RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12465
(434 letters)
>gnl|CDD|192929 pfam12062, HSNSD, heparan sulfate-N-deacetylase. This family of
proteins is are heparan sulfate N-deacetylase enzymes.
This protein is found in eukaryotes. This proteinenzyme
is often found associated with pfam00685.
Length = 487
Score = 285 bits (731), Expect = 8e-92
Identities = 130/310 (41%), Positives = 174/310 (56%), Gaps = 25/310 (8%)
Query: 7 RYKIEV-SGK-SLPVMTNQDKGKYGVIVFENVAKYLEMDKWNRELLDKYCREYSVGIVAF 64
+YK E+ GK LPV+T+ +G+Y +I++EN+ KYL MD WNRELLDKYC+EY VGI+ F
Sbjct: 87 KYKTEIAPGKGDLPVLTDSGRGRYSLIIYENILKYLNMDAWNRELLDKYCKEYGVGIIGF 146
Query: 65 FPPTETPRFDEPVRGFPLSRHSNMKLKDAGLNSLSPILRLTRAGETAWGDLPGDDWSVFL 124
F E ++GFPL N++LKD +N LSP+LR+T+ GE G LPGDDW+VF
Sbjct: 147 FKAPEDSLKSAQLKGFPLFLWQNLRLKDCSVNPLSPLLRITKIGEYEKGSLPGDDWTVFQ 206
Query: 125 TNHSTYETLEFAFNQSERHIDAGLNSLSPILRLTRAGETAWGDLP----------GDDWS 174
NHSTYE + A +S S RA T DL G++ +
Sbjct: 207 INHSTYEPVLLATVKSGEEAP------SLGQVALRA--TVVQDLGLHDGIQRVLFGNNLN 258
Query: 175 VFLTNHSTYETLEFAFNQS-----ERHIVLPQSGEEFGSGNQTFYSTVIQALLRTQKRIQ 229
+L + L F + +R+I++ G ++AL+ TQ ++
Sbjct: 259 FWLHKLVFLDALSFLSGKRLSLSLDRYILVDIDDIFVGKEGTRMVVEDVRALISTQNELR 318
Query: 230 KLVRGFKFNLGFSGKYFHHGESEENAGDDLLLENAHEFTWFSHMWNHQQPHLYENQTQLE 289
V F FNLGFSGK++H G EE+ GDD LLEN EF WF HMW+H QPHL+ N + LE
Sbjct: 319 TQVPNFTFNLGFSGKFYHTGTDEEDRGDDFLLENVEEFWWFPHMWSHMQPHLFHNFSYLE 378
Query: 290 VDMMLNKQFA 299
M LNK FA
Sbjct: 379 EQMALNKLFA 388
>gnl|CDD|216059 pfam00685, Sulfotransfer_1, Sulfotransferase domain.
Length = 254
Score = 38.9 bits (91), Expect = 0.003
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 382 LPRFLVIGPQKTGTTALYTFLSLHPNISSNSP 413
L++ K+GTT L LSL PN
Sbjct: 1 DDDVLIVTYPKSGTTWLQEILSLIPNRGDFEK 32
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 36.5 bits (85), Expect = 0.004
Identities = 12/22 (54%), Positives = 19/22 (86%)
Query: 413 PSPASEEEEEEEEEEEEEKKKT 434
+ A+ EE++EEEEEEEEK+++
Sbjct: 72 AAAAAAEEKKEEEEEEEEKEES 93
Score = 34.9 bits (81), Expect = 0.016
Identities = 11/21 (52%), Positives = 17/21 (80%)
Query: 413 PSPASEEEEEEEEEEEEEKKK 433
+ A+ EE++EEEEEEE+K+
Sbjct: 71 AAAAAAAEEKKEEEEEEEEKE 91
Score = 34.5 bits (80), Expect = 0.021
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 413 PSPASEEEEEEEEEEEEEKKK 433
+ A+ EE++EEEEEE++K
Sbjct: 70 AAAAAAAAEEKKEEEEEEEEK 90
Score = 31.8 bits (73), Expect = 0.16
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 413 PSPASEEEEEEEEEEEEEKKK 433
+ A+ EE++EEEEE+++
Sbjct: 69 AAAAAAAAAEEKKEEEEEEEE 89
Score = 31.8 bits (73), Expect = 0.17
