RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4926
(176 letters)
>gnl|CDD|214559 smart00209, TSP1, Thrombospondin type 1 repeats. Type 1 repeats
in thrombospondin-1 bind and activate TGF-beta.
Length = 53
Score = 39.5 bits (92), Expect = 3e-05
Identities = 19/53 (35%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 30 VGSWEAWSECDTECGPGTMVRTRKAI-QEPKNGGKHCPTL-TQKRSCLGTRCP 80
W WS C CG G RTR P+NGG C + R+C CP
Sbjct: 1 WSEWSEWSPCSVTCGGGVQTRTRSCCSPPPQNGGGPCTGEDVETRACNEQPCP 53
>gnl|CDD|240420 PTZ00441, PTZ00441, sporozoite surface protein 2 (SSP2);
Provisional.
Length = 576
Score = 34.6 bits (79), Expect = 0.019
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 31 GSWEAWSECDTECGPGTMVRTRKAIQEPKNGGKHCPTLTQKRSCLGTRCPHNP 83
G W+ W+ C CG GT R+R + E C T + C CP P
Sbjct: 241 GPWDEWTPCSVTCGKGTHSRSRPILHE------GCTTHMVEE-CEEEECPVEP 286
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 34.3 bits (79), Expect = 0.022
Identities = 17/45 (37%), Positives = 19/45 (42%), Gaps = 4/45 (8%)
Query: 6 GEEGRDKEEEEEEEEEEREMSDCQVGSW----EAWSECDTECGPG 46
RD EEEE+EEEEE E D E + E D E
Sbjct: 384 ANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDDVESKYE 428
>gnl|CDD|215709 pfam00090, TSP_1, Thrombospondin type 1 domain.
Length = 48
Score = 30.5 bits (69), Expect = 0.063
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 3/48 (6%)
Query: 33 WEAWSECDTECGPGTMVRTRKAIQEPKNGGKHCP-TLTQKRSCLGTRC 79
W WS C CG G R R GG C + + +C+ +C
Sbjct: 3 WSEWSPCSVTCGKGIRTRQRTCNSPF--GGPPCTGDVQETEACMMDKC 48
>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2
[Translation, ribosomal structure and biogenesis].
Length = 109
Score = 31.6 bits (72), Expect = 0.063
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 5 KGEEGRDKEEEEEEEEEEREMSD 27
E +EEE+EEE EE D
Sbjct: 80 AAEADEAEEEEKEEEAEEESDDD 102
Score = 31.2 bits (71), Expect = 0.084
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 5 KGEEGRDKEEEEEEEEEEREMSD 27
E + EEEE+EEE E E D
Sbjct: 79 AAAEADEAEEEEKEEEAEEESDD 101
Score = 27.4 bits (61), Expect = 1.8
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 6 GEEGRDKEEEEEEEEEERE 24
E + +E EEEE+EE
Sbjct: 77 AEAAAEADEAEEEEKEEEA 95
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 31.1 bits (71), Expect = 0.068
Identities = 10/14 (71%), Positives = 13/14 (92%)
Query: 12 KEEEEEEEEEEREM 25
K+EEEEEEEE+ +M
Sbjct: 70 KKEEEEEEEEDDDM 83
Score = 29.5 bits (67), Expect = 0.30
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 11 DKEEEEEEEEEEREMSD 27
EEE++EEEE E D
Sbjct: 64 AAAEEEKKEEEEEEEED 80
Score = 28.4 bits (64), Expect = 0.65
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 11 DKEEEEEEEEEEREM 25
++++EEEEEEEE +
Sbjct: 68 EEKKEEEEEEEEDDD 82
Score = 27.2 bits (61), Expect = 1.9
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 6 GEEGRDKEEEEEEEEEERE 24
++E++EEEEEEE +
Sbjct: 62 AAAAAEEEKKEEEEEEEED 80
>gnl|CDD|202558 pfam03159, XRN_N, XRN 5'-3' exonuclease N-terminus. This family
aligns residues towards the N-terminus of several
proteins with multiple functions. The members of this
family all appear to possess 5'-3' exonuclease activity
EC:3.1.11.-. Thus, the aligned region may be necessary
for 5' to 3' exonuclease function. The family also
contains several Xrn1 and Xrn2 proteins. The 5'-3'
exoribonucleases Xrn1p and Xrn2p/Rat1p function in the
degradation and processing of several classes of RNA in
Saccharomyces cerevisiae. Xrn1p is the main enzyme
catalyzing cytoplasmic mRNA degradation in multiple
decay pathways, whereas Xrn2p/Rat1p functions in the
processing of rRNAs and small nucleolar RNAs (snoRNAs)
in the nucleus.
