RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18074
(197 letters)
>gnl|CDD|217935 pfam04158, Sof1, Sof1-like domain. Sof1 is essential for cell
growth and is a component of the nucleolar rRNA
processing machinery.
Length = 88
Score = 106 bits (268), Expect = 1e-30
Identities = 48/88 (54%), Positives = 67/88 (76%)
Query: 106 AHASEKLGYVNNKQRQALDYSESLKQKYAHHPQIRRIARHRQVPRHIYNAQAEHRAIRSK 165
A+ASEKLG ++ ++RQAL+Y+E+LK+KY H P+I+RIARHR VP+ I AQ R ++
Sbjct: 1 ANASEKLGVLSPRERQALEYNEALKEKYKHMPEIKRIARHRHVPKAIKKAQKIKREMKEA 60
Query: 166 QKRKESNKRTHSAPGTVPQTKERQRAVV 193
+KRKE N+R HS PG+VP ER++ VV
Sbjct: 61 KKRKEENRRKHSKPGSVPPKPERKKHVV 88
>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 = 60.0 bits (146), Expect = 4e-11
Identities = 24/103 (23%), Positives = 44/103 (42%), Gaps = 7/103 (6%)
Query: 4 FVFTAANEDFNLYSYDIRQLNSPLNVHKDMTSAVTSVDYSPTGREFVAGGYDKSLRLYLA 63
FV +++ D + +D+R + T V SV +SP G + ++ D +++L+
Sbjct: 149 FVASSSQ-DGTIKLWDLRTG-KCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDL 206
Query: 64 HQGHSRDIY--HTKRMQHVTHTVWSLDNKFVISASDEMNLRVW 104
G H V +S D + S S++ +RVW
Sbjct: 207 STGKCLGTLRGHENG---VNSVAFSPDGYLLASGSEDGTIRVW 246
Score = 49.3 bits (118), Expect = 2e-07
Identities = 23/109 (21%), Positives = 48/109 (44%), Gaps = 19/109 (17%)
Query: 4 FVFTAANEDFNLYSYDIRQLNSPLNVHKDMTSAVTSVDYSPTGREFVAGGYDKSLRLY-- 61
++ + ++ D + +D+ + TS V+SV +SP GR + DK+++++
Sbjct: 65 YLASGSS-DKTIRLWDLET-GECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDV 122
Query: 62 ------LAHQGHSRDIYHTKRMQHVTHTVWSLDNKFVISASDEMNLRVW 104
+GH+ V +S D FV S+S + +++W
Sbjct: 123 ETGKCLTTLRGHTDW---------VNSVAFSPDGTFVASSSQDGTIKLW 162
Score = 44.6 bits (106), Expect = 8e-06
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 7/82 (8%)
Query: 34 TSAVTSVDYSPTGREFVAGGYDKSLRLYLAHQGHSRDIYHTKRMQH---VTHTVWSLDNK 90
T VT V +SP G+ G D +++++ G H V S D
Sbjct: 9 TGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGE----LLRTLKGHTGPVRDVAASADGT 64
Query: 91 FVISASDEMNLRVWKAHASEKL 112
++ S S + +R+W E +
Sbjct: 65 YLASGSSDKTIRLWDLETGECV 86
Score = 43.5 bits (103), Expect = 2e-05
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 34 TSAVTSVDYSPTGREFVAGG-YDKSLRLYLAHQGHSRDIY--HTKRMQHVTHTVWSLDNK 90
T V SV +SP G FVA D +++L+ G HT + V +S D +
Sbjct: 135 TDWVNSVAFSPDGT-FVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVA---FSPDGE 190
Query: 91 FVISASDEMNLRVWKAHASEKLG 113
++S+S + +++W + LG
Sbjct: 191 KLLSSSSDGTIKLWDLSTGKCLG 213
Score = 43.1 bits (102), Expect = 3e-05
Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 9/75 (12%)
Query: 34 TSAVTSVDYSPTGREFVAGGYDKSLRLYLAHQGHSRDIYHTKRMQHVTHTVWSL----DN 89
T V V S G +G DK++RL+ G H T V S+ D
