RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14680
(78 letters)
>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like.
Members of this group possess KH domains in a tandem
arrangement. Most members, similar to the poly(C)
binding proteins (PCBPs) and Nova, containing three KH
domains, with the first and second domains, which are
represented here, in tandem arrangement, followed by a
large spacer region, with the third domain near the
C-terminal end of the protein. The poly(C) binding
proteins (PCBPs) can be divided into two groups, hnRNPs
K/J and the alphaCPs, which share a triple KH domain
configuration and poly(C) binding specificity. They
play roles in mRNA stabilization, translational
activation, and translational silencing. Nova-1 and
Nova-2 are nuclear RNA-binding proteins that regulate
splicing. This group also contains plant proteins that
seem to have two tandem repeat arrrangements, like
Hen4, a protein that plays a role in AGAMOUS (AG)
pre-mRNA processing and important step in plant
development. In general, KH binds single-stranded RNA
or DNA. It is found in a wide variety of proteins
including ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA.
Length = 65
Score = 57.1 bits (139), Expect = 5e-13
Identities = 21/37 (56%), Positives = 32/37 (86%)
Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51
+++LVPS AG+IIGKGG TI +I+++TG+KI++SK
Sbjct: 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSK 37
>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional
modifiers of mRNA. There are two different KH domains
that belong to different protein folds, but they share
a single KH motif. The KH motif is folded into a beta
alpha alpha beta unit. In addition to the core, type II
KH domains (e.g. ribosomal protein S3) include
N-terminal extension and type I KH domains (e.g. hnRNP
K) contain C-terminal extension.
Length = 64
Score = 49.5 bits (119), Expect = 6e-10
Identities = 19/39 (48%), Positives = 28/39 (71%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
++LVPS G IIGKGG TI +I+++TG+KIK+ +
Sbjct: 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS 40
>gnl|CDD|215657 pfam00013, KH_1, KH domain. KH motifs bind RNA in vitro.
Autoantibodies to Nova, a KH domain protein, cause
paraneoplastic opsoclonus ataxia.
Length = 59
Score = 47.2 bits (113), Expect = 4e-09
Identities = 16/36 (44%), Positives = 24/36 (66%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51
+IL+P G IIGKGG I +I+++TG KI++
Sbjct: 2 ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIPD 37
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 44.6 bits (106), Expect = 5e-08
Identities = 17/40 (42%), Positives = 26/40 (65%)
Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
I++L+P+ G IIGKGG TI +I+++TG KI +
Sbjct: 4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS 43
>gnl|CDD|221895 pfam13014, KH_3, KH domain. KH motifs bind RNA in vitro. This
RNA-binding domain is required for the efficient
anchoring of ASH1-mRNA to the distal tip of the
daughter cell. ASH1 is a specific repressor of
transcription that localizes asymmetrically to the
daughter cell nucleus. RNA localisation is a widespread
mechanism for achieving localised protein synthesis.
Length = 42
Score = 41.8 bits (99), Expect = 4e-07
Identities = 17/30 (56%), Positives = 24/30 (80%)
Query: 25 AGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
GAIIGKGGETI +I+++TG+KI++ K
Sbjct: 2 VGAIIGKGGETIKEIREETGAKIQIPKPEP 31
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 38.5 bits (91), Expect = 8e-05
Identities = 11/22 (50%), Positives = 17/22 (77%)
Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
+IG GG+TI +I ++TG+KI
Sbjct: 566 RDVIGPGGKTIREITEETGAKI 587
>gnl|CDD|239092 cd02409, KH-II, KH-II (K homology RNA-binding domain, type II).
KH binds single-stranded RNA or DNA. It is found in a
wide variety of proteins including ribosomal proteins
(e.g. ribosomal protein S3), transcription factors
(e.g. NusA_K), and post-transcriptional modifiers of
mRNA (e.g. hnRNP K). There are two different KH domains
that belong to different protein folds, but they share
a single KH motif. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In addition to
their KH core domain, KH-II proteins have an N-terminal
alpha helical extension while KH-I proteins have a
C-terminal alpha helical extension.
Length = 68
Score = 34.5 bits (80), Expect = 5e-04
Identities = 12/45 (26%), Positives = 20/45 (44%)
Query: 7 FIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51
R +I I+V G +IGK G+ I +QK ++ +
Sbjct: 18 IERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLRKKR 62
>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding
domain_vigilin_like. The vigilin family is a large and
extended family of multiple KH-domain proteins,
including vigilin, also called high density lipoprotein
binding protien (HBP), fungal Scp160 and bicaudal-C.