Length = 237
Score = 31.5 bits (72), Expect = 0.14
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 2 RVRKGEEGRDKEEEEEEEEEEREMSDCQVGSWEAWSECDTEC-GPGT--MVRTRKAIQ 56
R R ++ ++KE E EE EE E ++ + D+ C PGT M R KA++
Sbjct: 100 RFRAAKDAKEKEAEAEENREELETEGIKLPEKVEKEKFDSNCITPGTPFMARLAKALR 157
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 31.5 bits (71), Expect = 0.23
Identities = 13/18 (72%), Positives = 15/18 (83%)
Query: 7 EEGRDKEEEEEEEEEERE 24
EE ++EEEEEEEEEE E
Sbjct: 871 EEEEEEEEEEEEEEEEEE 888
Score = 31.5 bits (71), Expect = 0.26
Identities = 13/18 (72%), Positives = 15/18 (83%)
Query: 7 EEGRDKEEEEEEEEEERE 24
EE ++EEEEEEEEEE E
Sbjct: 866 EEEEEEEEEEEEEEEEEE 883
Score = 31.1 bits (70), Expect = 0.32
Identities = 14/19 (73%), Positives = 15/19 (78%)
Query: 6 GEEGRDKEEEEEEEEEERE 24
G +G D EEEEEEEEEE E
Sbjct: 857 GSDGGDSEEEEEEEEEEEE 875
Score = 31.1 bits (70), Expect = 0.32
Identities = 13/18 (72%), Positives = 15/18 (83%)
Query: 7 EEGRDKEEEEEEEEEERE 24
EE ++EEEEEEEEEE E
Sbjct: 867 EEEEEEEEEEEEEEEEEE 884
Score = 31.1 bits (70), Expect = 0.34
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 7 EEGRDKEEEEEEEEEEREMSD 27
EE ++EEEEEEEEEE E +
Sbjct: 869 EEEEEEEEEEEEEEEEEEEEE 889
Score = 30.3 bits (68), Expect = 0.52
Identities = 13/18 (72%), Positives = 15/18 (83%)
Query: 7 EEGRDKEEEEEEEEEERE 24
EE ++EEEEEEEEEE E
Sbjct: 864 EEEEEEEEEEEEEEEEEE 881
Score = 30.3 bits (68), Expect = 0.60
Identities = 13/18 (72%), Positives = 15/18 (83%)
Query: 7 EEGRDKEEEEEEEEEERE 24
EE ++EEEEEEEEEE E
Sbjct: 868 EEEEEEEEEEEEEEEEEE 885
Score = 30.3 bits (68), Expect = 0.63
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 6 GEEGRDKEEEEEEEEEERE 24
G + ++EEEEEEEEEE E
Sbjct: 860 GGDSEEEEEEEEEEEEEEE 878
Score = 30.0 bits (67), Expect = 0.68
Identities = 13/18 (72%), Positives = 15/18 (83%)
Query: 7 EEGRDKEEEEEEEEEERE 24
EE ++EEEEEEEEEE E
Sbjct: 874 EEEEEEEEEEEEEEEENE 891
Score = 30.0 bits (67), Expect = 0.83
Identities = 13/18 (72%), Positives = 15/18 (83%)
Query: 7 EEGRDKEEEEEEEEEERE 24
EE ++EEEEEEEEEE E
Sbjct: 865 EEEEEEEEEEEEEEEEEE 882
Score = 29.2 bits (65), Expect = 1.2
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 7 EEGRDKEEEEEEEEEEREMS 26
EE ++EEEEEEEE E +S
Sbjct: 876 EEEEEEEEEEEEEENEEPLS 895
Score = 29.2 bits (65), Expect = 1.2
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 7 EEGRDKEEEEEEEEEERE 24
EE ++EEEEEEEEEE
Sbjct: 873 EEEEEEEEEEEEEEEEEN 890
Score = 29.2 bits (65), Expect = 1.3
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 7 EEGRDKEEEEEEEEEERE 24
EE ++EEEEEEEEE E
Sbjct: 875 EEEEEEEEEEEEEEENEE 892
Score = 28.8 bits (64), Expect = 1.6
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 6 GEEGRDKEEEEEEEEEERE 24
G+ ++EEEEEEEEEE E
Sbjct: 861 GDSEEEEEEEEEEEEEEEE 879
Score = 28.8 bits (64), Expect = 2.0
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 6 GEEGRDKEEEEEEEEEERE 24
+ G +EEEEEEEEEE E
Sbjct: 858 SDGGDSEEEEEEEEEEEEE 876
Score = 27.7 bits (61), Expect = 4.0
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 6 GEEGRDKEEEEEEEEEEREMSD 27
G G D + EEEEEEE E +
Sbjct: 854 GGGGSDGGDSEEEEEEEEEEEE 875
