RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5165
(169 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 = 114 bits (288), Expect = 5e-34
Identities = 42/71 (59%), Positives = 54/71 (76%)
Query: 88 SEVFITYIKPDITYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAIRLY 147
++ IT I P I+ + L EV++MC+F DQ FT+KW+DEEGDPC IS+QMELEEA RLY
Sbjct: 9 GDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWIDEEGDPCTISSQMELEEAFRLY 68
Query: 148 EVNHEPELVIH 158
E+N + EL IH
Sbjct: 69 ELNKDSELNIH 79
Score = 38.9 bits (91), Expect = 9e-05
Identities = 15/21 (71%), Positives = 17/21 (80%)
Query: 1 MELEEAIRLYEVNHEPELVIH 21
MELEEA RLYE+N + EL IH
Sbjct: 59 MELEEAFRLYELNKDSELNIH 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 = 63.1 bits (154), Expect = 6e-14
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 89 EVFITYIKPDITYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAIRLYE 148
+ I+++ L+ ++ E F +K+ DE+GD IS+ +LEEAI
Sbjct: 11 IRRFVVVSRSISFEDLRSKIAEKFGLD-AVSFKLKYPDEDGDLVTISSDEDLEEAIEEAR 69
Query: 149 VNHEPELVIH 158
+ +L +
Sbjct: 70 RSGSKKLRLF 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 = 62.2 bits (152), Expect = 2e-13
Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 89 EVFITYIKPDITYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAIRLYE 148
E + DI+++ L+ +V + +Q FT+K+ DE+GD +++ +LEEAI Y+
Sbjct: 11 ETRRLSVPRDISFEDLRSKVAKRFGLD-NQSFTLKYQDEDGDLVSLTSDEDLEEAIEEYD 69
Query: 149 VNHEPELVIH 158
+L +H
Sbjct: 70 SLGSKKLRLH 79
>gnl|CDD|215996 pfam00564, PB1, PB1 domain.
Length = 84
Score = 52.3 bits (126), Expect = 1e-09
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 92 ITYIKPDITYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAIRLYEVNH 151
+ P I+++ L+ +V++ F +K+ DE+GD I++ +LEEAI
Sbjct: 15 FLSVSPGISFEELRSKVEQRFG-LDRVDFKLKYPDEDGDLVSITSDEDLEEAIEEARSLG 73
Query: 152 EPELVIH 158
L +H
Sbjct: 74 SKTLRLH 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 = 36.6 bits (85), Expect = 6e-04
Identities = 15/50 (30%), Positives = 29/50 (58%)
Query: 96 KPDITYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAIR 145
+ D+ D L+E+V+E+ S D ++ + DE+GD + +L +AI+
Sbjct: 22 QLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQ 71
>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 = 31.4 bits (71), Expect = 0.056
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 106 EEVKEMCKFSTD-QVFTVKWVDEEGDPCLISTQMELEEAIRL 146
V+ M K S +K+VDEE + +++Q E EEA++
Sbjct: 25 ASVEAMVKVSFGLNDIQIKYVDEENEEVSVNSQGEYEEALKS 66
>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 = 30.8 bits (70), Expect = 0.073
Identities = 13/53 (24%), Positives = 29/53 (54%)
Query: 95 IKPDITYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAIRLY 147
+ P + L++E+ + K F +K++D++ + L++ +LEE I +Y
Sbjct: 16 LPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEECIDVY 68
>gnl|CDD|131724 TIGR02677, TIGR02677, TIGR02677 family protein. Members of this
protein belong to a conserved gene four-gene
neighborhood found sporadically in a phylogenetically
broad range of bacteria: Nocardia farcinica,
Symbiobacterium thermophilum, and Streptomyces
avermitilis (Actinobacteria), Geobacillus kaustophilus
(Firmicutes), Azoarcus sp. EbN1 and Ralstonia
solanacearum (Betaproteobacteria) [Hypothetical
proteins, Conserved].
Length = 494
Score = 32.1 bits (73), Expect = 0.12
Identities = 20/88 (22%), Positives = 32/88 (36%), Gaps = 8/88 (9%)
Query: 83 YFIIFSEVFITYIKPDITYDRLQ--EEVK--EMCKFSTDQVFTVKW--VDEEGDPCLIST 136
F E F TY++PD L+ V + + DQ+ VKW + + + T
Sbjct: 20 SFYAAKERFRTYLRPDDVLAFLRQYLPVADLTELQQALDQL--VKWGNLTAIPETSRVRT 77
Query: 137 QMELEEAIRLYEVNHEPELVIHGKSTYL 164
E LY+++ E T
Sbjct: 78 IEEFRRKRFLYQLSRIGEAAEAALRTLE 105
>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 = 29.2 bits (66), Expect = 0.32
Identities = 15/44 (34%), Positives = 22/44 (50%)
Query: 101 YDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAI 144
Y+ L E+V + + F + W DEEGD S+ EL A+
Sbjct: 29 YEYLVEKVAAVFPSLRGKNFQLFWKDEEGDLVAFSSDEELVMAL 72
>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 = 29.0 bits (65), Expect = 0.35
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 8/57 (14%)
Query: 98 DITYDRLQEEVKEMCKF-----STDQVFTVKWVDEEGDPCLISTQMELEEAIRLYEV 149
DITYD L + M + + +K+ DE+GD I +L AI+ +
Sbjct: 20 DITYDEL---LLMMQRVFRGKLGSSDDVLIKYKDEDGDLITIFDSSDLSFAIQCSRI 73
>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 = 28.4 bits (64), Expect = 0.58
Identities = 11/46 (23%), Positives = 23/46 (50%)
Query: 117 DQVFTVKWVDEEGDPCLISTQMELEEAIRLYEVNHEPELVIHGKST 162
++ + +VD+EGD LI++ +L A+ + +L +H
Sbjct: 41 THLYALSYVDDEGDIVLITSDSDLVAAVLVARSAGLKKLDLHLHYP 86
>gnl|CDD|130022 TIGR00947, 2A73, putative bicarbonate transporter, IctB family.