Yeast Scp160p has been shown to bind RNA and to
associate with both soluble and membrane-bound
polyribosomes as a mRNP component. Bicaudal-C is a
RNA-binding molecule believed to function in embryonic
development at the post-transcriptional level. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and
post-transcriptional modifiers of mRNA.
Length = 62
Score = 33.3 bits (77), Expect = 0.001
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 28 IIGKGGETIAQIQKDTGSKIKMSKAND 54
IIGK G I +I ++TG KI+
Sbjct: 14 IIGKKGSNIRKIMEETGVKIRFPDPGS 40
>gnl|CDD|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K
homology RNA-binding domain (KH). PNPase is a
polyribonucleotide nucleotidyl transferase that
degrades mRNA in prokaryotes and plant chloroplasts.
The C-terminal region of PNPase contains domains
homologous to those in other RNA binding proteins: a KH
domain and an S1 domain. KH domains bind
single-stranded RNA and are found in a wide variety of
proteins including ribosomal proteins, transcription
factors and post-transcriptional modifiers of mRNA.
Length = 61
Score = 32.5 bits (75), Expect = 0.002
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
+IG GG+TI +I ++TG KI
Sbjct: 14 RDVIGPGGKTIKKIIEETGVKI 35
>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase.
Members of this protein family are polyribonucleotide
nucleotidyltransferase, also called polynucleotide
phosphorylase. Some members have been shown also to have
additional functions as guanosine pentaphosphate
synthetase and as poly(A) polymerase (see model
TIGR02696 for an exception clade, within this family)
[Transcription, Degradation of RNA].
Length = 684
Score = 34.4 bits (80), Expect = 0.002
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
+IG GG+ I +I ++TG+KI
Sbjct: 563 RDVIGPGGKVIREITEETGAKI 584
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 32.9 bits (76), Expect = 0.008
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
+IG GG+TI I ++TG KI
Sbjct: 564 RDVIGPGGKTIKAITEETGVKI 585
>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase
I/polynucleotide phosphorylase. Sohlberg, et al present
characterization of two proteins from Streptomyces
coelicolor. The protein in this family was shown to have
poly(A) polymerase activity and may be responsible for
polyadenylating RNA in this species. Reference 2 showed
that a nearly identical plasmid-encoded protein from
Streptomyces antibioticus is a bifunctional enzyme that
acts also as a guanosine pentaphosphate synthetase.
Length = 719
Score = 31.7 bits (72), Expect = 0.018
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKI 47
I + +P G +IG G+ I QIQ +TG++I
Sbjct: 580 ITVKIPVDKIGEVIGPKGKMINQIQDETGAEI 611
>gnl|CDD|239049 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH). NusA
is an essential multifunctional transcription
elongation factor that is universally conserved among
prokaryotes and archaea. NusA anti-termination function
plays an important role in the expression of ribosomal
rrn operons. During transcription of many other genes,
NusA-induced RNAP pausing provides a mechanism for
synchronizing transcription and translation . The
N-terminal RNAP-binding domain (NTD) is connected
through a flexible hinge helix to three globular
domains, S1, KH1 and KH2. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices.
Length = 61
Score = 30.2 bits (69), Expect = 0.020
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKI 47
+++VP G IGKGG+ + K G KI
Sbjct: 27 ARVVVPDDQLGLAIGKGGQNVRLASKLLGEKI 58
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 31.3 bits (72), Expect = 0.023
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIK 48
+ VP +IGKGG+ I +I+K G I
Sbjct: 483 AVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDID 515
>gnl|CDD|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology
RNA-binding domain (KH). Splicing factor 1 (SF1)
specifically recognizes the intron branch point
sequence (BPS) UACUAAC in the pre-mRNA transcripts
during spliceosome assembly. We show that the KH-QUA2
region of SF1 defines an enlarged KH (hnRNP K) fold
which is necessary and sufficient for BPS binding. KH
binds single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional
modifiers of mRNA.
