RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17744
(326 letters)
>gnl|CDD|204879 pfam12317, IFT46_B_C, Intraflagellar transport complex B protein 46
C terminal. This family of proteins is found in
eukaryotes. Proteins in this family are typically
between 298 and 416 amino acids in length. IFT46 is a
flagellar protein of complex B. Like all IFT proteins,
it is required for transport of IFT particles into the
flagella.
Length = 214
Score = 307 bits (788), Expect = e-105
Identities = 121/210 (57%), Positives = 165/210 (78%)
Query: 95 AYDPLEFAHLATSTDLKEMFAYIEKYTPQPIDLTYKLRPFIPDYIPAVGDIDAFIKVARP 154
AYDP ++AHL + ++KE+F YI +Y PQ ++L KL+PFIPDYIPAVGDIDAFIKV RP
Sbjct: 2 AYDPADYAHLDVTPEIKELFQYITRYKPQTVELPTKLKPFIPDYIPAVGDIDAFIKVPRP 61
Query: 155 DGRPDSLGLTVLDEPCFEQSDPAILNLQLRQSSKCPTSSKATIIKKVEDADKNKKAIDRW 214
DG+PD+LGLTVLDEPC QSDP +L+LQLR++SK T K ++ +EDA+KN KAID W
Sbjct: 62 DGKPDNLGLTVLDEPCANQSDPTVLDLQLRETSKVATGGKDVVVGSIEDAEKNPKAIDTW 121
Query: 215 IKDIGDLHKNKPPPSVHYSRGMPDLDNLMQEWSNDVEQTISEVGLPPEDLDCDLTTYIDL 274
I+ I +LH++KPPP+VHYS+ MPD++ LMQEW + E+ ++ V LP DLD DL Y+ +
Sbjct: 122 IESIKELHRDKPPPTVHYSKNMPDIETLMQEWPQEFEEVLNSVQLPSADLDLDLKEYVKI 181
Query: 275 MAAILDIPRFESRIETLHVIFSLYAAIQSS 304
+ AILDIP + +RIE+LHV+F+LY+ +++
Sbjct: 182 ICAILDIPVYGNRIESLHVLFTLYSEFKNN 211
>gnl|CDD|221489 pfam12252, SidE, Dot/Icm substrate protein. This family of proteins
is found in bacteria. Proteins in this family are
typically between 397 and 1543 amino acids in length.
This family is the SidE protein in the Dot/Icm pathway of
Legionella pneumophila bacteria. There is little
literature describing the family.
Length = 1443
Score = 32.9 bits (75), Expect = 0.27
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 194 KATIIKKVEDADKNKKAIDRWI----KDIGDLHKNKPPPSVHYSRGMPDLDNLMQE 245
+A + V D +K ++ D I K I +L K K + + +L+NL QE
Sbjct: 1088 RAVVTPVVTDEEKVRERYDALIENTSKRITELEKAKLANLDVVKKAISNLNNLQQE 1143
>gnl|CDD|216652 pfam01698, FLO_LFY, Floricaula / Leafy protein. This family
consists of various plant development proteins which are
homologues of floricaula (FLO) and Leafy (LFY) proteins
which are floral meristem identity proteins. Mutations
in the sequences of these proteins affect flower and
leaf development.
Length = 382
Score = 32.7 bits (75), Expect = 0.27
Identities = 23/80 (28%), Positives = 32/80 (40%), Gaps = 9/80 (11%)
Query: 12 EEVQSPTGSVSSGENGEARVPMKIESSLRPGSAMKMQLSEHQTHIPLHSRTNSPRGDSSF 71
E VQ + SG G + + K + + Q R +
Sbjct: 150 EPVQQEKEAAGSG-GGGGGTWGLVGVPGHSSDSEKKKQRKKQ-------RRKRSKELRE- 200
Query: 72 DEDDYEDEDEDGDDGGEGGG 91
D+DD EDED+DG+ GGEGG
Sbjct: 201 DDDDDEDEDDDGEGGGEGGE 220
>gnl|CDD|240433 PTZ00482, PTZ00482, membrane-attack complex/perforin (MACPF)
Superfamily; Provisional.