Sbjct: 51 TGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRTLT----GH-TSYVSSVAFSPDG 105
Query: 90 KFVISASDEMNLRVW 104
+ + S+S + ++VW
Sbjct: 106 RILSSSSRDKTIKVW 120
Score = 43.1 bits (102), Expect = 3e-05
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 9/76 (11%)
Query: 34 TSAVTSVDYSPTGREFVAGGYDKSLRLYLAHQGHSRDIYHTKRMQHVTHTVWSL----DN 89
+ V SV +SP G +G D ++R++ R + + T++V SL D
Sbjct: 219 ENGVNSVAFSPDGYLLASGSEDGTIRVW-----DLRTGECVQTLSGHTNSVTSLAWSPDG 273
Query: 90 KFVISASDEMNLRVWK 105
K + S S + +R+W
Sbjct: 274 KRLASGSADGTIRIWD 289
Score = 38.9 bits (91), Expect = 7e-04
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 6 FTAANEDFNLYSYDIR--QLNSPLNVHKDMTSAVTSVDYSPTGREFVAGGYDKSLRLY 61
+ +ED + +D+R + L+ H T++VTS+ +SP G+ +G D ++R++
Sbjct: 234 LASGSEDGTIRVWDLRTGECVQTLSGH---TNSVTSLAWSPDGKRLASGSADGTIRIW 288
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 50.9 bits (120), Expect = 8e-08
Identities = 26/113 (23%), Positives = 49/113 (43%), Gaps = 9/113 (7%)
Query: 4 FVFTAANEDFNLYSYDIRQLNSPLNVHKDMTSAVTSVDYSPTGREFVAG-GYDKSLRLYL 62
+ + ++ D + +D+R PL+ T V+S+ +SP G +A D ++RL+
Sbjct: 169 LLASGSSLDGTIKLWDLRT-GKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWD 227
Query: 63 AHQG---HSRDIYHTKRMQHVTHTVWSLDNKFVISASDEMNLRVWKAHASEKL 112
G S H+ + +S D + S S + +R+W +S L
Sbjct: 228 LSTGKLLRSTLSGHSDS----VVSSFSPDGSLLASGSSDGTIRLWDLRSSSSL 276
Score = 48.5 bits (114), Expect = 6e-07
Identities = 26/113 (23%), Positives = 50/113 (44%), Gaps = 8/113 (7%)
Query: 5 VFTAANEDFNLYSYDIRQLNSPLNVHKDMTSAVTSVDYSPTGREFVAGGYDKSLRLYLAH 64
+ + + D + +D+R +S L +S+V SV +SP G+ +G D ++RL+
Sbjct: 255 LLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLE 314
Query: 65 QGHSRDIYHTKRMQHVTHTVWSLD-----NKFVISASDEMNLRVWKAHASEKL 112
G + + ++ V SL + V SD+ +R+W + L
Sbjct: 315 TG---KLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPL 364
Score = 44.3 bits (103), Expect = 1e-05
Identities = 20/102 (19%), Positives = 40/102 (39%), Gaps = 1/102 (0%)
Query: 4 FVFTAANEDFNLYSYDIRQLNSPLNVHKDMTSAVTSVDYSPTGREFVAGGYDKSLRLYLA 63
+ + + D + +D+ + + +V S +SP G +G D ++RL+
Sbjct: 212 LLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSS-FSPDGSLLASGSSDGTIRLWDL 270
Query: 64 HQGHSRDIYHTKRMQHVTHTVWSLDNKFVISASDEMNLRVWK 105
S + V +S D K + S S + +R+W
Sbjct: 271 RSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWD 312
Score = 43.5 bits (101), Expect = 3e-05
Identities = 21/103 (20%), Positives = 43/103 (41%), Gaps = 3/103 (2%)
Query: 12 DFNLYSYDIRQLNSPLNVHKDMTSAVTSVDYSPTGREFVAGG-YDKSLRLYLAHQGHSRD 70
D + +D+ + + + +VTS+ +SP G+ +G D +++L+ G
Sbjct: 133 DGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLS 192
Query: 71 IYHTKRMQHVTHTVWSLDNKFVI-SASDEMNLRVWKAHASEKL 112
V+ +S D +I S S + +R+W + L
