RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5840
(132 letters)
>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 = 98.5 bits (246), Expect = 2e-27
Identities = 44/116 (37%), Positives = 64/116 (55%), Gaps = 5/116 (4%)
Query: 3 LFQAVIGANAKEGEVHVVEVEAMGFR-ADIKLPIVVLKAAGVNNHAPLDLLFPDPPVTFK 61
L +G AK+ E +VVEVEAM + +K+PI VLK V L PPVTF+
Sbjct: 34 LRTICLGPEAKD-EFNVVEVEAMNYEGKKVKVPIAVLKP-SVLPMVSLGGFELTPPVTFR 91
Query: 62 LVKGSGPIYLFGNHSVGTGEPMGEDDDEESIDEDFSEEEVDESEILSKNLSQKFQV 117
L GSGP+++ G H V + E +DD+E+ +ED +EE D+ + + S +V
Sbjct: 92 LKSGSGPVHISGQHLVASEEDESDDDEEDEEEED--DEEDDDEDESEEEESPVKKV 145
>gnl|CDD|211905 TIGR04170, RNR_1b_NrdE, ribonucleoside-diphosphate reductase, class
1b, alpha subunit. Members of this family are NrdE, the
alpha subunit of class 1b ribonucleotide reductase. This
form uses a dimanganese moiety associated with a
tyrosine radical to reduce the cellular requirement for
iron.
Length = 698
Score = 32.0 bits (73), Expect = 0.064
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 56 PPVTFKLVKGSGPIYLFGNHSVGT--GEPMGEDDDEESIDEDFSEEEVDESEILSKNLSQ 113
P F+L K + +YLF + V G P + D E DE + + + +I +++ Q
Sbjct: 279 PDKFFELAKENKDMYLFSPYDVEREYGVPFDDIDITEKYDEMVANPRIRKKKINARDFFQ 338
Query: 114 K 114
Sbjct: 339 T 339
>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 = 30.0 bits (68), Expect = 0.25
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 83 MGEDDDEESIDEDFSEEEVDESE 105
+ E+++EE +D DF + E DE E
Sbjct: 45 IEEEEEEEEVDSDFDDSEDDEPE 67
Score = 25.8 bits (57), Expect = 8.5
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 89 EESIDEDFSEEEVDESEI 106
EE DE+F EE +E E
Sbjct: 36 EEEDDEEFEIEEEEEEEE 53
Score = 25.8 bits (57), Expect = 8.5
Identities = 9/32 (28%), Positives = 11/32 (34%)
Query: 74 NHSVGTGEPMGEDDDEESIDEDFSEEEVDESE 105
+ E E D + ED E DE E
Sbjct: 42 EFEIEEEEEEEEVDSDFDDSEDDEPESDDEEE 73
>gnl|CDD|115196 pfam06524, NOA36, NOA36 protein. This family consists of several
NOA36 proteins which contain 29 highly conserved
cysteine residues. The function of this protein is
unknown.
Length = 314
Score = 28.8 bits (64), Expect = 0.75
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 2/34 (5%)
Query: 73 GNHSVGTGEPMGEDDDEESIDEDFSEEEVDESEI 106
V G DDDE S D+ EEE + +
Sbjct: 263 DFKGVNYGY--ESDDDEGSSSNDYDEEEDGDDDD 294
>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 = 0.84
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 81 EPMGEDDDEESIDEDFSEEEVDESEILSK 109
E G DD++E D+D EEE ++ ++ +
Sbjct: 326 EEDGVDDEDEEDDDDDLEEEEEDVDLSDE 354
Score = 28.0 bits (63), Expect = 1.7
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 81 EPMGEDDDEESIDEDFSEEEVDESEILSK 109
+ E++DEE D D ++E +E E K
Sbjct: 350 DLSDEEEDEEDEDSDDEDDEEEEEEEKEK 378
Score = 26.1 bits (58), Expect = 6.6
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 76 SVGTGEPMGEDDDEESIDEDFSEEEVDESE 105
E + D+EE +++ S++E DE E
Sbjct: 342 LEEEEEDVDLSDEEEDEEDEDSDDEDDEEE 371
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 28.3 bits (63), Expect = 1.3
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 76 SVGTGEPMGEDDDEESIDEDFSEE 99
S+ E G+D EE DE+ ++
Sbjct: 215 SMDMAEETGDDGIEEDADEEDGDD 238
>gnl|CDD|179677 PRK03926, PRK03926, mevalonate kinase; Provisional.