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 30.0 bits (68), Expect = 0.27
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 6 GEEGRDKEEEEEEEEEEREMSD 27
++EEEEEEEEEE E S+
Sbjct: 72 AAAAEEEEEEEEEEEEEEEESE 93
Score = 28.5 bits (64), Expect = 0.94
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 7 EEGRDKEEEEEEEEEEREMS 26
EE ++EEEEEEE EE M+
Sbjct: 79 EEEEEEEEEEEEESEEEAMA 98
Score = 28.5 bits (64), Expect = 0.95
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 7 EEGRDKEEEEEEEEEERE 24
EE ++EEEEEEEE E E
Sbjct: 78 EEEEEEEEEEEEEESEEE 95
Score = 28.1 bits (63), Expect = 0.99
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 7 EEGRDKEEEEEEEEEERE 24
EE ++EEEEEEEEE E
Sbjct: 77 EEEEEEEEEEEEEEESEE 94
Score = 27.3 bits (61), Expect = 2.0
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 5 KGEEGRDKEEEEEEEEEERE 24
E ++EEEEEEEEEE
Sbjct: 73 AAAEEEEEEEEEEEEEEEES 92
Score = 26.9 bits (60), Expect = 2.5
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 5 KGEEGRDKEEEEEEEEEE 22
+ EE ++EEEEEE EEE
Sbjct: 78 EEEEEEEEEEEEEESEEE 95
Score = 26.2 bits (58), Expect = 5.3
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 6 GEEGRDKEEEEEEEEEERE 24
++EEEEEEEEEE E
Sbjct: 71 AAAAAEEEEEEEEEEEEEE 89
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 29.9 bits (68), Expect = 0.28
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 7 EEGRDKEEEEEEEEEEREMS 26
++ ++EEEE+EE EE +
Sbjct: 80 KKEEEEEEEEKEESEEEAAA 99
Score = 29.2 bits (66), Expect = 0.51
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 7 EEGRDKEEEEEEEEEERE 24
E+ ++EEEEE+EE E E
Sbjct: 79 EKKEEEEEEEEKEESEEE 96
Score = 28.8 bits (65), Expect = 0.67
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 7 EEGRDKEEEEEEEEEEREMSD 27
++++EEEEEEEE+E S+
Sbjct: 74 AAAAEEKKEEEEEEEEKEESE 94
Score = 28.8 bits (65), Expect = 0.75
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 5 KGEEGRDKEEEEEEEEEERE 24
EE +++EEEEEE+EE E
Sbjct: 76 AAEEKKEEEEEEEEKEESEE 95
Score = 28.4 bits (64), Expect = 0.86
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 5 KGEEGRDKEEEEEEEEEERE 24
E + +EEEEEEE+EE E
Sbjct: 75 AAAEEKKEEEEEEEEKEESE 94
Score = 26.1 bits (58), Expect = 5.1
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 6 GEEGRDKEEEEEEEEEERE 24
+E++EEEEEEE +
Sbjct: 72 AAAAAAEEKKEEEEEEEEK 90
Score = 26.1 bits (58), Expect = 6.3
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 5 KGEEGRDKEEEEEEEEE 21
K EE ++EE+EE EEE
Sbjct: 80 KKEEEEEEEEKEESEEE 96
>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II). Bone
sialoprotein (BSP) is a major structural protein of the
bone matrix that is specifically expressed by
fully-differentiated osteoblasts. The expression of bone
sialoprotein (BSP) is normally restricted to mineralised
connective tissues of bones and teeth where it has been
associated with mineral crystal formation. However, it
has been found that ectopic expression of BSP occurs in
various lesions, including oral and extraoral
carcinomas, in which it has been associated with the
formation of microcrystalline deposits and the
metastasis of cancer cells to bone.
