RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1652
(86 letters)
>gnl|CDD|212013 cd11623, HR1_PKN_2, Second Protein kinase C-related kinase
homology region 1 (HR1) Rho-binding domain of Protein
Kinase N. PKN, also called Protein-kinase C-related
kinase (PRK), is a serine/threonine protein kinase that
can be activated by the small GTPase Rho, and by fatty
acids such as arachidonic and linoleic acids. It is
involved in many biological processes including
cytoskeletal regulation, cell adhesion, vesicle
transport, glucose transport, regulation of meiotic
maturation and embryonic cell cycles, signaling to the
nucleus, and tumorigenesis. In some vertebrates, there
are three PKN isoforms from different genes (designated
PKN1, PKN2, and PKN3), which show different enzymatic
properties, tissue distribution, and varied functions.
PKN proteins contain three HR1 domains, a C2 domain,
and a kinase domain. This model characterizes the
second HR1 domain of PKN. HR1 domains are anti-parallel
coiled-coil (ACC) domains that bind small GTPases from
the Rho family.
Length = 71
Score = 70.0 bits (172), Expect = 8e-18
Identities = 31/44 (70%), Positives = 37/44 (84%)
Query: 1 MIQSLTSGGSRDKKLLAEAQQMLADSKAKIEFLRMRILKVKQSK 44
MIQ ++G S+D+KLLAEAQQML DSKAKIEFLRM+IL+ KQ
Sbjct: 28 MIQMYSNGKSKDRKLLAEAQQMLEDSKAKIEFLRMQILRAKQQA 71
>gnl|CDD|212022 cd11632, HR1_PKN3_2, Second Protein kinase C-related kinase
homology region 1 (HR1) Rho-binding domain of Protein
Kinase N3. PKN3, also called PKNbeta, is a
serine/threonine protein kinase that is activated by
the Rho family of small GTPases, preferentially by
RhoC. Both PKN1 and RhoC show limited and barely
detectable expression in normal tissues, but are both
upregulated in cancer cells, particularly in late-stage
malignancies. PKN3 has been implicated to play a role
in the metastatic growth and invasiveness of cancer
cells, downstream of the oncogenic phosphoinositide
3-kinase signaling network. PKN3 shares a common domain
architecture with other PKNs, containing three HR1
domains, a C2 domain, and a kinase domain. In addition,
PKN3 contains two proline-rich regions between its C2
and kinase domains, and has been shown to associate
with SH3 domain containing proteins like GRAFs, GAP for
RhoA, and Cdc42Hs. This model characterizes the second
HR1 domain of PKN3. HR1 domains are anti-parallel
coiled-coil (ACC) domains that bind small GTPases from
the Rho family; PKN3 binds Rho family GTPases,
preferentially RhoC.
Length = 74
Score = 53.8 bits (129), Expect = 2e-11
Identities = 27/43 (62%), Positives = 37/43 (86%)
Query: 1 MIQSLTSGGSRDKKLLAEAQQMLADSKAKIEFLRMRILKVKQS 43
MIQ+ +SG S+++KLLA AQQML DS+ KIE LRM+I+K++QS
Sbjct: 31 MIQTYSSGTSKERKLLATAQQMLQDSRTKIELLRMQIVKLEQS 73
>gnl|CDD|212021 cd11631, HR1_PKN2_2, Second Protein kinase C-related kinase
homology region 1 (HR1) Rho-binding domain of Protein
Kinase N2. PKN2, also called PKNgamma or
Protein-kinase C-related kinase 2 (PRK2), is a
serine/threonine protein kinase and an effector of the
small GTPase Rho/Rac. It regulates G2/M cell cycle
progression and the exit from cytokinesis. It also
phosphorylates hepatitis C virus (HCV) RNA polymerase
and thus, plays a role in HCV RNA replication. PKN2
shares a common domain architecture with other PKNs,
containing three HR1 domains, a C2 domain, and a kinase
domain. In addition, PKN2 contains a proline-rich
region in between its C2 and kinase domains and has
been shown to associate with SH3 domain containing
proteins like NCK and Grb4. This model characterizes
the second HR1 domain of PKN2. HR1 domains are
anti-parallel coiled-coil (ACC) domains that bind small
GTPases from the Rho family; PKN2 specifically binds to
RhoA GTPase in a GTP-dependent manner. The HR1 domains
of PKN2, together with its C2 domain, also facilitate
the recruitment of PKN2 to primordial junctions at
nascent cell-cell contacts, where it promotes
junctional maturation.
