RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11918
(285 letters)
>gnl|CDD|215968 pfam00520, Ion_trans, Ion transport protein. This family contains
Sodium, Potassium, Calcium ion channels. This family is
6 transmembrane helices in which the last two helices
flank a loop which determines ion selectivity. In some
sub-families (e.g. Na channels) the domain is repeated
four times, whereas in others (e.g. K channels) the
protein forms as a tetramer in the membrane. A bacterial
structure of the protein is known for the last two
helices but is not the Pfam family due to it lacking the
first four helices.
Length = 194
Score = 40.4 bits (95), Expect = 3e-04
Identities = 15/56 (26%), Positives = 29/56 (51%)
Query: 219 SVMGNFNNFFFAAHLLDVAVGFKTLRTILQSVTHNGKQLVLTVMLLTIIVYIYYLC 274
S + LL + F LRT+LQS+ + K L+ ++LL ++++I+ +
Sbjct: 56 SGLLRVLRLLRLLRLLRLLRRFPGLRTLLQSLGRSLKSLLNLLLLLLLLLFIFAII 111
>gnl|CDD|219038 pfam06459, RR_TM4-6, Ryanodine Receptor TM 4-6. This region covers
TM regions 4-6 of the ryanodine receptor 1 family.
Length = 217
Score = 35.1 bits (81), Expect = 0.021
Identities = 24/110 (21%), Positives = 37/110 (33%), Gaps = 18/110 (16%)
Query: 25 ILMSLMRGPAIEEPTVEVKEVEKSHMRSYPALPPPPDEGGKPL--EMFNLDVTKDDTGQY 82
+ G EE E E E S LP + + + + F LD+ K+ G
Sbjct: 5 PTQDEVHGDVPEEEGAEEVEPEGSGR----DLPETGEGEEEEVGVDAFGLDMKKEGGG-- 58
Query: 83 KMVPHE--------STPIKQTSTEEGVGGREMSQEGEGGEEHRAESEMPD 124
++ T EG + + E GEE ++E E D
Sbjct: 59 -YGHDASPGLGDMSEVEPEEPPTPEGAPAEKRELKEE-GEEPKSEPEKAD 106
>gnl|CDD|216260 pfam01040, UbiA, UbiA prenyltransferase family.
Length = 259
Score = 33.6 bits (77), Expect = 0.086
Identities = 16/81 (19%), Positives = 25/81 (30%), Gaps = 9/81 (11%)
Query: 200 AGVTITDNAFLYSLWYFTFSVMGNFNNFFFAAHLLDV----AVGFKTLRTILQSVTHNGK 255
G I L +L F S+ + DV G +TL L
Sbjct: 140 VGGDIPSPLLLLALPVFLLSL-----AILLTNDIRDVEGDRKAGIRTLPVRLGRKRALAL 194
Query: 256 QLVLTVMLLTIIVYIYYLCIP 276
+L L +++ + L P
Sbjct: 195 YALLLAAALLLLLLLLLLLAP 215
>gnl|CDD|240323 PTZ00233, PTZ00233, variable surface protein Vir18; Provisional.
Length = 509
Score = 31.9 bits (72), Expect = 0.41
Identities = 15/62 (24%), Positives = 21/62 (33%), Gaps = 5/62 (8%)
Query: 75 TKDDTGQYKMVPHESTPIKQTSTEEGVGGREMSQEGEGGEEHRAESEMPDPAVTLADLLG 134
D Q K+ P P K S E +E SQ +E ES + + +
Sbjct: 133 RVDTKSQSKLRP---VPSKAKSLE-IKDPQEQSQNQADAQESNKESVVL-QPQSDSMPSP 187
Query: 135 SF 136
S
Sbjct: 188 SS 189
>gnl|CDD|236332 PRK08668, PRK08668, NADH dehydrogenase subunit M; Validated.
Length = 610
Score = 30.7 bits (70), Expect = 0.91
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 4/57 (7%)
Query: 211 YSLWYFTFSVMGNFNNFFFAAHLLDVAVG---FKTLRTILQSVTHNGKQLVLTVMLL 264
SL YF S +G + +A L+ G F + L + T G L++ + LL
Sbjct: 148 ASLKYFVLSAIGAY-AMLYAIFLIYAKTGTFDFADISQGLINDTSTGFALIVFLFLL 203
>gnl|CDD|219521 pfam07695, 7TMR-DISM_7TM, 7TM diverse intracellular signalling.
This entry represents the transmembrane region of the
7TM-DISM (7TM Receptors with Diverse Intracellular
Signalling Modules).
