y
Sbjct: 211 GLILVDVKY 219
Score = 32.7 bits (75), Expect = 0.12
Identities = 12/47 (25%), Positives = 20/47 (42%)
Query: 10 DVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFP 56
+ + I IN+ P I V++ ++V F P A + Y Y
Sbjct: 62 ETEKEPIPPMINAKLPKDIWVLAGAKVPEDFDPRRWAHRKYYRYNLG 108
>gnl|CDD|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed.
Length = 245
Score = 46.3 bits (110), Expect = 4e-06
Identities = 17/61 (27%), Positives = 29/61 (47%)
Query: 179 VELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVG 238
+ + N FL MVR++V L+ + + ++++A R AP GL L +V
Sbjct: 185 IRVSGNGFLHNMVRIIVGALIEVGLGQLKAEDIKQILEAKDRNQANCTAPASGLYLENVE 244
Query: 239 Y 239
Y
Sbjct: 245 Y 245
Score = 30.5 bits (69), Expect = 0.59
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 16 IEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLY 53
I+ +N P I V +V +V FH ++ K + YLY
Sbjct: 76 IKKYLNEYLPNDIVVTNVEEVDERFHARYNVKSKTYLY 113
>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 = 45.5 bits (108), Expect = 6e-06
Identities = 21/68 (30%), Positives = 29/68 (42%)
Query: 172 EGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEG 231
+ + VE A FL VR +V L+ ++ +L+ PAP EG
Sbjct: 148 DLNPFVVVEFKAKSFLWHQVRRMVGFLMLVGEGLHSPSSVSRLLAGPAPPIPMVPAPAEG 207
Query: 232 LCLVDVGY 239
L LVDV Y
Sbjct: 208 LLLVDVKY 215
Score = 40.8 bits (96), Expect = 2e-04
Identities = 24/90 (26%), Positives = 35/90 (38%), Gaps = 6/90 (6%)
Query: 18 DAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYI---FPLNDGENREQSIDSEVEVE 74
+A+N PG IRV +V V FH R Y Y FPL+D + + +
Sbjct: 66 EALNGILPGDIRVFAVHSVPPDFHAPRYCDHRTYRYYIPSFPLDDERLKS-AASRFLGTH 124
Query: 75 NFHTSNNVGKQSNGCYENIENLLINDEGGF 104
+F N K + I ++ D F
Sbjct: 125 DFT--NFSKKDTRNTVRTIISIECKDLNPF 152
>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 = 44.6 bits (106), Expect = 1e-05
Identities = 20/63 (31%), Positives = 29/63 (46%)
Query: 172 EGRKVMCVELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEG 231
E + + +++ N FL MVR +V LV + + KL+DA R AP G
Sbjct: 165 ESGEYIIFDIIGNSFLWHMVRKIVGALVLVGRGKLPPEWVAKLLDAKKRNLAPTTAPANG 224
Query: 232 LCL 234
L L
Sbjct: 225 LYL 227
Score = 42.3 bits (100), Expect = 9e-05
Identities = 16/53 (30%), Positives = 27/53 (50%)
Query: 8 RKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLNDG 60
K++ + + +N+ P IRV +++ V+ FH FSA R Y YI +
Sbjct: 66 PKEIPDNKLNAKLNALLPPDIRVKALAPVNDNFHARFSASKRHYRYILYNHRH 118
>gnl|CDD|237759 PRK14589, PRK14589, tRNA pseudouridine synthase ACD; Provisional.
