RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11584
(573 letters)
>gnl|CDD|197548 smart00157, PRP, Major prion protein. The prion protein is a major
component of scrapie-associated fibrils in
Creutzfeldt-Jakob disease, kuru, Gerstmann-Straussler
syndrome and bovine spongiform encephalopathy.
Length = 218
Score = 34.1 bits (78), Expect = 0.13
Identities = 16/41 (39%), Positives = 17/41 (41%)
Query: 482 GGSPHKGGGKRSPHGDSGGGGGGVSPRLASKRKPGPIPKHV 522
G GGG PHG G GGG + KP KHV
Sbjct: 50 GWGQPHGGGWGQPHGGGWGQGGGTHNQWNKPSKPKTNMKHV 90
>gnl|CDD|214621 smart00327, VWA, von Willebrand factor (vWF) type A domain. VWA
domains in extracellular eukaryotic proteins mediate
adhesion via metal ion-dependent adhesion sites (MIDAS).
Intracellular VWA domains and homologues in prokaryotes
have recently been identified. The proposed VWA domains
in integrin beta subunits have recently been
substantiated using sequence-based methods.
Length = 175
Score = 32.4 bits (74), Expect = 0.34
Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 13/65 (20%)
Query: 29 NLTTFMTELKNLQ--CTGMTLLGAALKHTFDVLNMNRMQSGIDTYGQGRSPFFLEPAVIV 86
+ + L +L G T LGAAL++ + L S P V++
Sbjct: 60 SKDALLEALASLSYKLGGGTNLGAALQYALENLFSKSAGSRRG-----------APKVVI 108
Query: 87 VITDG 91
+ITDG
Sbjct: 109 LITDG 113
>gnl|CDD|238740 cd01463, vWA_VGCC_like, VWA Voltage gated Calcium channel like:
Voltage-gated calcium channels are a complex of five
proteins: alpha 1, beta 1, gamma, alpha 2 and delta. The
alpha 2 and delta subunits result from proteolytic
processing of a single gene product and carries at its
N-terminus the VWA and cache domains, The alpha 2 delta
gene family has orthologues in D. melanogaster and C.
elegans but none have been detected in aither A.
thaliana or yeast. The exact biochemical function of the
VWA domain is not known but the alpha 2 delta complex
has been shown to regulate various functional properties
of the channel complex.
Length = 190
Score = 30.8 bits (70), Expect = 1.2
Identities = 25/117 (21%), Positives = 42/117 (35%), Gaps = 14/117 (11%)
Query: 28 ENLTTFMTELKNLQCTGMTLLGAALKHTFDVLNMNRMQSGIDTYGQGRSPFFLEPAVIVV 87
N L L+ G+ AL+ F +L N + + Q I++
Sbjct: 77 SNKKVLKEALDMLEAKGIANYTKALEFAFSLLLKNLQSNHSGSRSQCNQ-------AIML 129
Query: 88 ITDGGKLSNATGVQEDFNLPMHSPIPGSEMTREPFRWDQRLFSLVLQRDMGVVACDN 144
ITDG N + + +N +S IP T + + + + M AC+N
Sbjct: 130 ITDGVP-ENYKEIFDKYNWDKNSEIPVRVFT---YLIGREVTDRREIQWM---ACEN 179
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 31.0 bits (71), Expect = 1.6
Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 9/73 (12%)
Query: 509 LASKRKPGPIPKHVQPLRRALIRMGMPAAISQSLI-------PDSMENSLSYSVLSYLKR 561
L+ R+ IP L + L R G+ I++ L+ P + Y +L L
Sbjct: 150 LSGLRQVERIPPEFAELYKRLKRSGLSPEIAEKLLKLLLEHMPPRERTAWRY-LLELLAN 208
Query: 562 M-KIQAKDEFDRN 573
M ++ +D +
Sbjct: 209 MIPVRVEDILKQG 221
>gnl|CDD|226538 COG4052, COG4052, Uncharacterized protein related to methyl
coenzyme M reductase subunit C [General function
prediction only].
Length = 310
Score = 30.6 bits (69), Expect = 2.0
Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 10/69 (14%)
Query: 427 HTMPISQMGNYQEYLKRMAAPLREVESTPVRQHMFGNPFKIDKRMMVDEADIDLVGGSPH 486
H + + G++++ +K+ L E PV + G P +ID D+ G +
Sbjct: 132 HDLAVFVFGSFEDCIKKKKPHLFEGIEIPVV--VTGGPEEIDTE--------DVPGADLY 181
Query: 487 KGGGKRSPH 495
G R H
Sbjct: 182 VGNIGRVSH 190
>gnl|CDD|219320 pfam07172, GRP, Glycine rich protein family. This family of
proteins includes several glycine rich proteins as well
as two nodulins 16 and 24. The family also contains
proteins that are induced in response to various
stresses.
