RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12012
(79 letters)
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 29.7 bits (66), Expect = 0.12
Identities = 11/22 (50%), Positives = 17/22 (77%)
Query: 25 FVCDVCDRRYKYKSGLYQHKKY 46
+ C+VCD+RYK +GL H+K+
Sbjct: 399 YRCEVCDKRYKNLNGLKYHRKH 420
Score = 27.8 bits (61), Expect = 0.59
Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 22/74 (29%)
Query: 25 FVCDV--CDRRYKYKSGLYQHKKYE------------------CGKEPRYQCPQCPHRTK 64
+ C V C+++YK ++GL H + K+ Y+C C R K
Sbjct: 350 YKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYK 409
Query: 65 QKSSLKTHMAVKHS 78
+ LK H KHS
Sbjct: 410 NLNGLKYH--RKHS 421
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 29.2 bits (66), Expect = 0.16
Identities = 15/51 (29%), Positives = 19/51 (37%), Gaps = 11/51 (21%)
Query: 22 AGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTH 72
A ++ C C R Y+S Y K CP C H+ LK H
Sbjct: 79 AKIYKCPKCPRPTCYQS-------YGSSKPDNPPCPGCGHKMT----LKRH 118
>gnl|CDD|206675 cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2
gamma). eIF2 is a heterotrimeric translation
initiation factor that consists of alpha, beta, and
gamma subunits. The GTP-bound gamma subunit also binds
initiator methionyl-tRNA and delivers it to the 40S
ribosomal subunit. Following hydrolysis of GTP to GDP,
eIF2:GDP is released from the ribosome. The gamma
subunit has no intrinsic GTPase activity, but is
stimulated by the GTPase activating protein (GAP) eIF5,
and GDP/GTP exchange is stimulated by the guanine
nucleotide exchange factor (GEF) eIF2B. eIF2B is a
heteropentamer, and the epsilon chain binds eIF2. Both
eIF5 and eIF2B-epsilon are known to bind strongly to
eIF2-beta, but have also been shown to bind directly to
eIF2-gamma. It is possible that eIF2-beta serves simply
as a high-affinity docking site for eIF5 and
eIF2B-epsilon, or that eIF2-beta serves a regulatory
role. eIF2-gamma is found only in eukaryotes and
archaea. It is closely related to SelB, the
selenocysteine-specific elongation factor from
eubacteria. The translational factor components of the
ternary complex, IF2 in eubacteria and eIF2 in
eukaryotes are not the same protein (despite their
unfortunately similar names). Both factors are GTPases;
however, eubacterial IF-2 is a single polypeptide,
while eIF2 is heterotrimeric. eIF2-gamma is a member of
the same family as eubacterial IF2, but the two
proteins are only distantly related. This family
includes translation initiation, elongation, and
release factors.
Length = 197
Score = 27.6 bits (62), Expect = 0.46
Identities = 9/43 (20%), Positives = 12/43 (27%), Gaps = 13/43 (30%)
Query: 22 AGLFVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTK 64
A ++ C C P +CP C TK
Sbjct: 45 AKIYKCPNCGC-------------PRPYDTPECECPGCGGETK 74
>gnl|CDD|153061 cd03591, CLECT_collectin_like, C-type lectin-like domain (CTLD)
of the type found in human collectins including lung
surfactant proteins A and D, mannose- or mannan binding
lectin (MBL), and CL-L1 (collectin liver 1).
CLECT_collectin_like: C-type lectin-like domain (CTLD)
of the type found in human collectins including lung
surfactant proteins A and D, mannose- or mannan binding
lectin (MBL), and CL-L1 (collectin liver 1). CTLD
refers to a domain homologous to the
carbohydrate-recognition domains (CRDs) of the C-type
lectins. The CTLDs of these collectins bind
carbohydrates on surfaces (e.g. pathogens, allergens,
necrotic, or apoptotic cells) and mediate functions
associated with killing and phagocytosis. MBPs
recognize high mannose oligosaccharides in a calcium
dependent manner, bind to a broad range of pathogens,
and trigger cell killing by activating the complement
pathway. MBP also acts directly as an opsonin. SP-A
and SP-D in addition to functioning as host defense
components, are components of pulmonary surfactant
which play a role in surfactant homeostasis. Pulmonary
surfactant is a phospholipid-protein complex which
reduces the surface tension within the lungs. SP-A
binds the major surfactant lipid:
dipalmitoylphosphatidylcholine (DPPC). SP-D binds two
minor components of surfactant that contain sugar
moieties: glucosylceramide and phosphatidylinositol
(PI). MBP and SP-A, -D monomers are homotrimers with
an N-terminal collagen region and three CTLDs.