Length = 207
Score = 29.9 bits (68), Expect = 1.1
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 5/66 (7%)
Query: 208 AFLYSLWYFTFSVMGNFNNFFFAAHLLDVAVGFKTLRTILQSVTHNGKQLVLTVMLLTII 267
L Y +++ F FA L++ L +L + L+L ++LL
Sbjct: 63 WLNNKLLYLFLALLVIFFALLFARSFLELKKYLPRLDRLLLGLA-----LLLLLLLLLAP 117
Query: 268 VYIYYL 273
++ Y L
Sbjct: 118 LFPYTL 123
>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 = 27.4 bits (61), Expect = 3.7
Identities = 11/42 (26%), Positives = 14/42 (33%), Gaps = 1/42 (2%)
Query: 171 TSFSSQEEEESSGIISFILRIDWRYQVWKAGVTITDNAFLYS 212
+ F Q + S +I I I I N FLY
Sbjct: 12 SGFQKQRTVQKS-LIRTIESIGIERDGELLVFEIKGNGFLYH 52
>gnl|CDD|223029 PHA03264, PHA03264, envelope glycoprotein D; Provisional.
Length = 416
Score = 28.8 bits (64), Expect = 3.8
Identities = 24/78 (30%), Positives = 26/78 (33%), Gaps = 19/78 (24%)
Query: 52 SYPALPPPPDEGGKPLEMFNLDVTKDDTGQYKMVPHESTPIKQTSTEEGVGGREMSQEGE 111
S PPP GG P DD + K P G GRE EGE
Sbjct: 261 SKGYEPPPAPSGGSPAP------PGDDRPEAKPEPGPVED--------GAPGRETGGEGE 306
Query: 112 G----GEEHRAESEMPDP 125
G G + A E P P
Sbjct: 307 GPEPAGRDGAAGGE-PKP 323
>gnl|CDD|200219 TIGR02927, SucB_Actino, 2-oxoglutarate dehydrogenase, E2 component,
dihydrolipoamide succinyltransferase. This model
represents an Actinobacterial clade of E2 enzyme, a
component of the 2-oxoglutarate dehydrogenase complex
involved in the TCA cycle. These proteins have multiple
domains including the catalytic domain (pfam00198), one
or two biotin domains (pfam00364) and an E3-component
binding domain (pfam02817).
Length = 579
Score = 28.8 bits (64), Expect = 3.8
Identities = 25/105 (23%), Positives = 36/105 (34%), Gaps = 23/105 (21%)
Query: 37 EPTVEVKEVEKSHMRSYPALPPPPDEGGKPLEMFNLDVTKDDTGQYKMVPHESTPIKQTS 96
EP + PA P P + P V+ D+G Y TP+ +
Sbjct: 224 EPAPDPAARAPHAAPDPPAPAPAPAKTAAPAAA--APVSSGDSGPY------VTPLVRKL 275
Query: 97 TEE-----------GVGGREMSQE----GEGGEEHRAESEMPDPA 126
++ GVGGR Q+ + EE RA + P A
Sbjct: 276 AKDKGVDLSTVKGTGVGGRIRKQDVLAAAKAAEEARAAAAAPAAA 320
>gnl|CDD|191716 pfam07263, DMP1, Dentin matrix protein 1 (DMP1). This family
consists of several mammalian dentin matrix protein 1
(DMP1) sequences. The dentin matrix acidic
phosphoprotein 1 (DMP1) gene has been mapped to human
chromosome 4q21. DMP1 is a bone and teeth specific
protein initially identified from mineralised dentin.
DMP1 is primarily localised in the nuclear compartment
of undifferentiated osteoblasts. In the nucleus, DMP1
acts as a transcriptional component for activation of
osteoblast-specific genes like osteocalcin. During the
early phase of osteoblast maturation, Ca(2+) surges into
the nucleus from the cytoplasm, triggering the
phosphorylation of DMP1 by a nuclear isoform of casein
kinase II. This phosphorylated DMP1 is then exported out
into the extracellular matrix, where it regulates
nucleation of hydroxyapatite. DMP1 is a unique molecule
that initiates osteoblast differentiation by
transcription in the nucleus and orchestrates
mineralised matrix formation extracellularly, at later
stages of osteoblast maturation. The DMP1 gene has been
found to be ectopically expressed in lung cancer
although the reason for this is unknown.