Length = 844
Score = 31.0 bits (70), Expect = 1.1
Identities = 10/49 (20%), Positives = 18/49 (36%)
Query: 55 HIPLHSRTNSPRGDSSFDEDDYEDEDEDGDDGGEGGGADKAYDPLEFAH 103
L+ R + D + YED+++D + G + LE
Sbjct: 77 ASFLNQRKSLDDDDDDEFDFLYEDDEDDAGNATSGESSTDDDSLLELPD 125
>gnl|CDD|217801 pfam03934, T2SK, Type II secretion system (T2SS), protein K.
Members of this family are involved in the Type II
protein secretion system. The T2SK family includes
proteins such as ExeK, PulK, OutX and XcpX.
Length = 282
Score = 29.6 bits (67), Expect = 2.4
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 5/58 (8%)
Query: 80 DEDGDDGGEGGGADKAYDPLEFAHLATSTDL--KEMFAYIEKYTPQPIDLTYKLRPFI 135
D D GG D Y L +LA + L + TP+ +LRP++
Sbjct: 122 DADDQPASPGGAEDSYYLSLSPPYLAANQPLADVSELRLVLGVTPELYA---RLRPYV 176
>gnl|CDD|223087 COG0008, GlnS, Glutamyl- and glutaminyl-tRNA synthetases
[Translation, ribosomal structure and biogenesis].
Length = 472
Score = 29.2 bits (66), Expect = 3.0
Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 7/57 (12%)
Query: 196 TIIKKVEDADKNKKAIDRWIKDIGDLHKNKPP----PS-VHYSRGM--PDLDNLMQE 245
+ + +D K+ I W+K + L K P P V + G P+L + ++
Sbjct: 400 KDAEGLITSDWTKENIIHWVKAVARLFGVKGPKLFPPLRVALTGGYVEPELADTIEL 456
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 29.2 bits (66), Expect = 3.6
Identities = 14/40 (35%), Positives = 17/40 (42%)
Query: 61 RTNSPRGDSSFDEDDYEDEDEDGDDGGEGGGADKAYDPLE 100
+ + R D FD+DD D D GGG D D E
Sbjct: 128 KDDDVRDDDDFDDDDLGDLASDDRAAHFGGGEDDEEDEEE 167
>gnl|CDD|203520 pfam06803, DUF1232, Protein of unknown function (DUF1232). This
family represents a conserved region of approximately 60
residues within a number of hypothetical bacterial and
archaeal proteins of unknown function.
Length = 40
Score = 25.9 bits (58), Expect = 3.6
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 7/23 (30%)
Query: 124 PIDLTYKLRPFIPDYIPAVGDID 146
PIDL IPD+IP +G +D
Sbjct: 17 PIDL-------IPDFIPVLGYLD 32
>gnl|CDD|143176 cd04975, Ig4_SCFR_like, Fourth immunoglobulin (Ig)-like domain of
stem cell factor receptor (SCFR) and similar proteins.
Ig4_SCFR_like; fourth immunoglobulin (Ig)-like domain
of stem cell factor receptor (SCFR). In addition to
SCFR this group also includes the fourth Ig domain of
platelet-derived growth factor receptors (PDGFR), alpha
and beta, the fourth Ig domain of macrophage colony
stimulating factor (M-CSF), and the Ig domain of the
receptor tyrosine kinase KIT. SCFR and the PDGFR alpha
and beta have similar organization: an extracellular
component having five Ig-like domains, a transmembrane
segment, and a cytoplasmic portion having protein
tyrosine kinase activity. SCFR and its ligand SCF are
critical for normal hematopoiesis, mast cell
development, melanocytes and gametogenesis. SCF binds
to the second and third Ig-like domains of SCFR, this
fourth Ig-like domain participates in SCFR
dimerization, which follows ligand binding. Deletion of
this fourth SCFR_Ig-like domain abolishes the
ligand-induced dimerization of SCFR and completely
inhibits signal transduction. PDGF is a potent mitogen
for connective tissue cells. PDGF-stimulated processes
are mediated by three different PDGFs (PDGF-A,-B, and
C). PDGFR alpha binds to all three PDGFs, whereas the
PDGFR beta, binds only to PDGF-B. In mice, PDGFR alpha,
and PDGFR beta, are essential for normal development.