Multiple homotrimeric units associate to form
supramolecular complexes. MBL deficiency results in an
increased susceptibility to a large number of different
infections and to inflammatory disease, such as
rheumatoid arthritis.
Length = 114
Score = 27.3 bits (61), Expect = 0.59
Identities = 10/25 (40%), Positives = 17/25 (68%), Gaps = 4/25 (16%)
Query: 3 GQFRFSE----SFTSWEASEPNHAG 23
GQF + + ++T+W+ EPN+AG
Sbjct: 61 GQFVYLDGGPLTYTNWKPGEPNNAG 85
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 26.4 bits (58), Expect = 1.1
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 3/54 (5%)
Query: 25 FVCDVCDRRYKYKSGLYQHKKYECGKEPRYQCPQCPHRTKQKSSLKTHMAVKHS 78
+VC +C + L QH +Y E CP C + S H+ KH+
Sbjct: 74 YVCPLCLMPFSSSVSLKQHIRY---TEHSKVCPVCGKEFRNTDSTLDHVCKKHN 124
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 25.1 bits (55), Expect = 1.2
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 54 YQCPQCPHRTKQKSSLKTHMAV 75
Y+CP+C K KS+L+ HM
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 24.9 bits (55), Expect = 1.2
Identities = 7/24 (29%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 54 YQCPQCPHRTKQKSSLKTHMAVKH 77
Y+C CP+ + L+ H+ + H
Sbjct: 1 YKCSHCPYSST-PKKLERHLKLHH 23
>gnl|CDD|227506 COG5179, TAF1, Transcription initiation factor TFIID, subunit TAF1
[Transcription].
Length = 968
Score = 26.2 bits (57), Expect = 1.7
Identities = 8/34 (23%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 45 KYECGKEPRYQCPQCPHRTKQKSSLKTHMAVKHS 78
K+ + Y + H++K +++L T + ++HS
Sbjct: 359 KFNISNDKYYGILKKTHQSKVRNTLST-LGIQHS 391
>gnl|CDD|219926 pfam08600, Rsm1, Rsm1-like. Rsm1 is a protein involved in mRNA
export from the nucleus.
Length = 91
Score = 25.5 bits (56), Expect = 2.0
Identities = 7/24 (29%), Positives = 9/24 (37%)
Query: 10 SFTSWEASEPNHAGLFVCDVCDRR 33
+ W+ GL C C RR
Sbjct: 5 ALFGWDGLPDGRLGLASCGTCFRR 28
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family
contains a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 24.1 bits (52), Expect = 2.9
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 54 YQCPQCPHRTKQKSSLKTHMAVKH 77
++CP C K +LK H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 25.8 bits (57), Expect = 2.9
Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 8/39 (20%)
Query: 23 GLFVCDVCDRRYKYKSGLYQHKKYECG--KEPRYQCPQC 59
G C C Y+++ +CG EP Y CP C
Sbjct: 666 GRRRCPSCGTE------TYENRCPDCGTHTEPVYVCPDC 698
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 23.0 bits (50), Expect = 5.6
Identities = 8/27 (29%), Positives = 11/27 (40%)
Query: 24 LFVCDVCDRRYKYKSGLYQHKKYECGK 50
+ C VC + + L HKK C
Sbjct: 1 VHTCGVCGKTFSSLQALGGHKKSHCSL 27
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 24.5 bits (54), Expect = 6.8
Identities = 5/9 (55%), Positives = 7/9 (77%)
Query: 51 EPRYQCPQC 59
E +Y CP+C
Sbjct: 96 EMKYTCPKC 104
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys.
The C2H2 zinc finger is composed of two short beta
strands followed by an alpha helix. The amino terminal
part of the helix binds the major groove in DNA binding
zinc fingers. The accepted consensus binding sequence
for Sp1 is usually defined by the asymmetric
hexanucleotide core GGGCGG but this sequence does not
include, among others, the GAG (=CTC) repeat that
constitutes a high-affinity site for Sp1 binding to the
wt1 promoter.
Length = 22
Score = 22.7 bits (49), Expect = 9.2
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 55 QCPQCPHRTKQKSSLKTHM 73
+CP C +KS+LK H+
Sbjct: 1 KCPDCGKSFSRKSNLKRHL 19
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 0.133 0.442
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,539,994
Number of extensions: 235885
Number of successful extensions: 271
Number of sequences better than 10.0: 1
Number of HSP's gapped: 269
Number of HSP's successfully gapped: 32
Length of query: 79
Length of database: 10,937,602
Length adjustment: 48
Effective length of query: 31
Effective length of database: 8,808,610
Effective search space: 273066910
Effective search space used: 273066910
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 (21.9 bits)
S2: 53 (24.3 bits)