RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7945
(288 letters)
>gnl|CDD|218540 pfam05291, Bystin, Bystin. Trophinin and tastin form a cell
adhesion molecule complex that potentially mediates an
initial attachment of the blastocyst to uterine
epithelial cells at the time of implantation. Trophinin
and tastin bind to an intermediary cytoplasmic protein
called bystin. Bystin may be involved in implantation
and trophoblast invasion because bystin is found with
trophinin and tastin in the cells at human implantation
sites and also in the intermediate trophoblasts at
invasion front in the placenta from early pregnancy.
This family also includes the yeast protein ENP1. ENP1
is an essential protein in Saccharomyces cerevisiae and
is localised in the nucleus. It is thought that ENP1
plays a direct role in the early steps of rRNA
processing as enp1 defective yeast cannot synthesise 20S
pre-rRNA and hence 18S rRNA, which leads to reduced
formation of 40S ribosomal subunits.
Length = 303
Score = 145 bits (369), Expect = 6e-42
Identities = 58/71 (81%), Positives = 67/71 (94%)
Query: 179 TAAALLKIAEMEYNGANSIFLRILLDKKYALPYRVVDAIVFHFLRFEREDRELPVLWHQS 238
++AALLK+AEM+YNGA S+F+R+LLDKKYALPYRVVDA+VFHFLRFE E+R LPVLWHQS
Sbjct: 189 SSAALLKLAEMDYNGATSVFIRVLLDKKYALPYRVVDALVFHFLRFENEERVLPVLWHQS 248
Query: 239 LLTFAQRYKQD 249
LLTFAQRYK D
Sbjct: 249 LLTFAQRYKND 259
Score = 112 bits (282), Expect = 3e-29
Identities = 45/87 (51%), Positives = 55/87 (63%), Gaps = 2/87 (2%)
Query: 95 FMNKHPGPQLTLRDILREKITEKHTELDTQFSDAASVQI--DNLDPKIKQMYEGVRDVLS 152
FMNK G TL DI+ EKI EK D LDPK+ ++YE V ++LS
Sbjct: 1 FMNKDDGGTRTLADIIMEKIQEKEASGQGAGRDEEGNPSPEIKLDPKVIEVYEKVGELLS 60
Query: 153 KYRSGKLPKAFKIVPKLRNWEQILYVT 179
+Y+SGKLPKAFKI+PKL NWE ILY+T
Sbjct: 61 RYKSGKLPKAFKIIPKLSNWEDILYLT 87
Score = 86.2 bits (214), Expect = 2e-19
Identities = 33/41 (80%), Positives = 40/41 (97%)
Query: 1 MLHSAAALLKIAEMEYNGANSIFLRILLDKKYALPYRVVDA 41
+LHS+AALLK+AEM+YNGA S+F+R+LLDKKYALPYRVVDA
Sbjct: 186 VLHSSAALLKLAEMDYNGATSVFIRVLLDKKYALPYRVVDA 226
>gnl|CDD|240453 cd12873, SPRY_DDX1, SPRY domain associated with DEAD box gene DDX1.
This SPRY domain is associated with the DEAD box gene,
DDX1, an RNA-dependent ATPase involved in HIV-1 Rev
function and virus replication. It is suggested that
DDX1 acts as a cellular cofactor by promoting
oligomerization of Rev on the Rev response element
(RRE). DDX1 RNA is overexpressed in breast cancer, data
showing a strong and independent association between
poor prognosis and deregulation of the DEAD box protein
DDX1, thus potentially serving as an effective
prognostic biomarker for early recurrence in primary
breast cancer. DDX1 also interacts with RelA and
enhances nuclear factor kappaB-mediated transcription.
DEAD-box proteins are associated with all levels of RNA
metabolism and function, and have been implicated in
translation initiation, transcription, RNA splicing,
ribosome assembly, RNA transport, and RNA decay.
Length = 155
Score = 34.9 bits (81), Expect = 0.017
Identities = 18/34 (52%), Positives = 21/34 (61%), Gaps = 4/34 (11%)
Query: 159 LPKAFKIVPKLRNWEQILYVTAAALLKIAEMEYN 192
L AF I PKLRN Q L+ A LK AE+E+N
Sbjct: 121 LGVAFDIPPKLRN--QALF--PAVCLKNAEVEFN 150
>gnl|CDD|240181 cd05381, SCP_PR-1_like, SCP_PR-1_like: SCP-like extracellular
protein domain, PR-1 like subfamily. The wider family of
SCP containing proteins includes plant
pathogenesis-related protein 1 (PR-1), which accumulates
after infections with pathogens, and may act as an
anti-fungal agent or be involved in cell wall loosening.
