RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16424
(295 letters)
>gnl|CDD|214879 smart00879, Brix, The Brix domain is found in a number of
eukaryotic proteins. Members include SSF proteins from
yeast and humans, Arabidopsis thaliana Peter Pan-like
protein and several hypothetical proteins.
Length = 180
Score = 183 bits (466), Expect = 6e-58
Identities = 69/180 (38%), Positives = 102/180 (56%), Gaps = 13/180 (7%)
Query: 97 MITTSRDPSSRLKMFVKELRLIFPNSQRMNRGNYEMKQLIHACRANDVTDFIVVHEH--R 154
+ITTSR PS R + K+LR +FP S ++NRG ++ +L+ TD +VV E +
Sbjct: 1 LITTSRKPSKRTRQLAKDLRRLFPPSTKINRGKNKLNELLEFASEKGNTDLLVVFESSSK 60
Query: 155 GIPDTLVICHLPYGPTAYFTMSDVIMRHDIPD---LGTMSEQYPHLVFHNFKTQLGQRVM 211
G P L I LP GPT F + +V +R ++ ++ P L+F+NF T+LG+ +
Sbjct: 61 GRPLNLTIYRLPNGPTLDFKILNVSLRKELKGFKTGNCLTGSRPLLIFNNFFTELGKLIK 120
Query: 212 SILKYLFPVPKED------SKRIVTFANHDDYISFRHHNYKRD--GKDIELKEVGPRFQL 263
+ + LFP P E +R+VTF+N DDYI FRH+ K +EL+E+GPRF L
Sbjct: 121 ELFQDLFPGPPEHKKSLPGLRRVVTFSNQDDYIFFRHYRIKFGKKKPRVELQEIGPRFTL 180
>gnl|CDD|218084 pfam04427, Brix, Brix domain.
Length = 176
Score = 179 bits (456), Expect = 2e-56
Identities = 72/180 (40%), Positives = 101/180 (56%), Gaps = 13/180 (7%)
Query: 98 ITTSRDPSSRLKMFVKELRLIFPNSQRMNRGNYEMKQLIHACRANDVTDFIVVHEHRGIP 157
ITTSR PS RL+ K+LRL+FPN++++NRG ++K L+ T +V EH+ P
Sbjct: 1 ITTSRKPSKRLRQLAKDLRLLFPNAKKLNRGKKKLKDLLEFAGEKGDTSLLVFGEHKK-P 59
Query: 158 DTLVICHLPYGPTAYFTMSDVIMRHDIPDLGTMS-EQYPHLVFHNFKTQ--LGQRVMSIL 214
L I LP GPT F +S+V + DI G + P LVF+ F + + +L
Sbjct: 60 LNLTIGRLPNGPTLEFRISNVKLLKDIKGKGKGNKGSRPLLVFNGFFFTRLGLKLIKELL 119
Query: 215 KYLFPVP------KEDSKRIVTFANHDDYISFRHHNYKRDGKDIELKEVGPRFQLKLYEI 268
+ LFP P + R++TF+N D I FRH+ YK K +EL+E+GPRF LKL I
Sbjct: 120 QDLFPGPNVHKIPLKGGDRVITFSNQRDTIFFRHYRYK---KKVELQEIGPRFTLKLRRI 176
>gnl|CDD|225047 COG2136, IMP4, Predicted exosome subunit/U3 small nucleolar
ribonucleoprotein (snoRNP) component, contains IMP4
domain [Translation, ribosomal structure and biogenesis
/ RNA processing and modification].
Length = 191
Score = 161 bits (410), Expect = 3e-49
Identities = 67/190 (35%), Positives = 96/190 (50%), Gaps = 8/190 (4%)
Query: 93 DPKIMITTSRDPSSRLKMFVKELRLIFPNSQRMNRGNYEMKQLIHACRANDVTDFIVVHE 152
PK+++TTSR PS R + F K+L + PN+ + RG + +L A TD ++V E
Sbjct: 1 MPKMLLTTSRKPSRRTRSFAKDLSRVLPNAYFLRRGKKSIIELSEEAIARGATDLLIVGE 60
Query: 153 HRGIPDTLVICHL-PYGPTAYFTMSDVIMRHDIPDLGT-MSEQYPHLVFHNFKTQLG-QR 209
RG P L L P G T F +S V +R +IP LG P L+F+NF T LG +
Sbjct: 61 RRGNPARLTFYDLEPEGLTFSFKLSGVKLRREIPVLGPKSRLHGPELIFNNFTTLLGFLK 120
Query: 210 VMSILKYLFPV-----PKEDSKRIVTFANHDDYISFRHHNYKRDGKDIELKEVGPRFQLK 264
V L V P + + + T AN D+ S R H + I L+EVGPR L+
Sbjct: 121 VAEAFSELLLVKFVPNPAWEHELVATGANKGDFKSLRRHRRVFEEDGIGLEEVGPRLTLR 180
Query: 265 LYEIKLGTLD 274
L+ ++ G +
Sbjct: 181 LWRMEDGRGE 190
>gnl|CDD|234867 PRK00933, PRK00933, ribosomal biogenesis protein; Validated.