Sbjct: 193 TLAGHT-DPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLL 234
Score = 39.3 bits (90), Expect = 6e-04
Identities = 25/104 (24%), Positives = 44/104 (42%), Gaps = 3/104 (2%)
Query: 4 FVFTAANEDFNLYSYDIRQLNSPLNVHKDMTSAVTSVDYSPTGREFVAGGYDKSLRLYLA 63
+ + ++D + +D+R + S V SV +SP GR +G D ++RL+
Sbjct: 342 LLVSGGSDDGTIRLWDLRTGKPLKTLEGH--SNVLSVSFSPDGRVVSSGSTDGTVRLWDL 399
Query: 64 HQGHSRDIYHTKRMQHVTHTVWSLDNKFVISASDEMNLRVWKAH 107
G + VT +S D K + S S + +R+W
Sbjct: 400 STGSLLRNLDGHTSR-VTSLDFSPDGKSLASGSSDNTIRLWDLK 442
Score = 33.1 bits (74), Expect = 0.080
Identities = 14/76 (18%), Positives = 32/76 (42%), Gaps = 4/76 (5%)
Query: 34 TSAVTSVDYSPTGREFVAGGYDKSLRLYLAHQGHS--RDIYHTKRMQHVTHTVWSLDNKF 91
++TS+ +SP G ++G D +++L+ G + + + S D
Sbjct: 65 EDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNS 124
Query: 92 VISASDE--MNLRVWK 105
++ AS +++W
Sbjct: 125 ILLASSSLDGTVKLWD 140
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats
(blades) of the beta propeller domain.
Length = 40
Score = 38.8 bits (91), Expect = 5e-05
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 25 SPLNVHKDMTSAVTSVDYSPTGREFVAGGYDKSLRLY 61
L K T VTSV +SP G+ +G D +++L+
Sbjct: 3 ELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
Score = 29.6 bits (67), Expect = 0.13
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 73 HTKRMQHVTHTVWSLDNKFVISASDEMNLRVWK 105
HT VT +S D K++ S SD+ +++W
Sbjct: 11 HTGP---VTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 37.7 bits (88), Expect = 1e-04
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 25 SPLNVHKDMTSAVTSVDYSPTGREFVAGGYDKSLRLY 61
L K T VTSV +SP G +G D ++R++
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVW 38
Score = 29.2 bits (66), Expect = 0.14
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 73 HTKRMQHVTHTVWSLDNKFVISASDEMNLRVWK 105
HT VT +S D + S SD+ +RVW
Sbjct: 10 HTGP---VTSVAFSPDGNLLASGSDDGTVRVWD 39
>gnl|CDD|226531 COG4044, COG4044, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 247
Score = 30.2 bits (68), Expect = 0.51
Identities = 9/41 (21%), Positives = 16/41 (39%)
Query: 44 PTGREFVAGGYDKSLRLYLAHQGHSRDIYHTKRMQHVTHTV 84
R + G + + L GH RD+ +R+ + V
Sbjct: 171 SYDRLIINGATREEIERALNRTGHGRDVVRIERLGLLETMV 211
>gnl|CDD|220455 pfam09883, DUF2110, Uncharacterized protein conserved in archaea
(DUF2110). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 226
Score = 30.0 bits (68), Expect = 0.58
Identities = 12/34 (35%), Positives = 15/34 (44%)
Query: 44 PTGREFVAGGYDKSLRLYLAHQGHSRDIYHTKRM 77
PT R V +R L GH RDI +R+
Sbjct: 160 PTDRLNVNSATRSEVRAALNRAGHGRDIVTIERL 193
>gnl|CDD|227657 COG5354, COG5354, Uncharacterized protein, contains Trp-Asp (WD)
repeat [General function prediction only].