Length = 514
Score = 28.5 bits (63), Expect = 4.5
Identities = 20/100 (20%), Positives = 40/100 (40%), Gaps = 4/100 (4%)
Query: 86 PHESTPIKQTSTEEGVGGREMSQEGEGGEEHRAESEMPDPAVTLADLLG---SFPVNYWD 142
P ++S E + +E S E + + + PD + ++ S + D
Sbjct: 326 QEVQDPSSESSQEADLPSQENSSESQEEVVSESRGDNPDNTTSHSEDQEDSESSEEDSLD 385
Query: 143 KFAKKKVRQKYSETYDFDSISNLLGMEKTSFSSQEEEESS 182
+ + Q E D +S +L E++ S+++E SS
Sbjct: 386 TPSSSE-SQSTEEQADSESNESLSSSEESPESTEDENSSS 424
>gnl|CDD|219166 pfam06764, DUF1223, Protein of unknown function (DUF1223). This
family consists of several hypothetical proteins of
around 250 residues in length which are found in both
plants and bacteria. The function of this family is
unknown.
Length = 200
Score = 28.0 bits (63), Expect = 4.9
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 9/30 (30%)
Query: 135 SFPVNYW------DKFAKK--KVRQK-YSE 155
+F V+YW D FA RQ+ Y+
Sbjct: 33 AFHVDYWDYLGWKDTFASPAFTERQRAYAR 62
>gnl|CDD|212914 cd11981, SH3_VAV3_1, First Src homology 3 domain of VAV3 protein.
VAV3 is ubiquitously expressed and functions as a
phosphorylation-dependent guanine nucleotide exchange
factor (GEF) for RhoA, RhoG, and Rac1. It has been
implicated to function in the hematopoietic, bone,
cerebellar, and cardiovascular systems. VAV3 is
essential in axon guidance in neurons that control
blood pressure and respiration. It is overexpressed in
prostate cancer cells and it plays a role in regulating
androgen receptor transcriptional activity. VAV
proteins contain several domains that enable their
function: N-terminal calponin homology (CH), acidic,
RhoGEF (also called Dbl-homologous or DH), Pleckstrin
Homology (PH), C1 (zinc finger), SH2, and two SH3
domains. The SH3 domain of VAV is involved in the
localization of proteins to specific sites within the
cell, by interacting with proline-rich sequences within
target proteins. SH3 domains are protein interaction
domains that bind to proline-rich ligands with moderate
affinity and selectivity, preferentially to PxxP
motifs. They play versatile and diverse roles in the
cell including the regulation of enzymes, changing the
subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 62
Score = 26.0 bits (57), Expect = 5.1
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 50 MRSYPALPPPPDEGGKPLEM 69
+R+Y +P P GG PL
Sbjct: 5 IRNYSGVPKPQLHGGPPLNA 24
>gnl|CDD|217354 pfam03073, TspO_MBR, TspO/MBR family. Tryptophan-rich sensory
protein (TspO) is an integral membrane protein that acts
as a negative regulator of the expression of specific
photosynthesis genes in response to oxygen/light. It is
involved in the efflux of porphyrin intermediates from
the cell. This reduces the activity of
coproporphyrinogen III oxidase, which is thought to lead
to the accumulation of a putative repressor molecule
that inhibits the expression of specific photosynthesis
genes. Several conserved aromatic residues are necessary
for TspO function: they are thought to be involved in
binding porphyrin intermediates. In, the rat
mitochondrial peripheral benzodiazepine receptor (MBR)
was shown to not only retain its structure within a
bacterial outer membrane, but also to be able to
functionally substitute for TspO in TspO- mutants, and
to act in a similar manner to TspO in its in situ
location: the outer mitochondrial membrane. The
biological significance of MBR remains unclear, however.
It is thought to be involved in a variety of cellular
functions, including cholesterol transport in
steroidogenic tissues.
Length = 147
Score = 27.5 bits (62), Expect = 5.3
Identities = 10/43 (23%), Positives = 18/43 (41%)
Query: 195 YQVWKAGVTITDNAFLYSLWYFTFSVMGNFNNFFFAAHLLDVA 237
Y VW+AG +L+ ++ ++ FF H +A
Sbjct: 56 YLVWRAGPGTKRRKLALALFALQLALNALWSPLFFGLHSPGLA 98
>gnl|CDD|224980 COG2069, CdhD, CO dehydrogenase/acetyl-CoA synthase delta subunit
(corrinoid Fe-S protein) [Energy production and
conversion].