Length = 165
Score = 44.7 bits (106), Expect = 1e-05
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 98 ITTSRDPSSRLKMFVKELRLIFPNSQRMNRGNYEMKQLIHACRANDVTDFIVVHEHRGIP 157
ITTSR PS R + VK+L N + +NRG +++L+ C A +++ E++G P
Sbjct: 3 ITTSRKPSQRTRSLVKDLARFL-NCKYVNRGKMSLQELLEECEAR---YLLIIGEYKGNP 58
Query: 158 DTLVI 162
L
Sbjct: 59 GALKF 63
>gnl|CDD|227483 COG5154, BRX1, RNA-binding protein required for 60S ribosomal
subunit biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 283
Score = 38.4 bits (89), Expect = 0.003
Identities = 43/195 (22%), Positives = 88/195 (45%), Gaps = 27/195 (13%)
Query: 95 KIMITTSRDPSSRLKMFVKELRLIFPNSQR-----MNRGNYEMKQLIHACRANDVTDFIV 149
+I +SR S R++ +K+L + P+S++ M + ++ +L N++ F
Sbjct: 32 TSLILSSRGVSYRIRHLMKDLSRLVPHSKKEQKLDMKKNLGQLNELAELYNCNNMLFF-- 89
Query: 150 VHEHRGIPDTLVICHLPYGPTAYFTMSDVIMRHDIPDLG----TMSEQYPHLVF-HNFKT 204
+ L+ +P GPT F M ++ H + +L ++ P L F F+
Sbjct: 90 -ESRKRSDLYLMGARIPNGPTVKFRMHNL---HTMDELNFTGNSLKGSRPVLSFDKEFED 145
Query: 205 -QLGQRVMSILKYLFPVPKEDSK------RIVTFANHDDYISFRHH----NYKRDGKDIE 253
+ +L+++F +PK + +++ F D I R + + KD++
Sbjct: 146 IPHLKYAKELLEHIFGIPKGARRSKPFIDKVLCFFILDGKIWVRCYEIGRENEDKSKDVK 205
Query: 254 LKEVGPRFQLKLYEI 268
L+E+GPRF + + +I
Sbjct: 206 LEEIGPRFVMTVIKI 220
>gnl|CDD|179689 PRK03972, PRK03972, ribosomal biogenesis protein; Validated.
Length = 208
Score = 34.1 bits (78), Expect = 0.054
Identities = 19/92 (20%), Positives = 43/92 (46%), Gaps = 3/92 (3%)
Query: 96 IMITTSRDPSSRLKMFVKELRLIFPNSQRMNRGNYEMKQLIHACRANDVTDFIVVHEHRG 155
++ITTS P+ R + F +L +FPNS + RG ++ L+ ++++ +G
Sbjct: 2 MLITTSHRPTRRTRSFGHDLERVFPNSLYLTRGKKTIQDLLMEAYDRGYERLLIINVWKG 61
Query: 156 IPDTLVICHL---PYGPTAYFTMSDVIMRHDI 184
P + + +G Y + + ++ ++
Sbjct: 62 NPLKMTFIKVGPEDWGYLGYLYLHGIKLQREM 93
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 30.5 bits (69), Expect = 0.79
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 5/61 (8%)
Query: 2 LRRQARLRREYLYRKSLEEKQRAIQEKKDRLRKSLDGNKKIPTDLKNQALSLQRKLDWED 61
LR ++++E K EE+++A +E+K R + L GN L N + + K W+D
Sbjct: 148 LRELEKIKKERAEEKEREEEEKAAEEEKAREEEILTGNP-----LLNTSGDFKVKRRWDD 202
Query: 62 E 62
+
Sbjct: 203 D 203
>gnl|CDD|227351 COG5018, KapD, Inhibitor of the KinA pathway to sporulation,
predicted exonuclease [General function prediction
only].
