RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5166
(76 letters)
>gnl|CDD|99725 cd06404, PB1_aPKC, PB1 domain is an essential modular domain of
the atypical protein kinase C (aPKC) which in complex
with Par6 and Par3 proteins is crucial for
establishment of apical-basal polarity of animal cells.
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. The aPKC protein contains a type
I/II PB1 domain.
Length = 83
Score = 108 bits (273), Expect = 3e-33
Identities = 42/75 (56%), Positives = 56/75 (74%)
Query: 2 YLFSDEVFITYIKPDITYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEA 61
++ ++ IT I P I+ + L EV++MC+F DQ FT+KW+DEEGDPC IS+QMELEEA
Sbjct: 5 AAYNGDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWIDEEGDPCTISSQMELEEA 64
Query: 62 IRLYEVNHEPELVIH 76
RLYE+N + EL IH
Sbjct: 65 FRLYELNKDSELNIH 79
>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 = 59.9 bits (146), Expect = 5e-14
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 4 FSDEVFITYIKPDITYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAIR 63
+ E + DI+++ L+ +V + +Q FT+K+ DE+GD +++ +LEEAI
Sbjct: 8 YGGETRRLSVPRDISFEDLRSKVAKRFGLD-NQSFTLKYQDEDGDLVSLTSDEDLEEAIE 66
Query: 64 LYEVNHEPELVIH 76
Y+ +L +H
Sbjct: 67 EYDSLGSKKLRLH 79
>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 = 59.6 bits (145), Expect = 9e-14
Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 5 SDEVFITYIKPDITYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAIRL 64
+ + I+++ L+ ++ E F +K+ DE+GD IS+ +LEEAI
Sbjct: 9 GEIRRFVVVSRSISFEDLRSKIAEKFGLD-AVSFKLKYPDEDGDLVTISSDEDLEEAIEE 67
Query: 65 YEVNHEPELVIH 76
+ +L +
Sbjct: 68 ARRSGSKKLRLF 79
>gnl|CDD|215996 pfam00564, PB1, PB1 domain.
Length = 84
Score = 50.0 bits (120), Expect = 5e-10
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 4 FSDEVFIT-YIKPDITYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAI 62
+ + + P I+++ L+ +V++ F +K+ DE+GD I++ +LEEAI
Sbjct: 8 YGGGIRRFLSVSPGISFEELRSKVEQRFG-LDRVDFKLKYPDEDGDLVSITSDEDLEEAI 66
Query: 63 RLYEVNHEPELVIH 76
L +H
Sbjct: 67 EEARSLGSKTLRLH 80
>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 = 33.9 bits (78), Expect = 0.001
Identities = 15/50 (30%), Positives = 29/50 (58%)
Query: 14 KPDITYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAIR 63
+ D+ D L+E+V+E+ S D ++ + DE+GD + +L +AI+
Sbjct: 22 QLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQ 71
>gnl|CDD|99728 cd06407, PB1_NLP, A PB1 domain is present in NIN like proteins
(NLP), a key enzyme in a process of establishment of
symbiosis betweeen legumes and nitrogen fixing bacteria
(Rhizobium). The PB1 domain is a modular domain
mediating specific protein-protein interaction which
play a role in many critical cell processes like
osteoclastogenesis, angiogenesis, early cardiovascular
development, and cell polarity. 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 = 82
Score = 31.1 bits (71), Expect = 0.012
Identities = 14/62 (22%), Positives = 32/62 (51%)
Query: 4 FSDEVFITYIKPDITYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAIR 63
+ +E + P + L++E+ + K F +K++D++ + L++ +LEE I
Sbjct: 7 YGEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEECID 66
Query: 64 LY 65
+Y
Sbjct: 67 VY 68
>gnl|CDD|99718 cd06396, PB1_NBR1, The PB1 domain is an essential part of NBR1
protein, next to BRCA1, a scaffold protein mediating
specific protein-protein interaction with both titin
protein kinase and with another scaffold protein p62. 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. The NBR1 protein
contains a type I PB1 domain.
Length = 81
Score = 29.0 bits (65), Expect = 0.071
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 40 VKWVDEEGDPCLISTQMELEEAIRL 64
+K+VDEE + +++Q E EEA++
Sbjct: 42 IKYVDEENEEVSVNSQGEYEEALKS 66
>gnl|CDD|129876 TIGR00794, kup, potassium uptake protein. Proteins of the KUP
family include the KUP (TrkD) protein of E. coli, a
partially sequenced ORF from Lactococcus lactis, high
affinity K+ uptake systems (Hak1) of the yeast
Debaryomyces occidentalis as well as the fungus,
Neurospora crassa, and several homologues in plants.