Length = 265
Score = 44.0 bits (104), Expect = 3e-05
Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 2/66 (3%)
Query: 180 ELVANRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY 239
E+ A FL MVR + L++ + D + +L+ C+R PAP EGL L DV
Sbjct: 167 EVTAQSFLWHMVRCMAGALLQIGEGEMEPDDIERLLSGPCKR-KVKPAPAEGLVLWDVDC 225
Query: 240 -TNFDP 244
F P
Sbjct: 226 GLTFTP 231
Score = 33.2 bits (76), Expect = 0.087
Identities = 15/45 (33%), Positives = 20/45 (44%)
Query: 12 KPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFP 56
KP +A+N P I ++V FHP + A R Y Y F
Sbjct: 71 KPERAVEALNGQLPPDIWCTGWAEVPESFHPRYDAISRTYRYYFS 115
>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 = 39.5 bits (93), Expect = 8e-04
Identities = 23/105 (21%), Positives = 43/105 (40%), Gaps = 6/105 (5%)
Query: 2 IILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFP--LND 59
+I+D D+ + +NS P IRV +++V++ F+ + R Y Y+ P +
Sbjct: 71 VIIDDPEGLGILEDLVEKLNSHLPSDIRVFGITRVTKSFNARKACDSRTYEYLLPTFALE 130
Query: 60 GENREQSIDSEVE-VENFH--TSNNVGKQSNGCYENIENLLINDE 101
R I E NFH T + I++ +++
Sbjct: 131 TLQRFNEILKEYVGTHNFHNFTVKK-KFEDPSANRFIKSFYVSEP 174
>gnl|CDD|215562 PLN03078, PLN03078, Putative tRNA pseudouridine synthase;
Provisional.
Length = 513
Score = 36.0 bits (83), Expect = 0.016
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 1 MIILDT-WRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFP 56
M I + W+ D + INS P IRV S+ R F P R+Y Y+ P
Sbjct: 147 MEIPENAWKDDPDGIALAKFINSHLPDNIRVFSILPAQRSFDPRRECDLRKYSYLLP 203
>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 = 35.0 bits (81), Expect = 0.022
Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 5 DTWRKDVKPSDIEDAI------NSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFPLN 58
DVK + E+ + N P IR+++ + V F FS R Y Y FP
Sbjct: 76 LDPSTDVKSTADEEELPYCKILNRVLPPDIRILAWAPVPPDFSARFSCVSRTYRYFFPKG 135
Query: 59 D 59
D
Sbjct: 136 D 136
>gnl|CDD|173051 PRK14587, PRK14587, tRNA pseudouridine synthase ACD; Provisional.
Length = 256
Score = 30.6 bits (69), Expect = 0.61
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 19 AINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLYIFP 56
+NS P + +V++V F+P AK RRYLY+ P
Sbjct: 63 YVNSKLPRGVWAWAVAEVPEGFNPR-RAKRRRYLYVAP 99
Score = 27.5 bits (61), Expect = 5.8
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 184 NRFLRKMVRVLVATLVREAAAGADEDALLKLMDATCRRATAPPAPPEGLCLVDVGY 239
N+ +RKM ++A R + D LL+ R P AP EGL L+D+ Y
Sbjct: 162 NKMIRKMAWAILAA-GRGVLSRRDIAELLE----RPRPGAVPSAPAEGLVLLDIEY 212
>gnl|CDD|199990 TIGR00072, hydrog_prot, hydrogenase maturation protease. HycI
and HoxM are well-characterized as responsible for
C-terminal protease activity on their respective
hydrogenase large chains. A large number of homologous
proteins appear responsible for the maturation of
various forms of hydrogenase.
Length = 145
Score = 29.4 bits (67), Expect = 1.00
Identities = 8/30 (26%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 18 DAINS-AAPGKIRVISVSQVSRVFHPNFSA 46
DA++S A PG +R + + S
Sbjct: 59 DAVDSGAEPGTVRRLDGEDLPAFLGGKLST 88
>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 = 29.5 bits (67), Expect = 1.2
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 8/74 (10%)
Query: 8 RKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSA--KWRRYLYIFPLNDGENREQ 65
+++ P ++ + +N+ P I V+ V +V P+ A Y PL+D E+ ++
Sbjct: 69 TEEIDPEEVLERLNAVLPEGIEVLEVEEVP-DKAPSLMALIDAADYRITLPLDDEEDLQE 127
Query: 66 SID-----SEVEVE 74
+I+ E+ VE
Sbjct: 128 AIEAFLAAEEIIVE 141
>gnl|CDD|185490 PTZ00163, PTZ00163, hypothetical protein; Provisional.
