RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy647
(190 letters)
>gnl|CDD|212550 cd11712, GINS_A_psf2, Alpha-helical domain of GINS complex protein
Psf2 (partner of Sld5 2). Psf2 is a component of GINS
tetrameric protein complex and has been found to play
important roles in normal eye development in Xenopus
laevis. GINS is a complex of four subunits (Sld5, Psf1,
Psf2 and Psf3) that is involved in both initiation and
elongation stages of eukaryotic chromosome replication.
Besides being essential for the maintenance of genomic
integrity, GINS plays a central role in coordinating DNA
replication with cell cycle checkpoints and is involved
in cell growth. The eukaryotic GINS subunits are
homologous and homologs are also found in the archaea;
the complex is not found in bacteria. The four subunits
of the complex consist of two domains each, termed the
alpha-helical (A) and beta-strand (B) domains. The A and
B domains of Sld5/Psf1 are permuted with respect to
Psf1/Psf3.
Length = 119
Score = 146 bits (371), Expect = 9e-46
Identities = 55/119 (46%), Positives = 80/119 (67%), Gaps = 1/119 (0%)
Query: 56 RQKCRLVLPTWMNLETLTEIKEEEKKSRFFIKMPSDHYMEMSHIILDIGADDIPNVDLIR 115
R KCR+V P W+ +E L EI EEEKKS F +P HY+E++ ++L++ +DDIP+ D IR
Sbjct: 1 RNKCRIVPPDWLTVEYLKEILEEEKKSETFSPLP-FHYLEIAKLLLEVASDDIPDADEIR 59
Query: 116 TLIKDIWDLRISKLRSSIDTFVKSGGGHATLNHLTQFEINSIRNILCDVLDTMSSLKDK 174
+L++DI D+R +KLRS ++ + SG HA L++LT EIN IR L LD + L+
Sbjct: 60 SLVEDIRDVRQAKLRSGLEKLLGSGEVHAKLDNLTAMEINEIRPFLSGALDKLRKLRAS 118
>gnl|CDD|227424 COG5093, COG5093, Uncharacterized conserved protein [Function
unknown].
Length = 185
Score = 97.7 bits (243), Expect = 8e-26
Identities = 52/172 (30%), Positives = 94/172 (54%), Gaps = 5/172 (2%)
Query: 3 PAEIEFIAEDQNVEIIPKFNHLNLIHLISGDVGPFRAGIPAKVPLWLAINLKQRQKCRLV 62
P EI FIA ++ +EI P L L P A+VPLW A+ LK++ C++V
Sbjct: 13 PEEILFIAYNELIEIEPMTTIPQLRLLERATYPPMMPLDIARVPLWAALLLKKQNMCKIV 72
Query: 63 LPTWMNLETL-TEIKEEEKKSRFFIKMPSDHYMEMSHIILDIGADDIPNVDLIRTLIKDI 121
LP+W+ LE+L I E +K+ F ++P +++ ++ +L+ DD+ +++ R +++DI
Sbjct: 73 LPSWLQLESLKMSIDVEIEKADEFSELPP-YWLPLATELLNENCDDVEDIEESRMIVEDI 131
Query: 122 WDLRISKLRSSIDTFVKSGGGHATLNHLTQFEINSIRNILCDVLDTMSSLKD 173
++R +K + L++LT FEIN IR ++ + +D ++D
Sbjct: 132 REIRQAKTLKGLKCL---NEKALNLDNLTLFEINEIRPLILESMDVGRRIED 180
>gnl|CDD|218810 pfam05916, Sld5, GINS complex protein. The eukaryotic GINS complex
is essential for the initiation and elongation phases of
DNA replication. It consists of four paralogous protein
subunits (Sld5, Psf1, Psf2 and Psf3), all of which are
included in this family. The GINS complex is conserved
from yeast to humans, and has been shown in human to
bind directly to DNA primase.
