RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16076
(161 letters)
>gnl|CDD|99724 cd06403, PB1_Par6, The PB1 domain is an essential part of Par6
protein which in complex with Par3 and aPKC proteins is
crucial for establishment of apical-basal polarity of
animal cells. The PB1 domain is a modular domain
mediating specific protein-protein interactions which
play a role in many critical cell processes. A
canonical PB1-PB1 interaction, which involves
heterodimerization of two PB1 domains, is required for
the formation of macromolecular signaling complexes
ensuring specificity and fidelity during cellular
signaling. The interaction between two PB1 domain
depends on the type of PB1. There are three types of
PB1 domains: type I which contains an OPCA motif,
acidic aminoacid cluster, type II which contains a
basic cluster, and type I/II which contains both an
OPCA motif and a basic cluster. Interactions of PB1
domains with other protein domains have been described
as noncanonical PB1-interactions. The PB1 domain module
is conserved in amoebas, fungi, animals, and plants.
The Par6 protein contains a type II PB1 domain.
Length = 80
Score = 84.7 bits (210), Expect = 2e-22
Identities = 33/69 (47%), Positives = 42/69 (60%), Gaps = 2/69 (2%)
Query: 32 FDAEFRRFSVPKPDISTYNEFKILVEKLHHLDEIPFHLTYIATDGDLLPINNDSNLGKAL 91
FDAEFRRFS+ + + +F L+E LHH+ + F + Y GDLLPINND N KAL
Sbjct: 7 FDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPNVDFLIGYTDPHGDLLPINNDDNFLKAL 66
Query: 92 L--NSFLRV 98
N LR+
Sbjct: 67 SSANPLLRI 75
>gnl|CDD|214770 smart00666, PB1, PB1 domain. Phox and Bem1p domain, present in
many eukaryotic cytoplasmic signalling proteins. The
domain adopts a beta-grasp fold, similar to that found
in ubiquitin and Ras-binding domains. A motif,
variously termed OPR, PC and AID, represents the most
conserved region of the majority of PB1 domains, and is
necessary for PB1 domain function. This function is the
formation of PB1 domain heterodimers, although not all
PB1 domain pairs associate.
Length = 81
Score = 54.1 bits (131), Expect = 1e-10
Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 30 LSFDAEFRRFSVPKPDISTYNEFKILVEKLHHLDEIPFHLTYIATDGDLLPINNDSNLGK 89
L + E RR SVP+ ++ + + V K LD F L Y DGDL+ + +D +L +
Sbjct: 6 LRYGGETRRLSVPRD--ISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDEDLEE 63
Query: 90 AL 91
A+
Sbjct: 64 AI 65
>gnl|CDD|99716 cd05992, PB1, The PB1 domain is a modular domain mediating
specific protein-protein interactions which play a role
in many critical cell processes, such as
osteoclastogenesis, angiogenesis, early cardiovascular
development, and cell polarity. A canonical PB1-PB1
interaction, which involves heterodimerization of two
PB1 domain, is required for the formation of
macromolecular signaling complexes ensuring specificity
and fidelity during cellular signaling. The interaction
between two PB1 domain depends on the type of PB1.
There are three types of PB1 domains: type I which
contains an OPCA motif, acidic aminoacid cluster, type
II which contains a basic cluster, and type I/II which
contains both an OPCA motif and a basic cluster.
Interactions of PB1 domains with other protein domains
have been described as a noncanonical PB1-interactions.
The PB1 domain module is conserved in amoebas, fungi,
animals, and plants.
Length = 81
Score = 50.4 bits (121), Expect = 4e-09
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 30 LSFDAEFRRFSVPKPDISTYNEFKILVEKLHHLDEIPFHLTYIATDGDLLPINNDSNLGK 89
+ + E RRF V IS + + + + + LD + F L Y DGDL+ I++D +L +
Sbjct: 5 VKYGGEIRRFVVVSRSIS-FEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSDEDLEE 63
Query: 90 AL 91
A+
Sbjct: 64 AI 65
>gnl|CDD|215996 pfam00564, PB1, PB1 domain.