Length = 230
Score = 28.5 bits (63), Expect = 3.3
Identities = 20/90 (22%), Positives = 44/90 (48%), Gaps = 11/90 (12%)
Query: 1 MIILDTWRKDVKPSDIEDAINSAAPGKIRVISVSQVSRVFHPNFSAKWRRYLY--IFPLN 58
++I K++ D++D N + +I+++ SR+ N +++Y+Y IF N
Sbjct: 15 LLIFKYSYKNIVKKDLQDKFNKS------IITINIASRILTENNKKWYKKYIYTSIFSGN 68
Query: 59 -DGENREQSIDSEVEVEN--FHTSNNVGKQ 85
+ + RE+ + E + +N NN+ +
Sbjct: 69 KNPQKRERKNEEENQKDNTKVDNDNNMENE 98
>gnl|CDD|198114 smart01046, c-SKI_SMAD_bind, c-SKI Smad4 binding domain. c-SKI
is an oncoprotein that inhibits TGF-beta signaling
through interaction with Smad proteins. This domain
binds to Smad4.
Length = 95
Score = 26.9 bits (60), Expect = 3.6
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 34 SQVSRVFHPNF-SAKWRRYLYIFPLNDGENREQ 65
S R H F SA WR YL++ E RE+
Sbjct: 50 SPEKRTCHWGFDSANWRSYLHVAKDYGTEEREK 82
>gnl|CDD|233802 TIGR02258, 2_5_ligase, 2'-5' RNA ligase. This protein family
consists of bacterial and archaeal proteins with two
tandem copies of Pfam domain pfam02834. Members for
which activity has been measured perform a reversible,
ATP-independent 2'-5'-ligation of what is presumably a
non-phyiological substrate: half-tRNA splice
intermediates from an intron-containing yeast tRNA. The
physiological substrate(s) in prokaryotes may include
small 2'-5'-link-containing oligonucleotides, perhaps
with regulatory or biosynthetic roles [Transcription,
RNA processing].
Length = 179
Score = 27.6 bits (62), Expect = 4.5
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 12/57 (21%)
Query: 71 VEVENFH-TSNNVGKQSNGCYENIENLL-----------INDEGGFGSHEKPRNFTI 115
V EN H T +G+ E +E+ L + G FG+ ++PR
Sbjct: 34 VPPENLHITLKFLGEVDEEQVEELEDALAKIAEPPFTLKLEGIGVFGNPKRPRVLWA 90
>gnl|CDD|183698 PRK12715, flgK, flagellar hook-associated protein FlgK;
Provisional.
Length = 649
Score = 28.2 bits (62), Expect = 4.7
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 205 GADEDALLKLMDATCRRAT---APPAPPEGLCLVD 236
GA+E L++ D T T +PPAPP G ++D
Sbjct: 368 GANELRLIRKSDGTSTTLTWSSSPPAPPAGQVVID 402
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 27.8 bits (63), Expect = 5.3
Identities = 14/27 (51%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 185 RFLRKMVRVLVATLVREAAAGADEDAL 211
RF + VLVAT V AA G D AL
Sbjct: 287 RFANRSCSVLVATDV--AARGLDIKAL 311
>gnl|CDD|236441 PRK09269, PRK09269, chorismate mutase; Provisional.
Length = 193
Score = 27.3 bits (61), Expect = 6.1
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 193 VLVATLVREAAAGADEDALLKLMDATCRR-ATAPP 226
L+ L AAA D+ AL L+D +R A A P
Sbjct: 16 ALLLLLGPPAAAAGDDSALTPLVDLAAQRLALADP 50
>gnl|CDD|235485 PRK05471, PRK05471, CDP-diacylglycerol pyrophosphatase;
Provisional.