Length = 74
Score = 49.7 bits (118), Expect = 1e-09
Identities = 26/43 (60%), Positives = 34/43 (79%)
Query: 1 MIQSLTSGGSRDKKLLAEAQQMLADSKAKIEFLRMRILKVKQS 43
MIQ ++G S+D+KLLA AQQML DSK KIE +RM+IL+ Q+
Sbjct: 31 MIQMYSNGSSKDRKLLATAQQMLQDSKTKIEVIRMQILQAVQT 73
>gnl|CDD|212020 cd11630, HR1_PKN1_2, Second Protein kinase C-related kinase
homology region 1 (HR1) Rho-binding domain of Protein
Kinase N1. PKN1, also called PKNalpha or
Protein-kinase C-related kinase 1 (PRK1), is a
serine/threonine protein kinase that is activated by
the Rho family of small GTPases, and by fatty acids
such as arachidonic and linoleic acids. It is expressed
ubiquitously and is the most abundant PKN isoform in
neurons. PKN1 is implicated in a variety of functions
including cytoskeletal reorganization, cardiac cell
survival, cell adhesion, and glucose transport, among
others. PKN1 contains three HR1 domains, a C2 domain,
and a kinase domain. This model characterizes the
second HR1 domain of PKN1. HR1 domains are
anti-parallel coiled-coil (ACC) domains that bind small
GTPases from the Rho family; PKN1 binds the GTPases
RhoA, RhoB, and RhoC, and can also interact weakly with
Rac.
Length = 78
Score = 45.4 bits (107), Expect = 5e-08
Identities = 23/43 (53%), Positives = 32/43 (74%)
Query: 1 MIQSLTSGGSRDKKLLAEAQQMLADSKAKIEFLRMRILKVKQS 43
MIQ+ +G ++D+KLL AQQML DSK KI+ +RM+I K Q+
Sbjct: 30 MIQTYANGSTKDRKLLQTAQQMLQDSKTKIDIIRMQIRKAMQA 72
>gnl|CDD|216921 pfam02185, HR1, Hr1 repeat.
Length = 60
Score = 33.3 bits (77), Expect = 0.002
Identities = 14/42 (33%), Positives = 28/42 (66%), Gaps = 3/42 (7%)
Query: 1 MIQSLTSGGSRDKKLLAEAQQMLADSKAKIEFLRMRILKVKQ 42
M+++L + +KK+L EA+ L +S KIE L+ ++ K+++
Sbjct: 22 MLRALETD---NKKVLQEAESELRESNQKIELLKEQLEKLQK 60
>gnl|CDD|128981 smart00742, Hr1, Rho effector or protein kinase C-related kinase
homology region 1 homologues. Alpha-helical domain
found in vertebrate PRK1 and yeast PKC1 protein kinases
C. The HR1 in rhophilin bind RhoGTP; those in PRK1 bind
RhoA and RhoB. Also called RBD - Rho-binding domain.
Length = 57
Score = 31.8 bits (73), Expect = 0.005
Identities = 13/39 (33%), Positives = 24/39 (61%), Gaps = 4/39 (10%)
Query: 1 MIQSLTSGGSRDKKLLAEAQQMLADSKAKIEFLRMRILK 39
M + ++ D+K+L+EAQ ML +S K++ L+ + K
Sbjct: 23 MRKLTSN----DRKVLSEAQSMLRESNQKLDLLKEELEK 57
>gnl|CDD|212015 cd11625, HR1_PKN_3, Third Protein kinase C-related kinase
homology region 1 (HR1) Rho-binding domain of Protein
Kinase N. PKN, also called Protein-kinase C-related
kinase (PRK), is a serine/threonine protein kinase that
can be activated by the small GTPase Rho, and by fatty
acids such as arachidonic and linoleic acids. It is
involved in many biological processes including
cytoskeletal regulation, cell adhesion, vesicle
transport, glucose transport, regulation of meiotic
maturation and embryonic cell cycles, signaling to the
nucleus, and tumorigenesis. In some vertebrates, there
are three PKN isoforms from different genes (designated
PKN1, PKN2, and PKN3), which show different enzymatic
properties, tissue distribution, and varied functions.
