RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8580
(274 letters)
>gnl|CDD|190975 pfam04410, Gar1, Gar1/Naf1 RNA binding region. Gar1 is a small
nucleolar RNP that is required for pre-mRNA processing
and pseudouridylation. It is co-immunoprecipitated with
the H/ACA families of snoRNAs. This family represents
the conserved central region of Gar1. This region is
necessary and sufficient for normal cell growth, and
specifically binds two snoRNAs snR10 and snR30. This
region is also necessary for nucleolar targeting, and it
is thought that the protein is co-transported to the
nucleolus as part of a nucleoprotein complex. In humans,
Gar1 is also component of telomerase in vivo. Naf1 is an
essentail protein that plays a role in ribosome
biogenesis, modification of spliceosomal small nuclear
RNAs and telomere synthesis, and is homologous to Gar1.
Length = 154
Score = 122 bits (308), Expect = 9e-35
Identities = 50/155 (32%), Positives = 77/155 (49%), Gaps = 8/155 (5%)
Query: 8 GELDLGDLPPIEDLQISV-PEDQCLPVGKILNIVDTLVLIKTLKNTPTLDLDSVLFLDKG 66
E + PP ++ P + +G I ++V+ V+IK+ + LD S+L L+
Sbjct: 1 NEGGGEEGPPGGPPDYTIGPPTEIEELGTISSVVENQVVIKSTNSEKVLDFGSILCLEDK 60
Query: 67 QRSLGKIFDVIGPVSGPVYCVRFNSHQHIVDSNIKIDQDVYCAPQTEHTSYVPLPDLIK- 125
+GK+ ++ GPV+ P Y V+F S + I ++K+ VY P L +K
Sbjct: 61 T-VIGKVDEIFGPVNNPFYSVKF-SSEGIQAKSLKVGDKVYYVPD--PAQRF-LTQPLKQ 115
Query: 126 VKGSDASWERDQEPPPEV-VEFSDDEEERRVKRNQ 159
KG+DAS D+E P E EFSDDE E KR +
Sbjct: 116 QKGTDASNGHDEELPEEERGEFSDDEAEAEAKRGR 150
>gnl|CDD|183872 PRK13149, PRK13149, H/ACA RNA-protein complex component Gar1;
Reviewed.
Length = 73
Score = 35.3 bits (82), Expect = 0.004
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 33 VGKILNIVDTLVLIKTLKNTPTLDLDSVLFLDKGQRSLGKIFDVIGPVSGP 83
+GK+L+ LI L P + SV++ K ++ +GK+ DV GPV P
Sbjct: 4 LGKVLHYAPKGKLIIRLDKQP--PIGSVVYDKKLKK-IGKVVDVFGPVKEP 51
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 36.5 bits (84), Expect = 0.016
Identities = 26/94 (27%), Positives = 30/94 (31%), Gaps = 4/94 (4%)
Query: 169 SSTDGTDPPDVPPEPKTRRPTPFEQRMNLRNLLMTASYERRNRINDTATTSRPANKSFTP 228
S T DPP PP P+ P L A A + TP
Sbjct: 2694 SLTSLADPPPPPPTPEPA-PHALVSATPLPPGPAAARQASPALPAAPAPPA-VPAGPATP 2751
Query: 229 GSIIR--APTLPDIPPLPLPMSQPSAPPPRFTPP 260
G R P PP P P + P+A PPR
Sbjct: 2752 GGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTR 2785
Score = 29.9 bits (67), Expect = 1.6
Identities = 25/104 (24%), Positives = 32/104 (30%), Gaps = 2/104 (1%)
Query: 169 SSTDGTDPPDVPPEPKTRRPTPFEQRMNLRNLLMTASYERRNRINDTA--TTSRPANKSF 226
G PP +P +R R+ + R + A SR
Sbjct: 2840 PPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFA 2899
Query: 227 TPGSIIRAPTLPDIPPLPLPMSQPSAPPPRFTPPQHQHQQETPL 270
P P P PP P P QP PP PP + + PL
