RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7107
(76 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 67.1 bits (165), Expect = 5e-17
Identities = 24/45 (53%), Positives = 32/45 (71%)
Query: 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
RR RTTFT QL+ELE+ F++ YP REE+A K+ LTE +V+
Sbjct: 1 RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVK 45
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved
in the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 59.2 bits (144), Expect = 6e-14
Identities = 22/46 (47%), Positives = 31/46 (67%)
Query: 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76
RR RT FT QL+ELE+ F++ YP REE+A ++ LTE +V+
Sbjct: 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKI 46
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 58.0 bits (141), Expect = 2e-13
Identities = 23/46 (50%), Positives = 33/46 (71%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
+RR RT+FT QL+ELE+ FQ+ YP REE+A K+ L+E +V+
Sbjct: 1 KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVK 46
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 40.5 bits (95), Expect = 9e-06
Identities = 14/49 (28%), Positives = 23/49 (46%)
Query: 28 RKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76
+ R T QL LER F+ YP TR ++++ +++ VQ
Sbjct: 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQI 97
>gnl|CDD|238988 cd02030, NDUO42, NADH:Ubiquinone oxioreductase, 42 kDa (NDUO42) is
a family of proteins that are highly similar to
deoxyribonucleoside kinases (dNK). Members of this
family have been identified as one of the subunits of
NADH:Ubiquinone oxioreductase (complex I), a
multi-protein complex located in the inner mitochondrial
membrane. The main function of the complex is to
transport electrons from NADH to ubiquinone, which is
accompanied by the translocation of protons from the
mitochondrial matrix to the inter membrane space.
Length = 219
Score = 29.6 bits (67), Expect = 0.094
Identities = 17/49 (34%), Positives = 29/49 (59%), Gaps = 4/49 (8%)
Query: 27 KRKQRRIRT---TFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEA 72
KR ++R TSA L+++E A+++T P+I E+ ++ D TEA
Sbjct: 158 KRIKKRGDPHEMKVTSAYLQDIENAYKKTFLPEISEHSEV-LQYDWTEA 205
>gnl|CDD|235705 PRK06127, PRK06127, enoyl-CoA hydratase; Provisional.
Length = 269
Score = 26.6 bits (59), Expect = 1.2
Identities = 8/26 (30%), Positives = 10/26 (38%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYP 55
Q + F S +E AF E P
Sbjct: 239 QALVAACFDSEDYREGRAAFMEKRKP 264
>gnl|CDD|183523 PRK12427, PRK12427, flagellar biosynthesis sigma factor;
Provisional.
Length = 231
Score = 26.4 bits (58), Expect = 1.5
Identities = 14/35 (40%), Positives = 22/35 (62%)
Query: 40 AQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 74
+QL E E+ +Y + +EIA+ +DLTEAR+
Sbjct: 182 SQLDEREQLILHLYYQHEMSLKEIALVLDLTEARI 216
>gnl|CDD|173336 PTZ00039, PTZ00039, 40S ribosomal protein S20; Provisional.
Length = 115
Score = 25.9 bits (57), Expect = 1.8
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 26 EKRKQRRIRTTFTSAQLKELERA 48
E+ + +IR T TS LK +E+
Sbjct: 12 EQNRLHKIRITLTSKNLKSIEKV 34
>gnl|CDD|237336 PRK13288, PRK13288, pyrophosphatase PpaX; Provisional.
Length = 214
Score = 25.4 bits (56), Expect = 3.2
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 51 ETHYPDIYTREEIAMKI 67
+T+YP+ Y RE++ I
Sbjct: 30 KTYYPNQYKREDVLPFI 46
>gnl|CDD|223098 COG0019, LysA, Diaminopimelate decarboxylase [Amino acid transport
and metabolism].
Length = 394
Score = 25.3 bits (56), Expect = 3.2
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 7/40 (17%)
Query: 37 FTSAQLKELERAFQ------ETHY-PDIYTREEIAMKIDL 69
F A L ELE A + + EEIA ++L
Sbjct: 78 FDVASLGELELALAAGFPPERIVFSGPAKSEEEIAFALEL 117
>gnl|CDD|236872 PRK11183, PRK11183, D-lactate dehydrogenase; Provisional.
Length = 564
Score = 25.2 bits (56), Expect = 3.5
Identities = 10/23 (43%), Positives = 11/23 (47%)
Query: 19 GHEGVLTEKRKQRRIRTTFTSAQ 41
G VLT+ K R R F S Q
Sbjct: 14 GSSHVLTDPAKTERYRKGFRSGQ 36
>gnl|CDD|148314 pfam06632, XRCC4, DNA double-strand break repair and V(D)J
recombination protein XRCC4. This family consists of
several eukaryotic DNA double-strand break repair and
V(D)J recombination protein XRCC4 sequences. In the
non-homologous end joining pathway of DNA double-strand
break repair, the ligation step is catalyzed by a
complex of XRCC4 and DNA ligase IV. It is thought that
XRCC4 and ligase IV are essential for alignment-based
gap filling, as well as for final ligation of the
breaks.
Length = 331
Score = 25.2 bits (55), Expect = 3.7
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 27 KRKQRRIRTTFTSAQLKELERAFQETHYPD 56
KR+QR + T ++ E+ QE PD
Sbjct: 270 KRRQRMQKNLGTEPKMATQEQQLQEKEKPD 299
>gnl|CDD|220966 pfam11072, DUF2859, Protein of unknown function (DUF2859). This is
a bacterial family of uncharacterized proteins.
Length = 142
Score = 24.9 bits (55), Expect = 3.9
Identities = 6/21 (28%), Positives = 8/21 (38%)
Query: 44 ELERAFQETHYPDIYTREEIA 64
+L HYP + T I
Sbjct: 122 DLAERLGLRHYPVLITATGIE 142
>gnl|CDD|183733 PRK12769, PRK12769, putative oxidoreductase Fe-S binding subunit;
Reviewed.