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 416 ASEEEEEEEEEEEEE 430
EEEEEEE+EE EE
Sbjct: 81 KEEEEEEEEKEESEE 95
Score = 31.5 bits (72), Expect = 0.26
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 415 PASEEEEEEEEEEEEE 430
EEEEEE+EE EEE
Sbjct: 81 KEEEEEEEEKEESEEE 96
Score = 30.7 bits (70), Expect = 0.36
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 415 PASEEEEEEEEEEEEE 430
EEEEEEEE+EE E
Sbjct: 79 EKKEEEEEEEEKEESE 94
Score = 29.5 bits (67), Expect = 1.0
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 413 PSPASEEEEEEEEEEEEEKKK 433
+ A+ EE++EEEE+++
Sbjct: 68 AAAAAAAAAAEEKKEEEEEEE 88
Score = 28.8 bits (65), Expect = 2.2
Identities = 5/21 (23%), Positives = 12/21 (57%)
Query: 413 PSPASEEEEEEEEEEEEEKKK 433
+ A+ EE++EE+++
Sbjct: 66 AAAAAAAAAAAAEEKKEEEEE 86
Score = 28.0 bits (63), Expect = 3.9
Identities = 6/22 (27%), Positives = 14/22 (63%)
Query: 412 SPSPASEEEEEEEEEEEEEKKK 433
+ + A+ EE++EEE+++
Sbjct: 66 AAAAAAAAAAAAEEKKEEEEEE 87
>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 = 36.2 bits (84), Expect = 0.005
Identities = 12/22 (54%), Positives = 18/22 (81%)
Query: 412 SPSPASEEEEEEEEEEEEEKKK 433
+ + A+ EEEEEEEEEEE+++
Sbjct: 68 AAAAAAAAEEEEEEEEEEEEEE 89
Score = 34.6 bits (80), Expect = 0.016
Identities = 14/22 (63%), Positives = 20/22 (90%)
Query: 412 SPSPASEEEEEEEEEEEEEKKK 433
+ + A+EEEEEEEEEEEEE+++
Sbjct: 70 AAAAAAEEEEEEEEEEEEEEEE 91
Score = 32.3 bits (74), Expect = 0.11
Identities = 14/19 (73%), Positives = 16/19 (84%)
Query: 415 PASEEEEEEEEEEEEEKKK 433
A EEEEEEEEEEEEE++
Sbjct: 74 AAEEEEEEEEEEEEEEEES 92
Score = 31.9 bits (73), Expect = 0.14
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 413 PSPASEEEEEEEEEEEEEKKK 433
+ A+ EEEEEEEEE+++
Sbjct: 67 AAAAAAAAAEEEEEEEEEEEE 87
Score = 31.6 bits (72), Expect = 0.24
Identities = 13/20 (65%), Positives = 15/20 (75%)
Query: 413 PSPASEEEEEEEEEEEEEKK 432
+ EEEEEEEEEEEEE+
Sbjct: 73 AAAEEEEEEEEEEEEEEEES 92
Score = 30.8 bits (70), Expect = 0.35
Identities = 12/18 (66%), Positives = 12/18 (66%)
Query: 413 PSPASEEEEEEEEEEEEE 430
EEEEEEEEEE EE
Sbjct: 77 EEEEEEEEEEEEEEESEE 94
Score = 29.6 bits (67), Expect = 0.86
Identities = 12/16 (75%), Positives = 12/16 (75%)
Query: 415 PASEEEEEEEEEEEEE 430
EEEEEEEEE EEE
Sbjct: 80 EEEEEEEEEEEESEEE 95
Score = 29.6 bits (67), Expect = 1.0
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 413 PSPASEEEEEEEEEEEEEKKK 433
+ A+ EEEEEEE+++
Sbjct: 65 AAAAAAAAAAAEEEEEEEEEE 85
Score = 28.1 bits (63), Expect = 3.3
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 412 SPSPASEEEEEEEEEEEEEKKK 433