Sbjct: 2900 LPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPL 2943
>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
Length = 333
Score = 33.5 bits (77), Expect = 0.086
Identities = 26/136 (19%), Positives = 36/136 (26%), Gaps = 27/136 (19%)
Query: 134 ERDQEPPPEVVEFSDDEEERRVKRNQLRTRNNRNTSSTDGTDPPDVPPEPKTRRPTPFEQ 193
+RD + E VE + E RV R P E + RP+P Q
Sbjct: 47 KRDDDSYDEDVEDDEGVGEVRVHR---------------VNHAPANAQEHEAARPSPQHQ 91
Query: 194 RMNLRNLLMTASYERRNRINDTATTSRPANKSFTPGSIIRAPTLPDIPPLPLPMSQPSAP 253
Y+ + ++ P P P P+ P QP
Sbjct: 92 ------------YQPPYASAQPRQPVQQPPEAQVPPQHAPRPAQPAPQPVQQPAYQPQPE 139
Query: 254 PPRFTPPQHQHQQETP 269
P P Q
Sbjct: 140 QPLQQPVSPQVAPAPQ 155
>gnl|CDD|225816 COG3277, GAR1, RNA-binding protein involved in rRNA processing
[Translation, ribosomal structure and biogenesis].
Length = 98
Score = 31.2 bits (71), Expect = 0.15
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 4/81 (4%)
Query: 31 LPVGKILNIVDTLVLIKTLKNTPTLDLDSVLFLDKGQRSLGKIFDVIGPVSGPVYCVRFN 90
+GK+L++ T ++I N L++ ++ +R +GK+ DV GPV P V+ +
Sbjct: 2 KRLGKVLHVCGTGMVIVRD-NDRIPPLNAPVYDANLKR-IGKVVDVFGPVDEPYILVKPD 59
Query: 91 SHQHIVDSNIKIDQDVYCAPQ 111
V + +Y P
Sbjct: 60 D--RDVKLESLVGDTLYIPPD 78
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 31.2 bits (71), Expect = 0.57
Identities = 19/102 (18%), Positives = 34/102 (33%), Gaps = 24/102 (23%)
Query: 40 VDTLVLIKTLKNTPTLDLDSVLFLDKGQR-------SLGKIFDVIGPV--------SGPV 84
++T L++TLK T + V G +++D+ + V
Sbjct: 38 LETGELLRTLKG-HTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLTGHTSYV 96
Query: 85 YCVRFNSHQHIV-----DSNIKI---DQDVYCAPQTEHTSYV 118
V F+ I+ D IK+ + HT +V
Sbjct: 97 SSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWV 138
>gnl|CDD|215145 PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygenase NCED.
Length = 590
Score = 29.7 bits (67), Expect = 2.0
Identities = 14/56 (25%), Positives = 18/56 (32%), Gaps = 3/56 (5%)
Query: 215 TATTSRPANKSFTPGSIIRAPTLPDIPPLPLPMSQPSAPPPRFTPPQHQHQQETPL 270
++T+ RP + S P I PLP S Q Q PL
Sbjct: 28 SSTSPRPRRRKP---SASSLLHTPSILPLPKLSSPSPPSVTLPPAATTQTPQLNPL 80
Score = 27.7 bits (62), Expect = 8.2
Identities = 10/55 (18%), Positives = 17/55 (30%), Gaps = 1/55 (1%)
Query: 213 NDTATTSRPANKSFTPGSIIRAPTLPDIPPLPLPMSQPSAPPPRFTPPQHQHQQE 267
+ ++ S + + + LPLP +PP PP Q
Sbjct: 22 SQSSPPSSTSPRPRRRKPSASSLLHT-PSILPLPKLSSPSPPSVTLPPAATTQTP 75
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 29.3 bits (66), Expect = 2.0
Identities = 13/37 (35%), Positives = 15/37 (40%)
Query: 234 APTLPDIPPLPLPMSQPSAPPPRFTPPQHQHQQETPL 270
+ PP P + PS PP PP QQ PL
Sbjct: 218 SFQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVPPL 254
>gnl|CDD|172376 PRK13855, PRK13855, type IV secretion system protein VirB10;
Provisional.