Length = 120
Score = 30.7 bits (70), Expect = 0.027
Identities = 11/22 (50%), Positives = 17/22 (77%)
Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
G I+G G T+ Q++K+TG+KI
Sbjct: 18 GLILGPRGNTLKQLEKETGAKI 39
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 31.2 bits (71), Expect = 0.034
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 18 ILVPSYAAGAIIGKGGETIAQIQKDTGSKIK 48
+ VP +IGKGG+ I +I+K G KI
Sbjct: 490 VKVPEKYIPKVIGKGGKRIKEIEKKLGIKID 520
>gnl|CDD|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional.
Length = 180
Score = 30.6 bits (70), Expect = 0.047
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 20 VPSYAAGAIIGKGGETIAQIQKDTGSKIK 48
+P G +IGK GET +I++ TG K++
Sbjct: 9 IPKDRIGVLIGKKGETKKEIEERTGVKLE 37
Score = 25.2 bits (56), Expect = 3.3
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
G IIG+GG+T I++ TG I
Sbjct: 107 GRIIGEGGKTRRIIEELTGVDI 128
>gnl|CDD|211858 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain
protein. This family of proteins is universal among
the 41 archaeal genomes analyzed in and is not observed
outside of the archaea. The proteins contain a single
KH domain (pfam00013) which is likely to confer the
ability to bind RNA.
Length = 172
Score = 29.1 bits (66), Expect = 0.12
Identities = 12/22 (54%), Positives = 17/22 (77%)
Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
G +IGKGGET +I++ TG K+
Sbjct: 10 GVLIGKGGETKKEIEERTGVKL 31
Score = 25.6 bits (57), Expect = 2.2
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
G IIG+GG+T I++ TG I
Sbjct: 101 GRIIGEGGKTRRIIEELTGVSI 122
>gnl|CDD|181413 PRK08406, PRK08406, transcription elongation factor NusA-like
protein; Validated.
Length = 140
Score = 29.0 bits (66), Expect = 0.14
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKI 47
I +V G IGKGGE + ++++ G I
Sbjct: 34 IIFVVKEGDMGLAIGKGGENVKRLEEKLGKDI 65
>gnl|CDD|239095 cd02412, 30S_S3_KH, K homology RNA-binding (KH) domain of the
prokaryotic 30S small ribosomal subunit protein S3. S3
is part of the head region of the 30S ribosomal subunit
and is believed to interact with mRNA as it threads its
way from the latch into the channel. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In general, KH
binds single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional
modifiers of mRNA.
Length = 109
Score = 27.8 bits (63), Expect = 0.25
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 10/44 (22%)
Query: 9 RADGVCQIKILVPSYAA--GAIIGKGGETI----AQIQKDTGSK 46
R ++ I + A G IIGK G I ++QK G+K
Sbjct: 58 RKADRVEVTI----HTARPGIIIGKKGAGIEKLRKELQKLLGNK 97
>gnl|CDD|234722 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed.
Length = 232
Score = 28.2 bits (64), Expect = 0.27
Identities = 10/40 (25%), Positives = 22/40 (55%), Gaps = 8/40 (20%)
Query: 15 QIKILVPSYAA--GAIIGKGGETI----AQIQKDTGSKIK 48
++++ + + A G +IGK G I +++K TG ++
Sbjct: 63 RVRVTI--HTARPGIVIGKKGAEIEKLRKELEKLTGKPVQ 100
>gnl|CDD|203707 pfam07650, KH_2, KH domain.
Length = 77
Score = 27.1 bits (61), Expect = 0.44
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 26 GAIIGKGGETIAQIQKDTGSKIK 48
G +IGKGG I ++ K+ I+
Sbjct: 37 GIVIGKGGSNIKKLGKELRKLIE 59
>gnl|CDD|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH
domains) [General function prediction only].
Length = 194
Score = 27.3 bits (61), Expect = 0.61
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKM 49
+ +P G +IGK GE I++ TG K+++
Sbjct: 10 EAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRI 43
Score = 24.9 bits (55), Expect = 4.8
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
G IIG+ G+T I++ TG I
Sbjct: 114 GRIIGREGKTRRAIEELTGVYI 135
>gnl|CDD|211958 TIGR04235, seadorna_VP4, seadornavirus VP4 protein. This protein
family occurs in the seadornavirus virus group, with
designation VP4 in Banna virus, Kadipiro virus, and Liao
ning virus. Although this family has been suggested to
resemble methyltransferases, members show apparent
N-terminal sequence similarity to the outer capsid
protein VP5 of the orbivirus group, such as bluetongue
virus, which also belong to the Reoviridae.