It also includes CRISPs, mammalian cysteine-rich
secretory proteins, and allergen 5 from vespid venom. It
has been proposed that SCP domains may function as
endopeptidases.
Length = 136
Score = 30.3 bits (69), Expect = 0.51
Identities = 20/63 (31%), Positives = 26/63 (41%), Gaps = 17/63 (26%)
Query: 232 PVLWHQSLLTFAQRYKQDTSAQNRGKPCSI------YSGLNPIQPLPWKYDGNFRAPS-V 284
P+ W +L +AQRY A R C++ Y G N L W GN+ A V
Sbjct: 19 PLKWDDTLAAYAQRY-----ANQRRGDCALVHSNGPY-GEN----LFWGSGGNWSAADAV 68
Query: 285 EMW 287
W
Sbjct: 69 ASW 71
>gnl|CDD|226223 COG3700, AphA, Acid phosphatase (class B) [General function
prediction only].
Length = 237
Score = 30.2 bits (68), Expect = 1.00
Identities = 14/54 (25%), Positives = 24/54 (44%)
Query: 10 KIAEMEYNGANSIFLRILLDKKYALPYRVVDAIKEQTTKLHTGDSDNDLDADDD 63
K ++ N + DK Y I+++ ++H GDSDND+ A +
Sbjct: 149 KTLAKNFHITNMNPVIFAGDKPKPGQYTKTQWIQDKNIRIHYGDSDNDITAAKE 202
>gnl|CDD|183905 PRK13233, nifH, nitrogenase reductase; Reviewed.
Length = 275
Score = 30.2 bits (68), Expect = 1.0
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 65 KSTTSDDPNFSGDYYNE--IIIDPEDEKALSLFMNKHPGPQLTLRDILREKITEKHTE-- 120
KSTT+ + + Y+++ + I D KA S + PQ T+ D LRE EK T
Sbjct: 15 KSTTTQNTAAAMAYFHDKKVFIHGCDPKADSTRLILGGKPQTTMMDTLRELGEEKVTPDK 74
Query: 121 -LDTQFSDAASVQ 132
+ T F D V+
Sbjct: 75 VIKTGFKDIRCVE 87
>gnl|CDD|222798 PHA00454, PHA00454, ATP-dependent DNA ligase.
Length = 315
Score = 30.0 bits (68), Expect = 1.3
Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 14/94 (14%)
Query: 81 EIIIDPEDEKALSLFMNKHPGPQLTLRDILREKITEKHTELDTQFSDAASV----QIDNL 136
+++ ED +SL M +H + + E E+D S++ V + L
Sbjct: 134 DVLESGEDYDVMSLLMYEH-------VRAMVPLLMEYFPEIDWFLSESYEVYDMESLQEL 186
Query: 137 DPKIKQM-YEG--VRDVLSKYRSGKLPKAFKIVP 167
K + +EG V+D YR GK +K+ P
Sbjct: 187 YEKKRAEGHEGLVVKDPSLIYRRGKKSGWWKMKP 220
>gnl|CDD|215205 PLN02357, PLN02357, serine acetyltransferase.
Length = 360
Score = 28.7 bits (64), Expect = 3.5
Identities = 21/72 (29%), Positives = 28/72 (38%), Gaps = 9/72 (12%)
Query: 30 KKYALPYRVVDAIKEQTTKLHTGDSDNDLDADDD--------DKSTTSDDPNFSGDYYNE 81
K + P T +HT ++DLD DDD KS +P S YY
Sbjct: 61 KNFCRPSFS-PFSGNHTKTIHTRPVEDDLDRDDDVWLKIQEEAKSDVEQEPILSSYYYAS 119
Query: 82 IIIDPEDEKALS 93
I+ E AL+
Sbjct: 120 ILSHRSLESALA 131
>gnl|CDD|147601 pfam05505, Ebola_NP, Ebola nucleoprotein. This family consists of
Ebola and Marburg virus nucleoproteins. These proteins
are responsible for encapsidation of genomic RNA. It has
been found that nucleoprotein DNA vaccines can offer
protection from the virus.
