RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11447
(360 letters)
>gnl|CDD|238732 cd01455, vWA_F11C1-5a_type, Von Willebrand factor type A (vWA)
domain was originally found in the blood coagulation
protein von Willebrand factor (vWF). Typically, the vWA
domain is made up of approximately 200 amino acid
residues folded into a classic a/b para-rossmann type of
fold. The vWA domain, since its discovery, has drawn
great interest because of its widespread occurrence and
its involvement in a wide variety of important cellular
functions. These include basal membrane formation, cell
migration, cell differentiation, adhesion, haemostasis,
signaling, chromosomal stability, malignant
transformation and in immune defenses In integrins
these domains form heterodimers while in vWF it forms
multimers. There are different interaction surfaces of
this domain as seen by the various molecules it
complexes with. Ligand binding in most cases is mediated
by the presence of a metal ion dependent adhesion site
termed as the MIDAS motif that is a characteristic
feature of most, if not all A domains. Not much is known
about the functions of the members of this subgroup. The
members of this subgroup are fused to the ancient AAA
domain.
Length = 191
Score = 217 bits (554), Expect = 3e-70
Identities = 85/160 (53%), Positives = 125/160 (78%), Gaps = 2/160 (1%)
Query: 200 LEAFQDFDQRISLDIIGHSGETHSIPFVTSNNLPRDNKQRLEVIKIMHAHAQFCASGDYT 259
+EAF F+ +I DIIGHSG+ +PFV +N+ P++NK+RLE +K+MHAH+QFC SGD+T
Sbjct: 34 MEAFDGFEDKIQYDIIGHSGDGPCVPFVKTNHPPKNNKERLETLKMMHAHSQFCWSGDHT 93
Query: 260 LESIRASIQDLTTECAQHDDSILIVLSDANLDRYGIAPREMGEALNAEAASVRAYAIFIG 319
+E+ +I++L + D++I+IVLSDANL+RYGI P+++ +AL A +V A+ IFIG
Sbjct: 94 VEATEFAIKELAAK-EDFDEAIVIVLSDANLERYGIQPKKLADAL-AREPNVNAFVIFIG 151
Query: 320 SLGDQAKRLTQELPAGRGFVCMDLTEIPQILQQIFSASLL 359
SL D+A +L +ELPAG+ FVCMD +E+P I+QQIF+++LL
Sbjct: 152 SLSDEADQLQRELPAGKAFVCMDTSELPHIMQQIFTSTLL 191
Score = 99 bits (249), Expect = 5e-25
Identities = 39/68 (57%), Positives = 54/68 (79%), Gaps = 1/68 (1%)
Query: 119 KFNGYDGRLDRELEAVIMVLEAFQDFDQRIRLDIIGHSGETHSIPFVTSIKNLPRDNKQR 178
+FNGYDGRLDR LEAV+MV+EAF F+ +I+ DIIGHSG+ +PFV + + P++NK+R
Sbjct: 15 RFNGYDGRLDRSLEAVVMVMEAFDGFEDKIQYDIIGHSGDGPCVPFVKT-NHPPKNNKER 73
Query: 179 LEVIKVHH 186
LE +K+ H
Sbjct: 74 LETLKMMH 81
>gnl|CDD|235170 PRK03881, PRK03881, hypothetical protein; Provisional.
Length = 467
Score = 32.9 bits (76), Expect = 0.28
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 8/54 (14%)
Query: 282 LIVLSDANLDRYGIAPREMGEALNAEAASVRAYAIFIGSLGDQAKRLTQELPAG 335
LS L ++G+A RE E L + I S GD + RLT + P G
Sbjct: 150 YGGLSPEELYKFGMAIREAAEELGRKVV-------LIAS-GDLSHRLTPDGPYG 195
>gnl|CDD|222192 pfam13519, VWA_2, von Willebrand factor type A domain.