Length = 91
Score = 28.6 bits (64), Expect = 2.1
Identities = 11/23 (47%), Positives = 11/23 (47%)
Query: 482 GGSPHKGGGKRSPHGDSGGGGGG 504
GG GGG G GGGGG
Sbjct: 63 GGYYGGGGGYGGGGGGYPGGGGG 85
>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 = 29.8 bits (67), Expect = 2.5
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 15/65 (23%)
Query: 27 KENLTTFMTELKNLQCTGMTLLGAALKHTFDVLNMNRMQSGIDTYGQGRSPFFLEPAVIV 86
K +L + LK G T +GAAL+ ++L + VI+
Sbjct: 62 KADLLEAIDALKK-GLGGGTNIGAALRLALELLK--------------SAKRPNARRVII 106
Query: 87 VITDG 91
++TDG
Sbjct: 107 LLTDG 111
>gnl|CDD|238728 cd01451, vWA_Magnesium_chelatase, Magnesium chelatase: Mg-chelatase
catalyses the insertion of Mg into protoporphyrin IX
(Proto). In chlorophyll biosynthesis, insertion of Mg2+
into protoporphyrin IX is catalysed by magnesium
chelatase in an ATP-dependent reaction. Magnesium
chelatase is a three sub-unit (BchI, BchD and BchH)
enzyme with a novel arrangement of domains: the
C-terminal helical domain is located behind the
nucleotide binding site. The BchD domain contains a AAA
domain at its N-terminus and a VWA domain at its
C-terminus. The VWA domain has been speculated to be
involved in mediating protein-protein interactions.
Length = 178
Score = 29.2 bits (66), Expect = 3.7
Identities = 16/56 (28%), Positives = 21/56 (37%), Gaps = 13/56 (23%)
Query: 36 ELKNLQCTGMTLLGAALKHTFDVLNMNRMQSGIDTYGQGRSPFFLEPAVIVVITDG 91
L L G T L A L +++ G+ P +IVVITDG
Sbjct: 66 RLARLPTGGGTPLAAGLLAAYELAAEQA-------RDPGQRP------LIVVITDG 108
>gnl|CDD|112426 pfam03608, EII-GUT, PTS system enzyme II sorbitol-specific factor.
Length = 168
Score = 28.4 bits (64), Expect = 6.6
Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 8/47 (17%)
Query: 385 LLPLIDDFFKVHRMKVTPEWRGNF--QKYIGTMPSYYAAYSSSIHTM 429
+LP++ FF + M T G F +KY PSYY A S H
Sbjct: 67 VLPVLSVFFLTNPMAYT---LGRFLPEKY---KPSYYDAAVSFCHPS 107
>gnl|CDD|238326 cd00583, MutH_Sau3AI, MutH is a 28kD endonuclease involved in
methyl-directed DNA mismatch repair in gram negative
bacteria. MutH is both sequence-specific and
methylation-specific, introducing a nick in the
unmethylated strand of a hemi-methylated d(GATC) DNA
duplex. MutH is homologous to the type II restriction
endonuclease Sau3AI which also recognizes the d(GATC)
sequence however, Sau3AI cleaves both strands regardless
of their methylation state. The active form of MutH is
monomeric while that of Sau3AI is homodimeric. In
addition to MutH, MutS, involved in mismatch
recognition, and MutL, involved in mediating the
interactions between MutH and MutS, are essential in
initiating mismatch repair in Escherichia coli.
Length = 210
Score = 28.5 bits (64), Expect = 7.0
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 230 NSTAWHNCRKLIYVPRSAQKGFPVGFWPIPESF 262
S WH +K++++P ++G P I E F
Sbjct: 94 TSHVWHKLKKILWIPYEGERGIPKADRIIGEPF 126
>gnl|CDD|238759 cd01482, vWA_collagen_alphaI-XII-like, Collagen: The extracellular
matrix represents a complex alloy of variable members of
diverse protein families defining structural integrity
and various physiological functions. The most abundant
family is the collagens with more than 20 different
collagen types identified thus far. Collagens are
centrally involved in the formation of fibrillar and
microfibrillar networks of the extracellular matrix,
basement membranes as well as other structures of the
extracellular matrix. Some collagens have about 15-18
vWA domains in them. The VWA domains present in these
collagens mediate protein-protein interactions.
Length = 164
Score = 28.4 bits (64), Expect = 7.2
Identities = 17/67 (25%), Positives = 24/67 (35%), Gaps = 22/67 (32%)
Query: 43 TGMTLLGAALKHTFD--VLNMNRMQSGIDTYGQGRSPFFLEPAVIVVITDGGKLSNATGV 100
G T G AL H + + G+ P V+++ITDG
Sbjct: 76 GGNTRTGKALTHVREKNFTPDAGARPGV-------------PKVVILITDGKS------- 115
Query: 101 QEDFNLP 107
Q+D LP
Sbjct: 116 QDDVELP 122
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 0.136 0.420
Gapped
Lambda K H
0.267 0.0660 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,525,709
Number of extensions: 2888459
Number of successful extensions: 2458
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2445
Number of HSP's successfully gapped: 17
Length of query: 573
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 471
Effective length of database: 6,413,494
Effective search space: 3020755674
Effective search space used: 3020755674
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 (21.8 bits)
S2: 62 (27.8 bits)