Length = 252
Score = 27.3 bits (61), Expect = 7.8
Identities = 22/69 (31%), Positives = 27/69 (39%), Gaps = 15/69 (21%)
Query: 193 VLVATLVREAAAGADEDALLKLMDATC---RRATAPPAPPEGLCLV---DVGYT----NF 242
VL A L GAD DAL K++ C ++ PAP C GY
Sbjct: 16 VLAAGLGYWKLRGADRDALWKIVSEQCLPNQQQNQNPAP----CAEVDPQAGYVLLKDRN 71
Query: 243 DP-QNSLIP 250
P Q L+P
Sbjct: 72 GPLQYLLMP 80
>gnl|CDD|112953 pfam04163, Tht1, Tht1-like nuclear fusion protein.
Length = 554
Score = 27.4 bits (60), Expect = 8.0
Identities = 15/41 (36%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 130 LSYKTFARDTKASRNIGPPTECFIYH---ARATEAILPCPV 167
L Y+ +DT+ S I EC IYH A E I C +
Sbjct: 507 LKYRNSKKDTELSLFIPAKEECNIYHNEHAALLEDIYLCAI 547
>gnl|CDD|173671 cd05580, STKc_PKA, Catalytic domain of the Protein Serine/Threonine
Kinase, cAMP-dependent protein kinase. Serine/Threonine
Kinases (STKs), cAMP-dependent protein kinase (PKA)
subfamily, catalytic (c) subunit. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The PKA
subfamily is part of a larger superfamily that includes
the catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase (PI3K). This subfamily is composed of the
cAMP-dependent proteins kinases, PKA and PRKX. The
inactive PKA holoenzyme is a heterotetramer composed of
two phosphorylated and active catalytic (C) subunits
with a dimer of regulatory (R) subunits. Activation is
achieved through the binding of the important second
messenger cAMP to the R subunits, which leads to the
dissociation of PKA into the R dimer and two active C
subunits. PKA is present ubiquitously in cells and
interacts with many different downstream targets. It
plays a role in the regulation of diverse processes such
as growth, development, memory, metabolism, gene
expression, immunity, and lipolysis.
Length = 290
Score = 27.1 bits (61), Expect = 8.4
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 7/30 (23%)
Query: 94 ENLLINDEG-------GFGSHEKPRNFTIC 116
ENLL++ +G GF K R +T+C
Sbjct: 130 ENLLLDSDGYIKITDFGFAKRVKGRTYTLC 159
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 27.6 bits (61), Expect = 9.4
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 9/81 (11%)
Query: 61 ENREQSIDSEVEVENFHTSNNVGKQSNGCYENIENLLINDEGGFGSHE-KPR-----NFT 114
RE + ++V + +N K S+ + + L +N++ FG+H +P N T
Sbjct: 414 VEREPYVPKFIDV-TYTEGSNDKKWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINAT 472
Query: 115 I--CRVNLLLQRLEGKLLSYK 133
+ V +L+ GK L+Y+
Sbjct: 473 MSGYDVFVLMPTGGGKSLTYQ 493
>gnl|CDD|235629 PRK05858, PRK05858, hypothetical protein; Provisional.
Length = 542
Score = 27.4 bits (61), Expect = 9.7
Identities = 9/36 (25%), Positives = 15/36 (41%)
Query: 194 LVATLVREAAAGADEDALLKLMDATCRRATAPPAPP 229
VA + + AA + +L+D + A P P
Sbjct: 121 FVAPVTKFAATAQSAENAGRLVDQALQAAVTPHRGP 156
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
0.320 0.136 0.410
Gapped
Lambda K H
0.267 0.0701 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,701,571
Number of extensions: 1183742
Number of successful extensions: 1007
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1001
Number of HSP's successfully gapped: 49
Length of query: 250
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 155
Effective length of database: 6,723,972
Effective search space: 1042215660
Effective search space used: 1042215660
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 (21.8 bits)
S2: 58 (26.2 bits)