Length = 376
Score = 29.5 bits (66), Expect = 2.2
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 6/49 (12%)
Query: 224 KSFTPGSIIRAPTLPDIPPLPLPMSQPSAPPPRFTPPQHQHQQ--ETPL 270
K F P I P PP QP+APP + P+ + ETP+
Sbjct: 71 KPFHPAPIDVPPD----PPAAQEAVQPTAPPSAQSEPERNEPRPEETPI 115
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 29.6 bits (67), Expect = 2.3
Identities = 16/87 (18%), Positives = 32/87 (36%), Gaps = 3/87 (3%)
Query: 134 ERDQEPPPEVVEFSDDEEERRVKRNQLRTRNNRNTSSTDGTDPPDVPPEPKTRRPTPFEQ 193
+ +P + ++ + ER+ R + R N R+ + T E + R E
Sbjct: 583 GEETKPQEQPAPKAEAKPERQQDRRKPRQNNRRDRNERRDTRDNRTRREGRENRE---EN 639
Query: 194 RMNLRNLLMTASYERRNRINDTATTSR 220
R N R + R ++ + +R
Sbjct: 640 RRNRRQAQQQTAETRESQQAEVTEKAR 666
>gnl|CDD|177475 PHA02693, PHA02693, hypothetical protein; Provisional.
Length = 710
Score = 29.2 bits (65), Expect = 2.9
Identities = 25/106 (23%), Positives = 40/106 (37%), Gaps = 16/106 (15%)
Query: 132 SWERDQEPPPEVVEFSDDEEER----------RVKRNQLRTRNNRNTSSTDGTDP-PDVP 180
S R + P E V+F DE + + R+ TR+ R+ + TD TDP D
Sbjct: 254 SKSRSRRLPEEHVDFHYDESDTADSCSRSFSTQSTRSTRSTRSTRSGAETDTTDPDLDPD 313
Query: 181 PEPKTRRPTPFEQRMNLRNLLMTASYERRNRINDTATTSRPANKSF 226
+ P +R T+ R + + +A+ A S
Sbjct: 314 DDESFDEVGPLTRRFT-----ATSFAPRASVRSSSASMRLHARGST 354
>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 28.7 bits (64), Expect = 4.0
Identities = 27/146 (18%), Positives = 34/146 (23%), Gaps = 26/146 (17%)
Query: 136 DQEPPPEVVEFSDDEEERRVKRNQLRTRNNRNTSSTDGTDPPDVPPEPKTRRPTPFEQRM 195
D P + +S + PP P+ R PTP
Sbjct: 483 DAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPPTPAAAAP 542
Query: 196 N------------LRNLLMTASYERRNRINDTA------------TTSRPANKSFTPGSI 231
LRN M S +R R A R A + TP +
Sbjct: 543 AARAGGAAAALDVLRNAGMRVSSDRGARAAAAAKPAAAPAAAPKPAAPRVAVQVPTPRAR 602
Query: 232 IRAPTLPDIP--PLPLPMSQPSAPPP 255
P APPP
Sbjct: 603 AATGDAPPNGAARAEQAAESRGAPPP 628
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 28.6 bits (64), Expect = 4.6
Identities = 10/53 (18%), Positives = 15/53 (28%), Gaps = 5/53 (9%)
Query: 214 DTATTSRPANKSFTPGSIIRAPTLPDI-----PPLPLPMSQPSAPPPRFTPPQ 261
+ PA + P + +P P P + P P R T
Sbjct: 357 EALLVPVPAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATP 409
>gnl|CDD|237042 PRK12291, PRK12291, apolipoprotein N-acyltransferase; Reviewed.
Length = 418
Score = 28.4 bits (64), Expect = 4.7
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 3/37 (8%)
Query: 89 FNSHQHIVDSNIKIDQDVYCAPQTEHTSYVPLPDLIK 125
+NS N++I V P E +PLP K
Sbjct: 280 YNSTYIFSKGNVQIADKVILVPFGE---EIPLPKFFK 313
>gnl|CDD|171499 PRK12438, PRK12438, hypothetical protein; Provisional.