PKN proteins contain three HR1 domains, a C2 domain,
and a kinase domain. This model characterizes the third
HR1 domain of PKN. HR1 domains are anti-parallel
coiled-coil (ACC) domains that bind small GTPases from
the Rho family.
Length = 74
Score = 30.0 bits (68), Expect = 0.035
Identities = 14/35 (40%), Positives = 23/35 (65%)
Query: 1 MIQSLTSGGSRDKKLLAEAQQMLADSKAKIEFLRM 35
+I+ L + DKK L EAQ+ L++S K++ LR+
Sbjct: 31 VIKLLQNAKKDDKKALQEAQKSLSESSQKLDLLRL 65
>gnl|CDD|212027 cd11637, HR1_PKN3_3, Third Protein kinase C-related kinase
homology region 1 (HR1) Rho-binding domain of Protein
Kinase N3. PKN3, also called PKNbeta, is a
serine/threonine protein kinase that is activated by
the Rho family of small GTPases, preferentially by
RhoC. Both PKN1 and RhoC show limited and barely
detectable expression in normal tissues, but are both
upregulated in cancer cells, particularly in late-stage
malignancies. PKN3 has been implicated to play a role
in the metastatic growth and invasiveness of cancer
cells, downstream of the oncogenic phosphoinositide
3-kinase signaling network. PKN3 shares a common domain
architecture with other PKNs, containing three HR1
domains, a C2 domain, and a kinase domain. In addition,
PKN3 contains two proline-rich regions between its C2
and kinase domains, and has been shown to associate
with SH3 domain containing proteins like GRAFs, GAP for
RhoA, and Cdc42Hs. This model characterizes the third
HR1 domain of PKN3. HR1 domains are anti-parallel
coiled-coil (ACC) domains that bind small GTPases from
the Rho family; PKN3 binds Rho family GTPases,
preferentially RhoC.
Length = 74
Score = 29.1 bits (65), Expect = 0.10
Identities = 16/30 (53%), Positives = 21/30 (70%), Gaps = 2/30 (6%)
Query: 8 GGSR--DKKLLAEAQQMLADSKAKIEFLRM 35
GG R D+K+LAEAQ L +S KI+ LR+
Sbjct: 36 GGRRFQDRKILAEAQARLQESSQKIDLLRL 65
>gnl|CDD|185513 PTZ00203, PTZ00203, cathepsin L protease; Provisional.
Length = 348
Score = 27.7 bits (61), Expect = 0.60
Identities = 20/71 (28%), Positives = 28/71 (39%), Gaps = 16/71 (22%)
Query: 16 LAEAQQMLADSKAKIEFLRMRILKVKQSKNHHHHHSSG---DLNS--------NGDQHSH 64
L E QQ LA+ + +E +R Q++N H DL+ NG +
Sbjct: 52 LTEEQQRLANFERNLELMREH-----QARNPHARFGITKFFDLSEAEFAARYLNGAAYFA 106
Query: 65 KGKLLESQHYR 75
K QHYR
Sbjct: 107 AAKQHAGQHYR 117
>gnl|CDD|212008 cd00089, HR1, Protein kinase C-related kinase homology region 1
(HR1) domain that binds Rho family small GTPases. The
HR1 domain, also called the ACC (anti-parallel
coiled-coil) finger domain or Rho-binding domain binds
small GTPases from the Rho family. It is found in Rho
effector proteins including PKC-related kinases such as
vertebrate PRK1 (or PKN) and yeast PKC1 protein kinases
C, as well as in rhophilins and Rho-associated kinase
(ROCK). Rho family members function as molecular
switches, cycling between inactive and active forms,
controlling a variety of cellular processes. HR1
domains may occur in repeat arrangements (PKN contains
three HR1 domains), separated by a short linker region.
