RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10479
(222 letters)
>gnl|CDD|150884 pfam10278, Med19, Mediator of RNA pol II transcription subunit 19.
Med19 represents a family of conserved proteins which
are members of the multi-protein co-activator Mediator
complex. Mediator is required for activation of RNA
polymerase II transcription by DNA binding
transactivators.
Length = 178
Score = 202 bits (516), Expect = 1e-66
Identities = 112/170 (65%), Positives = 131/170 (77%), Gaps = 7/170 (4%)
Query: 51 GPFYLMKEPPGKSEKTGSVNLMASYGLEHTYNKFCGKKLKESLSSFLPNLPGIIDAPGSQ 110
GPFYL+KE PG SE TGS NL+ YGLEH+Y+KFCGKK+KE LSSFLP+LPG+ID PG+
Sbjct: 1 GPFYLLKELPGYSELTGSTNLLTHYGLEHSYSKFCGKKVKEKLSSFLPHLPGMIDLPGTP 60
Query: 111 DNSSLRSVIEKPPICGKEILPLTSVQLAGFRLHPGNLPEQYRIANQVASKR-HKNKHKKH 169
+NSSLRS+IEKPPI GKE+LPLTSVQLAGFRLHPG LPEQYR+ + K+ HK+KHKKH
Sbjct: 61 ENSSLRSLIEKPPIGGKELLPLTSVQLAGFRLHPGPLPEQYRLMHIQPPKKKHKHKHKKH 120
Query: 170 KYK-TGDTSNPDANMGDVSYSDSHEKKHKKQKRHNDDKERKKRKKEKKKK 218
+ + P D HEKKHKK+K DDKERKK+KKEKKKK
Sbjct: 121 RTQDPLPEETPS----DSEGLKGHEKKHKKKKHE-DDKERKKKKKEKKKK 165
>gnl|CDD|219547 pfam07741, BRF1, Brf1-like TBP-binding domain. This region covers
both the Brf homology II and III regions. This region is
involved in binding TATA binding protein.
Length = 95
Score = 29.9 bits (68), Expect = 0.28
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 193 EKKHKKQKRHNDDKERKKRKKEKKKKN 219
E K K + +N K++KKRK +KK+
Sbjct: 36 ELKQKADEGNNSGKKKKKRKAKKKRDE 62
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 31.4 bits (72), Expect = 0.32
Identities = 21/82 (25%), Positives = 35/82 (42%), Gaps = 13/82 (15%)
Query: 141 RLHPGNLPEQYRIANQVASKRHKNKHKKHKYKTGDTSNPDANMGDVSYSDSHEKKHKKQK 200
R HP Y A A + + H K G+ + G++S + KK +K++
Sbjct: 368 RSHPF-----YFKAALGAIEIYLKLHDKPLLAEGEE--EEGENGNLS--PAERKKLRKKQ 418
Query: 201 RHNDDKERKKRKKEKKKKNRIE 222
R K KK +KE+ +K +
Sbjct: 419 R----KAEKKAEKEEAEKAAAK 436
>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein
complex aNOP56 subunit; Provisional.
Length = 414
Score = 29.6 bits (67), Expect = 1.4
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 193 EKKHKKQKRHNDDKERKKRKKEKKKKNR 220
++ K QKR K +KK KK KKK +
Sbjct: 387 REEKKPQKRKKKKKRKKKGKKRKKKGRK 414
Score = 29.2 bits (66), Expect = 1.7
Identities = 11/27 (40%), Positives = 20/27 (74%)
Query: 194 KKHKKQKRHNDDKERKKRKKEKKKKNR 220
KK +++K+ K++KKRKK+ KK+ +
Sbjct: 384 KKKREEKKPQKRKKKKKRKKKGKKRKK 410
Score = 28.0 bits (63), Expect = 4.0
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 194 KKHKKQKRHNDDKERKKRKKEKKKKNR 220
KK +++K K++K++KK KK+K +
Sbjct: 385 KKREEKKPQKRKKKKKRKKKGKKRKKK 411
Score = 27.2 bits (61), Expect = 7.3
Identities = 8/27 (29%), Positives = 19/27 (70%)
Query: 194 KKHKKQKRHNDDKERKKRKKEKKKKNR 220
K K++++ +++KK++K+K KK +
Sbjct: 383 PKKKREEKKPQKRKKKKKRKKKGKKRK 409
>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal. This
domain is found to the N-terminus of bacterial signal
peptidases of the S49 family (pfam01343).
Length = 154
Score = 28.6 bits (65), Expect = 1.4
Identities = 10/29 (34%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 193 EKKHKKQKRHNDDKERKKRKKEKKKKNRI 221
EK KK ++ K KK+ K+++ K R+
Sbjct: 72 EKAEKKAEK-AKAKAEKKKAKKEEPKPRL 99
Score = 28.3 bits (64), Expect = 2.1
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 7/35 (20%)
Query: 190 DSHEKK--HKKQKRHNDDKERKKRKKEKKKKNRIE 222
D E K K +K K K + K +KKK + E
Sbjct: 64 DKKELKAWEKAEK-----KAEKAKAKAEKKKAKKE 93
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 29.1 bits (66), Expect = 1.7
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 193 EKKHKKQKRHNDDKERKKRKKEKKKKNR 220
++K K +KRH D K KR+K
Sbjct: 407 KEKPKVKKRHRDTKNIGKRRKPSGTSEE 434
>gnl|CDD|221012 pfam11169, DUF2956, Protein of unknown function (DUF2956). This
family of proteins with unknown function appears to be
restricted to Gammaproteobacteria.