Length = 717
Score = 28.8 bits (64), Expect = 4.1
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 4/50 (8%)
Query: 30 KKYALPYRVVDAIKEQTTKLHTGDSDND----LDADDDDKSTTSDDPNFS 75
K +L Y+ + ++E+ D D+ L++DDD S + +
Sbjct: 532 GKTSLRYQELTPVQEEDEPEDQTDDDDSSLPPLESDDDPGSDNEQGVDLT 581
>gnl|CDD|221568 pfam12419, DUF3670, SNF2 Helicase protein. This domain family is
found in bacteria, archaea and eukaryotes, and is
approximately 140 amino acids in length. The family is
found in association with pfam00271, pfam00176. Most of
the proteins in this family are annotated as SNF2
helicases but there is little accompanying literature to
confirm this.
Length = 141
Score = 27.6 bits (62), Expect = 4.7
Identities = 10/31 (32%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 82 IIIDPED-EKALSLFMNKHPGPQLTLRDILR 111
+ +DPE+ AL L+L D LR
Sbjct: 107 VELDPEELRAALKFLEKAKKEGGLSLGDALR 137
>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota). DNA
Topoisomerase I (eukaryota), DNA topoisomerase V,
Vaccina virus topoisomerase, Variola virus
topoisomerase, Shope fibroma virus topoisomeras.
Length = 391
Score = 28.5 bits (64), Expect = 4.9
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 78 YYNEIIIDPEDEKALSLFM-NKHPGPQL 104
YYNE+ +D + K L +FM K PG L
Sbjct: 172 YYNEVEVDKQVFKNLKIFMKPKKPGDDL 199
>gnl|CDD|182379 PRK10325, PRK10325, heat shock protein GrpE; Provisional.
Length = 197
Score = 27.7 bits (61), Expect = 5.4
Identities = 13/48 (27%), Positives = 26/48 (54%)
Query: 112 EKITEKHTELDTQFSDAASVQIDNLDPKIKQMYEGVRDVLSKYRSGKL 159
E I ++H E++ +A++ Q+D D KI + + + ++ R G L
Sbjct: 16 EIIMDQHEEIEAVEPEASAEQVDPRDEKIANLEAQLAEAQTRERDGIL 63
>gnl|CDD|153307 cd07623, BAR_SNX1_2, The Bin/Amphiphysin/Rvs (BAR) domain of
Sorting Nexins 1 and 2. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs. This
subfamily consists of SNX1, SNX2, and similar proteins.
SNX1 and SNX2 are components of the retromer complex, a
membrane coat multimeric complex required for endosomal
retrieval of lysosomal hydrolase receptors to the Golgi.
The retromer consists of a cargo-recognition subcomplex
and a subcomplex formed by a dimer of sorting nexins
(SNX1 and/or SNX2), which ensures efficient cargo
sorting by facilitating proper membrane localization of
the cargo-recognition subcomplex. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 224
Score = 28.0 bits (63), Expect = 5.6
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 113 KITEKHTELDTQFSDAASVQIDNLDPKIKQMYEGVRDVLSKYR 155
KIT K E D F + QI+NLD ++++++ V + L +R
Sbjct: 2 KITIKMDETDQWFEEKQQ-QIENLDQQLRKLHASV-ESLVNHR 42
>gnl|CDD|178346 PLN02745, PLN02745, Putative pectinesterase/pectinesterase
inhibitor.
Length = 596
Score = 27.9 bits (62), Expect = 6.8
Identities = 22/93 (23%), Positives = 38/93 (40%), Gaps = 11/93 (11%)
Query: 89 EKALSLFMNKHPGPQLTLRDILREKITEKHTELDTQFSDAASVQIDNLDPK--------- 139
E L K P +D+L+ I + +LD S + +N D K
Sbjct: 96 ENTLKKGTEKDP-SLAQPKDLLKSAIKAVNDDLDKVLKKVLSFKFENPDEKDAIEDCKLL 154
Query: 140 IKQMYEGVRDVLSKYRSGKLPKAFKIVPKLRNW 172
++ E ++ +S+ + ++ K K VP L NW
Sbjct: 155 VEDAKEELKASISRI-NDEVNKLAKNVPDLNNW 186
>gnl|CDD|233522 TIGR01672, AphA, HAD superfamily (subfamily IIIB) phosphatase,
TIGR01672. This family of proteins is a member of the
IIIB subfamily (pfam02767) of the haloacid dehalogenase
(HAD) superfamily of hydrolases. All characterized
members of subfamily III and most characterized members
of the HAD superfamily are phosphatases. HAD superfamily
phosphatases contain active site residues in several
conserved catalytic motifs, all of which are found
conserved here. The AphA gene from E. coli has been
characterized and shown to be an active phosphatase
enzyme. This family has been previously described as the
"class B non-specific bacterial acid phosphatase"
(B-NSAP) family where it is noted that the enzyme is
secreted and has a broad substrate range. The
possibility exists, however, that the enzyme is specific
for an as yet undefined substrate. Supporting evidence
for the inclusion in the HAD superfamily, whose
phosphatase members are magnesium dependent, is the
inhibition by EDTA and calcium ions, and stimulation by
magnesium ion.