+ + A+ EEEEEEEE+++
Sbjct: 65 AAAAAAAAAAAEEEEEEEEEEE 86
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 35.7 bits (83), Expect = 0.006
Identities = 12/19 (63%), Positives = 17/19 (89%)
Query: 412 SPSPASEEEEEEEEEEEEE 430
+ + A+EEE++EEEEEEEE
Sbjct: 61 AAAAAAEEEKKEEEEEEEE 79
Score = 33.8 bits (78), Expect = 0.024
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 412 SPSPASEEEEEEEEEEEEE 430
+ + A EE++EEEEEEEE+
Sbjct: 62 AAAAAEEEKKEEEEEEEED 80
Score = 32.6 bits (75), Expect = 0.061
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 413 PSPASEEEEEEEEEEEEE 430
+ E++EEEEEEEE++
Sbjct: 64 AAAEEEKKEEEEEEEEDD 81
Score = 32.6 bits (75), Expect = 0.069
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 412 SPSPASEEEEEEEEEEEEE 430
+ + A+ EEE++EEEEEEE
Sbjct: 60 AAAAAAAEEEKKEEEEEEE 78
Score = 30.3 bits (69), Expect = 0.38
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 413 PSPASEEEEEEEEEEEEE 430
+ A+ EEE++EEEEE
Sbjct: 59 AAAAAAAAEEEKKEEEEE 76
Score = 29.9 bits (68), Expect = 0.53
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 413 PSPASEEEEEEEEEEEEEKK 432
+ A+ EEE++EEE++
Sbjct: 57 AAAAAAAAAAEEEKKEEEEE 76
Score = 29.9 bits (68), Expect = 0.55
Identities = 6/22 (27%), Positives = 14/22 (63%)
Query: 412 SPSPASEEEEEEEEEEEEEKKK 433
+ + A+ EEE++EE+++
Sbjct: 55 AAAAAAAAAAAAEEEKKEEEEE 76
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 36.0 bits (84), Expect = 0.030
Identities = 15/26 (57%), Positives = 21/26 (80%)
Query: 408 ISSNSPSPASEEEEEEEEEEEEEKKK 433
+S+ + + A+EEEEEEEEEEEEE+
Sbjct: 292 LSAQAQAAAAEEEEEEEEEEEEEEPS 317
Score = 35.6 bits (83), Expect = 0.039
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 406 PNISSNSPSPASEEEEEEEEEEEEEKKK 433
+ S A+ EEEEEEEEEEEE++
Sbjct: 289 KEVLSAQAQAAAAEEEEEEEEEEEEEEP 316
Score = 30.6 bits (70), Expect = 1.7
Identities = 11/16 (68%), Positives = 11/16 (68%)
Query: 415 PASEEEEEEEEEEEEE 430
EEEEEEEEE EE
Sbjct: 304 EEEEEEEEEEEEPSEE 319
Score = 30.2 bits (69), Expect = 2.1
Identities = 11/18 (61%), Positives = 11/18 (61%)
Query: 413 PSPASEEEEEEEEEEEEE 430
EEEEEEEE EEE
Sbjct: 303 EEEEEEEEEEEEEPSEEE 320
>gnl|CDD|216269 pfam01056, Myc_N, Myc amino-terminal region. The myc family
belongs to the basic helix-loop-helix leucine zipper
class of transcription factors, see pfam00010. Myc forms
a heterodimer with Max, and this complex regulates cell
growth through direct activation of genes involved in
cell replication. Mutations in the C-terminal 20
residues of this domain cause unique changes in the
induction of apoptosis, transformation, and G2 arrest.