Length = 210
Score = 28.7 bits (64), Expect = 2.8
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 2/54 (3%)
Query: 105 SSRLKMFVKELRLIFP--NSQRMNRGNYEMKQLIHACRANDVTDFIVVHEHRGI 156
S + F+++L P NS GN +MK L C N + F +
Sbjct: 80 SMVFEDFIRKLNEHDPRKNSTWATWGNMDMKVLKQNCMFNHIPPFPFKGPMVDL 133
>gnl|CDD|129249 TIGR00144, beta_RFAP_syn, beta-RFAP synthase. This protein family
contains several archaeal examples of
beta-ribofuranosylaminobenzene 5-prime-phosphate
synthase (beta-RFAP synthase), an enzyme involved in
methanopterin biosynthesis. In some species, two members
of this family are found. It is unclear whether both act
as beta-RFAP synthase. This family is related to the
GHMP kinases (Galactokinase, Homoserine kinase,
Mevalonate kinase, Phosphomevalonate kinase). Members
are found so far only in the Archaea and in
Methylobacterium extorquens [Unknown function, Enzymes
of unknown specificity].
Length = 324
Score = 29.1 bits (65), Expect = 2.9
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 6/51 (11%)
Query: 178 VIMRHDIPDLGTMSEQYPHLVFHNFKTQLGQRVMSILKYLFPVPKEDSKRI 228
VI R+D PD + L + G+R ++I + PVP D +RI
Sbjct: 173 VIARYDFPDWNII------LAIPEIDSVSGRREVNIFQKYCPVPLRDVERI 217
>gnl|CDD|192773 pfam11559, ADIP, Afadin- and alpha -actinin-Binding. This family
is found in mammals where it is localised at cell-cell
adherens junctions, and in Sch. pombe and other fungi
where it anchors spindle-pole bodies to spindle
microtubules. It is a coiled-coil structure, and in
pombe, it is required for anchoring the minus end of
spindle microtubules to the centrosome equivalent, the
spindle-pole body. The name ADIP derives from the
family being composed of Afadin- and alpha
-Actinin-Binding Proteins Localised at Cell-Cell
Adherens Junctions.
Length = 149
Score = 28.0 bits (63), Expect = 3.4
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 7/52 (13%)
Query: 7 RLRREYLYRKSLEEKQRAIQEKKDRLRKSLDGNKKIPTDLKNQALSLQRKLD 58
+ R+ +R+SLEE R ++ + +RL+ +++ LK Q L+R+L
Sbjct: 44 QRDRDLEFRESLEETLRKLEAEIERLQNTIE-------RLKTQLEDLERELA 88
>gnl|CDD|220078 pfam08939, DUF1917, Domain of unknown function (DUF1917). This
domain is found in various hypothetical and basophilic
leukaemia proteins. It has no known function.
Length = 237
Score = 28.6 bits (64), Expect = 3.6
Identities = 15/62 (24%), Positives = 23/62 (37%), Gaps = 5/62 (8%)
Query: 167 YGPTAYFTMSDVIMRHDIP-----DLGTMSEQYPHLVFHNFKTQLGQRVMSILKYLFPVP 221
Y P Y++ +R I + G +E PH +F N +T + L L P
Sbjct: 9 YDPEPYWSEIHPRLRSTIQARLSVESGPDAETDPHELFRNRRTPYNEPAEDFLARLPPST 68
Query: 222 KE 223
Sbjct: 69 TP 70
>gnl|CDD|223596 COG0522, RpsD, Ribosomal protein S4 and related proteins
[Translation, ribosomal structure and biogenesis].
Length = 205
Score = 28.4 bits (64), Expect = 3.8
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 8/61 (13%)
Query: 4 RQARLRREYLYRKSLEEKQ-----RAIQEKKDRLRKSLDGNKKIPTDLKNQALS-LQRKL 57
Q R ++ Y L EKQ + EK+ R+ L ++ L+ L+R+L
Sbjct: 39 GQERWKKLSDYGLQLREKQKLRAFYGVLEKQ--FRRYLKEAGRLKGVTGLNLLALLERRL 96
Query: 58 D 58
D
Sbjct: 97 D 97
>gnl|CDD|131739 TIGR02692, tRNA_CCA_actino, tRNA adenylyltransferase. The enzyme
tRNA adenylyltransferase, also called
tRNA-nucleotidyltransferase and CCA-adding enzyme, can
add or repair the required CCA triplet at the 3'-end of
tRNA molecules. Genes encoding tRNA include the CCA tail
in some but not all bacteria, and this enzyme may be
required for viability. Members of this family represent
a distinct clade within the larger family pfam01743
(tRNA nucleotidyltransferase/poly(A) polymerase family
protein). The example from Streptomyces coelicolor was
shown to act as a CCA-adding enzyme and not as a poly(A)
polymerase [Protein synthesis, tRNA and rRNA base
modification].
Length = 466
Score = 28.5 bits (64), Expect = 4.5
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 5/40 (12%)
Query: 3 RRQARLRREYLYRKSLEEKQRAIQEKKD--RLRKSLDGNK 40
R+ ARL+ Y LEE+ + ++D R+R LDGN+
Sbjct: 386 RKAARLQAAY---DDLEERIAELAAQEDLARVRPDLDGNE 422
>gnl|CDD|201249 pfam00472, RF-1, RF-1 domain. This domain is found in peptide
chain release factors such as RF-1 and RF-2, and a
number of smaller proteins of unknown function. This
domain contains the peptidyl-tRNA hydrolase activity.