Length = 291
Score = 30.8 bits (69), Expect = 0.33
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 4 RKGEEGRDKEEEEEEEEEEREMSDCQVG 31
++ E D+EEEEEEEEEE E+ + + G
Sbjct: 131 KEDESDEDEEEEEEEEEEEAEVEENEQG 158
Score = 27.4 bits (60), Expect = 4.5
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 2 RVRKGEEGRDKEEEEEEEEEEREMSD 27
+ + +E ++EEEEEEEE E E ++
Sbjct: 131 KEDESDEDEEEEEEEEEEEAEVEENE 156
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 30.1 bits (68), Expect = 0.48
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 5 KGEEGRDKEEEEEEEEEEREMSD 27
E+ +D+EEEEEEEEE+ + D
Sbjct: 169 DEEDEKDEEEEEEEEEEDEDFDD 191
>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A. The
CAF-1 or chromatin assembly factor-1 consists of three
subunits, and this is the first, or A. The A domain is
uniquely required for the progression of S phase in
mouse cells, independent of its ability to promote
histone deposition but dependent on its ability to
interact with HP1 - heterochromatin protein 1-rich
heterochromatin domains next to centromeres that are
crucial for chromosome segregation during mitosis. This
HP1-CAF-1 interaction module functions as a built-in
replication control for heterochromatin, which, like a
control barrier, has an impact on S-phase progression
in addition to DNA-based checkpoints.
Length = 76
Score = 28.3 bits (64), Expect = 0.50
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 7 EEGRDKEEEEEEEEEEREMSD 27
EEG D E E+EE+EEE + D
Sbjct: 52 EEGEDLESEDEEDEEEDDDDD 72
Score = 27.6 bits (62), Expect = 0.96
Identities = 8/22 (36%), Positives = 16/22 (72%)
Query: 6 GEEGRDKEEEEEEEEEEREMSD 27
GE+ ++EE+EEE+++ +M
Sbjct: 54 GEDLESEDEEDEEEDDDDDMDG 75
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 30.2 bits (69), Expect = 0.56
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 7 EEGRDKEEEEEEEEEEREMSD 27
EE ++EEEEEEE E E +
Sbjct: 303 EEEEEEEEEEEEEPSEEEAAA 323
Score = 29.1 bits (66), Expect = 1.3
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 5 KGEEGRDKEEEEEEEEEE 22
+ EE ++EEEEEE EE
Sbjct: 302 EEEEEEEEEEEEEEPSEE 319
Score = 28.7 bits (65), Expect = 1.8
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 7 EEGRDKEEEEEEEEEERE 24
E ++EEEEEEEEE E
Sbjct: 301 AEEEEEEEEEEEEEEPSE 318
Score = 27.9 bits (63), Expect = 2.9
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 7 EEGRDKEEEEEEEEEERE 24
EE ++EEEEEEEE E
Sbjct: 302 EEEEEEEEEEEEEEPSEE 319
Score = 27.1 bits (61), Expect = 4.8
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 5 KGEEGRDKEEEEEEEEE 21
+ EE ++EEEE EEE
Sbjct: 304 EEEEEEEEEEEEPSEEE 320
Score = 26.8 bits (60), Expect = 6.8
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 7 EEGRDKEEEEEEEEEERE 24
++EEEEEEEEEE
Sbjct: 300 AAEEEEEEEEEEEEEEPS 317
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is
functionally equivalent to L7/L12 in bacteria and the
P1 and P2 proteins in eukaryotes. L12p is homologous to
P1 and P2 but is not homologous to bacterial L7/L12. It
is located in the L12 stalk, with proteins L10, L11,
and 23S rRNA. L12p is the only protein in the ribosome
to occur as multimers, always appearing as sets of
dimers. Recent data indicate that most archaeal species
contain six copies of L12p (three homodimers), while
eukaryotes have four copies (two heterodimers), and
bacteria may have four or six copies (two or three
homodimers), depending on the species. The organization
of proteins within the stalk has been characterized
primarily in bacteria, where L7/L12 forms either two or
three homodimers and each homodimer binds to the
extended C-terminal helix of L10. L7/L12 is attached to
the ribosome through L10 and is the only ribosomal
protein that does not directly interact with rRNA.
Archaeal L12p is believed to function in a similar
fashion. However, hybrid ribosomes containing the large
subunit from E. coli with an archaeal stalk are able to
bind archaeal and eukaryotic elongation factors but not
bacterial elongation factors. In several mesophilic and
thermophilic archaeal species, the binding of 23S rRNA
to protein L11 and to the L10/L12p pentameric complex
was found to be temperature-dependent and cooperative.