Length = 84
Score = 48.4 bits (116), Expect = 2e-08
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 30 LSFDAEFRRF-SVPKPDISTYNEFKILVEKLHHLDEIPFHLTYIATDGDLLPINNDSNLG 88
L + RRF SV ++ E + VE+ LD + F L Y DGDL+ I +D +L
Sbjct: 6 LRYGGGIRRFLSVSPG--ISFEELRSKVEQRFGLDRVDFKLKYPDEDGDLVSITSDEDLE 63
Query: 89 KAL 91
+A+
Sbjct: 64 EAI 66
>gnl|CDD|99719 cd06397, PB1_UP1, Uncharacterized protein 1. The PB1 domain is a
modular domain mediating specific protein-protein
interaction which play a role in many critical cell
processes, such as osteoclastogenesis, angiogenesis,
early cardiovascular development, and cell polarity. A
canonical PB1-PB1 interaction, which involves
heterodimerization of two PB1 domain, is required for
the formation of macromolecular signaling complexes
ensuring specificity and fidelity during cellular
signaling. The interaction between two PB1 domain
depends on the type of PB1. There are three types of
PB1 domains: type I which contains an OPCA motif,
acidic aminoacid cluster, type II which contains a
basic cluster, and type I/II which contains both an
OPCA motif and a basic cluster. Interactions of PB1
domains with other protein domains have been described
as noncanonical PB1-interactions.
Length = 82
Score = 32.5 bits (74), Expect = 0.021
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 28 FTLSFDAEFRRFSVPKPDISTYNEFKILVEKLHHLDEIPFHLTYIATDGDLLPINNDSNL 87
F SF + RR PDI T+ +E L++L EI +TYI D D + ++++ L
Sbjct: 3 FKSSFLGDTRRIV--FPDIPTWEALASKLENLYNLPEIKVGVTYIDNDNDEITLSSNKEL 60
>gnl|CDD|99723 cd06402, PB1_p62, The PB1 domain is an essential part of p62
scaffold protein (alias sequestosome 1,SQSTM) involved
in cell signaling, receptor internalization, and
protein turnover. The PB1 domain is a modular domain
mediating specific protein-protein interaction which
play roles in many critical cell processes. A canonical
PB1-PB1 interaction, which involves heterodimerization
of two PB1 domains, is required for the formation of
macromolecular signaling complexes ensuring specificity
and fidelity during cellular signaling. The interaction
between two PB1 domain depends on the type of PB1.
There are three types of PB1 domains: type I which
contains an OPCA motif, acidic aminoacid cluster, type
II which contains a basic cluster, and type I/II which
contains both an OPCA motif and a basic cluster.
Interactions of PB1 domains with other protein domains
have been described as noncanonical PB1-interactions.
The PB1 domain module is conserved in amoebas, fungi,
animals, and plants.
Length = 87
Score = 28.8 bits (65), Expect = 0.36
Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 34 AEFRRFSVPKPDISTYNEFKILVEKLH----HLDEIPFHLTYIATDGDLLPINNDSNLGK 89
AE RRF++ D ++ LVEK+ L F L + +GDL+ ++D L
Sbjct: 14 AEIRRFAI---DEDVSTSYEYLVEKVAAVFPSLRGKNFQLFWKDEEGDLVAFSSDEELVM 70
Query: 90 AL 91
AL
Sbjct: 71 AL 72
>gnl|CDD|99720 cd06398, PB1_Joka2, The PB1 domain is present in the Nicotiana
plumbaginifolia Joka2 protein which interacts with
sulfur stress inducible UP9 protein. The PB1 domain is a
modular domain mediating specific protein-protein
interactions which play a role in many critical cell
processes, such as osteoclastogenesis, angiogenesis,
early cardiovascular development and cell polarity. A
canonical PB1-PB1 interaction, which involves
heterodimerization of two PB1 domain, is required for
the formation of macromolecular signaling complexes
ensuring specificity and fidelity during cellular
signaling. The interaction between two PB1 domain
depends on the type of PB1. There are three types of PB1
domains: type I which contains an OPCA motif, acidic
aminoacid cluster, type II which contains a basic
cluster, and type I/II which contains both an OPCA motif
and a basic cluster. Interactions of PB1 domains with
other protein domains have been described as
noncanonical PB1-interactions. The PB1 domain module is
conserved in amoebas, fungi, animals, and plants.
Length = 91
Score = 28.1 bits (63), Expect = 0.72
Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 15/88 (17%)
Query: 31 SFDAEFRRFSVP----KPDISTYNEFKILVEKLHHLD-EIPFHLTYIATDGDLLPINNDS 85
+ RRF+ P + D++ + + VE+L L + LTY DGD++ + +D+
Sbjct: 6 KYGGTLRRFTFPVAENQLDLN-MDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDN 64
Query: 86 NLGKAL--------LNSFLRVSQIIDVD 105
+L A+ LN LR+ +D D
Sbjct: 65 DLTDAIQYFCSGSRLN-PLRIDVTVDYD 91
>gnl|CDD|200465 cd11326, AmyAc_Glg_debranch, Alpha amylase catalytic domain found
in glycogen debranching enzymes. Debranching enzymes
facilitate the breakdown of glycogen through
glucosyltransferase and glucosidase activity. These
activities are performed by a single enzyme in mammals,
yeast, and some bacteria, but by two distinct enzymes in
Escherichia coli and other bacteria. Debranching enzymes
perform two activities: 4-alpha-D-glucanotransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33).