The domain contains a highly conserved motif GGQ, where
the glutamine is thought to coordinate the water that
mediates the hydrolysis.
Length = 114
Score = 27.1 bits (61), Expect = 4.6
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 3 RRQARLR-REYLYRKSLEEKQRAIQEKKDRLRKSLDGNKKIPTDLKNQ 49
R +A R + LY L++K+ + + + D +KI T Q
Sbjct: 60 REKALERLKAKLYEAELQKKREKTKPTRASQVRRGDRKEKIRTYNFPQ 107
>gnl|CDD|217011 pfam02388, FemAB, FemAB family. The femAB operon codes for two
nearly identical approximately 50-kDa proteins involved
in the formation of the Staphylococcal pentaglycine
interpeptide bridge in peptidoglycan. These proteins are
also considered as a factor influencing the level of
methicillin resistance.
Length = 408
Score = 28.0 bits (63), Expect = 6.2
Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 10/66 (15%)
Query: 14 YRKSLEEKQRAIQEKKDRLRKSLDGN-----KKIPTDLKNQALSLQRKLDWEDE-----G 63
Y L+EK +++ +L + L+ N K +L+ Q SL++++D E G
Sbjct: 243 YLDELQEKLEKLEKDLAKLEEKLEKNPNSKKKNKLAELEQQLASLEKRIDEAKELIAKYG 302
Query: 64 PELAVS 69
E+ ++
Sbjct: 303 NEVPLA 308
>gnl|CDD|217408 pfam03177, Nucleoporin_C, Non-repetitive/WGA-negative nucleoporin
C-terminal. This is the C-termainl half of a family of
nucleoporin proteins. Nucleoporins are the main
components of the nuclear pore complex in eukaryotic
cells, and mediate bidirectional nucleocytoplasmic
transport, especially of mRNA and proteins. Two
nucleoporin classes are known: one is characterized by
the FG repeat pfam03093; the other is represented by
this family, and lacks any repeats. RNA undergoing
nuclear export first encounters the basket of the
nuclear pore and many nucleoporins are accessible on the
basket side of the pore.
Length = 559
Score = 27.9 bits (62), Expect = 6.8
Identities = 16/50 (32%), Positives = 18/50 (36%), Gaps = 4/50 (8%)
Query: 13 LYRKSLEEKQRAIQEKKDRLRKSLDGNKKIPTDLKN-QALSLQRKLDWED 61
L + LE QR EK LDG T L N AL + D
Sbjct: 438 LLEQLLEADQRISDEKAAAALAKLDGLILSLTKLFNDYALPAE---YLID 484
>gnl|CDD|220942 pfam11014, DUF2852, Protein of unknown function (DUF2852). This
bacterial family of proteins has no known function.
Length = 115
Score = 26.4 bits (59), Expect = 8.9
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 7/34 (20%)
Query: 4 RQARLRREYLYRKSLEEKQRAIQEKKDRLRKSLD 37
R LRR LEE+QRA ++ +RLR++ D
Sbjct: 76 RAETLRR-------LEEEQRAFEDFLERLRRAKD 102
>gnl|CDD|218640 pfam05565, Sipho_Gp157, Siphovirus Gp157. This family contains
both viral and bacterial proteins which are related to
the Gp157 protein of the Streptococcus thermophilus SFi
bacteriophages. It is thought that bacteria possessing
the gene coding for this protein have an increased
resistance to the bacteriophage.
Length = 162
Score = 26.8 bits (60), Expect = 9.7
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 6/38 (15%)
Query: 15 RKSLEEKQRAIQEKKDRLRKSLDGN------KKIPTDL 46
K L E++++I+ K RL+ L+ KKI T L
Sbjct: 63 IKRLAERKKSIENKVKRLKDYLEEAMEATGIKKIKTPL 100
>gnl|CDD|234723 PRK00311, panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase;
Reviewed.
Length = 264
Score = 27.3 bits (62), Expect = 9.9
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 10/37 (27%)
Query: 132 MKQLIHACRANDVTDFIVVHEHRGIPDTLVICHLPYG 168
+ +I+ +A V RG P LV+ +P+G
Sbjct: 60 LDDMIYHTKA-------VA---RGAPRALVVADMPFG 86
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
0.321 0.138 0.409
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,520,413
Number of extensions: 1514191
Number of successful extensions: 1707
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1690
Number of HSP's successfully gapped: 46
Length of query: 295
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 199
Effective length of database: 6,679,618
Effective search space: 1329243982
Effective search space used: 1329243982
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: 59 (26.5 bits)