Length = 329
Score = 34.9 bits (80), Expect = 0.076
Identities = 18/29 (62%), Positives = 20/29 (68%), Gaps = 3/29 (10%)
Query: 405 HPNISSNSPS---PASEEEEEEEEEEEEE 430
PN SS+S S +EEEEEEEEEEEE
Sbjct: 215 PPNSSSSSGSDSESEEDEEEEEEEEEEEE 243
>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 = 32.5 bits (74), Expect = 0.088
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 413 PSPASEEEEEEEEEEEEEKKKT 434
+ EE+EEE+++EEEK++
Sbjct: 73 AAEEKAEEKEEEKKKEEEKEEE 94
Score = 31.7 bits (72), Expect = 0.19
Identities = 9/21 (42%), Positives = 17/21 (80%)
Query: 413 PSPASEEEEEEEEEEEEEKKK 433
+ A E+ EE+EEE+++E++K
Sbjct: 71 AAAAEEKAEEKEEEKKKEEEK 91
Score = 30.5 bits (69), Expect = 0.53
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 413 PSPASEEEEEEEEEEEEEKK 432
+ A+ EE+ EE+EEE+KK
Sbjct: 68 AAAAAAAEEKAEEKEEEKKK 87
Score = 29.4 bits (66), Expect = 1.4
Identities = 8/19 (42%), Positives = 17/19 (89%)
Query: 416 ASEEEEEEEEEEEEEKKKT 434
+EE+EEE+++EEE++++
Sbjct: 77 KAEEKEEEKKKEEEKEEEE 95
Score = 29.0 bits (65), Expect = 1.6
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 415 PASEEEEEEEEEEEEEKKK 433
A+ EE+ EE+EEEKKK
Sbjct: 69 AAAAAAEEKAEEKEEEKKK 87
Score = 28.6 bits (64), Expect = 2.3
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 413 PSPASEEEEEEEEEEEEE 430
E+++EEE+EEEEE
Sbjct: 79 EEKEEEKKKEEEKEEEEE 96
Score = 28.2 bits (63), Expect = 2.7
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 415 PASEEEEEEEEEEEEE 430
+++EEE+EEEEEE
Sbjct: 82 EEEKKKEEEKEEEEEE 97
Score = 27.8 bits (62), Expect = 4.2
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 413 PSPASEEEEEEEEEEEEEKKK 433
P+ A+ EE+ EE+EE+KK
Sbjct: 66 PAAAAAAAAEEKAEEKEEEKK 86
>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2
[Translation, ribosomal structure and biogenesis].
Length = 109
Score = 32.0 bits (73), Expect = 0.16
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 413 PSPASEEEEEEEEEEEEEKKK 433
+ A+ E +E EEEE+EE+ +
Sbjct: 76 GAEAAAEADEAEEEEKEEEAE 96
Score = 31.6 bits (72), Expect = 0.23
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 412 SPSPASEEEEEEEEEEEEEK 431
+ + A +E EEEE+EEE +
Sbjct: 77 AEAAAEADEAEEEEKEEEAE 96
Score = 30.4 bits (69), Expect = 0.60
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 412 SPSPASEEEEEEEEEEEEE 430
+ + A E EEEE+EEE EE
Sbjct: 79 AAAEADEAEEEEKEEEAEE 97
Score = 30.1 bits (68), Expect = 0.76
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 413 PSPASEEEEEEEEEEEEE 430
+ +EEEE+EEE EEE
Sbjct: 82 EADEAEEEEKEEEAEEES 99
Score = 29.7 bits (67), Expect = 1.1
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 409 SSNSPSPASEEEEEEEEEEEEEKKK 433
+ + + A E E +E EEE+K+
Sbjct: 68 GAAAAAAAGAEAAAEADEAEEEEKE 92
Score = 29.3 bits (66), Expect = 1.3
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 416 ASEEEEEEEEEEEEE 430
A EEE+EEE EEE +
Sbjct: 86 AEEEEKEEEAEEESD 100
Score = 29.3 bits (66), Expect = 1.5
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 409 SSNSPSPASEEEEEEEEEEEEEKKK 433
++ + + +E E +E EEEEK++
Sbjct: 69 AAAAAAAGAEAAAEADEAEEEEKEE 93
Score = 28.5 bits (64), Expect = 2.6
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 416 ASEEEEEEEEEEEEE 430
EE+EEE EEE ++
Sbjct: 87 EEEEKEEEAEEESDD 101
Score = 28.1 bits (63), Expect = 3.5
Identities = 7/26 (26%), Positives = 16/26 (61%)