Length = 561
Score = 29.8 bits (67), Expect = 0.88
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 14 NLYSYDIRQLNSPLNVHKDMTSAVTSVDYSPTGREFV 50
NLY I + + P V KD+ V + P F
Sbjct: 256 NLYLLRITERSIP--VEKDLKDPVHDFTWEPLSSRFA 290
>gnl|CDD|219958 pfam08660, Alg14, Oligosaccharide biosynthesis protein Alg14 like.
Alg14 is involved dolichol-linked oligosaccharide
biosynthesis and anchors the catalytic subunit Alg13 to
the ER membrane.
Length = 166
Score = 28.4 bits (64), Expect = 1.7
Identities = 8/49 (16%), Positives = 22/49 (44%), Gaps = 2/49 (4%)
Query: 73 HTKRMQHVTHTVWSLDNK--FVISASDEMNLRVWKAHASEKLGYVNNKQ 119
HT M + + +L++ +V++ +D+ +L + G + +
Sbjct: 10 HTAEMLRLLPFLKNLEDPRRYVVTETDKDSLSKASKFEKSRGGILKIPR 58
>gnl|CDD|178768 PLN03229, PLN03229, acetyl-coenzyme A carboxylase carboxyl
transferase subunit alpha; Provisional.
Length = 762
Score = 29.1 bits (65), Expect = 1.7
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 11/51 (21%)
Query: 109 SEKLGYVNNKQRQALDYSESLKQKYAHHPQIRR--IARHRQVPR---HIYN 154
S+++ + +K +QAL K Y H I+R IARH P HI+N
Sbjct: 125 SDQIISLESKYQQAL------KDLYTHLTPIQRVNIARHPNRPTFLDHIFN 169
>gnl|CDD|236474 PRK09350, PRK09350, poxB regulator PoxA; Provisional.
Length = 306
Score = 28.0 bits (63), Expect = 3.5
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 4/41 (9%)
Query: 37 VTSVDYSPTGREFVAGGYDKSLRLYLAHQGHSRDIYHTKRM 77
VT + P FV G + L+L + YH KR+
Sbjct: 37 VTDIHLVPFETRFVGPGASQGKTLWL----MTSPEYHMKRL 73
>gnl|CDD|217428 pfam03213, Pox_P35, Poxvirus P35 protein.
Length = 325
Score = 27.3 bits (61), Expect = 4.9
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 9/58 (15%)
Query: 19 DIRQLNSPLNVHKDMTSAVTSVD---YSPTGREFVAGGYDKSLRLYLAHQGHSRDIYH 73
DI QL L+ + T S + YS TG GYD SL Y+ ++ +Y
Sbjct: 150 DILQLRETLHNNNVRTLLNQSGNPSLYSYTG------GYDVSLSAYIIRVSTAKKLYA 201
>gnl|CDD|99786 cd06189, flavin_oxioreductase, NAD(P)H dependent flavin
oxidoreductases use flavin as a substrate in mediating
electron transfer from iron complexes or iron proteins.
Structurally similar to ferredoxin reductases, but with
only 15% sequence identity, flavin reductases reduce
FAD, FMN, or riboflavin via NAD(P)H. Flavin is used as a
substrate, rather than a tightly bound prosthetic group
as in flavoenzymes; weaker binding is due to the absence
of a binding site for the AMP moeity of FAD.
Length = 224
Score = 27.1 bits (61), Expect = 5.0
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 49 FVAGG----YDKSLRLYLAHQGHSRDIY 72
+AGG KS+ +L QG R I+
Sbjct: 103 LIAGGTGFAPIKSILEHLLAQGSKRPIH 130
>gnl|CDD|236796 PRK10922, PRK10922, 3-octaprenyl-4-hydroxybenzoate decarboxylase;
Provisional.