Length = 106
Score = 28.2 bits (63), Expect = 0.98
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 5 KGEEGRDKEEEEEEEEEE 22
+ EE + KEEE+EEEEEE
Sbjct: 80 EKEEEKKKEEEKEEEEEE 97
Score = 28.2 bits (63), Expect = 1.1
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 5 KGEEGRDKEEEEEEEEEERE 24
EE +++EEE+++EEE+E
Sbjct: 73 AAEEKAEEKEEEKKKEEEKE 92
Score = 27.8 bits (62), Expect = 1.5
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 7 EEGRDKEEEEEEEEEEREMS 26
+E K+EEE+EEEEE ++
Sbjct: 81 KEEEKKKEEEKEEEEEEALA 100
Score = 27.5 bits (61), Expect = 1.7
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 5 KGEEGRDKEEEEEEEEEERE 24
E+ +K++EEE+EEEE E
Sbjct: 78 AEEKEEEKKKEEEKEEEEEE 97
Score = 27.5 bits (61), Expect = 2.0
Identities = 7/20 (35%), Positives = 14/20 (70%)
Query: 5 KGEEGRDKEEEEEEEEEERE 24
+ + +EE+++EEE+E E
Sbjct: 75 EEKAEEKEEEKKKEEEKEEE 94
Score = 26.7 bits (59), Expect = 3.4
Identities = 8/20 (40%), Positives = 16/20 (80%)
Query: 5 KGEEGRDKEEEEEEEEEERE 24
+ E +++E+++EEE+EE E
Sbjct: 76 EKAEEKEEEKKKEEEKEEEE 95
>gnl|CDD|185582 PTZ00373, PTZ00373, 60S Acidic ribosomal protein P2; Provisional.
Length = 112
Score = 27.6 bits (61), Expect = 1.8
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 6 GEEGRDKEEEEEEEEEEREM 25
E + +E++EEEEEEE ++
Sbjct: 87 KAEAKKEEKKEEEEEEEDDL 106
Score = 26.4 bits (58), Expect = 4.5
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 5 KGEEGRDKEEEEEEEEEE 22
K E +++++EEEEEEE+
Sbjct: 87 KAEAKKEEKKEEEEEEED 104
>gnl|CDD|100109 cd05831, Ribosomal_P1, Ribosomal protein P1. This subfamily
represents the eukaryotic large ribosomal protein P1.
Eukaryotic P1 and P2 are functionally equivalent to the
bacterial protein L7/L12, but are not homologous to
L7/L12. P1 is located in the L12 stalk, with proteins
P2, P0, L11, and 28S rRNA. P1 and P2 are the only
proteins in the ribosome to occur as multimers, always
appearing as sets of heterodimers. Recent data indicate
that eukaryotes have four copies (two heterodimers),
while most archaeal species contain six copies of L12p
(three homodimers) and bacteria may have four or six
copies (two or three homodimers), depending on the
species. Experiments using S. cerevisiae P1 and P2
indicate that P1 proteins are positioned more
internally with limited reactivity in the C-terminal
domains, while P2 proteins seem to be more externally
located and are more likely to interact with other
cellular components. In lower eukaryotes, P1 and P2 are
further subdivided into P1A, P1B, P2A, and P2B, which
form P1A/P2B and P1B/P2A heterodimers. Some plant
species have a third P-protein, called P3, which is not
homologous to P1 and P2. In humans, P1 and P2 are
strongly autoimmunogenic. They play a significant role
in the etiology and pathogenesis of systemic lupus
erythema (SLE). In addition, the ribosome-inactivating
protein trichosanthin (TCS) interacts with human P0,
P1, and P2, with its primary binding site located in
the C-terminal region of P2. TCS inactivates the
ribosome by depurinating a specific adenine in the
sarcin-ricin loop of 28S rRNA.
Length = 103
Score = 27.3 bits (61), Expect = 2.1
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 6 GEEGRDKEEEEEEEEEEREM 25
KEE++EEEEEE +
Sbjct: 77 AAAEAKKEEKKEEEEEESDD 96
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein. This
family includes the radial spoke head proteins RSP4 and
RSP6 from Chlamydomonas reinhardtii, and several
eukaryotic homologues, including mammalian RSHL1, the
protein product of a familial ciliary dyskinesia
candidate gene.