Length = 403
Score = 27.9 bits (62), Expect = 6.3
Identities = 30/146 (20%), Positives = 53/146 (36%), Gaps = 17/146 (11%)
Query: 22 FARILMSLMRGPAIEEPTVEVKEVEKSHMRSYPALPPPPDEGGKPLEMFNLDVTKDDTGQ 81
+L+ + G IE+ +++ E+ + M YP P + + + KD
Sbjct: 13 LKGMLVEAVEGIEIEDIEIDLDELRLALMFGYPVAIGAPAAPAEKPAVEEPKLEKDLPPA 72
Query: 82 YKMVPHESTP-------IKQTSTEEGVGGREMSQEGEGGEE--HRAESEMPDPAVTLADL 132
P E P I T + G G+ + GGE +R E P+P V D+
Sbjct: 73 KFEPPIEEYPGEIAEVQIGATKADGGSRGKVVML---GGERAFYRFEEPQPNPPVVTFDV 129
Query: 133 LGSFPVNYWDKFAKKKVRQKYSETYD 158
+ K +R+ Y + +
Sbjct: 130 F-----DIPRPGLPKPIREHYDDVME 150
>gnl|CDD|110122 pfam01098, FTSW_RODA_SPOVE, Cell cycle protein. This entry
includes the following members; FtsW, RodA, SpoVE.
Length = 356
Score = 27.6 bits (62), Expect = 7.7
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 209 FLYSLWYFTFSVMGNFNNFFFAAHLLDVAVGF 240
+YS T V+ FFF L+ + +GF
Sbjct: 18 MIYSASGVTSLVLFGDPFFFFKRQLVYLLLGF 49
>gnl|CDD|227829 COG5542, COG5542, Predicted integral membrane protein [Function
unknown].
Length = 420
Score = 27.8 bits (62), Expect = 7.8
Identities = 20/96 (20%), Positives = 34/96 (35%), Gaps = 12/96 (12%)
Query: 185 ISFILRIDWRYQ--VWKAGVTITDNAFLYSL-----WYF--TFSVMGNFNNFFFAAHLLD 235
I WR + G +YS W + N F L+
Sbjct: 253 AFEIFLGYWRQSNGFKEQGKNAP---NIYSWIPNNYWNVGLPKYWISNNIPNFLFILLII 309
Query: 236 VAVGFKTLRTILQSVTHNGKQLVLTVMLLTIIVYIY 271
+ VGF L Q ++H+ L++ + L +IV ++
Sbjct: 310 IVVGFSKLYFTKQYLSHSLAALIVLLRPLILIVCMH 345
>gnl|CDD|149504 pfam08475, Baculo_VP91_N, Viral capsid protein 91 N-terminal. This
domain is found in Baculoviridae including the
nucleopolyhedrovirus at the N-terminus of the viral
capsid protein 91 (VP91).
Length = 185
Score = 27.2 bits (61), Expect = 7.9
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 257 LVLTVMLLTIIVYIYYLCIP 276
L+L ++L II IYYL I
Sbjct: 1 LLLVAIILLIIFLIYYLFIY 20
>gnl|CDD|237164 PRK12664, PRK12664, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 527
Score = 27.8 bits (62), Expect = 8.8
Identities = 20/114 (17%), Positives = 35/114 (30%), Gaps = 46/114 (40%)
Query: 182 SGIISFILRIDWRYQVWKAGVTITDNAFLYSLWYFTFSVMGNFNNFFFAAHLLDVAVGFK 241
G I+F + IDW Y+ F V+ FNNF
Sbjct: 438 LGRINFKMDIDWIYRA------------------FLPYVILLFNNFVLYV--------RS 471
Query: 242 TLRTILQSVTHNGKQL--------------------VLTVMLLTIIVYIYYLCI 275
++LQ+V ++ L + +L + + + LC+
Sbjct: 472 ISASVLQNVLNSKTLLYFNNGEKVKEVSSYNSLGFAISASLLFLMSIVLVVLCL 525
>gnl|CDD|217486 pfam03311, Cornichon, Cornichon protein.
Length = 128
Score = 26.4 bits (59), Expect = 9.8
Identities = 18/68 (26%), Positives = 26/68 (38%), Gaps = 10/68 (14%)
Query: 209 FLYSLWYFTFSVMG-----NFNNFFFAAHLLDVAVGFKTLRTILQSVTHNGKQLVLTVML 263
FL + +F F + N ++ HLLD F+TL S + L L
Sbjct: 65 FLLTGHWFVFLLNLPLLAYNVYLYYKRTHLLDATEIFRTL-----SKHKRESFIKLAFYL 119
Query: 264 LTIIVYIY 271
L Y+Y
Sbjct: 120 LLFFYYLY 127
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
0.319 0.135 0.405
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,625,671
Number of extensions: 1392857
Number of successful extensions: 1198
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1194
Number of HSP's successfully gapped: 27
Length of query: 285
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 189
Effective length of database: 6,679,618
Effective search space: 1262447802
Effective search space used: 1262447802
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 (21.7 bits)
S2: 58 (26.1 bits)