Length = 172
Score = 31.9 bits (73), Expect = 0.30
Identities = 22/143 (15%), Positives = 49/143 (34%), Gaps = 16/143 (11%)
Query: 214 IIGHSGETHSIPFVTSNNLPRDNKQRLEVIKIMHAHAQFCASGDYTLESIRASIQDLTTE 273
+I +G + + +T + L + G ++ +++ L
Sbjct: 43 LIAFAGSAYLVLPLTDD--RAALAAALPALSPRIMPGG----GTNLAAALALALRLLAG- 95
Query: 274 CAQHDDSILIVLSDANLDRYGIAPREMGEALNAEAASVRAYAIFIGSLGDQAKRLTQ--E 331
A +++++D P + A + A VR Y + +G+ L + +
Sbjct: 96 -AGGGSGAIVLITDG-----EDTPSLLEAASALKQAGVRVYVLGVGTDEGAEDALQRLAK 149
Query: 332 LPAGRGF-VCMDLTEIPQILQQI 353
GR D ++ +LQ I
Sbjct: 150 ATGGRYVDATADAADLDALLQAI 172
>gnl|CDD|238119 cd00198, vWFA, Von Willebrand factor type A (vWA) domain was
originally found in the blood coagulation protein von
Willebrand factor (vWF). Typically, the vWA domain is
made up of approximately 200 amino acid residues folded
into a classic a/b para-rossmann type of fold. The vWA
domain, since its discovery, has drawn great interest
because of its widespread occurrence and its involvement
in a wide variety of important cellular functions. These
include basal membrane formation, cell migration, cell
differentiation, adhesion, haemostasis, signaling,
chromosomal stability, malignant transformation and in
immune defenses In integrins these domains form
heterodimers while in vWF it forms multimers. There are
different interaction surfaces of this domain as seen by
the various molecules it complexes with. Ligand binding
in most cases is mediated by the presence of a metal ion
dependent adhesion site termed as the MIDAS motif that
is a characteristic feature of most, if not all A
domains.
Length = 161
Score = 30.6 bits (69), Expect = 0.72
Identities = 18/142 (12%), Positives = 48/142 (33%), Gaps = 12/142 (8%)
Query: 200 LEAFQDFDQRISLDIIGHSGETHS-IPFVTSNNLPRDNKQRLEVIKIMHAHAQFCASGDY 258
+ + + ++ +P T + ++++ + A + G
Sbjct: 29 VSSLSASPPGDRVGLVTFGSNARVVLPLTTDTDKA-------DLLEAIDALKKGLGGGTN 81
Query: 259 TLESIRASIQDLTTECAQHDDSILIVLSDANLDRYGIAPREMGEALNAEAASVRAYAIFI 318
++R +++ L + + ++I+L+D + E A + Y I I
Sbjct: 82 IGAALRLALELLKSAKRPNARRVIILLTDGEPNDGPELLAE--AARELRKLGITVYTIGI 139
Query: 319 GSLGDQA--KRLTQELPAGRGF 338
G ++ K + + G F
Sbjct: 140 GDDANEDELKEIADKTTGGAVF 161
>gnl|CDD|222505 pfam14028, SpaB_C, SpaB C-terminal domain. This presumed domain is
found at the C-terminus of the SpaB protein. SpaB is
involved in the synthesis of the lantibiotic subtilin.
This family of proteins is found in bacteria and
eukaryotes. Proteins in this family are typically
between 317 and 1029 amino acids in length. The family
is often found in association with pfam04737, pfam04738.
This domain is found in isolation in some proteins. This
domain is also found in EpiB involved in epidermin
biosynthesis.
Length = 259
Score = 30.2 bits (68), Expect = 1.5
Identities = 24/108 (22%), Positives = 36/108 (33%), Gaps = 5/108 (4%)
Query: 248 AHAQFCASGDYTLESIRASIQDLTTECAQHDDSILIVLS--DANLDRYGIAPREMGEALN 305
A F A L +RA+ L D L+ S D +G+ P E G+ L
Sbjct: 104 AEELFAADSRLALAQLRAARARLGLA---LDLLALLAASLLDLAAGAFGLDPEEGGDWLA 160
Query: 306 AEAASVRAYAIFIGSLGDQAKRLTQELPAGRGFVCMDLTEIPQILQQI 353
AA A + +Q + LP G + + Q+
Sbjct: 161 RLAAQREGRAELDRARREQLLAALRALPGGDAVARAWAALLAEAWQRR 208
>gnl|CDD|234734 PRK00349, uvrA, excinuclease ABC subunit A; Reviewed.
