RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8114
(111 letters)
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in
vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the hnRNA
in the nucleus and in processing of pre-mRNA such as
splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 30.7 bits (70), Expect = 0.031
Identities = 7/18 (38%), Positives = 13/18 (72%)
Query: 83 VKRQDMDHVFLRYGKITS 100
V ++D++ +F +YGKI
Sbjct: 13 VSKEDLEEIFSKYGKILG 30
>gnl|CDD|214355 CHL00076, chlB, photochlorophyllide reductase subunit B.
Length = 513
Score = 29.6 bits (67), Expect = 0.25
Identities = 21/57 (36%), Positives = 26/57 (45%), Gaps = 6/57 (10%)
Query: 11 LMVTLFMKKSLAMPPLQCTP-GFVDQIPFKIRKICVAL----STIYELSNAMESYID 62
LM +++K MP + TP G VD IR+I L S I E E YID
Sbjct: 227 LMTAKYLEKEFGMPYISTTPMGIVDTAEC-IRQIQKILNKLASDILEKKVDYEKYID 282
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 29.5 bits (66), Expect = 0.29
Identities = 13/45 (28%), Positives = 23/45 (51%)
Query: 62 DDNGSMDQFVNPEINQLMENGVKRQDMDHVFLRYGKITSDGWVSP 106
+ +D ++ + L ENG + D+ R GK+TSD ++ P
Sbjct: 437 NGVDEIDYYIESSLKFLKENGFIKGDVTLRATRLGKLTSDLYIDP 481
>gnl|CDD|202669 pfam03495, Binary_toxB, Clostridial binary toxin B/anthrax toxin
PA. The N-terminal region of this family contains a
calcium-binding motif that may be an EF-hand.
Length = 406
Score = 28.2 bits (63), Expect = 0.86
Identities = 17/76 (22%), Positives = 24/76 (31%), Gaps = 20/76 (26%)
Query: 47 LSTIYELSNAMESYIDDNGS-------------MDQFVNPEI----NQLME---NGVKRQ 86
++TI N I + MD F + I NQL E
Sbjct: 203 IATIKAKENQTALSIAPGETYPSKGLNPIALNTMDDFNSRPITLNYNQLKELDNGKPLML 262
Query: 87 DMDHVFLRYGKITSDG 102
+ D V+ Y S+G
Sbjct: 263 ETDQVYGNYATYNSNG 278
>gnl|CDD|203917 pfam08360, TetR_C_5, QacR-like protein, C-terminal region. This
family features the C-terminal region of a number of
proteins that bear similarity to the QacR protein, a
transcriptional regulator of the TetR family. QacR is
able to bind various environmental agents, which
include a number of cationic lipophilic compounds, and
thus regulate the transcription of QacA, a multidrug
efflux pump. The C-terminal region contains the
multifaceted, expansive drug-binding pocket, which is
composed of several separate, but linked, binding
sites.
Length = 131
Score = 27.6 bits (61), Expect = 1.1
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 8/48 (16%)
Query: 51 YELSNAMESYIDDNGSMDQFVNPEINQLMENGVKRQ--DMDHVFLRYG 96
Y L NA+ + + + IN+ M N ++ + D HV + G
Sbjct: 36 YPLQNAIIEF-----YTEYYKTNSINEKM-NKLENKYIDAYHVIFKEG 77
>gnl|CDD|180177 PRK05636, PRK05636, replicative DNA helicase; Provisional.
Length = 505
Score = 27.5 bits (61), Expect = 1.3
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 32 FVDQIPFKIRKICVALSTIYELSNAMESYIDDNGSMDQFVNPEINQLMENGVKRQDMDHV 91
F Q+ +++ V L I +L+ ES D P++ L E+G QD D V
Sbjct: 403 FSRQLKLLAKELDVPLIAISQLNRGPESRTDKR--------PQLADLRESGSLEQDADMV 454
Query: 92 FLRY 95
L Y
Sbjct: 455 MLLY 458
>gnl|CDD|180705 PRK06806, PRK06806, fructose-bisphosphate aldolase; Provisional.
Length = 281
Score = 26.6 bits (59), Expect = 2.6
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 40 IRKICVALSTIYELSNAMESYIDDNGSMDQFV--NPEINQLMENGVKR 85
IRKI VA +T + A+ + + + D F I EN VK+
Sbjct: 224 IRKINVATATFNSVITAVNNLVLNTPYSDYFTYHQDVIKAAYEN-VKK 270
>gnl|CDD|219018 pfam06419, COG6, Conserved oligomeric complex COG6. COG6 is a
component of the conserved oligomeric golgi complex,
which is composed of eight different subunits and is
required for normal golgi morphology and localisation.
Length = 615
Score = 26.9 bits (60), Expect = 2.8
Identities = 9/43 (20%), Positives = 21/43 (48%)
Query: 39 KIRKICVALSTIYELSNAMESYIDDNGSMDQFVNPEINQLMEN 81
++++I LS + M+S +++ + + E + LME
Sbjct: 46 QLKRIGEDLSKLNNTCEEMKSQLNNAKQDTKDLLEEASTLMEQ 88
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair
protein alkB homolog 8 (ALKBH8) and similar proteins.
This subfamily corresponds to the RRM of ALKBH8, also
termed alpha-ketoglutarate-dependent dioxygenase ABH8,
or S-adenosyl-L-methionine-dependent tRNA
methyltransferase ABH8, expressed in various types of
human cancers. It is essential in urothelial carcinoma
cell survival mediated by NOX-1-dependent ROS signals.
ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation of
tRNA modification. ALKBH8 localizes to the cytoplasm. It
contains the characteristic AlkB domain that is composed
of a tRNA methyltransferase motif, a motif homologous to
the bacterial AlkB DNA/RNA repair enzyme, and a
dioxygenase catalytic core domain encompassing
cofactor-binding sites for iron and 2-oxoglutarate. In
addition, unlike other AlkB homologs, ALKBH8 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal S-adenosylmethionine (SAM)-dependent
methyltransferase (MT) domain. .
Length = 80
Score = 24.5 bits (54), Expect = 6.7
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 81 NGVKRQDMDHVFLRYGKITS 100
NGV R+++ VF +YG +
Sbjct: 13 NGVSREELLRVFEKYGTVED 32
>gnl|CDD|168658 PRK06749, PRK06749, replicative DNA helicase; Provisional.
Length = 428
Score = 25.7 bits (56), Expect = 7.0
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 13/76 (17%)
Query: 41 RKICVALSTIYELSNAMESYIDDNGSMDQFVNPEINQLMENGVKRQDMDHVFLR-----Y 95
R++ V + + +LS ++ES D P ++ L E G QD D + L Y
Sbjct: 337 RELNVCVVALSQLSRSVESRQDKR--------PLLSDLRETGQIEQDADVIMLMYREDYY 388
Query: 96 GKITSDGWVSPVHVYK 111
K T ++ +HV K
Sbjct: 389 DKETMQKEMTEIHVAK 404
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
0.325 0.139 0.430
Gapped
Lambda K H
0.267 0.0594 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,739,057
Number of extensions: 475456
Number of successful extensions: 602
Number of sequences better than 10.0: 1
Number of HSP's gapped: 602
Number of HSP's successfully gapped: 21
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.5 bits)