Length = 106
Score = 69.5 bits (170), Expect = 6e-16
Identities = 24/115 (20%), Positives = 51/115 (44%), Gaps = 12/115 (10%)
Query: 43 AKVPLWLAINLKQRQKCRLVLPTWMNLETLTEIKEEEKKSRF---FIKMPSDHYMEMSHI 99
++PLWLA L +R + P ++LE L +K E K K+P ++ E++ +
Sbjct: 1 PELPLWLAEELVERVLVEIEAPDELSLEVLNALKAEPKNVDTKLQLSKLPP-YFYELAEL 59
Query: 100 ILDIGADDIPNVDLIRTLIKDIWDLRISKLRSSIDTFVKSGGGHATLNHLTQFEI 154
+L++ + L+++ +R+ K+ L++L++ E
Sbjct: 60 LLELLR--------NKRLLREYLRIRLRKIEKLAWHLAGGNESEDLLDNLSEEER 106
>gnl|CDD|240380 PTZ00362, PTZ00362, hypothetical protein; Provisional.
Length = 479
Score = 34.7 bits (80), Expect = 0.020
Identities = 19/105 (18%), Positives = 41/105 (39%), Gaps = 14/105 (13%)
Query: 46 PLWLAINLKQRQKCRLVLPTWMNLETLTEIKEEE-KKSRFFIKMPSDHYMEMSHIILDIG 104
P+++A L + P W ++ L I E E + +PS ++ E+S + L+
Sbjct: 320 PIYIAKELSHFGLVTVEFPFWFYIKNLKNIYEREFEDQNELTDLPSPYFFEISSMFLENN 379
Query: 105 ADD---IPN----------VDLIRTLIKDIWDLRISKLRSSIDTF 136
+ + L++DI R+ K+ + ++
Sbjct: 380 IFKKVTPIETIGQRTVYKYISKVAGLVEDIRYKRLKKIMNHLENQ 424
>gnl|CDD|182333 PRK10250, PRK10250, hypothetical protein; Provisional.
Length = 122
Score = 29.4 bits (66), Expect = 0.52
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 92 HYMEMSHIILDIGADDIPNVDLIRTLIKDIWDLRISKL 129
++M H I +DI + L+R LI D W+L + L
Sbjct: 75 YHMNKKHWISVYPGEDI-SEALLRDLINDSWNLVVDGL 111
>gnl|CDD|175986 cd04019, C2C_MCTP_PRT_plant, C2 domain third repeat found in
Multiple C2 domain and Transmembrane region Proteins
(MCTP); plant subset. MCTPs are involved in Ca2+
signaling at the membrane. Plant-MCTPs are composed of
a variable N-terminal sequence, four C2 domains, two
transmembrane regions (TMRs), and a short C-terminal
sequence. It is one of four protein classes that are
anchored to membranes via a transmembrane region; the
others being synaptotagmins, extended synaptotagmins,
and ferlins. MCTPs are the only membrane-bound C2 domain
proteins that contain two functional TMRs. MCTPs are
unique in that they bind Ca2+ but not phospholipids. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the third C2
repeat, C2C, and has a type-II topology.
Length = 150
Score = 29.6 bits (67), Expect = 0.68
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 25 NLIHLISGDVGPFRAGIPAKVPLWLAINLKQRQKCRLVLPTWMNLETLTEIKEEEKKSRF 84
+LI + VGP + + + L +++R R V W +LE E++KK +F
Sbjct: 63 HLILSVEDRVGPNKDEPLGRAVIPLND-IERRVDDRPVPSRWFSLERPGGAMEQKKKRKF 121
>gnl|CDD|211427 cd11602, Ndc10, Ndc10 component of the yeast centromere-binding
factor 3. Ndc10 is a multidomain protein conserved in
Saccharomycotina that interacts with kinetochore
components. This model characterizes the majority of the
protein; some family members may have an additional
C-terminal domain that is homologous to transcriptional
activators (GCR1_C). Ndc10 is part of the
centromere-binding factor 3 (CBF3) complex in budding
yeast. The CBF3 complex contains four essential
proteins, Ndc10, Cep3, Ctf13, and Skp1. CBF3/Ndc10 is
essential for the recruitment of the centromeric
nucleosome and formation of the kinetochore. The
Kinetochore is the large, multiprotein assembly that
serves to connect condensed sister chromatids to the
mitotic spindle. Ndc10 forms a dimer and it has
non-sequence-specific DNA binding activity via the DNA
backbone. Ndc10 also plays an important role in the
coordination of cell division. It has been noted that
the protein bears resemblance to the tyrosine
recombinases (type IB topoisomerase/lambda-integrase).