Query: 409 SSNSPSPASEEEEEEEEEEEEEKKKT 434
++ + + A E +E EEEE++++
Sbjct: 70 AAAAAAGAEAAAEADEAEEEEKEEEA 95
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 33.4 bits (76), Expect = 0.28
Identities = 14/17 (82%), Positives = 17/17 (100%)
Query: 417 SEEEEEEEEEEEEEKKK 433
SEEEEEEEEEEEEE+++
Sbjct: 863 SEEEEEEEEEEEEEEEE 879
Score = 32.3 bits (73), Expect = 0.56
Identities = 13/16 (81%), Positives = 16/16 (100%)
Query: 418 EEEEEEEEEEEEEKKK 433
EEEEEEEEEEEEE+++
Sbjct: 872 EEEEEEEEEEEEEEEE 887
Score = 32.3 bits (73), Expect = 0.58
Identities = 13/16 (81%), Positives = 16/16 (100%)
Query: 418 EEEEEEEEEEEEEKKK 433
EEEEEEEEEEEEE+++
Sbjct: 874 EEEEEEEEEEEEEEEE 889
Score = 32.3 bits (73), Expect = 0.62
Identities = 14/20 (70%), Positives = 17/20 (85%)
Query: 414 SPASEEEEEEEEEEEEEKKK 433
S EEEEEEEEEEEEE+++
Sbjct: 863 SEEEEEEEEEEEEEEEEEEE 882
Score = 32.3 bits (73), Expect = 0.66
Identities = 13/16 (81%), Positives = 15/16 (93%)
Query: 418 EEEEEEEEEEEEEKKK 433
EEEEEEEEEEEEE ++
Sbjct: 877 EEEEEEEEEEEEENEE 892
Score = 32.3 bits (73), Expect = 0.68
Identities = 13/16 (81%), Positives = 16/16 (100%)
Query: 418 EEEEEEEEEEEEEKKK 433
EEEEEEEEEEEEE+++
Sbjct: 871 EEEEEEEEEEEEEEEE 886
Score = 32.3 bits (73), Expect = 0.68
Identities = 13/16 (81%), Positives = 15/16 (93%)
Query: 418 EEEEEEEEEEEEEKKK 433
EEEEEEEEEEEEE+ +
Sbjct: 876 EEEEEEEEEEEEEENE 891
Score = 31.9 bits (72), Expect = 0.72
Identities = 13/16 (81%), Positives = 16/16 (100%)
Query: 418 EEEEEEEEEEEEEKKK 433
EEEEEEEEEEEEE+++
Sbjct: 873 EEEEEEEEEEEEEEEE 888
Score = 31.9 bits (72), Expect = 0.81
Identities = 13/16 (81%), Positives = 16/16 (100%)
Query: 418 EEEEEEEEEEEEEKKK 433
EEEEEEEEEEEEE+++
Sbjct: 870 EEEEEEEEEEEEEEEE 885
Score = 31.9 bits (72), Expect = 0.84
Identities = 13/16 (81%), Positives = 16/16 (100%)
Query: 418 EEEEEEEEEEEEEKKK 433
EEEEEEEEEEEEE+++
Sbjct: 868 EEEEEEEEEEEEEEEE 883
Score = 31.9 bits (72), Expect = 0.84
Identities = 13/16 (81%), Positives = 16/16 (100%)
Query: 418 EEEEEEEEEEEEEKKK 433
EEEEEEEEEEEEE+++
Sbjct: 869 EEEEEEEEEEEEEEEE 884
>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 = 33.2 bits (76), Expect = 0.28
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 397 ALYTFLSLHPNISSNSPSPASEEEEEEEEEEEEE 430
L F +L ++ EE+EEEEEEE+E+
Sbjct: 372 ILDAFSALEIEDANTERDDEEEEDEEEEEEEDED 405
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 31.7 bits (72), Expect = 0.91
Identities = 13/17 (76%), Positives = 16/17 (94%)
Query: 418 EEEEEEEEEEEEEKKKT 434
EEE +EEEE+EE+KKKT
Sbjct: 58 EEEVDEEEEKEEKKKKT 74
Score = 31.3 bits (71), Expect = 1.2
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 414 SPASEEEEEEEEEEEEEKKK 433
+EEE +EEEE+EEKKK
Sbjct: 53 KTTDKEEEVDEEEEKEEKKK 72
Score = 30.9 bits (70), Expect = 1.7
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 409 SSNSPSPASEEEEEEEEEEEEEKKK 433
+ EE +EEEE+EE++KK
Sbjct: 50 EEEKTTDKEEEVDEEEEKEEKKKKT 74
Score = 28.6 bits (64), Expect = 6.8
Identities = 13/20 (65%), Positives = 17/20 (85%)
Query: 415 PASEEEEEEEEEEEEEKKKT 434
P EEEEE+EE++EEE+K T
Sbjct: 36 PDEEEEEEKEEKKEEEEKTT 55
>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein. The proteins in this family
are designated YL1. These proteins have been shown to be
DNA-binding and may be a transcription factor.