Length = 237
Score = 27.6 bits (61), Expect = 7.3
Identities = 13/54 (24%), Positives = 23/54 (42%)
Query: 10 KIAEMEYNGANSIFLRILLDKKYALPYRVVDAIKEQTTKLHTGDSDNDLDADDD 63
K ++ + DK Y I+++ ++H GDSDND+ A +
Sbjct: 149 KTLAKNFHIPAMNPVIFAGDKPGQYQYTKTQWIQDKNIRIHYGDSDNDITAAKE 202
>gnl|CDD|200478 cd11339, AmyAc_bac_CMD_like_2, Alpha amylase catalytic domain
found in bacterial cyclomaltodextrinases and related
proteins. Cyclomaltodextrinase (CDase; EC3.2.1.54),
neopullulanase (NPase; EC 3.2.1.135), and maltogenic
amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of
alpha-(1,4) glycosidic linkages on a number of
substrates including cyclomaltodextrins (CDs),
pullulan, and starch. These enzymes hydrolyze CDs and
starch to maltose and pullulan to panose by cleavage of
alpha-1,4 glycosidic bonds whereas alpha-amylases
essentially lack activity on CDs and pullulan. They
also catalyze transglycosylation of oligosaccharides to
the C3-, C4- or C6-hydroxyl groups of various acceptor
sugar molecules. Since these proteins are nearly
indistinguishable from each other, they are referred to
as cyclomaltodextrinases (CMDs). This group of CMDs is
bacterial. The Alpha-amylase family comprises the
largest family of glycoside hydrolases (GH), with the
majority of enzymes acting on starch, glycogen, and
related oligo- and polysaccharides. These proteins
catalyze the transformation of alpha-1,4 and alpha-1,6
glucosidic linkages with retention of the anomeric
center. The protein is described as having 3 domains:
A, B, C. A is a (beta/alpha) 8-barrel; B is a loop
between the beta 3 strand and alpha 3 helix of A; C is
the C-terminal extension characterized by a Greek key.
The majority of the enzymes have an active site cleft
found between domains A and B where a triad of
catalytic residues (Asp, Glu and Asp) performs
catalysis. Other members of this family have lost the
catalytic activity as in the case of the human 4F2hc,
or only have 2 residues that serve as the catalytic
nucleophile and the acid/base, such as Thermus A4
beta-galactosidase with 2 Glu residues (GH42) and human
alpha-galactosidase with 2 Asp residues (GH31). The
family members are quite extensive and include: alpha
amylase, maltosyltransferase, cyclodextrin
glycotransferase, maltogenic amylase, neopullulanase,
isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 344
Score = 27.6 bits (62), Expect = 8.3
Identities = 8/29 (27%), Positives = 11/29 (37%)
Query: 46 TTKLHTGDSDNDLDADDDDKSTTSDDPNF 74
T + + GD ND D D + D
Sbjct: 10 TDRFYDGDPSNDNGGGDGDPRSNPTDNGP 38
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 27.7 bits (62), Expect = 9.8
Identities = 21/71 (29%), Positives = 30/71 (42%), Gaps = 5/71 (7%)
Query: 28 LDKKYALPYRVVDAIKEQTTKLHTGDSDNDLDA-----DDDDKSTTSDDPNFSGDYYNEI 82
LDK L Y + Q D D+DLD DDDD+ DD + D +E
Sbjct: 112 LDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEE 171
Query: 83 IIDPEDEKALS 93
+ ++ + LS
Sbjct: 172 KKEAKELEKLS 182
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
0.318 0.136 0.399
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: 15,187,282
Number of extensions: 1489543
Number of successful extensions: 1465
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1449
Number of HSP's successfully gapped: 39
Length of query: 288
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 192
Effective length of database: 6,679,618
Effective search space: 1282486656
Effective search space used: 1282486656
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: 58 (26.2 bits)