Length = 68
Score = 25.8 bits (57), Expect = 1.2
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 1 MIQSLTSGGSRDKKLLAEAQQMLADSKAKIEFLRMRILK 39
+++ ++ KK LAE Q L +SK KI+ L+ ++ +
Sbjct: 27 LLKLYSNPK--VKKDLAEVQLNLKESKEKIDLLKRQLER 63
>gnl|CDD|202317 pfam02625, XdhC_CoxI, XdhC and CoxI family. This domain is often
found in association with an NAD-binding region,
related to TrkA-N (pfam02254; personal obs:C. Yeats).
XdhC is believed to be involved in the attachment of
molybdenum to Xanthine Dehydrogenase.
Length = 71
Score = 26.0 bits (58), Expect = 1.3
Identities = 5/25 (20%), Positives = 15/25 (60%)
Query: 7 SGGSRDKKLLAEAQQMLADSKAKIE 31
GG + ++ A+++LA+ + ++
Sbjct: 43 GGGCLEAAVIERARELLAEGRPRLV 67
>gnl|CDD|212026 cd11636, HR1_PKN1_3, Third Protein kinase C-related kinase
homology region 1 (HR1) Rho-binding domain of Protein
Kinase N1. PKN1, also called PKNalpha or
Protein-kinase C-related kinase 1 (PRK1), is a
serine/threonine protein kinase that is activated by
the Rho family of small GTPases, and by fatty acids
such as arachidonic and linoleic acids. It is expressed
ubiquitously and is the most abundant PKN isoform in
neurons. PKN1 is implicated in a variety of functions
including cytoskeletal reorganization, cardiac cell
survival, cell adhesion, and glucose transport, among
others. PKN1 contains three HR1 domains, a C2 domain,
and a kinase domain. This model characterizes the third
HR1 domain of PKN1. HR1 domains are anti-parallel
coiled-coil (ACC) domains that bind small GTPases from
the Rho family; PKN1 binds the GTPases RhoA, RhoB, and
RhoC, and can also interact weakly with Rac.
Length = 74
Score = 26.1 bits (57), Expect = 1.3
Identities = 12/34 (35%), Positives = 25/34 (73%)
Query: 1 MIQSLTSGGSRDKKLLAEAQQMLADSKAKIEFLR 34
+++ L +G ++D+K ++EAQ L++S K++ LR
Sbjct: 31 VLRLLGAGKAQDRKAISEAQSKLSESSQKLDLLR 64
>gnl|CDD|178695 PLN03150, PLN03150, hypothetical protein; Provisional.
Length = 623
Score = 25.9 bits (57), Expect = 2.9
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 1 MIQSLTSG-GSRDKKLLAEAQQMLADSKAKIEF 32
I SL SG S D+++ AEA L D A I F
Sbjct: 123 QISSLKSGWSSHDEQVFAEALVFLTDGSASICF 155
>gnl|CDD|217843 pfam04012, PspA_IM30, PspA/IM30 family. This family includes PspA
a protein that suppresses sigma54-dependent
transcription. The PspA protein, a negative regulator of
the Escherichia coli phage shock psp operon, is produced
when virulence factors are exported through secretins in
many Gram-negative pathogenic bacteria and its homologue
in plants, VIPP1, plays a critical role in thylakoid
biogenesis, essential for photosynthesis. Activation of
transcription by the enhancer-dependent bacterial
sigma(54) containing RNA polymerase occurs through ATP
hydrolysis-driven protein conformational changes enabled
by activator proteins that belong to the large AAA(+)
mechanochemical protein family. It has been shown that
PspA directly and specifically acts upon and binds to
the AAA(+) domain of the PspF transcription activator.
Length = 220
Score = 25.4 bits (56), Expect = 3.4
Identities = 7/44 (15%), Positives = 18/44 (40%)
Query: 2 IQSLTSGGSRDKKLLAEAQQMLADSKAKIEFLRMRILKVKQSKN 45
I +L + L + + + + ++ L +I ++K K
Sbjct: 93 IATLEKQAEALETQLTQQRSAVEQLRKQLAALETKIQQLKAKKT 136
>gnl|CDD|236641 PRK10019, PRK10019, nickel/cobalt efflux protein RcnA; Provisional.