4-alpha-D-glucanotransferase catalyzes the
endohydrolysis of 1,6-alpha-D-glucoside linkages at
points of branching in chains of 1,4-linked
alpha-D-glucose residues. Amylo-alpha-1,6-glucosidase
catalyzes the endohydrolysis of 1,6-alpha-D-glucoside
linkages at points of branching in chains of 1,4-linked
alpha-D-glucose residues. In Escherichia coli, GlgX is
the debranching enzyme and malQ is the
4-alpha-glucanotransferase. TreX, an archaeal
glycogen-debranching enzyme has dual activities like
mammals and yeast, but is structurally similar to GlgX.
TreX exists in two oligomeric states, a dimer and
tetramer. Isoamylase (EC 3.2.1.68) is one of the
starch-debranching enzymes that catalyzes the hydrolysis
of alpha-1,6-glucosidic linkages specific in
alpha-glucans such as amylopectin or glycogen and their
beta-limit dextrins. 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 = 433
Score = 28.2 bits (64), Expect = 2.2
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 25 YNAFTLSFDAEFRRFSVPKPDISTYNEFKILVEKLH 60
YN TL+F A R++ +EFK +V+ LH
Sbjct: 86 YN--TLNFFAPDPRYASDDAPGGPVDEFKAMVKALH 119
>gnl|CDD|224685 COG1771, COG1771, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 471
Score = 28.0 bits (62), Expect = 2.4
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 35 EFRRFSVPKPDISTYNEFKILVEKLHHLDEIPFHLTYI 72
E R F P ++ I+ EKL +IP HL+YI
Sbjct: 52 ERREFDSPYKNVGELGPTPIIKEKLS---KIPSHLSYI 86
>gnl|CDD|223165 COG0087, RplC, Ribosomal protein L3 [Translation, ribosomal
structure and biogenesis].
Length = 218
Score = 26.8 bits (60), Expect = 4.3
Identities = 16/83 (19%), Positives = 29/83 (34%), Gaps = 14/83 (16%)
Query: 23 HKYNAFTLSFDAEFRRFS-VPKPDISTYNEFKILVEKLHHLDEIPFHLTYIATDGDLLPI 81
Y A + R+ V KP + + K V+ HL E GD +
Sbjct: 43 DGYRAVQVGAGD--RKAKRVNKPLVGHFA--KAGVKPKRHLAEFR------VGGGD---V 89
Query: 82 NNDSNLGKALLNSFLRVSQIIDV 104
+G+ + + +++DV
Sbjct: 90 AEKFEVGQEITVDVFKEGELVDV 112
>gnl|CDD|217514 pfam03362, Herpes_UL47, Herpesvirus UL47 protein.
Length = 452
Score = 27.4 bits (61), Expect = 4.4
Identities = 7/36 (19%), Positives = 14/36 (38%)
Query: 91 LLNSFLRVSQIIDVDVVPETCRRVRLLKSPNSERPL 126
LL++ LRV+ + ++ +PL
Sbjct: 83 LLDAALRVAANCHALGRRRRAELGGNFRLLSALQPL 118
>gnl|CDD|211851 TIGR03611, RutD, pyrimidine utilization protein D. This protein is
observed in operons extremely similar to that
characterized in E. coli K-12 responsible for the import
and catabolism of pyrimidines, primarily uracil. This
protein is a member of the hydrolase, alpha/beta fold
family defined by pfam00067.
Length = 248
Score = 26.6 bits (59), Expect = 5.3
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 60 HHLDEIPFHLTYIATDGDLL-PINNDSNLGKALLNSFLRV 98
LD I + IA D+L P L AL N+ L++
Sbjct: 191 ARLDRIRHPVLLIAARDDMLVPYTCSLRLAAALPNAQLKL 230
>gnl|CDD|219850 pfam08455, SNF2_assoc, Bacterial SNF2 helicase associated. This
domain is found in bacterial proteins of the SWF/SNF/SWI
helicase family to the N-terminus of the SNF2 family
N-terminal domain (pfam00176) and together with the
Helicase conserved C-terminal domain (pfam00271). The
function of the domain is not clear.