Length = 238
Score = 31.2 bits (71), Expect = 0.91
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 407 NISSNSPSPASEEEEEEEEEEEEEKKK 433
+ S + + +EEE E+E + EE+ K
Sbjct: 59 DDSEDDEPESDDEEEGEKELQREERLK 85
Score = 29.3 bits (66), Expect = 3.3
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 409 SSNSPSPASEEEEEEEEEEEEEKKK 433
+ P EEE E+E + EE KK
Sbjct: 62 EDDEPESDDEEEGEKELQREERLKK 86
>gnl|CDD|235302 PRK04456, PRK04456, acetyl-CoA decarbonylase/synthase complex
subunit beta; Reviewed.
Length = 463
Score = 31.2 bits (71), Expect = 1.2
Identities = 14/15 (93%), Positives = 15/15 (100%)
Query: 416 ASEEEEEEEEEEEEE 430
A+EEEEEEEEEEEEE
Sbjct: 403 AAEEEEEEEEEEEEE 417
Score = 30.4 bits (69), Expect = 1.8
Identities = 14/15 (93%), Positives = 14/15 (93%)
Query: 416 ASEEEEEEEEEEEEE 430
A EEEEEEEEEEEEE
Sbjct: 404 AEEEEEEEEEEEEEE 418
Score = 28.9 bits (65), Expect = 5.7
Identities = 13/13 (100%), Positives = 13/13 (100%)
Query: 418 EEEEEEEEEEEEE 430
EEEEEEEEEEEEE
Sbjct: 407 EEEEEEEEEEEEE 419
>gnl|CDD|240285 PTZ00135, PTZ00135, 60S acidic ribosomal protein P0; Provisional.
Length = 310
Score = 30.8 bits (70), Expect = 1.3
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 413 PSPASEEEEEEEEEEEEE 430
+ A+ EEEEEEE+
Sbjct: 285 AAAAAAAAPAEEEEEEED 302
Score = 28.8 bits (65), Expect = 5.6
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 414 SPASEEEEEEEEEEEEE 430
+ A+ EEEEEEE++
Sbjct: 287 AAAAAAPAEEEEEEEDD 303
Score = 28.4 bits (64), Expect = 7.6
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 411 NSPSPASEEEEEEEEEEEE 429
+ + A+ EEEEEEE++
Sbjct: 285 AAAAAAAAPAEEEEEEEDD 303
>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 = 29.2 bits (65), Expect = 1.3
Identities = 11/22 (50%), Positives = 17/22 (77%)
Query: 409 SSNSPSPASEEEEEEEEEEEEE 430
++ P+ +EE +EEEEEEE+E
Sbjct: 77 ATAEPAEKAEEAKEEEEEEEDE 98
>gnl|CDD|217576 pfam03466, LysR_substrate, LysR substrate binding domain. The
structure of this domain is known and is similar to the
periplasmic binding proteins.