Length = 302
Score = 27.7 bits (62), Expect = 1.7
Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 62 LVKGSGP--IYLFGNHSVGTGEP 82
+V S P IYLFG H+V G+P
Sbjct: 1 MVLCSAPGKIYLFGEHAVVYGKP 23
>gnl|CDD|218601 pfam05477, SURF2, Surfeit locus protein 2 (SURF2). Surfeit locus
protein 2 is part of a group of at least six sequence
unrelated genes (Surf-1 to Surf-6). The six Surfeit
genes have been classified as housekeeping genes, being
expressed in all tissue types tested and not containing
a TATA box in their promoter region. The exact function
of SURF2 is unknown.
Length = 244
Score = 26.8 bits (59), Expect = 3.6
Identities = 21/58 (36%), Positives = 25/58 (43%), Gaps = 4/58 (6%)
Query: 68 PIYLFGNHSVGTGEPMGEDDDEESIDEDFSEEEVDESEILSKNLSQKFQVSSLLLSFK 125
P LF + G + EDDD E+ DED E E E + K Q SL FK
Sbjct: 176 PPELFTLKNPGKEQNGDEDDDFETDDEDEMEVESPELQ----QKRSKKQSGSLTKKFK 229
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 26.7 bits (59), Expect = 4.1
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 3/47 (6%)
Query: 70 YLFGNHSVGTGEPMGEDDDEESIDEDFSEEEVDESEILSKNLSQKFQ 116
YL H G + + + E + + EE +E E L L + F
Sbjct: 782 YLMQAHQKGQLKDTIDVAEPEEPGDPLTAEEQEEKEQL---LEEGFS 825
>gnl|CDD|218555 pfam05320, Pox_RNA_Pol_19, Poxvirus DNA-directed RNA polymerase 19
kDa subunit. This family contains several DNA-directed
RNA polymerase 19 kDa polypeptides. The Poxvirus
DNA-directed RNA polymerase (EC: 2.7.7.6) catalyzes
DNA-template-directed extension of the 3'-end of an RNA
strand by one nucleotide at a time.
Length = 167
Score = 26.2 bits (58), Expect = 4.5
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 85 EDDDEESIDEDFSEEEVDESEILSKNLSQKFQVSSLLLSFKVGIE 129
+DDD E +E+ +EE ES S S K Q + + S IE
Sbjct: 13 DDDDSEEYEEEEEDEEDAESLESSDVSSLK-QSNYKIESASENIE 56
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 26.6 bits (59), Expect = 4.8
Identities = 8/27 (29%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 79 TGEPMGEDDDEESIDEDFSEEEVDESE 105
+ G+ D++ DED E ++D+S+
Sbjct: 248 DSDDEGDGSDDD-DDEDAIESDLDDSD 273
>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 = 26.3 bits (58), Expect = 4.8
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 85 EDDDEESIDEDFSEEEVDE 103
E+++EE DEDF +++ D+
Sbjct: 178 EEEEEEEEDEDFDDDDDDD 196
>gnl|CDD|226961 COG4598, HisP, ABC-type histidine transport system, ATPase
component [Amino acid transport and metabolism].
Length = 256
Score = 26.2 bits (58), Expect = 5.3
Identities = 14/50 (28%), Positives = 23/50 (46%)
Query: 7 VIGANAKEGEVHVVEVEAMGFRADIKLPIVVLKAAGVNNHAPLDLLFPDP 56
V+ A+EG VV MGF D+ ++ L + P + +F +P
Sbjct: 194 VMQDLAEEGRTMVVVTHEMGFARDVSSHVIFLHQGKIEEEGPPEQVFGNP 243
>gnl|CDD|236179 PRK08188, PRK08188, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 714
Score = 26.6 bits (59), Expect = 5.6
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 9/66 (13%)
Query: 56 PPVTFKLVKGSGPIYLFGNHSVG--TGEPMGEDDDEESIDEDFSEEEVDESEILSKNLSQ 113
P +TF+L K + +YLF + V G+P + S+ E + +E V + I K ++
Sbjct: 293 PDITFELAKENEDMYLFSPYDVERVYGKPFA----DISVTEKY-DEMVADERIRKKKINA 347
Query: 114 K--FQV 117
+ FQ
Sbjct: 348 REFFQT 353
>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 = 26.2 bits (57), Expect = 6.9
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 78 GTGEPMGEDDDEESIDEDFSEEEVDESE 105
T E ++D+EE +E+ E EV+E+E
Sbjct: 129 ATKEDESDEDEEEEEEEEEEEAEVEENE 156
>gnl|CDD|220605 pfam10156, Med17, Subunit 17 of Mediator complex. This Mediator
complex subunit was formerly known as Srb4 in yeasts or
Trap80 in Drosophila and human. The Med17 subunit is
located within the head domain and is essential for cell
viability to the extent that a mutant strain of
cerevisiae lacking it shows all RNA polymerase
II-dependent transcription ceasing at non-permissive
temperatures.