Length = 101
Score = 27.3 bits (61), Expect = 4.0
Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 3/58 (5%)
Query: 9 VNAEEVQSPTGSVSSGENGEARVPMKIESSLRPGSAMKMQ--LSEHQTHIPLHSRTNS 64
+N Q+ T V+ GEN V ++ + L+ T I S S
Sbjct: 3 INLSPEQNTTIFVNLGENLNLVVEVEAYPPPPHINWTYDNRTLTNKLTEIVT-SENES 59
>gnl|CDD|216334 pfam01153, Glypican, Glypican.
Length = 559
Score = 28.9 bits (65), Expect = 4.1
Identities = 11/44 (25%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 58 LHSRTNSPRGDSSFDEDDYEDEDEDGDDGGEGGGADKAYDPLEF 101
L T+ R S ++ D++D ++ GG G G+ L
Sbjct: 461 LKIMTSRLRAAYSGNDVDFQDASDES-SGGSGSGSGCVDKRLRI 503
>gnl|CDD|113452 pfam04684, BAF1_ABF1, BAF1 / ABF1 chromatin reorganising factor.
ABF1 is a sequence-specific DNA binding protein involved
in transcription activation, gene silencing and
initiation of DNA replication. ABF1 is known to remodel
chromatin, and it is proposed that it mediates its
effects on transcription and gene expression by
modifying local chromatin architecture. These functions
require a conserved stretch of 20 amino acids in the
C-terminal region of ABF1 (amino acids 639 to 662 S.
cerevisiae). The N-terminal two thirds of the protein
are necessary for DNA binding, and the N-terminus (amino
acids 9 to 91 in S. cerevisiae) is thought to contain a
novel zinc-finger motif which may stabilise the protein
structure.
Length = 508
Score = 28.9 bits (64), Expect = 4.1
Identities = 34/135 (25%), Positives = 50/135 (37%), Gaps = 13/135 (9%)
Query: 15 QSPTGSVSSGENGEARVPMKIESSLRPGSAMKMQLSEHQTHIPLHSRTNSPRGDSSFDED 74
Q S + + G E G M H H H+ + D ED
Sbjct: 78 QGANNSGQNED-GSPGGGSGDEGGHHHGH--NMHAHHHHHHHNGHTNGHGLAEDDR-AED 133
Query: 75 DYEDEDEDGDDGGEGGGADKAYDPLEFAHLATSTD-LKEMFAY--IEKYTPQPIDLTYKL 131
+ +D+DED D A A A +A S + +K FA IE Y P++ L
Sbjct: 134 EAQDDDEDDD------AAVTAAIAAAVAAVADSQETIKGPFAVTKIEPYHNHPLESNLSL 187
Query: 132 RPFIPDYIPAVGDID 146
+ F+ IP + +D
Sbjct: 188 QRFVLSKIPKILQVD 202
>gnl|CDD|204463 pfam10369, ALS_ss_C, Small subunit of acetolactate synthase.
ALS_ss_C is the C-terminal half of a family of proteins
which are the small subunits of acetolactate synthase.
Acetolactate synthase is a tetrameric enzyme, containing
probably two large and two small subunits, which
catalyzes the first step in branched-chain amino acid
biosynthesis. This reaction is sensitive to certain
herbicides.
Length = 75
Score = 26.6 bits (60), Expect = 4.7
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 12/57 (21%)
Query: 105 ATSTDLKEMFAYIEKYTPQPIDLTYKLRPFIPDY--IPAVGD---IDAFIKVARPDG 156
AT E+ + + + +D+T PD I GD IDAFI + RP G
Sbjct: 11 ATGETRAEILRIADIFRAKIVDVT-------PDSYTIELTGDPEKIDAFIDLLRPFG 60
>gnl|CDD|111382 pfam02477, Nairo_nucleo, Nucleocapsid N protein. The nucleoprotein
of the ssRNA negative-strand Nairovirus is an internal
part of the virus particle.