Length = 103
Score = 28.0 bits (63), Expect = 1.7
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 194 KKHKKQKRHNDDKERKKRKKEKKK 217
KK +K K DK RK++ K K++
Sbjct: 40 KKQQKAKAREADKARKQQLKAKQR 63
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase; Provisional.
Length = 330
Score = 28.6 bits (65), Expect = 2.5
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 190 DSHEKK--HKKQKRHNDDKERKKRKKEKKKK 218
D E K HK QK+ +K+ K K K K
Sbjct: 62 DKKELKAWHKAQKKK--EKQEAKAAKAKSKP 90
Score = 27.9 bits (63), Expect = 4.1
Identities = 14/67 (20%), Positives = 24/67 (35%), Gaps = 20/67 (29%)
Query: 146 NLPEQYR-IANQVASKRHKNKHKKHKYKTGDTSNPDANMGDVSYSDSHEKKHKKQKRHND 204
NL EQY+ + ++ + K K +K +KK +KQ+
Sbjct: 44 NLNEQYKEMKEELKAALLDKKELKAWHKA-------------------QKKKEKQEAKAA 84
Query: 205 DKERKKR 211
+ K R
Sbjct: 85 KAKSKPR 91
Score = 26.7 bits (60), Expect = 9.5
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 192 HEKKHKKQKRHNDDKERKKRKKEKKKKNRIE 222
E K + + D KE K K +KKK + E
Sbjct: 50 KEMKEELKAALLDKKELKAWHKAQKKKEKQE 80
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional.
Length = 813
Score = 28.6 bits (64), Expect = 3.1
Identities = 18/67 (26%), Positives = 24/67 (35%), Gaps = 5/67 (7%)
Query: 161 RHKNKHKKHKYKTGDTSNPDANMGDVSYS-----DSHEKKHKKQKRHNDDKERKKRKKEK 215
R+ K + K K GD V DS + KK K K+ +K KK
Sbjct: 732 RNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKAKKPS 791
Query: 216 KKKNRIE 222
K +I
Sbjct: 792 AKTQKIA 798
>gnl|CDD|201659 pfam01201, Ribosomal_S8e, Ribosomal protein S8e.
Length = 129
Score = 27.5 bits (62), Expect = 3.2
Identities = 11/32 (34%), Positives = 13/32 (40%), Gaps = 4/32 (12%)
Query: 183 MGDVSYSDSHEKKHKKQKRHNDDKERKKRKKE 214
MG S K+ + H RKKRK E
Sbjct: 1 MGINQGIRSKRKRTGGRLDH----HRKKRKFE 28
>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit
RPA34.5. This is a family of proteins conserved from
yeasts to human. Subunit A34.5 of RNA polymerase I is a
non-essential subunit which is thought to help Pol I
overcome topological constraints imposed on ribosomal
DNA during the process of transcription.
Length = 193
Score = 27.8 bits (62), Expect = 3.4
Identities = 11/31 (35%), Positives = 22/31 (70%)
Query: 189 SDSHEKKHKKQKRHNDDKERKKRKKEKKKKN 219
++ E++ K++K+ + K+ KK KK+KK+K
Sbjct: 147 AEVEEEEKKEKKKKKEVKKEKKEKKDKKEKM 177
Score = 27.0 bits (60), Expect = 6.2
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 189 SDSHEKKHKKQKRHNDDKERKKRKKEKKK 217
+ EKK KK+K +KK+KK+KKK
Sbjct: 165 KEKKEKKDKKEKMVEPKGSKKKKKKKKKK 193
>gnl|CDD|237747 PRK14530, PRK14530, adenylate kinase; Provisional.
Length = 215
Score = 27.8 bits (62), Expect = 4.3
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 50 SGPFYLMKEPPGKSEKTGSVNLMASYGLEH 79
S P L+ PG + T S NL +G+EH
Sbjct: 2 SQPRILLLGAPGAGKGTQSSNLAEEFGVEH 31
>gnl|CDD|115057 pfam06375, BLVR, Bovine leukaemia virus receptor (BLVR). This
family consists of several bovine specific leukaemia
virus receptors which are thought to function as
transmembrane proteins, although their exact function is
unknown.
Length = 561
Score = 27.7 bits (61), Expect = 5.4
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 188 YSDSHEKKHKKQKRHNDDKERKKRKKEKKKKNR 220
Y E++ +Q+ D +E+KKR+KEK+ + R
Sbjct: 81 YVKLEEERRHRQRLEKDKREKKKREKEKRGRRR 113
>gnl|CDD|222665 pfam14303, NAM-associated, No apical meristem-associated C-terminal
domain. This domain is found in a number of different
types of plant proteins including NAM-like proteins.
Length = 147
Score = 27.0 bits (60), Expect = 5.6
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 5/64 (7%)
Query: 160 KRHKNKHKKHKYKTGDTSNPDANMGDVSYSDSHEK-----KHKKQKRHNDDKERKKRKKE 214
K+ K KK + +++ + N + S + K K K+K D + KK + E
Sbjct: 26 KKASKKKKKRSNSSPGSTSNEENEDEDDESTAESKRPEGRKKAKEKLRRDKLKAKKEEAE 85
Query: 215 KKKK 218
K+K+
Sbjct: 86 KEKE 89
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
0.309 0.128 0.366
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: 10,798,550
Number of extensions: 961777
Number of successful extensions: 1954
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1772
Number of HSP's successfully gapped: 116
Length of query: 222
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 129
Effective length of database: 6,812,680
Effective search space: 878835720
Effective search space used: 878835720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 57 (25.8 bits)