Length = 454
Score = 25.8 bits (57), Expect = 7.5
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 7/58 (12%)
Query: 74 NHSVGTGEPMGEDDDEESIDEDFSEEEVDESEI-------LSKNLSQKFQVSSLLLSF 124
+ E E++D+E D D SEE D E + + L+Q SSL L F
Sbjct: 62 AAKIDFSEESDEEEDDEEDDNDDSEENKDTVEEFPKARDEVLEQLNQALNESSLALDF 119
>gnl|CDD|224493 COG1577, ERG12, Mevalonate kinase [Lipid metabolism].
Length = 307
Score = 25.7 bits (57), Expect = 7.7
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 62 LVKGSGPIYLFGNHSVGTGEP 82
V G + LFG H+V G P
Sbjct: 2 SVSAPGKLILFGEHAVVYGYP 22
>gnl|CDD|219069 pfam06512, Na_trans_assoc, Sodium ion transport-associated.
Members of this family contain a region found
exclusively in eukaryotic sodium channels or their
subunits, many of which are voltage-gated. Members very
often also contain between one and four copies of
pfam00520 and, less often, one copy of pfam00612.
Length = 230
Score = 25.8 bits (57), Expect = 7.8
Identities = 12/30 (40%), Positives = 13/30 (43%)
Query: 84 GEDDDEESIDEDFSEEEVDESEILSKNLSQ 113
GE D E DED S E + SK S
Sbjct: 110 GESDLENLNDEDTSSESSYGFKEESKKGSA 139
>gnl|CDD|178493 PLN02905, PLN02905, beta-amylase.
Length = 702
Score = 26.1 bits (57), Expect = 8.4
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 85 EDDDEESIDEDFSEEEVDESEILSKNLSQKFQVS 118
E+DDEE +D D EE+ + K++ VS
Sbjct: 13 EEDDEEEMDMDVKEEDDGDRRNREKHIPVTGMVS 46
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 25.6 bits (57), Expect = 9.3
Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 25/72 (34%)
Query: 52 LFPDPPVTFKLVKGSGPIYLFGNHSVGTGEPMGEDDDEESIDE------DFSEEEVDES- 104
F +PPVT ++ + EP D+E I E DFSEE V ++
Sbjct: 232 FFLNPPVT-------------DDYELKWKEP-----DKEGIIEFLVEEHDFSEERVKKAL 273
Query: 105 EILSKNLSQKFQ 116
E L K + +K Q
Sbjct: 274 ERLEKAVKEKKQ 285
>gnl|CDD|217059 pfam02480, Herpes_gE, Alphaherpesvirus glycoprotein E.
Glycoprotein E (gE) of Alphaherpesvirus forms a complex
with glycoprotein I (gI) (pfam01688), functioning as an
immunoglobulin G (IgG) Fc binding protein. gE is
involved in virus spread but is not essential for
propagation.
Length = 437
Score = 25.5 bits (56), Expect = 9.8
Identities = 10/35 (28%), Positives = 14/35 (40%)
Query: 71 LFGNHSVGTGEPMGEDDDEESIDEDFSEEEVDESE 105
L V T P E ++ S D + +EE D
Sbjct: 388 LNPFSPVYTSLPTNELFEDVSSDSESDDEEFDSDS 422
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
0.316 0.138 0.388
Gapped
Lambda K H
0.267 0.0785 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,856,662
Number of extensions: 633039
Number of successful extensions: 1184
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1087
Number of HSP's successfully gapped: 75
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
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 (21.6 bits)
S2: 53 (24.1 bits)