Length = 207
Score = 30.4 bits (69), Expect = 1.3
Identities = 14/66 (21%), Positives = 21/66 (31%), Gaps = 2/66 (3%)
Query: 98 LSPILRLTRAGETAWGDLPGDDWSVFLTNHSTYETLEFAFNQSERHIDAGL--NSLSPIL 155
P L R + DL + + + L+ A + L NSL +L
Sbjct: 82 APPDHPLARGEPVSLEDLADEPLILLEPGSGLRDLLDRALRAAGLRPRVALEVNSLEALL 141
Query: 156 RLTRAG 161
AG
Sbjct: 142 AAVAAG 147
>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 = 29.2 bits (66), Expect = 1.4
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 412 SPSPASEEEEEEEEEEEEE 430
+ EE++EEEEEE ++
Sbjct: 78 AAEAKKEEKKEEEEEESDD 96
>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 = 30.4 bits (69), Expect = 1.9
Identities = 13/19 (68%), Positives = 13/19 (68%)
Query: 412 SPSPASEEEEEEEEEEEEE 430
PSP EEEEEEEEE E
Sbjct: 299 PPSPPEPEEEEEEEEEVPE 317
Score = 29.2 bits (66), Expect = 4.7
Identities = 13/19 (68%), Positives = 13/19 (68%)
Query: 412 SPSPASEEEEEEEEEEEEE 430
SP EEEEEEEE EEE
Sbjct: 301 SPPEPEEEEEEEEEVPEEE 319
Score = 28.8 bits (65), Expect = 6.1
Identities = 12/25 (48%), Positives = 12/25 (48%)
Query: 406 PNISSNSPSPASEEEEEEEEEEEEE 430
P EEEEEEEEEEE
Sbjct: 303 PEPEEEEEEEEEVPEEEEEEEEEEE 327
Score = 28.8 bits (65), Expect = 6.8
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 412 SPSPASEEEEEEEEEEEEEKKKT 434
EE EEEEEEEEE+++T
Sbjct: 307 EEEEEEEEVPEEEEEEEEEEERT 329
Score = 28.5 bits (64), Expect = 8.4
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 413 PSPASEEEEEEEEEEEEE 430
P P+ E EEEEEEEEE
Sbjct: 298 PPPSPPEPEEEEEEEEEV 315
Score = 28.5 bits (64), Expect = 9.4
Identities = 12/25 (48%), Positives = 12/25 (48%)
Query: 406 PNISSNSPSPASEEEEEEEEEEEEE 430
P E EEEEEEEEEE
Sbjct: 302 PPEPEEEEEEEEEVPEEEEEEEEEE 326
>gnl|CDD|178132 PLN02517, PLN02517, phosphatidylcholine-sterol O-acyltransferase.
Length = 642
Score = 30.1 bits (68), Expect = 2.4
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 14/39 (35%)
Query: 94 GLNSLSPILRLTR-----------AGETAWGDLPGDDWS 121
GL +L ++R+TR GET WGDL DWS
Sbjct: 298 GLQTLQHVMRMTRTWDSTMSMLPKGGETIWGDL---DWS 333
Score = 30.1 bits (68), Expect = 2.4
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 14/39 (35%)
Query: 147 GLNSLSPILRLTR-----------AGETAWGDLPGDDWS 174
GL +L ++R+TR GET WGDL DWS
Sbjct: 298 GLQTLQHVMRMTRTWDSTMSMLPKGGETIWGDL---DWS 333
>gnl|CDD|214818 smart00784, SPT2, SPT2 chromatin protein. This entry includes the
Saccharomyces cerevisiae protein SPT2 which is a
chromatin protein involved in transcriptional
regulation.
Length = 106
Score = 28.5 bits (64), Expect = 2.6
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 418 EEEEEEEEEEEEEKKK 433
EEE E+EEE EK+
Sbjct: 87 REEERLEKEEEREKRA 102
Score = 27.3 bits (61), Expect = 5.8
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 418 EEEEEEEEEEEEEKKK 433
EE E+EEE E+ +K
Sbjct: 89 EERLEKEEEREKRARK 104
Score = 27.0 bits (60), Expect = 9.1
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 418 EEEEEEEEEEEEEKKK 433
EEE E+EEE E++ +
Sbjct: 88 EEERLEKEEEREKRAR 103
>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 = 30.0 bits (68), Expect = 2.8
Identities = 12/20 (60%), Positives = 16/20 (80%)
Query: 413 PSPASEEEEEEEEEEEEEKK 432
P EEEE+E+EEEEEE++
Sbjct: 344 PEQKDEEEEQEDEEEEEEEE 363
>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 = 28.6 bits (64), Expect = 2.9
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 418 EEEEEEEEEEEEEKK 432
+EEEEEEEE EK+
Sbjct: 94 TRQEEEEEEEENEKQ 108
>gnl|CDD|224530 COG1614, CdhC, CO dehydrogenase/acetyl-CoA synthase beta subunit
[Energy production and conversion].