Length = 991
Score = 28.7 bits (64), Expect = 4.8
Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 1/60 (1%)
Query: 211 RINDTATTSRPANKSFTPGS-IIRAPTLPDIPPLPLPMSQPSAPPPRFTPPQHQHQQETP 269
R+ T + ++ F PG+ + D P P + P APP PP+ P
Sbjct: 880 RVGYAPTLAEALDQVFGPGTGRVATAPGGDAASAPPPGAGPPAPPQAVPPPRTTQPPAAP 939
>gnl|CDD|216908 pfam02159, Oest_recep, Oestrogen receptor.
Length = 139
Score = 27.2 bits (60), Expect = 6.0
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 3/45 (6%)
Query: 225 SFTPGSIIRAPTLPDIPPLPLPMSQPSAPPPRFTPPQHQHQQETP 269
P S+ +L +PP PL P+ +P H H Q+ P
Sbjct: 46 VHGPPSLGGLQSLGSVPPSPLMFLPS---SPQLSPFLHPHGQQVP 87
>gnl|CDD|219006 pfam06388, DUF1075, Protein of unknown function (DUF1075). This
family consists of several eukaryotic proteins of
unknown function.
Length = 146
Score = 27.1 bits (60), Expect = 6.2
Identities = 16/64 (25%), Positives = 27/64 (42%), Gaps = 11/64 (17%)
Query: 154 RVKRNQLRTRNNRNTSSTDGTDPPDVPPE-----PKTRRPTPFEQRMNLRNLLMTASYER 208
R++R R N T + P P + P T RP+ FE+++ LL + ++
Sbjct: 18 RLRRPSDLKRIN--GFCTKPQESPGAPTQHIHRVPGTHRPSDFEKKI----LLWSGRFKS 71
Query: 209 RNRI 212
I
Sbjct: 72 EEEI 75
>gnl|CDD|185628 PTZ00449, PTZ00449, 104 kDa microneme/rhoptry antigen; Provisional.
Length = 943
Score = 28.1 bits (62), Expect = 6.6
Identities = 18/89 (20%), Positives = 31/89 (34%), Gaps = 1/89 (1%)
Query: 172 DGTDPPDVPPEPKTRRPTPFEQRMNLRNLLMTASYERRNRINDTATTSRPANKSFTPGSI 231
+G P PK+ +P PF+ + + +++ T + +S ++
Sbjct: 649 EGPKIIKSPKPPKSPKP-PFDPKFKEKFYDDYLDAAAKSKETKTTVVLDESFESILKETL 707
Query: 232 IRAPTLPDIPPLPLPMSQPSAPPPRFTPP 260
P P P PLP P F P
Sbjct: 708 PETPGTPFTTPRPLPPKLPRDEEFPFEPI 736
>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106). This
family of proteins are found in large numbers in the
Trichomonas vaginalis proteome. The function of this
protein is unknown.
Length = 422
Score = 27.7 bits (61), Expect = 7.0
Identities = 21/93 (22%), Positives = 32/93 (34%), Gaps = 11/93 (11%)
Query: 179 VPPEPKTRRPTPFEQRMNLRNLLMTASYERRNR----INDTATTSRPANKSFTPGSIIRA 234
+PP P P P + T+S+ R+R T PA + T + +
Sbjct: 172 IPPNPPREAPAPGLPKT------FTSSHGHRHRHAPKPTQQPTVQNPAQQP-TVQNPAQQ 224
Query: 235 PTLPDIPPLPLPMSQPSAPPPRFTPPQHQHQQE 267
P P QP+ P PPQ + +
Sbjct: 225 PQQQPQQQPVQPAQQPTPQNPAQQPPQTEQGHK 257
>gnl|CDD|218621 pfam05518, Totivirus_coat, Totivirus coat protein.