While the E. coli KUP protein is assumed to be a
secondary transporter, and uptake is blocked by
protonophores such as CCCP (but not arsenate), the
energy coupling mechanism has not been defined. However,
the N. crassa protein has been shown to be a K+:H+
symporter, establishing that the KUP family consists of
secondary carriers. The plant high affinity (20mM) K+
transporter can complement K+ uptake defects in E. coli
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 688
Score = 29.0 bits (65), Expect = 0.20
Identities = 13/71 (18%), Positives = 22/71 (30%), Gaps = 3/71 (4%)
Query: 2 YLFSDEVFITYIKPDITYDRLQEEVKEMCKFS--TDQVFTVKWVDEEGDPCLISTQMELE 59
Y F D + + E V+ C F+ + + K + ME +
Sbjct: 569 YGFMDTPNEPKELAAHIVNSIVEFVEHECGFNLNNLEELSDKRCRMPIEEI-FENAMETK 627
Query: 60 EAIRLYEVNHE 70
E Y + E
Sbjct: 628 EHGYSYFMGEE 638
>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 = 27.7 bits (62), Expect = 0.23
Identities = 15/44 (34%), Positives = 22/44 (50%)
Query: 19 YDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAI 62
Y+ L E+V + + F + W DEEGD S+ EL A+
Sbjct: 29 YEYLVEKVAAVFPSLRGKNFQLFWKDEEGDLVAFSSDEELVMAL 72
>gnl|CDD|99730 cd06409, PB1_MUG70, The MUG70 protein is a product of the
meiotically up-regulated gene 70 which has a role in
meiosis and harbors a PB1 domain. 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 domains, is required for
the formation of macromolecular signaling complexes
ensuring specificity and fidelity during cellular
signaling. The interaction between two PB1 domains
depends on the type of PB1. There are three types of
PB1 domains: type I which contains an OPCA motif,
acidic amino acid 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 = 86
Score = 26.9 bits (60), Expect = 0.48
Identities = 11/42 (26%), Positives = 23/42 (54%)
Query: 35 DQVFTVKWVDEEGDPCLISTQMELEEAIRLYEVNHEPELVIH 76
++ + +VD+EGD LI++ +L A+ + +L +H
Sbjct: 41 THLYALSYVDDEGDIVLITSDSDLVAAVLVARSAGLKKLDLH 82
>gnl|CDD|99722 cd06401, PB1_TFG, The PB1 domain found in TFG protein, an
oncogenic gene product and fusion partner to nerve
growth factor tyrosine kinase receptor TrkA and to the
tyrosine kinase ALK. The PB1 domain is a modular domain
mediating specific protein-protein interaction 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 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. The PB1 domains of TFG
represent a type I/II PB1 domain. The physiological
function of TFG remains unknown.
Length = 81
Score = 25.9 bits (57), Expect = 1.1
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 8/57 (14%)
Query: 16 DITYDRLQEEVKEMCKF-----STDQVFTVKWVDEEGDPCLISTQMELEEAIRLYEV 67
DITYD L + M + + +K+ DE+GD I +L AI+ +
Sbjct: 20 DITYDEL---LLMMQRVFRGKLGSSDDVLIKYKDEDGDLITIFDSSDLSFAIQCSRI 73
>gnl|CDD|220652 pfam10250, O-FucT, GDP-fucose protein O-fucosyltransferase. This
is a family of conserved proteins representing the
enzyme responsible for adding O-fucose to EGF (epidermal
growth factor-like) repeats. Six highly conserved
cysteines are present in O-FucT-1 as well as a DXD-like
motif (ERD), conserved in mammals, Drosophila, and C.
elegans. Both features are characteristic of several
glycosyltransferase families. The enzyme is a
membrane-bound protein released by proteolysis and, as
for most glycosyltransferases, is strongly activated by
manganese.