Length = 481
Score = 28.1 bits (63), Expect = 2.4
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 5 KGEEGRDKEEEEEEEEEERE 24
EE ++ EEEEEEEEE E
Sbjct: 348 DEEEEQEDEEEEEEEEEPEE 367
Score = 27.7 bits (62), Expect = 3.7
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 5 KGEEGRDKEEEEEEEEEEREMSDCQVG 31
K EE ++EEEEEEEEE E + + G
Sbjct: 347 KDEEEEQEDEEEEEEEEEPEEPEPEEG 373
>gnl|CDD|111875 pfam03032, Brevenin, Brevenin/esculentin/gaegurin/rugosin family.
This family contains a number of defence peptides
secreted from the skin of amphibians, including the
opiate-like dermorphins and deltorphins, and the
antimicrobial dermoseptins and temporins. The alignment
for this family includes the signal peptide.
Length = 46
Score = 25.8 bits (57), Expect = 2.4
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 7 EEGRDKEEEEEEEEEERE 24
EE + ++EEE E+EEE E
Sbjct: 22 EEEKREDEEENEDEEEGE 39
Score = 25.0 bits (55), Expect = 5.1
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 7 EEGRDKEEEEEEEEEER 23
EE D+EE EE+ E +R
Sbjct: 30 EENEDEEEGEEQSEVKR 46
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 28.5 bits (63), Expect = 2.7
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 7 EEGRDKEEEEEEEEEEREMSD 27
++ D EEEEEEEEE + D
Sbjct: 165 DDEEDDEEEEEEEEEIKGFDD 185
Score = 27.7 bits (61), Expect = 3.8
Identities = 7/24 (29%), Positives = 18/24 (75%)
Query: 7 EEGRDKEEEEEEEEEEREMSDCQV 30
+E D+++++EE++EE E + ++
Sbjct: 157 DEDEDEDDDDEEDDEEEEEEEEEI 180
Score = 27.7 bits (61), Expect = 4.5
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 6 GEEGRDKEEEEEEEEEERE 24
+E D EE++EEEEEE E
Sbjct: 160 EDEDDDDEEDDEEEEEEEE 178
>gnl|CDD|217433 pfam03223, V-ATPase_C, V-ATPase subunit C.
Length = 371
Score = 28.0 bits (63), Expect = 2.7
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 141 MRLQVESALRPGLVDNFIS 159
+R+ VES LR GL NF +
Sbjct: 300 LRVFVESVLRYGLPPNFQA 318
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 28.2 bits (63), Expect = 2.8
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 5 KGEEGRDKEEEEEEEEEERE 24
+ E+ DKEEE +EEEE+ E
Sbjct: 50 EEEKTTDKEEEVDEEEEKEE 69
>gnl|CDD|221581 pfam12446, DUF3682, Protein of unknown function (DUF3682). This
domain family is found in eukaryotes, and is typically
between 125 and 136 amino acids in length.
Length = 133
Score = 27.1 bits (60), Expect = 3.0
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 10 RDKEEEEEEEEEEREMSD 27
R +EEEEEEE E+++ SD
Sbjct: 95 RQEEEEEEEENEKQQQSD 112
Score = 25.9 bits (57), Expect = 8.9
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 11 DKEEEEEEEEEEREM 25
+EEEEEEEE E
Sbjct: 93 HTRQEEEEEEEENEK 107
Score = 25.5 bits (56), Expect = 9.8
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 6 GEEGRDKEEEEEEEEEEREMSDCQV 30
G +++EEEEEE E++++ + QV
Sbjct: 92 GHTRQEEEEEEEENEKQQQSDEAQV 116
Score = 25.5 bits (56), Expect = 10.0
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 6 GEEGRDKEEEEEEEEEERE 24
G +EEEEEEEE E++
Sbjct: 90 GTGHTRQEEEEEEEENEKQ 108
>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2. PPP4R2 (protein phosphatase 4 core
regulatory subunit R2) is the regulatory subunit of the
histone H2A phosphatase complex. It has been shown to
confer resistance to the anticancer drug cisplatin in
yeast, and may confer resistance in higher eukaryotes.
Length = 285
Score = 27.9 bits (62), Expect = 3.1
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 7 EEGRDKEEEEEEEEEERE 24
EE KE+EEEEE EE E
Sbjct: 261 EEKELKEDEEEEETEEEE 278
>gnl|CDD|240285 PTZ00135, PTZ00135, 60S acidic ribosomal protein P0; Provisional.