Length = 413
Score = 28.1 bits (63), Expect = 3.0
Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 2/44 (4%)
Query: 57 QKCRLVLPTWMN--LETLTEIKEEEKKSRFFIKMPSDHYMEMSH 98
Q +L P W + T E E S F +P D+ M+
Sbjct: 300 QDSQLQYPDWSDEEYNTFFEAYPSESDSAFPYNIPLDYIRIMNL 343
>gnl|CDD|212547 cd11581, GINS_A, Alpha-helical domain of GINS complex proteins;
Sld5, Psf1, Psf2 and Psf3. The GINS complex is involved
in both initiation and elongation stages of eukaryotic
chromosome replication, with GINS being the component
that most likely serves as the replicative helicase that
unwinds duplex DNA ahead of the moving replication fork.
In eukaryotes, GINS is a tetrameric arrangement of four
subunits Sld5, Psf1, Psf2 and Psf3. The GINS complex has
been found in eukaryotes and archaea, but not in
bacteria. The four subunits of the complex are
homologous and consist of two domains each, termed the
alpha-helical (A) and beta-strand (B) domains. The A and
B domains of Sld5/Psf1 are permuted with respect to
Psf1/Psf3.
Length = 103
Score = 26.7 bits (59), Expect = 3.8
Identities = 20/105 (19%), Positives = 35/105 (33%), Gaps = 21/105 (20%)
Query: 70 ETLTEIKEEEKKSRFFIKMPSDHYM----EMSHIILDIGADD---------IPNVDLIRT 116
E L E E+KS + P D + + ++ I + IR
Sbjct: 2 EKLAEAIHNERKSENLLPPPPDFMEEVKELLHRLSKRQRSETQEILEHRLKILELSYIRD 61
Query: 117 LIKDIWDLRISKLRSSIDTFVKSGGGHATLNHLTQFEINSIRNIL 161
L+K + R+ K+R ++LT+ EI +
Sbjct: 62 LLKTYLNSRLDKIRDLSP--------EFLPSNLTEEEIGYFQTYW 98
>gnl|CDD|180263 PRK05799, PRK05799, coproporphyrinogen III oxidase; Provisional.
Length = 374
Score = 27.3 bits (61), Expect = 5.7
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 10/63 (15%)
Query: 111 VDLIRTLIKDIWDLRISKLRSSIDTFVKSGGGHATLNHLTQFEINSIRNILCDVLDTMSS 170
++ I+ L K+I + +K SI F+ GGG T +L+ + IL + + ++
Sbjct: 33 MEYIKALSKEIRNSTKNKKIKSI--FI--GGG--TPTYLSLEAL----EILKETIKKLNK 82
Query: 171 LKD 173
+D
Sbjct: 83 KED 85
>gnl|CDD|212552 cd11714, GINS_A_archaea, Alpha-helical domain of archaeal GINS
complex proteins. The GINS complex is involved in
replication of archaeal and eukayotic genomes. The
archaeal DNA replication system is a simplified version
of that of the eukaryotes. Like its eukaryotic
counterpart, the archaeal GINS complex is tetrameric,
but instead of four different subunits (Sld5, Psf1, Psf2
and Psf3) it consists of two different proteins named
Gins51 and Gins23. All GINS subunits are homologs and
they can be classified into two groups. One group (the
eukayotic Sld5 and Psf1, as well as the archaeal Gins51)
has the alpha-helical (A) domain at the N-terminus and
the beta-strand domain (B) at the C-terminus (this
arrangement is called ABtype). The arrangement of the A
and B domains is reversed in the second group
(eukaryotic Psf2 and Psf3 and archaeal Gins23, also
referred to as BAtype). The overall fold of each
archaeal subunit and the overall tetrameric assembly of
GINS are similar, but the relative locations of the
C-terminal small domains are different with respect to
the alpha helical domain characterized by this model,
resulting in different subunit contacts in the archaeal
GINS complex.Some archaea may have a homotetrameric GINS
complex (4 copies of an AB-type module).