This family of proteins is suggested to transport
inorganic carbon (HCO3-), based on the phenotype of a
mutant of IctB in Synechococcus sp. strain PCC 7942.
Bicarbonate uptake is used by many photosynthetic
organisms including cyanobacteria. These organisms are
able to concentrate CO2/HCO3- against a greater than
ten-fold concentration gradient. Cyanobacteria may have
several such carriers operating with different
efficiencies. Note that homology to various O-antigen
ligases, with possible implications for mutant cell
envelope structure, might allow alternatives to the
interpretation of IctB as a bicarbonate transport
protein [Transport and binding proteins, Carbohydrates,
organic alcohols, and acids].
Length = 425
Score = 29.7 bits (67), Expect = 0.73
Identities = 10/25 (40%), Positives = 10/25 (40%), Gaps = 1/25 (4%)
Query: 24 LWTWQWWNKFWRTWAPVPTLFGITI 48
LW FWR W P P L G
Sbjct: 237 LWWSPRLPPFWRRWVP-PALLGGAA 260
>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 = 26.7 bits (59), Expect = 2.4
Identities = 13/51 (25%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 97 PDI-TYDRLQEEVKEMCKFSTDQVFTVKWVDEEGDPCLISTQMELEEAIRL 146
PDI T++ L +++ + + V ++D + D +S+ EL++ RL
Sbjct: 17 PDIPTWEALASKLENLYNLPEIK-VGVTYIDNDNDEITLSSNKELQDFYRL 66
>gnl|CDD|223383 COG0306, PitA, Phosphate/sulphate permeases [Inorganic ion
transport and metabolism].
Length = 326
Score = 26.4 bits (59), Expect = 7.8
Identities = 10/62 (16%), Positives = 18/62 (29%), Gaps = 10/62 (16%)
Query: 29 WWNKFWRT---WAPVPTL-FGITIFIVWQYSRKLQHRELVRKKRSYCKFLHI------SF 78
W + W P L + + R + ++ RK + L I +F
Sbjct: 128 DWGVLGKIVASWVLSPILGGVLAYLLYSLLRRLIVGKDGKRKVERIFRILLIISASLVAF 187
Query: 79 TL 80
Sbjct: 188 AH 189
>gnl|CDD|146320 pfam03620, IBV_3C, IBV 3C protein. Product of ORF 3C from Avian
infectious bronchitis virus (IBV). Currently, the
function of this protein remains unknown.
Length = 93
Score = 25.6 bits (56), Expect = 8.0
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 33 FWRTWAPVPTLFGITIFIVWQYSRKLQHREL 63
FW TW +P G Y ++L + EL
Sbjct: 48 FWYTWVALPGAKGTAFVYNNTYGKRLNNPEL 78
>gnl|CDD|226684 COG4231, COG4231, Indolepyruvate ferredoxin oxidoreductase, alpha
and beta subunits [Energy production and conversion].
Length = 640
Score = 26.6 bits (59), Expect = 9.0
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 125 VDEEGDPCLISTQMELEEAIRLYEVNHEPELVIHGKSTYLISLHG 169
V EEG+P + EE ++ + + +HGK L+ + G
Sbjct: 301 VVEEGEPFI-------EEQVKALLYDAGLPVEVHGKDEGLLPMEG 338
>gnl|CDD|215943 pfam00487, FA_desaturase, Fatty acid desaturase.
Length = 251
Score = 26.1 bits (57), Expect = 9.4
Identities = 7/42 (16%), Positives = 13/42 (30%), Gaps = 3/42 (7%)
Query: 8 RLYEVNHEPELVIHGNLWTWQWWNKFWRTWAPVPTLFGITIF 49
L + HE HG L+ + N + + +
Sbjct: 19 ILGGLAHE---AAHGALFRSRRLNDLLGRLLALLLGISYSAW 57
>gnl|CDD|223385 COG0308, PepN, Aminopeptidase N [Amino acid transport and
metabolism].
Length = 859
Score = 26.3 bits (58), Expect = 9.5
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 22 GNLWTWQWWNKFW 34
GNL T +WW+ W
Sbjct: 321 GNLVTMKWWDDLW 333
>gnl|CDD|107384 cd06389, PBP1_iGluR_AMPA_GluR2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR2 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR2 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 370
Score = 26.1 bits (57), Expect = 9.8
Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 40 VPTLFGITIFIVWQYSRKL------QHRELVRKKRSYCKFLHISFTLHCYFIIFSEVFIT 93
V F +T Q+SR + ++ V S+C LH+SF + + F+
Sbjct: 40 VANSFAVTNAFCSQFSRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVI 99
Query: 94 YIKPDI 99
++PD+
Sbjct: 100 QMRPDL 105
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
0.325 0.140 0.467
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: 9,007,327
Number of extensions: 833524
Number of successful extensions: 1253
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1245
Number of HSP's successfully gapped: 51
Length of query: 169
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 79
Effective length of database: 6,945,742
Effective search space: 548713618
Effective search space used: 548713618
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (24.9 bits)