Length = 310
Score = 27.7 bits (62), Expect = 3.2
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 12 KEEEEEEEEEEREM 25
EEEEEEE +M
Sbjct: 291 AAPAEEEEEEEDDM 304
>gnl|CDD|220376 pfam09745, DUF2040, Coiled-coil domain-containing protein 55
(DUF2040). This entry is a conserved domain of
approximately 130 residues of proteins conserved from
fungi to humans. The proteins do contain a coiled-coil
domain, but the function is unknown.
Length = 128
Score = 27.0 bits (60), Expect = 3.3
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 4 RKGEEGRDKEEEEEEEEEEREMSD 27
+K E K EEEE+E EE E +
Sbjct: 96 KKQLEENRKLEEEEKEREELEEEN 119
Score = 25.8 bits (57), Expect = 9.1
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 4 RKGEEGRDKEEEEEEEEEEREMSD 27
++ EE R EEEE+E EE E +D
Sbjct: 97 KQLEENRKLEEEEKEREELEEEND 120
>gnl|CDD|216906 pfam02153, PDH, Prephenate dehydrogenase. Members of this family
are prephenate dehydrogenases EC:1.3.1.12 involved in
tyrosine biosynthesis.
Length = 258
Score = 27.3 bits (61), Expect = 3.9
Identities = 9/33 (27%), Positives = 11/33 (33%)
Query: 9 GRDKEEEEEEEEEEREMSDCQVGSWEAWSECDT 41
G D + E E + D S A E D
Sbjct: 16 GYDIDPEAAVAAVELGLIDEATDSISAVQEADI 48
>gnl|CDD|215067 PLN00129, PLN00129, succinate dehydrogenase [ubiquinone]
iron-sulfur subunit.
Length = 276
Score = 27.4 bits (61), Expect = 4.1
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 15/62 (24%)
Query: 42 ECGPGTMVRTRKAIQEPKNGGKHCPTLTQKRSCLGTRCPHNPRSALKGRESINMRGKVCV 101
+CGP MV + + KN + P+LT +RSC R + G ++N+ GK +
Sbjct: 70 DCGP--MVL--DVLIKIKN--EQDPSLTFRRSC---------REGICGSCAMNIDGKNTL 114
Query: 102 RC 103
C
Sbjct: 115 AC 116
>gnl|CDD|150531 pfam09871, DUF2098, Uncharacterized protein conserved in archaea
(DUF2098). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 91
Score = 26.1 bits (58), Expect = 4.2
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 4 RKGEEGRDKEEEEEEEEEEREM 25
+K E DKEE E ++E E
Sbjct: 55 KKEEREEDKEELIERIKKEEET 76
>gnl|CDD|218756 pfam05797, Rep_4, Yeast trans-acting factor (REP1/REP2). This
family consists of the yeast trans-acting factor B and C
(REP1 and 2) proteins. The yeast plasmid stability
system consists of two plasmid-coded proteins, Rep1 and
Rep2, and a cis-acting locus, STB. The Rep proteins show
both self- and cross-interactions in vivo and in vitro,
and bind to the STB DNA with assistance from host
factor(s). Within the yeast nucleus, the Rep1 and Rep2
proteins tightly associate with STB-containing plasmids
into well organised plasmid foci that form a cohesive
unit in partitioning. It is generally accepted that the
protein-protein and DNA-protein interactions engendered
by the Rep-STB system are central to plasmid
partitioning. Point mutations in Rep1 that knock out
interaction with Rep2 or with STB simultaneously block
the ability of these Rep1 variants to support plasmid
stability.
Length = 337
Score = 27.5 bits (61), Expect = 4.3
Identities = 10/37 (27%), Positives = 14/37 (37%)
Query: 4 RKGEEGRDKEEEEEEEEEEREMSDCQVGSWEAWSECD 40
K + D+ E+ E E + D GS E E
Sbjct: 212 NKQDTVPDQPPLEDPELFEHIVQDESNGSPEQDDEAS 248
>gnl|CDD|198151 smart01083, Cir_N, N-terminal domain of CBF1 interacting
co-repressor CIR. This is a 45 residue conserved
region at the N-terminal end of a family of proteins
referred to as CIRs (CBF1-interacting co-repressors).
CBF1 (centromere-binding factor 1) acts as a
transcription factor that causes repression by binding
specifically to GTGGGAA motifs in responsive promoters,
and it requires CIR as a co-repressor. CIR binds to
histone deacetylase and to SAP30 and serves as a linker
between CBF1 and the histone deacetylase complex.