Length = 497
Score = 27.6 bits (61), Expect = 5.4
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 8/38 (21%)
Query: 73 HTKRMQHVTHTVWS-----LDNKFVISASDEMNLRVWK 105
H KR V VWS + KFVI D++N R W
Sbjct: 377 HAKR---VMMGVWSFLRQFMYTKFVIVCDDDVNARDWN 411
>gnl|CDD|226081 COG3551, COG3551, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 402
Score = 27.3 bits (60), Expect = 5.8
Identities = 21/91 (23%), Positives = 27/91 (29%), Gaps = 11/91 (12%)
Query: 55 DKSLRLYLAHQGHSRDIYHTKRMQHVTHTVWSLDNKFVI------SASDEMNLRVWKAHA 108
+KSL L+ H R R QHV D +N RV +A
Sbjct: 160 EKSLILWPYHGNKQR-----IREQHVEEGADIYDVHLSDLRQHPDRLVAAVNQRVGRAPK 214
Query: 109 SEKLGYVNNKQRQALDYSESLKQKYAHHPQI 139
L V +L + S A Q
Sbjct: 215 KRFLDDVRLFLDHSLKHFASALAAAAGSFQA 245
>gnl|CDD|238755 cd01478, Sec23-like, Sec23-like: Protein and membrane traffic in
eukaryotes is mediated by at least in part by the
budding and fusion of intracellular transport vesicles
that selectively carry cargo proteins and lipids from
donor to acceptor organelles. The two main classes of
vesicular carriers within the endocytic and the
biosynthetic pathways are COP- and clathrin-coated
vesicles. Formation of COPII vesicles requires the
ordered assembly of the coat built from several
cytosolic components GTPase Sar1, complexes of
Sec23-Sec24 and Sec13-Sec31. The process is initiated by
the conversion of GDP to GTP by the GTPase Sar1 which
then recruits the heterodimeric complex of Sec23 and
Sec24. This heterodimeric complex generates the
pre-budding complex. The final step leading to membrane
deformation and budding of COPII-coated vesicles is
carried by the heterodimeric complex Sec13-Sec31. The
members of this CD belong to the Sec23-like family. Sec
23 is very similar to Sec24. The Sec23 and Sec24
polypeptides fold into five distinct domains: a
beta-barrel, a zinc finger, a vWA or trunk, an all
helical region and a carboxy Gelsolin domain. The
members of this subgroup lack the consensus MIDAS motif
but have the overall Para-Rossmann type fold that is
characteristic of this superfamily.
Length = 267
Score = 26.9 bits (60), Expect = 6.7
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 19/58 (32%)
Query: 21 RQLNSPLNVHKDMTSAVTSVDYSPTGREFVAGGYDKSLRLY------LAHQGHSRDIY 72
+L P+ H D+ D + Y K+++ Y LA GH+ DI+
Sbjct: 183 TELKDPIRSHHDIDK-----DNAKY--------YKKAVKFYDSLAKRLAANGHAVDIF 227
>gnl|CDD|235668 PRK06007, fliF, flagellar MS-ring protein; Reviewed.
Length = 542
Score = 26.8 bits (60), Expect = 10.0
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 158 EHRAIRSKQKRKESNKRTHSAPGTVP 183
+RS+Q +E++ PG VP
Sbjct: 286 NQGVVRSEQTVEETSTGQGGNPGGVP 311
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
0.317 0.127 0.369
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,812,817
Number of extensions: 863230
Number of successful extensions: 847
Number of sequences better than 10.0: 1
Number of HSP's gapped: 839
Number of HSP's successfully gapped: 42
Length of query: 197
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 105
Effective length of database: 6,857,034
Effective search space: 719988570
Effective search space used: 719988570
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 (21.7 bits)
S2: 56 (25.4 bits)