Length = 376
Score = 26.8 bits (60), Expect = 6.4
Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 9/47 (19%)
Query: 23 HKYNAFTL--SFDAEFRRFSVPKPDISTYNEFKILVEKLHHLDEIPF 67
KY A L + E + FK LVE L H +++ F
Sbjct: 334 PKYRALYLDDLLEEELSF-------VKFSKSFKELVEDLKHPEKLEF 373
>gnl|CDD|177037 CHL00112, rpl28, ribosomal protein L28; Provisional.
Length = 63
Score = 24.9 bits (54), Expect = 7.1
Identities = 7/25 (28%), Positives = 15/25 (60%)
Query: 137 RVTSTGLDKFLRISSSTKYINDLTK 161
++ S ++++++ STK I L K
Sbjct: 37 KIWSNTQNRWVKLKISTKAIKTLKK 61
>gnl|CDD|129482 TIGR00387, glcD, glycolate oxidase, subunit GlcD. This protein,
the glycolate oxidase GlcD subunit, is similar in
sequence to that of several D-lactate dehydrogenases,
including that of E. coli. The glycolate oxidase has
been found to have some D-lactate dehydrogenase activity
[Energy metabolism, Other].
Length = 413
Score = 26.3 bits (58), Expect = 7.9
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 89 KALLNSFLRVSQIIDVDVVPETCRR---VRLLKSPNSERPLG-FYIRDGTSLRVTSTG 142
L+ F +++I+++DVV T VR L+ + FY D +S ++ G
Sbjct: 42 GGLVLVFKHMNKILEIDVVNLTAVVQPGVRNLELEQAVEEHNLFYPPDPSSQISSTIG 99
>gnl|CDD|176863 cd07821, PYR_PYL_RCAR_like, Pyrabactin resistance 1 (PYR1),
PYR1-like (PYL), regulatory component of abscisic acid
receptors (RCARs), and related proteins. The
PYR/PYL/RCAR-like family belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. PYR/PYL/RCAR plant proteins are receptors
involved in signal transduction. They bind abscisic
acid (ABA) and mediate its signaling. ABA is a vital
plant hormone, which regulates plant growth,
development, and response to environmental stresses.
Upon binding ABA, these plant proteins interact with a
type 2C protein phosphatase (PP2C), such as ABI1 and
ABI2, and inhibit their activity. When ABA is bound, a
loop (designated the gate/CL2 loop) closes over the
ligand binding pocket, resulting in the weakening of
the inactive PYL dimer and facilitating type 2C protein
phosphatase binding. In the ABA:PYL1:ABI1 complex, the
gate blocks substrate access to the phosphatase active
site. A conserved Trp from PP2C inserts into PYL to
lock the receptor in a closed formation. This group
also contains Methylobacterium extorquens AM1 MxaD. The
mxaD gene is located within the mxaFJGIR(S)ACKLDEHB
cluster which encodes proteins involved in methanol
oxidation. MxaD may participate in the periplasmic
electron transport chain for oxidation of methanol.
Mutants lacking MxaD exhibit a reduced growth on
methanol, and a lower rate of respiration with
methanol.
Length = 140
Score = 25.7 bits (57), Expect = 8.6
Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 48 TYNEFKILVEKLHHLDEIPFHLTYIATDGDLLPINN 83
T + + E+L LD+ +Y +G LP+ N
Sbjct: 52 TLKDGGTVRERLLALDDAERRYSYRIVEGP-LPVKN 86
>gnl|CDD|227688 COG5401, COG5401, Spore germination protein [General function
prediction only].
Length = 250
Score = 25.9 bits (57), Expect = 9.3
Identities = 20/68 (29%), Positives = 26/68 (38%), Gaps = 15/68 (22%)
Query: 83 NDSNLGKALLNSFLRVSQIIDVDVVPETCRRV-------------RLLKSPNSERPLGFY 129
ND+ GKA+ FL V D V + +R LLK P+ L
Sbjct: 104 NDAQPGKAITLYFLAVDP--DGYFVRQVVKRANYYPKNILEEALKELLKGPSLVSGLLTL 161
Query: 130 IRDGTSLR 137
I +GT L
Sbjct: 162 IPEGTKLL 169
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
0.321 0.139 0.401
Gapped
Lambda K H
0.267 0.0786 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,361,990
Number of extensions: 772484
Number of successful extensions: 624
Number of sequences better than 10.0: 1
Number of HSP's gapped: 621
Number of HSP's successfully gapped: 29
Length of query: 161
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 72
Effective length of database: 6,990,096
Effective search space: 503286912
Effective search space used: 503286912
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: 55 (24.9 bits)