Length = 37
Score = 24.8 bits (55), Expect = 5.0
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 2 RVRKGEEGRDKEEEEEEEEEER 23
RV K E+ K EEE+++ EER
Sbjct: 12 RVWKAEQ---KAEEEKKKIEER 30
>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein. This
protein is covalently attached to the terminii of
replicating DNA in vivo.
Length = 548
Score = 27.3 bits (61), Expect = 5.2
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 6 GEEGRDKEEEEEEEEEEREMSD 27
EE +EEEEEEEEEER +
Sbjct: 311 EEEEVPEEEEEEEEEEERTFEE 332
>gnl|CDD|100108 cd04411, Ribosomal_P1_P2_L12p, Ribosomal protein P1, P2, and
L12p. Ribosomal proteins P1 and P2 are the eukaryotic
proteins that are functionally equivalent to bacterial
L7/L12. L12p is the archaeal homolog. Unlike other
ribosomal proteins, the archaeal L12p and eukaryotic P1
and P2 do not share sequence similarity with their
bacterial counterparts. They are part of the ribosomal
stalk (called the L7/L12 stalk in bacteria), along with
28S rRNA and the proteins L11 and P0 in eukaryotes (23S
rRNA, L11, and L10e in archaea). In bacterial
ribosomes, L7/L12 homodimers bind the extended
C-terminal helix of L10 to anchor the L7/L12 molecules
to the ribosome. Eukaryotic P1/P2 heterodimers and
archaeal L12p homodimers are believed to bind the L10
equivalent proteins, eukaryotic P0 and archaeal L10e,
in a similar fashion. P1 and P2 (L12p, L7/L12) are the
only proteins in the ribosome to occur as multimers,
always appearing as sets of dimers. Recent data
indicate that most archaeal species contain six copies
of L12p (three homodimers), while eukaryotes have two
copies each of P1 and P2 (two heterodimers). Bacteria
may have four or six copies (two or three homodimers),
depending on the species. As in bacteria, the stalk is
crucial for binding of initiation, elongation, and
release factors in eukaryotes and archaea.
Length = 105
Score = 26.1 bits (57), Expect = 6.4
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 6 GEEGRDKEEEEEEEEEEREMSD 27
E +K EE +EEEEE E D
Sbjct: 78 TAEPAEKAEEAKEEEEEEEDED 99
>gnl|CDD|227496 COG5167, VID27, Protein involved in vacuole import and degradation
[Intracellular trafficking and secretion].
Length = 776
Score = 26.9 bits (59), Expect = 6.4
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 4 RKGEEGRDKEEEEEEEEEERE 24
+ E R+ EE E EEE E
Sbjct: 372 KMEIENRNPEESEHEEEVEDY 392
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 26.8 bits (59), Expect = 6.9
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 5 KGEEGRDKEEEEEEEEEEREMSDCQVGSWEAWSECDTE 42
+E ++E EEEEEEE E + + S E E + E
Sbjct: 435 ASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEE 472
>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon.
Length = 431
Score = 26.5 bits (58), Expect = 8.0
Identities = 14/40 (35%), Positives = 17/40 (42%)
Query: 3 VRKGEEGRDKEEEEEEEEEEREMSDCQVGSWEAWSECDTE 42
V + E+ +EE EE EE E Q W EC E
Sbjct: 111 VEEEEKEESREEREEVEETEGVTKSEQKNDWRDAEECQKE 150
>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin. Nucleoplasmins are also
known as chromatin decondensation proteins. They bind to
core histones and transfer DNA to them in a reaction
that requires ATP. This is thought to play a role in the
assembly of regular nucleosomal arrays.
Length = 146
Score = 25.7 bits (57), Expect = 9.0
Identities = 7/24 (29%), Positives = 18/24 (75%)
Query: 7 EEGRDKEEEEEEEEEEREMSDCQV 30
++ D+EEE++EE+++ + S+ +
Sbjct: 116 DDEEDEEEEDDEEDDDEDESEEEE 139
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 26.3 bits (59), Expect = 9.3
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 7 EEGRDKEEEEEEEEEEREMSD 27
E D +E+EEEEE+E + S
Sbjct: 189 LEELDDDEDEEEEEDENDDSL 209
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
0.317 0.133 0.437
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,624,682
Number of extensions: 716536
Number of successful extensions: 2727
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2455
Number of HSP's successfully gapped: 156
Length of query: 176
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 86
Effective length of database: 6,945,742
Effective search space: 597333812
Effective search space used: 597333812
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 (21.7 bits)
S2: 56 (25.2 bits)