Length = 753
Score = 27.8 bits (62), Expect = 8.3
Identities = 15/111 (13%), Positives = 26/111 (23%), Gaps = 10/111 (9%)
Query: 151 EERRVKRNQLRTRNNRNTSSTDGTDPPDVPPEPKTRRPTPFEQRMNLRNLLMTASYERRN 210
E+ V+R RTR R + V + P F+ + +
Sbjct: 601 EDPEVRR--ARTRGARALAQARTFGRATVGEMIISGFPPVFKTALP--------RPDYNR 650
Query: 211 RINDTATTSRPANKSFTPGSIIRAPTLPDIPPLPLPMSQPSAPPPRFTPPQ 261
P R + P+ + P+ P
Sbjct: 651 GGEAGGPGVPGPVPVGMPAHTARPSRVARGDPVRPTAHHAALRAPQAPRPG 701
>gnl|CDD|215523 PLN02969, PLN02969, 9-cis-epoxycarotenoid dioxygenase.
Length = 610
Score = 27.4 bits (61), Expect = 8.7
Identities = 12/30 (40%), Positives = 13/30 (43%), Gaps = 3/30 (10%)
Query: 241 PPLPLPMSQPSAPPPRFTPPQHQHQQETPL 270
P P+P PPP PP H H PL
Sbjct: 1 PSHPIP---TKFPPPLKLPPIHHHPSPPPL 27
>gnl|CDD|233376 TIGR01363, strep_his_triad, streptococcal histidine triad protein.
This model represents the N-terminal half of a family of
Streptococcal proteins that contain a signal peptide and
then up to five repeats of a region that includes a
His-X-X-His-X-His (histidine triad) motif. Three repeats
are found in the seed alignment. Members of this family
from Streptococcus pneumoniae are suggested to cleave
human C3, and the member PhpA has been shown in vaccine
studies to be a protective antigen in mice [Cellular
processes, Pathogenesis].
Length = 348
Score = 27.2 bits (60), Expect = 9.5
Identities = 19/83 (22%), Positives = 29/83 (34%), Gaps = 17/83 (20%)
Query: 105 DVYCAPQTEHTSYVPLPDL--IKVKGSDASWERDQEPPPEVVEFSDDEEERRVKRNQLRT 162
D Y P +H Y+P +L ++ ++A W Q R R
Sbjct: 202 DAYIVPHGDHYHYIPKNELSASELAAAEAYWSGKQG---------------RGARPSDYR 246
Query: 163 RNNRNTSSTDGTDPPDVPPEPKT 185
+ +R S D T P P P+
Sbjct: 247 QGSRKASIPDVTPNPGQPAPPRP 269
>gnl|CDD|114709 pfam06003, SMN, Survival motor neuron protein (SMN). This family
consists of several eukaryotic survival motor neuron
(SMN) proteins. The Survival of Motor Neurons (SMN)
protein, the product of the spinal muscular
atrophy-determining gene, is part of a large
macromolecular complex (SMN complex) that functions in
the assembly of spliceosomal small nuclear
ribonucleoproteins (snRNPs). The SMN complex functions
as a specificity factor essential for the efficient
assembly of Sm proteins on U snRNAs and likely protects
cells from illicit, and potentially deleterious,
non-specific binding of Sm proteins to RNAs.
Length = 264
Score = 27.3 bits (60), Expect = 9.7
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 3/58 (5%)
Query: 129 SDASWERDQEPPPEVVEFSDDEEERRVKRNQLRTRNNRNT---SSTDGTDPPDVPPEP 183
D + +E E S DE +R +++R+++N S + PP PP P
Sbjct: 123 PDVDEDALKEANVNETESSTDESDRSSHSHEVRSKSNFPMGPPSPWNPRFPPGPPPPP 180
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 0.135 0.406
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,303,404
Number of extensions: 1357637
Number of successful extensions: 1603
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1476
Number of HSP's successfully gapped: 96
Length of query: 274
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 179
Effective length of database: 6,723,972
Effective search space: 1203590988
Effective search space used: 1203590988
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: 42 (22.0 bits)
S2: 58 (26.3 bits)