Length = 470
Score = 29.8 bits (67), Expect = 3.0
Identities = 13/16 (81%), Positives = 14/16 (87%)
Query: 416 ASEEEEEEEEEEEEEK 431
+EEEEEEEEEEEEE
Sbjct: 401 WAEEEEEEEEEEEEEA 416
Score = 28.6 bits (64), Expect = 6.4
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 418 EEEEEEEEEEEEEKK 432
EEEEEEEEEEEE+
Sbjct: 402 AEEEEEEEEEEEEEA 416
Score = 28.2 bits (63), Expect = 8.5
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 416 ASEEEEEEEEEEEEEKKKT 434
EEEEEEEEEEE + +
Sbjct: 403 EEEEEEEEEEEEEAAEAEA 421
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 28.5 bits (64), Expect = 5.3
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 383 PRFLVIGPQKTGTTALYTFLSL 404
P ++ G +G T+L+T L+
Sbjct: 4 PAVIIAGLCDSGKTSLFTLLTT 25
>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 = 28.1 bits (63), Expect = 5.7
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 401 FLSLHPNISSNSPSPASEEEEEEEEEEEEE 430
+S ++S +EE+EEEE++EE+
Sbjct: 100 HISGQHLVASEEDESDDDEEDEEEEDDEED 129
Score = 28.1 bits (63), Expect = 6.1
Identities = 7/17 (41%), Positives = 15/17 (88%)
Query: 417 SEEEEEEEEEEEEEKKK 433
EEE++EE+++E+E ++
Sbjct: 121 EEEEDDEEDDDEDESEE 137
Score = 27.7 bits (62), Expect = 7.9
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 418 EEEEEEEEEEEEEKKKT 434
EE+++E+E EEEE
Sbjct: 127 EEDDDEDESEEEESPVK 143
>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 = 26.4 bits (59), Expect = 7.0
Identities = 7/14 (50%), Positives = 14/14 (100%)
Query: 417 SEEEEEEEEEEEEE 430
SE+EE+EEE+++++
Sbjct: 59 SEDEEDEEEDDDDD 72
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 28.8 bits (65), Expect = 7.3
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 409 SSNSPSPASEEEEEEEEEEEEEKKK 433
+ S++E++EEEEEEE++KK
Sbjct: 355 EEDEEDEDSDDEDDEEEEEEEKEKK 379
>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366). This
family of proteins is found in bacteria and eukaryotes.
Proteins in this family are typically between 227 and
387 amino acids in length.
Length = 213
Score = 28.1 bits (63), Expect = 7.8
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 409 SSNSPSPASEEEEEEEEEEEEEKKKT 434
S N E E E E EEE +KK+
Sbjct: 131 SVNMTECTGPEPEPEPEPEEEPEKKS 156
>gnl|CDD|145910 pfam03012, PP_M1, Phosphoprotein. This family includes the M1
phosphoprotein non-structural RNA polymerase alpha
subunit, which is thought to be a component of the
active polymerase, and may be involved in template
binding.
Length = 298
Score = 28.2 bits (63), Expect = 8.1
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 407 NISSNSPSPASEEEEEEEEEEEEE 430
IS PS +EEE+E+E EE+
Sbjct: 57 QISDAKPSQFTEEEDEDEGSSEED 80
>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 = 28.1 bits (62), Expect = 8.3
Identities = 12/13 (92%), Positives = 13/13 (100%)
Query: 418 EEEEEEEEEEEEE 430
E+EEEEEEEEEEE
Sbjct: 137 EDEEEEEEEEEEE 149
Score = 28.1 bits (62), Expect = 9.0
Identities = 12/15 (80%), Positives = 15/15 (100%)
Query: 417 SEEEEEEEEEEEEEK 431
S+E+EEEEEEEEEE+
Sbjct: 135 SDEDEEEEEEEEEEE 149
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 0.134 0.413
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,504,358
Number of extensions: 2164194
Number of successful extensions: 5279
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5031
Number of HSP's successfully gapped: 157
Length of query: 434
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 334
Effective length of database: 6,502,202
Effective search space: 2171735468
Effective search space used: 2171735468
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: 60 (27.0 bits)