Length = 315
Score = 26.1 bits (58), Expect = 1.8
Identities = 10/55 (18%), Positives = 19/55 (34%), Gaps = 1/55 (1%)
Query: 3 LFSDEVFITYIKPDITYDR-LQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQM 56
F E FI+Y+ + + L +E+ + D V + P +
Sbjct: 51 FFDVEHFISYLSRVVEIVKFLPKELPSAKRLQYDTFKVDFRVCVQSSPSYYLESV 105
>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 = 25.2 bits (55), Expect = 2.1
Identities = 13/51 (25%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 15 PDI-TYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAIRL 64
PDI T++ L +++ + + V ++D + D +S+ EL++ RL
Sbjct: 17 PDIPTWEALASKLENLYNLPEIK-VGVTYIDNDNDEITLSSNKELQDFYRL 66
>gnl|CDD|220286 pfam09544, DUF2381, Protein of unknown function (DUF2381). This
family consists of at least 8 paralogs in Myxococcus
xanthus, a member of the Deltaproteobacteria. The
function is unknown.
Length = 289
Score = 25.4 bits (56), Expect = 2.7
Identities = 7/27 (25%), Positives = 10/27 (37%)
Query: 26 VKEMCKFSTDQVFTVKWVDEEGDPCLI 52
E S D FT++ +G L
Sbjct: 257 EAEAPPLSADGPFTLELWGADGLRTLT 283
>gnl|CDD|173571 PTZ00378, PTZ00378, hypothetical protein; Provisional.
Length = 518
Score = 25.2 bits (55), Expect = 3.4
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 15 PDITYDRLQEEVKEMCKFSTDQV 37
PD+T D+L E V+E + D V
Sbjct: 324 PDVTGDQLSEYVREQLQAVPDIV 346
>gnl|CDD|185104 PRK15182, PRK15182, Vi polysaccharide biosynthesis protein TviB;
Provisional.
Length = 425
Score = 24.6 bits (53), Expect = 5.7
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 15 PDITYDRLQEEVKEMCKFSTDQVFTVKWVDEE 46
PDI R+ + VKE+ K+S WVD E
Sbjct: 329 PDIRNTRIIDVVKELGKYSCKVDIFDPWVDAE 360
>gnl|CDD|184829 PRK14807, PRK14807, histidinol-phosphate aminotransferase;
Provisional.
Length = 351
Score = 24.4 bits (53), Expect = 6.9
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 13 IKPDITYDRLQEEVKEMCKFSTDQVFTVKWVDE 45
I PD T ++L+EE+ C +F DE
Sbjct: 55 IYPDPTAEKLREELARYCSVVPTNIFVGNGSDE 87
>gnl|CDD|203570 pfam07058, Myosin_HC-like, Myosin II heavy chain-like. This family
represents a conserved region within a number of myosin
II heavy chain-like proteins that seem to be specific to
Arabidopsis thaliana.
Length = 351
Score = 24.2 bits (52), Expect = 7.3
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 15 PDITYDRLQEEVKEMCKFSTDQVFTVKWVDEE 46
P + YD LQ+EV + K ++ ++ DE
Sbjct: 288 PGVLYDLLQKEVIALRKACEEKDQSLNDKDEA 319
>gnl|CDD|233249 TIGR01051, topA_bact, DNA topoisomerase I, bacterial. This model
describes DNA topoisomerase I among the members of
bacteria. DNA topoisomerase I transiently cleaves one
DNA strand and thus relaxes negatively supercoiled DNA
during replication, transcription and recombination
events [DNA metabolism, DNA replication, recombination,
and repair].
Length = 610
Score = 24.3 bits (53), Expect = 9.4
Identities = 17/69 (24%), Positives = 26/69 (37%), Gaps = 10/69 (14%)
Query: 9 FITYIKPDITYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQ-----MELEEAIR 63
ITY++ D T RL + + D+ + +++ G E EAIR
Sbjct: 293 LITYMRTDST--RLSNQAVNEARNLIDKNYGKEYL---GPKPKRYKSKEKNAQEAHEAIR 347
Query: 64 LYEVNHEPE 72
V PE
Sbjct: 348 PTSVFRTPE 356
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
0.320 0.138 0.410
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: 3,981,414
Number of extensions: 309940
Number of successful extensions: 375
Number of sequences better than 10.0: 1
Number of HSP's gapped: 372
Number of HSP's successfully gapped: 27
Length of query: 76
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 30
Effective length of database: 8,897,318
Effective search space: 266919540
Effective search space used: 266919540
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: 53 (24.1 bits)