RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16628
(107 letters)
>gnl|CDD|238756 cd01479, Sec24-like, Sec24-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
24 is very similar to Sec23. 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 carry a partial MIDAS motif and
have the overall Para-Rossmann type fold that is
characteristic of this superfamily.
Length = 244
Score = 74.2 bits (183), Expect = 2e-17
Identities = 26/56 (46%), Positives = 38/56 (67%), Gaps = 1/56 (1%)
Query: 53 EVLLNQLKSMPGDR-RTSIAIITYDSAVHFYSLAEGQTQPSQMILTDIDDIFLPSP 107
E LL+ L ++PGD RT + IT+DS +HF++L QP M+++D+DD FLP P
Sbjct: 27 EALLSNLDNLPGDDPRTRVGFITFDSTLHFFNLKSSLEQPQMMVVSDLDDPFLPLP 82
>gnl|CDD|238745 cd01468, trunk_domain, trunk domain. COPII-coated vesicles carry
proteins from the endoplasmic reticulum to the Golgi
complex. This vesicular transport can be reconstituted
by using three cytosolic components containing five
proteins: the small GTPase Sar1p, the Sec23p/24p
complex, and the Sec13p/Sec31p complex. This domain is
known as the trunk domain and has an alpha/beta vWA fold
and forms the dimer interface. Some members of this
family possess a partial MIDAS motif that is a
characteristic feature of most vWA domain proteins.
Length = 239
Score = 66.5 bits (163), Expect = 1e-14
Identities = 29/60 (48%), Positives = 40/60 (66%), Gaps = 1/60 (1%)
Query: 48 QALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAEGQTQPSQMILTDIDDIFLPSP 107
QAL+ E LL L +PGD R + +ITYDS VHFY+L+ QP +++D+ D+FLP P
Sbjct: 23 QALK-ESLLASLDLLPGDPRARVGLITYDSTVHFYNLSSDLAQPKMYVVSDLKDVFLPLP 81
>gnl|CDD|147125 pfam04811, Sec23_trunk, Sec23/Sec24 trunk domain. COPII-coated
vesicles carry proteins from the endoplasmic reticulum
to the Golgi complex. This vesicular transport can be
reconstituted by using three cytosolic components
containing five proteins: the small GTPase Sar1p, the
Sec23p/24p complex, and the Sec13p/Sec31p complex. This
domain is known as the trunk domain and has an
alpha/beta vWA fold and forms the dimer interface.
Length = 241
Score = 65.0 bits (159), Expect = 4e-14
Identities = 24/55 (43%), Positives = 36/55 (65%)
Query: 53 EVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAEGQTQPSQMILTDIDDIFLPSP 107
E LL L +PGD R + IT+DS VHF++L+ QP ++++D+ D+FLP P
Sbjct: 27 ESLLQSLDLLPGDPRALVGFITFDSTVHFFNLSSSLRQPKMLVVSDLQDMFLPLP 81
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 39.3 bits (91), Expect = 1e-04
Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 29/98 (29%)
Query: 32 PLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDR---------RTSIAIITYDSAVHFY 82
P YF+ V C Y A+ + L+ G R +T IAIIT++S+++FY
Sbjct: 952 PPYFVFV----VECSYNAIYNNITYTILE---GIRYAVQNVKCPQTKIAIITFNSSIYFY 1004
Query: 83 SLAEGQTQPSQ-------------MILTDIDDIFLPSP 107
G+ + ++++D+DD FLP P
Sbjct: 1005 HCKGGKGVSGEEGDGGGGSGNHQVIVMSDVDDPFLPLP 1042
>gnl|CDD|227361 COG5028, COG5028, Vesicle coat complex COPII, subunit SEC24/subunit
SFB2/subunit SFB3 [Intracellular trafficking and
secretion].
Length = 861
Score = 37.5 bits (87), Expect = 5e-04
Identities = 22/56 (39%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 53 EVLLNQLKSMPG-DRRTSIAIITYDSAVHFYSLAEGQTQPSQMILTDIDDIFLPSP 107
+L L +P D RT IAII +DS++HF+ L+ +I++D+D+ FLP P
Sbjct: 300 RAILENLDQIPNFDPRTKIAIICFDSSLHFFKLSPD-LDEQMLIVSDLDEPFLPFP 354
>gnl|CDD|238741 cd01464, vWA_subfamily, VWA subfamily: 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. Members of this subgroup have no assigned
function. This subfamily is typified by the presence of
a conserved MIDAS motif.
Length = 176
Score = 31.2 bits (71), Expect = 0.058
Identities = 14/59 (23%), Positives = 21/59 (35%), Gaps = 15/59 (25%)
Query: 48 QALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAEGQTQPSQMILTDIDDIFLPS 106
Q LQ E+ + I++IT+DSA P LT ++ P
Sbjct: 29 QMLQSELRQDPYAL----ESVEISVITFDSAAR-------VIVP----LTPLESFQPPR 72
>gnl|CDD|226696 COG4245, TerY, Uncharacterized protein encoded in toxicity
protection region of plasmid R478, contains von
Willebrand factor (vWF) domain [General function
prediction only].
Length = 207
Score = 28.6 bits (64), Expect = 0.57
Identities = 16/82 (19%), Positives = 28/82 (34%), Gaps = 19/82 (23%)
Query: 30 KCPLYFMV-----VKGYACYCKYQALQREVLLNQLKSMP-GDRRTSIAIITYDSAVHFYS 83
+ P Y ++ + G LQ +++ LK P R ++I+T+
Sbjct: 3 RLPCYLLLDTSGSMIGEPIEALNAGLQM--MIDTLKQDPYALERVELSIVTFGGPARVI- 59
Query: 84 LAEGQTQPSQMILTDIDDIFLP 105
QP TD + P
Sbjct: 60 ------QP----FTDAANFNPP 71
>gnl|CDD|177811 PLN02150, PLN02150, terpene synthase/cyclase family protein.
Length = 96
Score = 26.7 bits (59), Expect = 1.5
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 37 VVKGYACYCKYQALQREVLLNQLKSMPGD 65
V G CY K + +E +++LK M D
Sbjct: 6 VANGVNCYMKQHGVTKEEAVSELKKMIRD 34
>gnl|CDD|222021 pfam13279, 4HBT_2, Thioesterase-like superfamily. This family
contains a wide variety of enzymes, principally
thioesterases. These enzymes are part of the Hotdog fold
superfamily.
Length = 120
Score = 25.1 bits (55), Expect = 5.8
Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 1/62 (1%)
Query: 41 YACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHF-YSLAEGQTQPSQMILTDI 99
A Y +Y RE L + R ++ +S + + L G ++ L D
Sbjct: 14 NARYLRYFDEAREDFLARTGLGELLRAAGWGLVVVESHIRYLRELKLGDELEVRLRLLDW 73
Query: 100 DD 101
D+
Sbjct: 74 DE 75
>gnl|CDD|150203 pfam09450, DUF2019, Domain of unknown function (DUF2019).
Protein of unknown function found in bacteria.
Length = 106
Score = 24.7 bits (54), Expect = 7.4
Identities = 6/16 (37%), Positives = 12/16 (75%)
Query: 55 LLNQLKSMPGDRRTSI 70
+ ++LKS GD+R ++
Sbjct: 37 ISDELKSRDGDQRRAL 52
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
0.326 0.140 0.435
Gapped
Lambda K H
0.267 0.0603 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,401,154
Number of extensions: 433098
Number of successful extensions: 406
Number of sequences better than 10.0: 1
Number of HSP's gapped: 404
Number of HSP's successfully gapped: 13
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.5 bits)