Length = 442
Score = 28.7 bits (64), Expect = 4.8
Identities = 22/68 (32%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 191 TSSKATIIKKVEDADKNKKAIDRWIKDIGDLHKNKPPPS--VHYSRGMPDLDNLMQEWSN 248
TSS + K +E DKNK I W DL K P P V Y + +W
Sbjct: 83 TSSTGVVKKGLEWFDKNKDTIKLWDAKYMDLKKEIPEPEQLVSYQQA-------ALKWRK 135
Query: 249 DVEQTISE 256
DV I++
Sbjct: 136 DVGFEINQ 143
>gnl|CDD|113290 pfam04514, BTV_NS2, Bluetongue virus non-structural protein NS2.
This family includes NS2 proteins from other members of
the Orbivirus genus. NS2 is a non-specific
single-stranded RNA-binding protein that forms large
homomultimers and accumulates in viral inclusion bodies
of infected cells. Three RNA binding regions have been
identified in Bluetongue virus serotype 17 at residues
2-11, 153-166 and 274-286. NS2 multimers also possess
nucleotidyl phosphatase activity. The precise function
of NS2 is not known, but it may be involved in the
transport and condensation of viral mRNAs.
Length = 363
Score = 28.7 bits (64), Expect = 4.8
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 73 EDDYEDEDEDGDDGGEGGGADKAY 96
E D +DEDE G+D +G ++Y
Sbjct: 253 ERDSDDEDEHGEDSEDGETKPESY 276
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 28.8 bits (64), Expect = 5.2
Identities = 14/41 (34%), Positives = 18/41 (43%)
Query: 58 LHSRTNSPRGDSSFDEDDYEDEDEDGDDGGEGGGADKAYDP 98
L + N D S DD +D D DG+D A K +P
Sbjct: 344 LKGKKNGLDKDDSDSGDDSDDSDIDGEDSVSLVTAKKQKEP 384
>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366). This
family of proteins is found in bacteria and eukaryotes.
Proteins in this family are typically between 227 and
387 amino acids in length.
Length = 213
Score = 28.1 bits (63), Expect = 5.5
Identities = 11/21 (52%), Positives = 12/21 (57%)
Query: 68 DSSFDEDDYEDEDEDGDDGGE 88
D DE DY DEDE+ DD
Sbjct: 192 DDDLDEYDYGDEDEEEDDEPP 212
>gnl|CDD|177565 PHA03239, PHA03239, envelope glycoprotein M; Provisional.
Length = 429
Score = 28.4 bits (63), Expect = 5.5
Identities = 11/54 (20%), Positives = 22/54 (40%)
Query: 29 ARVPMKIESSLRPGSAMKMQLSEHQTHIPLHSRTNSPRGDSSFDEDDYEDEDED 82
ARV K++ + ++ PL + + PR + F+ E + +D
Sbjct: 372 ARVAQKVKGRAQKEKNGPHSHKKYVDARPLDAYADDPRDNIPFERRSREGDADD 425
>gnl|CDD|237969 PRK15452, PRK15452, putative protease; Provisional.
Length = 443
Score = 27.9 bits (63), Expect = 7.9
Identities = 13/54 (24%), Positives = 21/54 (38%)
Query: 3 DESIDVVNAEEVQSPTGSVSSGENGEARVPMKIESSLRPGSAMKMQLSEHQTHI 56
D+ D+V+ + + G +E + RPG M EH T+I
Sbjct: 209 DDVGDIVHKHPIPVQNVEPTLGIGAPTDKVFLLEEAQRPGEYMPAFEDEHGTYI 262
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
0.312 0.133 0.387
Gapped
Lambda K H
0.267 0.0563 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,021,766
Number of extensions: 1651617
Number of successful extensions: 1776
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1729
Number of HSP's successfully gapped: 49
Length of query: 326
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 229
Effective length of database: 6,635,264
Effective search space: 1519475456
Effective search space used: 1519475456
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 (21.8 bits)
S2: 59 (26.9 bits)