Length = 943
Score = 30.0 bits (69), Expect = 2.3
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 173 RDNKQRLEVIKVHHNNLRN 191
+ N + L++ NNL+N
Sbjct: 609 KGNGKFLKLKGARENNLKN 627
>gnl|CDD|219330 pfam07201, HrpJ, HrpJ-like domain. This family represents a
conserved region approximately 200 residues long within
a number of bacterial hypersensitivity response
secretion protein HrpJ and similar proteins. HrpJ forms
part of a type III secretion system through which, in
phytopathogenic bacterial species, virulence factors
are thought to be delivered to plant cells. This family
also includes the InvE invasion protein from
Salmonella. This protein is involved in host parasite
interactions and mutations in the InvE gene render
Salmonella typhimurium non-invasive. InvE S.
typhimurium mutants fail to elicit a rapid Ca2+
increase in cultured cells, an important event in the
infection procedure and internalisation of S.
typhimurium into epithelial cells. This family includes
bacterial SepL and SsaL proteins. SepL plays an
essential role in the infection process of
enterohemorrhagic Escherichia coli and is thought to be
responsible for the secretion of EspA, EspD, and EspB.
SsaL of Salmonella typhimurium is thought to be a
component of the type III secretion system.
Length = 161
Score = 28.1 bits (63), Expect = 4.8
Identities = 18/89 (20%), Positives = 30/89 (33%), Gaps = 1/89 (1%)
Query: 1 MGLKAFKQKLKEIQMSEYDAKVYSEYSLPVQNQQNDQHRDLFSVHVIDNPSPESELALLS 60
L K+ + SE ++ + + ++ R+L + S LA L
Sbjct: 7 KALSQRKRSDRRKSESEKLEELSDLLERVLDLEAEEKLRELRQLLKSGRSSLPQLLAYLE 66
Query: 61 SYGPDVPRDTLIRLVRAFGEFRELSDKSL 89
S PD P D + L + R L
Sbjct: 67 SLFPD-PSDQDLALRALLQQARPLKRALK 94
>gnl|CDD|133022 cd04179, DPM_DPG-synthase_like, DPM_DPG-synthase_like is a member
of the Glycosyltransferase 2 superfamily. DPM1 is the
catalytic subunit of eukaryotic dolichol-phosphate
mannose (DPM) synthase. DPM synthase is required for
synthesis of the glycosylphosphatidylinositol (GPI)
anchor, N-glycan precursor, protein O-mannose, and
C-mannose. In higher eukaryotes,the enzyme has three
subunits, DPM1, DPM2 and DPM3. DPM is synthesized from
dolichol phosphate and GDP-Man on the cytosolic surface
of the ER membrane by DPM synthase and then is flipped
onto the luminal side and used as a donor substrate. In
lower eukaryotes, such as Saccharomyces cerevisiae and
Trypanosoma brucei, DPM synthase consists of a single
component (Dpm1p and TbDpm1, respectively) that
possesses one predicted transmembrane region near the C
terminus for anchoring to the ER membrane. In contrast,
the Dpm1 homologues of higher eukaryotes, namely
fission yeast, fungi, and animals, have no
transmembrane region, suggesting the existence of
adapter molecules for membrane anchoring. This family
also includes bacteria and archaea DPM1_like enzymes.
However, the enzyme structure and mechanism of function
are not well understood. The
UDP-glucose:dolichyl-phosphate glucosyltransferase
(DPG_synthase) is a transmembrane-bound enzyme of the
endoplasmic reticulum involved in protein N-linked
glycosylation. This enzyme catalyzes the transfer of
glucose from UDP-glucose to dolichyl phosphate. This
protein family belongs to Glycosyltransferase 2
superfamily.
Length = 185
Score = 28.3 bits (64), Expect = 5.0
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 46 VIDNPSPESELALLSSYGPDVPRDTLIRLVRAFG 79
V+D+ S + + VPR +IRL R FG
Sbjct: 33 VVDDGSTDGTAEIARELAARVPRVRVIRLSRNFG 66
>gnl|CDD|221287 pfam11881, DUF3401, Domain of unknown function (DUF3401). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 231 to 250 amino acids in length. This domain
is found associated with pfam02145, pfam00595.