Length = 654
Score = 25.1 bits (55), Expect = 4.0
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 21 EGVLTEKRKQRRIRTTFTSAQ 41
E L+ K RR+RT Q
Sbjct: 147 EQALSGMAKSRRLRTARQEHQ 167
>gnl|CDD|225623 COG3081, COG3081, Nucleoid-associated protein [General function
prediction only].
Length = 335
Score = 25.1 bits (55), Expect = 4.3
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 52 THYPDIYTREEIAMKIDLTEARVQK 76
THY DI + +I +IDLTE
Sbjct: 138 THYLDI-NQADIVARIDLTEWETNP 161
>gnl|CDD|237528 PRK13840, PRK13840, sucrose phosphorylase; Provisional.
Length = 495
Score = 25.0 bits (55), Expect = 5.0
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 6/32 (18%)
Query: 11 GLPYKVYSGHEGVLTEKRKQRRIRTTFTSAQL 42
GLP+ Y+ +G K R + TTFT Q+
Sbjct: 137 GLPFTTYTLADG------KTRLVWTTFTPQQI 162
>gnl|CDD|215695 pfam00075, RNase_H, RNase H. RNase H digests the RNA strand of
an RNA/DNA hybrid. Important enzyme in retroviral
replication cycle, and often found as a domain
associated with reverse transcriptases. Structure is a
mixed alpha+beta fold with three a/b/a layers.
Length = 126
Score = 24.5 bits (54), Expect = 5.6
Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 8 SCGGLPYKVYSGHEGVLTEKRKQRRIRTTFTSAQLKELE 46
SC G P G G +T+ KQR T+ Q EL
Sbjct: 11 SCNGNPGP---GGAGYVTDGGKQRSKPLPGTTNQRAELL 46
>gnl|CDD|106307 PRK13349, PRK13349, superantigen-like protein; Reviewed.
Length = 241
Score = 24.6 bits (53), Expect = 6.6
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 14 YKVYSGHEGVLTEKRKQRRIRTTF 37
+ VY G++ VLT K RIR T
Sbjct: 160 FPVYEGNKPVLTLKELDFRIRQTL 183
>gnl|CDD|221903 pfam13030, DUF3891, Protein of unknown function (DUF3891). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and archaea.
Proteins in this family are approximately 250 amino
acids in length.
Length = 221
Score = 24.2 bits (53), Expect = 6.8
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 26 EKRKQRRIRTTFTSAQLKELERAFQ 50
E+++Q R+ T E+ER +
Sbjct: 128 EEQRQERLLATLGIEPKAEVERHYA 152
>gnl|CDD|218187 pfam04637, Herpes_pp85, Herpesvirus phosphoprotein 85 (HHV6-7
U14/HCMV UL25). This family includes UL25 proteins from
HCMV, as well as U14 proteins from HHV 6 and HHV7. These
85 kD phosphoproteins appear to act as structural
antigens, but their precise function is otherwise
unknown.
Length = 502
Score = 24.3 bits (53), Expect = 7.0
Identities = 12/59 (20%), Positives = 16/59 (27%)
Query: 4 LVVLSCGGLPYKVYSGHEGVLTEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREE 62
L L Y L K +R + E RA+ P +T E
Sbjct: 125 SESLGDLDLTDGQYKAALRTLYRLLKSLGLRESPELESCYETLRAYNLLFKPPRFTTRE 183
>gnl|CDD|143650 cd07934, RHD-n_NFkB2, N-terminal sub-domain of the Rel homology
domain (RHD) of nuclear factor kappa B2 (NF-kappa B2).
Proteins containing the Rel homology domain (RHD) are
metazoan transcription factors. The RHD is composed of
two structural sub-domains; this model characterizes the
N-terminal RHD sub-domain of the NF-kappa B2 family of
transcription factors, a class I member of the NF-kappa
B family. In class I NF-kappa Bs, the RHD domain
co-occurs with C-terminal ankyrin repeats. NF-kappa B2
is commonly referred to as p100 or p52 (proteolytically
processed form). NF-kappa B proteins are part of a
protein complex that acts as a transcription factor,
which is responsible for regulating a host of cellular
responses to a variety of stimuli. This complex tightly
regulates the expression of a large number of genes, and
is involved in processes such as adaptive and innate
immunity, stress response, inflammation, cell adhesion,
proliferation and apoptosis. The cytosolic NF-kappa B
complex is activated via phosphorylation of the
ankyrin-repeat containing inhibitory protein I-kappa B,
which dissociates from the complex and exposes the
nuclear localization signal of the heterodimer (NF-kappa
B and REL). NF-kappa B2 is involved in the alternative
NF-kappa B signaling pathway which is activated by few
agonists and plays an important role in secondary
lymphoid organogenesis, maturation of B-cells, and
adaptive humoral immunity. p100 may also act as an
I-kappa B due to its C-terminal ankyrin repeats.
Length = 185
Score = 24.1 bits (52), Expect = 9.8
Identities = 12/34 (35%), Positives = 21/34 (61%), Gaps = 4/34 (11%)
Query: 22 GVLTEKRKQRRIRTT----FTSAQLKELERAFQE 51
+L EK K++++R T T A+ +ELE+ +E
Sbjct: 111 EILKEKLKRQKLRNTGPYKLTEAEERELEQEAKE 144
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 0.135 0.379
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,867,552
Number of extensions: 296455
Number of successful extensions: 361
Number of sequences better than 10.0: 1
Number of HSP's gapped: 361
Number of HSP's successfully gapped: 28
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 (21.9 bits)
S2: 53 (24.1 bits)