RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9880
(280 letters)
>gnl|CDD|227571 COG5246, PRP11, Splicing factor 3a, subunit 2 [RNA processing and
modification].
Length = 222
Score = 197 bits (502), Expect = 5e-63
Identities = 74/243 (30%), Positives = 106/243 (43%), Gaps = 47/243 (19%)
Query: 1 MDYQNRPGGKTGGGGVASWSESNRDRRERLRQLALETIDLNKDPYFMKNHLGSYECKLCL 60
M+Y R G KTGGGG AS + N+ RR R L DL DPY KNH G Y C LC
Sbjct: 1 MNYGGRGGSKTGGGGTASEIKKNKKRRSRQLLLEAYGQDLMDDPYLSKNHTGKYVCLLCK 60
Query: 61 TLHNNEGSYLAHTQGKKHQANLARRAAKEAKDAPQQSCDELLLTSDAVYTHKDSILISTL 120
T H E SY+ H +GKKH+ N +RR+ +++ + + K S+
Sbjct: 61 TKHLTEMSYVKHREGKKHKENSSRRSEEKSSLGRENQTTHDFRQQQKIIEAKQSL----- 115
Query: 121 DWGPPAPEKPRVEPKKFVKIGRPGYRVTKQRDPSNGQQSLLFQVDYPEIADDVFPRHRFM 180
+ G P Y+V +P G+
Sbjct: 116 -----------------KRSGIPSYKVRSLVEPKGGR----------------------- 135
Query: 181 SAYSLLFQVDYPEIADDVFPRHRFMSAYEQRIEPPDRKWQYLLFAAEPYETIAFKVSDRT 240
L QV+Y + + P++R +S+ EQ +E D ++YL+FA EPYE IAFK ++
Sbjct: 136 --RGLGIQVNYEDDLAEEMPQYRIVSSLEQNVEEYDESFRYLVFACEPYENIAFKFENKE 193
Query: 241 GLY 243
+
Sbjct: 194 IDF 196
>gnl|CDD|214996 smart01050, CactinC_cactus, Cactus-binding C-terminus of cactin
protein. CactinC_cactus is the C-terminal 200 residues
of the cactin protein which are necessary for the
association of cactin with IkappaB-cactus as one of the
intracellular members of the Rel complex. The Rel
(NF-kappaB) pathway is conserved in invertebrates and
vertebrates. In mammals, it controls the activities of
the immune and inflammatory response genes as well as
viral genes, and is critical for cell growth and
survival. In Drosophila, the Rel pathway functions in
the innate cellular and humoral immune response, in
muscle development, and in the establishment of
dorsal-ventral polarity in the early embryo. Most
members of the family also have a Cactin_mid domain
further upstream.
Length = 129
Score = 91.3 bits (227), Expect = 5e-23
Identities = 30/118 (25%), Positives = 39/118 (33%), Gaps = 30/118 (25%)
Query: 127 PEKPRVEPKKFVKIGRPGYRVTK---QRDPSNGQQSLLFQVDYPEIADDVFPRHRFMSAY 183
KPR + Y T P Q F + YP++ D
Sbjct: 7 LRKPRYFNRVKTGYDWNKYNQTHYDNDNPPPKIVQGYKFNIFYPDLID------------ 54
Query: 184 SLLFQVDYPEIADDVFPRHRFMSAYEQRIEPPDRKWQYLLF-AAEPYETIAFKVSDRT 240
PR+R S++E E PD L F A PYE IAFK+ +R
Sbjct: 55 ------------KGKAPRYRIESSFEI--EKPDDDTCLLRFSAGPPYEDIAFKIVNRE 98
>gnl|CDD|197732 smart00451, ZnF_U1, U1-like zinc finger. Family of C2H2-type
zinc fingers, present in matrin, U1 small nuclear
ribonucleoprotein C and other RNA-binding proteins.
Length = 35
Score = 48.4 bits (116), Expect = 3e-08
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 52 GSYECKLCLTLHNNEGSYLAHTQGKKHQANLARR 85
G + CKLC +E S AH +GKKH+ N+ +R
Sbjct: 2 GGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a
zinc-finger domain with the CxxCx(12)Hx(6)H motif,
found in multiple copies in a wide range of proteins
from plants to metazoans. Some member proteins,
particularly those from plants, are annotated as being
RNA-binding.
Length = 25
Score = 40.6 bits (96), Expect = 2e-05
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 54 YECKLCLTLHNNEGSYLAHTQGKKH 78
+ C+LC +E +H +GKKH
Sbjct: 1 FYCELCNVTFTSESQLKSHLRGKKH 25
>gnl|CDD|234807 PRK00648, PRK00648, Maf-like protein; Reviewed.
Length = 191
Score = 31.8 bits (73), Expect = 0.22
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 59 CLTLHNNEGSYLAHTQGKKHQANLARRAAKEAKDAPQQSCDELLLTSDAVYTHKDSIL 116
+ E SY ++ LAR A+ + DEL++T+D + + +L
Sbjct: 27 VVPSPFVEESYPYSLDPEEITLELARLKAEAVR--SDLFPDELIITADTIVWYDGKVL 82
>gnl|CDD|204069 pfam08799, PRP4, pre-mRNA processing factor 4 (PRP4) like. This
small domain is found on PRP4 ribonuleoproteins. PRP4
is a U4/U6 small nuclear ribonucleoprotein that is
involved in pre-mRNA processing.
Length = 30
Score = 26.9 bits (61), Expect = 1.3
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 21 ESNRDRRERLRQL 33
E++ DRRERLR+L
Sbjct: 17 ETDADRRERLRKL 29
>gnl|CDD|128776 smart00500, SFM, Splicing Factor Motif, present in Prp18 and
Pr04.