Length = 240
Score = 28.6 bits (64), Expect = 5.0
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 9/50 (18%)
Query: 40 DLFSVHVIDNPSPESELALLSSYGPDVPRDTLIRLVRAFGEFRELSDKSL 89
DL + + D+P PE E GP PR +L R LSD+S+
Sbjct: 38 DLKKLIIPDSPPPEEERDKTPFPGPPSPRRSL---------QRTLSDESI 78
>gnl|CDD|236843 PRK11092, PRK11092, bifunctional (p)ppGpp synthetase II/
guanosine-3',5'-bis pyrophosphate
3'-pyrophosphohydrolase; Provisional.
Length = 702
Score = 28.9 bits (65), Expect = 5.5
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 101 HIVKHLQ--EGVLGQHENTRKFNGYDGRLDRELEAVIMVLEAFQDFDQRIRLDIIGHSG 157
I+ H+ +G++ HE+ R GY ++ + AV E Q+F I++++ H G
Sbjct: 581 PIIAHVSPGKGLVIHHESCRNIRGYQKEPEKFM-AVEWDKETEQEFIAEIKVEMFNHQG 638
>gnl|CDD|239823 cd04331, RNAP_E_N, RNAP_E_N: RpoE, N-terminal ribonucleoprotein
(RNP) domain. RpoE (subunit E) is a subunit of the
archaeal RNA polymerase (RNAP) that is homologous to
Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP
III, and Rpa43 of eukaryotic RNAP I. RpoE
heterodimerizes with RpoF, another RNA polymerase
subunit. RpoE has an elongated two-domain structure that
includes an N-terminal RNP domain and a C-terminal
oligonucleotide-binding (OB) domain. Both domains of
RpoE bind single-stranded RNA.
Length = 80
Score = 26.4 bits (59), Expect = 6.4
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 123 YDGRLDRELEAVIMVLEA 140
Y+GRLD++L ++ VL+
Sbjct: 33 YEGRLDKDLGKIVSVLDV 50
>gnl|CDD|215980 pfam00535, Glycos_transf_2, Glycosyl transferase family 2.
Diverse family, transferring sugar from UDP-glucose,
UDP-N-acetyl- galactosamine, GDP-mannose or
CDP-abequose, to a range of substrates including
cellulose, dolichol phosphate and teichoic acids.
Length = 168
Score = 27.4 bits (61), Expect = 8.7
Identities = 12/44 (27%), Positives = 21/44 (47%)
Query: 36 DQHRDLFSVHVIDNPSPESELALLSSYGPDVPRDTLIRLVRAFG 79
+Q F + V+D+ S + + + Y + PR +IRL G
Sbjct: 22 NQTYKNFEIIVVDDGSTDGTVEIAEEYAKNDPRVRVIRLEENLG 65
>gnl|CDD|215851 pfam00310, GATase_2, Glutamine amidotransferases class-II.
Length = 223
Score = 27.7 bits (62), Expect = 8.8
Identities = 21/108 (19%), Positives = 34/108 (31%), Gaps = 27/108 (25%)
Query: 208 QRISLDIIGHSGETHSIPFVTSNNLPRDNKQRLEVIKIMHAHAQFCASGDYTLE------ 261
R ++ H+GE I N L R + + + + + D LE
Sbjct: 108 FRREGWVLAHNGE---I-----NTL-RGLRNWMRAREGVFNSGSDSEAFDNLLELLVRAG 158
Query: 262 ---SIRASIQDLTTECAQH----DDSILIVLSD-----ANLDRYGIAP 297
+ + A D +V +D A LDR G+ P
Sbjct: 159 RSPDMDPEERAFYEYLAGLMEPWDGPAALVFTDGRYVGATLDRNGLRP 206
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 0.383
Gapped
Lambda K H
0.267 0.0624 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,441,557
Number of extensions: 1808227
Number of successful extensions: 1603
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1599
Number of HSP's successfully gapped: 30
Length of query: 360
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 262
Effective length of database: 6,590,910
Effective search space: 1726818420
Effective search space used: 1726818420
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: 60 (27.1 bits)