Length = 105
Score = 26.1 bits (58), Expect = 6.4
Identities = 21/105 (20%), Positives = 48/105 (45%), Gaps = 15/105 (14%)
Query: 69 LETLTEIKEEEKKSRFFIKMPSDHYMEMSHIILDIGAD---------DIPNVDLIRTLIK 119
+E L +I +E+KS K+P D Y I ++ + + ++ ++ ++
Sbjct: 1 IEELRKILFKERKSASLQKLPEDFYERAKEYIKELEEEARKSPEAQELLDELEKAKSTLR 60
Query: 120 DIWDLRISKLRSSIDTFVKSGGGHATLNHLTQFE---INSIRNIL 161
+++ LR+ K+ + + S L +LT E +S++ I+
Sbjct: 61 ELFRLRLRKI---VKLALLSAEDREELENLTPEEKELYDSLKEII 102
>gnl|CDD|133168 cd05036, PTKc_ALK_LTK, Catalytic domain of the Protein Tyrosine
Kinases, Anaplastic Lymphoma Kinase and Leukocyte
Tyrosine Kinase. Protein Tyrosine Kinase (PTK) family;
Anaplastic Lymphoma Kinase (ALK) and Leukocyte Tyrosine
(tyr) Kinase (LTK); catalytic (c) domain. The PTKc
family is part of a larger superfamily that includes
the catalytic domains of other kinases such as protein
serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to tyr
residues in protein substrates. ALK and LTK are orphan
receptor tyr kinases (RTKs) whose ligands are not yet
well-defined. RTKs contain an extracellular
ligand-binding domain, a transmembrane region, and an
intracellular tyr kinase domain. They are usually
activated through ligand binding, which causes
dimerization and autophosphorylation of the
intracellular tyr kinase catalytic domain. ALK appears
to play an important role in mammalian neural
development as well as visceral muscle differentiation
in Drosophila. ALK is aberrantly expressed as fusion
proteins, due to chromosomal translocations, in about
60% of anaplastic large cell lymphomas (ALCLs). ALK
fusion proteins are also found in rare cases of diffuse
large B cell lymphomas (DLBCLs). LTK is mainly
expressed in B lymphocytes and neuronal tissues. It is
important in cell proliferation and survival.
Transgenic mice expressing TLK display retarded growth
and high mortality rate. In addition, a polymorphism in
mouse and human LTK is implicated in the pathogenesis
of systemic lupus erythematosus.
Length = 277
Score = 27.0 bits (60), Expect = 7.1
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 4 AEIEFIAEDQNVEIIPKFNHLNLIHLI 30
E +F+ E I+ KFNH N++ LI
Sbjct: 52 DESDFLME---ALIMSKFNHQNIVRLI 75
>gnl|CDD|227085 COG4742, COG4742, Predicted transcriptional regulator
[Transcription].
Length = 260
Score = 26.4 bits (59), Expect = 8.2
Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 4/84 (4%)
Query: 58 KCRLVLPTWMNL-ETLTEIKEEEKKSRFFIKMPSDHYMEMSHIILDIGADDIPNVDLIRT 116
C L+ P +L E E E S+ + S + + L++ I +V LI T
Sbjct: 114 DCELLEPDLDHLFEPPPEFLENLSSSKRIMGFSSYFHPSYPSLYLELAEKGI-DVSLILT 172
Query: 117 LIKDIWDLRISKLRSSIDTFVKSG 140
+ +++ S + + F+K
Sbjct: 173 --EPVFERLKSDYKEELKEFLKLE 194
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 0.137 0.404
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,578,812
Number of extensions: 890911
Number of successful extensions: 791
Number of sequences better than 10.0: 1
Number of HSP's gapped: 782
Number of HSP's successfully gapped: 28
Length of query: 190
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 99
Effective length of database: 6,901,388
Effective search space: 683237412
Effective search space used: 683237412
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: 56 (25.3 bits)