Length = 44
Score = 26.6 bits (59), Expect = 2.2
Identities = 10/23 (43%), Positives = 17/23 (73%)
Query: 21 ESNRDRRERLRQLALETIDLNKD 43
E +++RR+RLRQL + +L+K
Sbjct: 22 EDDQERRQRLRQLLIVQDELDKG 44
>gnl|CDD|192352 pfam09732, CactinC_cactus, Cactus-binding C-terminus of cactin
protein. CactinC_cactus is the C-terminal 200 residues
of the cactin protein which are necessary for the
association of cactin with IkappaB-cactus as one of the
intracellular members of the Rel complex. The Rel
(NF-kappaB) pathway is conserved in invertebrates and
vertebrates. In mammals, it controls the activities of
the immune and inflammatory response genes as well as
viral genes, and is critical for cell growth and
survival. In Drosophila, the Rel pathway functions in
the innate cellular and humoral immune response, in
muscle development, and in the establishment of
dorsal-ventral polarity in the early embryo. Most
members of the family also have a Cactin_mid domain
pfam10312 further upstream.
Length = 125
Score = 27.6 bits (62), Expect = 3.3
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 10/57 (17%)
Query: 187 FQVDYPEIADDVFPRHRFMSAYEQRIEPPDRKWQY--LLFAAE-PYETIAFKVSDRT 240
F + YP++ D R+ RIEP + L F A PYE IAF++ ++
Sbjct: 45 FNIFYPDLIDKGKA-PRY------RIEPCEDPDDTCLLRFHAGPPYEDIAFRIVNKE 94
>gnl|CDD|114912 pfam06220, zf-U1, U1 zinc finger. This family consists of
several U1 small nuclear ribonucleoprotein C (U1-C)
proteins. The U1 small nuclear ribonucleoprotein (U1
snRNP) binds to the pre-mRNA 5' splice site (ss) at
early stages of spliceosome assembly. Recruitment of U1
to a class of weak 5' ss is promoted by binding of the
protein TIA-1 to uridine-rich sequences immediately
downstream from the 5' ss. Binding of TIA-1 in the
vicinity of a 5' ss helps to stabilise U1 snRNP
recruitment, at least in part, via a direct interaction
with U1-C, thus providing one molecular mechanism for
the function of this splicing regulator. This domain is
probably a zinc-binding. It is found in multiple copies
in some members of the family.
Length = 38
Score = 25.5 bits (56), Expect = 5.3
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 2/35 (5%)
Query: 53 SYECKLCLT--LHNNEGSYLAHTQGKKHQANLARR 85
Y C C H++ +H G+KH+ N+
Sbjct: 3 KYYCDYCDCYLTHDSPSVRKSHNGGRKHKDNVKDY 37
>gnl|CDD|233988 TIGR02734, crtI_fam, phytoene desaturase. Phytoene is converted to
lycopene by desaturation at four (two symmetrical pairs
of) sites. This is achieved by two enzymes (crtP and
crtQ) in cyanobacteria (Gloeobacter being an exception)
and plants, but by a single enzyme in most other
bacteria and in fungi. This single enzyme is called the
bacterial-type phytoene desaturase, or CrtI. Most
members of this family, part of the larger Pfam family
pfam01593, which also contains amino oxidases, are CrtI
itself; it is likely that all members act on either
phytoene or on related compounds such as
dehydrosqualene, for carotenoid biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 502
Score = 28.0 bits (63), Expect = 5.5
Identities = 24/103 (23%), Positives = 39/103 (37%), Gaps = 8/103 (7%)
Query: 98 CDELLLTSDAVYTHKDSILISTLDWGPPA--PEKPRVEPKKFVKIGRPGYRVTKQRDPSN 155
D ++ +D +T++ +L + PA + R P FV G P
Sbjct: 265 ADAVVSNADLHHTYRR-LLPNHPRRRYPAARLSRKRPSPSLFVLY--FGLLGVDGHWPQL 321
Query: 156 GQQSLLFQVDYPEIADDVFPRHRFMSAYSLLFQ---VDYPEIA 195
+L F Y E+ D++F + R SL V P +A
Sbjct: 322 AHHTLCFGPRYKELFDEIFRKGRLAEDPSLYLHRPTVTDPSLA 364
>gnl|CDD|218422 pfam05088, Bac_GDH, Bacterial NAD-glutamate dehydrogenase. This
family consists of several bacterial proteins which are
closely related to NAD-glutamate dehydrogenase found in
Streptomyces clavuligerus. Glutamate dehydrogenases
(GDHs) are a broadly distributed group of enzymes that
catalyze the reversible oxidative deamination of
glutamate to ketoglutarate and ammonia.
Length = 1526
Score = 27.9 bits (63), Expect = 8.6
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 6 RPGGKTGGGGVASWSESNRDRRERLRQL 33
G+ VA+W E+N R ER R++
Sbjct: 1474 SGPGEDAEAAVAAWLEANASRLERWRRM 1501
>gnl|CDD|234400 TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa. This
model represents the N-terminal domain or EccCa subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 661
Score = 27.6 bits (62), Expect = 9.5
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 12 GGGGVASWSESNRDRRERLRQLA 34
GG S E + DRR+ LR L
Sbjct: 54 RGGAGKSTPELDEDRRDYLRYLD 76
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
0.319 0.135 0.412
Gapped
Lambda K H
0.267 0.0708 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,509,237
Number of extensions: 1365641
Number of successful extensions: 1085
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1078
Number of HSP's successfully gapped: 20
Length of query: 280
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 184
Effective length of database: 6,679,618
Effective search space: 1229049712
Effective search space used: 1229049712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.2 bits)