Length = 279
Score = 25.5 bits (56), Expect = 4.1
Identities = 6/20 (30%), Positives = 9/20 (45%)
Query: 46 HHHHHSSGDLNSNGDQHSHK 65
HHHH + Q +H+
Sbjct: 140 GHHHHHEHGATAEEYQDAHE 159
>gnl|CDD|218462 pfam05140, ResB, ResB-like family. This family includes both ResB
and cytochrome c biogenesis proteins. Mutations in ResB
indicate that they are essential for growth. ResB is
predicted to be a transmembrane protein.
Length = 437
Score = 25.3 bits (56), Expect = 4.2
Identities = 9/59 (15%), Positives = 19/59 (32%), Gaps = 4/59 (6%)
Query: 30 IEFLR-MRILKVKQSKNH---HHHHSSGDLNSNGDQHSHKGKLLESQHYRAIVFQGNSI 84
L+ +R V+ + + + + LL+ + YR G S+
Sbjct: 76 PPLLKALRRWPVRTPERSLSRLPLSAELTTPAPEEALEQLAALLKKRGYRVFEEGGRSL 134
>gnl|CDD|180941 PRK07352, PRK07352, F0F1 ATP synthase subunit B; Validated.
Length = 174
Score = 25.3 bits (56), Expect = 4.2
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 17 AEAQQMLADSKAKIEFLRMRILK 39
EA+++ AD+KA+ E +R I K
Sbjct: 85 QEAERIRADAKARAEAIRAEIEK 107
>gnl|CDD|148955 pfam07631, PSD4, Protein of unknown function (DUF1592). A region
of similarity shared by several Rhodopirellula baltica
cytochrome-like proteins that are predicted to be
secreted. These proteins also match pfam07627,
pfam07626, and pfam07624.
Length = 128
Score = 24.8 bits (55), Expect = 5.9
Identities = 10/24 (41%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 7 SGGSRDKK-LLAEAQQMLADSKAK 29
+G RD + L A+ ++MLAD +A+
Sbjct: 29 AGELRDPEVLRAQVERMLADPRAR 52
>gnl|CDD|178754 PLN03215, PLN03215, ascorbic acid mannose pathway regulator 1;
Provisional.
Length = 373
Score = 24.9 bits (54), Expect = 6.7
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 18 EAQQMLADSKAKIE---FLRMRILKVKQSKNHHH 48
EA Q+L +K + + R ++KVK+ NH
Sbjct: 140 EAYQVLDWAKRRETRPGYQRSALVKVKEGDNHRD 173
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 24.8 bits (54), Expect = 6.8
Identities = 11/51 (21%), Positives = 18/51 (35%), Gaps = 4/51 (7%)
Query: 1 MIQSLTSGGSRDKKLLAEAQ----QMLADSKAKIEFLRMRILKVKQSKNHH 47
M +++ + LL EA + LA + + R KV S
Sbjct: 23 MAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKVIISTRTK 73
>gnl|CDD|109486 pfam00430, ATP-synt_B, ATP synthase B/B' CF(0). Part of the
CF(0) (base unit) of the ATP synthase. The base unit is
thought to translocate protons through membrane (inner
membrane in mitochondria, thylakoid membrane in plants,
cytoplasmic membrane in bacteria). The B subunits are
thought to interact with the stalk of the CF(1)
subunits. This domain should not be confused with the
ab CF(1) proteins (in the head of the ATP synthase)
which are found in pfam00006.
Length = 132
Score = 24.5 bits (54), Expect = 7.0
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 14 KLLAEAQQMLADSKAKIEFLRM----RILKVKQSK 44
LLAEA+Q LA ++A+ + K+K+
Sbjct: 51 ALLAEAEQQLAQARAEASEIINNAKKEAQKLKEEI 85
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
0.316 0.127 0.353
Gapped
Lambda K H
0.267 0.0794 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,993,827
Number of extensions: 293691
Number of successful extensions: 463
Number of sequences better than 10.0: 1
Number of HSP's gapped: 458
Number of HSP's successfully gapped: 37
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.1 bits)