Length = 618
Score = 27.2 bits (60), Expect = 0.96
Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 4/57 (7%)
Query: 8 IRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK-ANDFYPVYQVIT 63
ADGV + + PS A GA K G A+ +T +K S V+
Sbjct: 156 AAADGVGVVPVFGPSVANGA---KVGIDTAESVAETAIAVKASGIITQLNDVFHAFQ 209
>gnl|CDD|223273 COG0195, NusA, Transcription elongation factor [Transcription].
Length = 190
Score = 26.0 bits (58), Expect = 1.7
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 24 AAGAIIGKGGETIAQIQKDTGSKI 47
GA IGK G + + ++ G KI
Sbjct: 86 PVGACIGKRGSRVKAVSEELGEKI 109
Score = 25.7 bits (57), Expect = 2.2
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIK 48
++VP IGKGG+ + + TG +I
Sbjct: 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEID 176
>gnl|CDD|139075 PRK12568, PRK12568, glycogen branching enzyme; Provisional.
Length = 730
Score = 26.5 bits (58), Expect = 1.7
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 6 PFIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQ 40
P +ADG Q+++L P A +I G+ +A++Q
Sbjct: 32 PHPQADGRRQVRVLAPGAEAMGLIDGRGKLLARMQ 66
>gnl|CDD|227503 COG5176, MSL5, Splicing factor (branch point binding protein) [RNA
processing and modification].
Length = 269
Score = 26.1 bits (57), Expect = 2.2
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 6/41 (14%)
Query: 13 VCQIKILVP------SYAAGAIIGKGGETIAQIQKDTGSKI 47
Q KI +P S G +IG G T+ Q+++ + +KI
Sbjct: 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKI 187
>gnl|CDD|223170 COG0092, RpsC, Ribosomal protein S3 [Translation, ribosomal
structure and biogenesis].
Length = 233
Score = 25.7 bits (57), Expect = 2.7
Identities = 9/22 (40%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 23 YAA--GAIIGKGGETIAQIQKD 42
+AA G +IGK G I +++K+
Sbjct: 58 HAARPGLVIGKKGSNIEKLRKE 79
>gnl|CDD|188365 TIGR03675, arCOG00543, arCOG00543 universal archaeal
KH-domain/beta-lactamase-domain protein. This family of
proteins is universal in the archaea and consistsof an
N-terminal type-1 KH-domain (pfam00013) a central
beta-lactamase-domain (pfam00753) with a C-terminal
motif associated with RNA metabolism (pfam07521).
KH-domains are associated with RNA-binding, so taken
together, this protein is a likely metal-dependent
RNAase. This family was defined in as arCOG01782.
Length = 630
Score = 25.3 bits (56), Expect = 3.4
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 26 GAIIGKGGETIAQIQKDTG 44
G +IGKGG T+ +I K+TG
Sbjct: 105 GLVIGKGGSTLREITKETG 123
>gnl|CDD|233653 TIGR01952, nusA_arch, NusA family KH domain protein, archaeal.
This model represents a family of archaeal proteins
found in a single copy per genome. It contains two KH
domains (pfam00013) and is most closely related to the
central region bacterial NusA, a transcription
termination factor named for its iteraction with phage
lambda protein N in E. coli. The proteins required for
antitermination by N include NusA, NusB, nusE
(ribosomal protein S10), and nusG. This system, on the
whole, appears not to be present in the Archaea.
Length = 141
Score = 24.7 bits (54), Expect = 4.6
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
GA IGKGGE + ++++ G I
Sbjct: 45 GAAIGKGGENVKRLEELIGKSI 66
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 25.0 bits (56), Expect = 4.8
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 28 IIGKGGETIAQI 39
IIGKGG + +I
Sbjct: 241 IIGKGGAMLKKI 252
>gnl|CDD|239093 cd02410, archeal_CPSF_KH, The archaeal cleavage and polyadenylation
specificity factor (CPSF) contains an N-terminal K
homology RNA-binding domain (KH). The archeal CPSFs are
predicted to be metal-dependent RNases belonging to the
beta-CASP family, a subgroup enzymes within the
metallo-beta-lactamase fold. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In general, KH
domains are known to bind single-stranded RNA or DNA and
are found in a wide variety of proteins including
ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA.
Length = 145
Score = 24.6 bits (54), Expect = 4.8
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 26 GAIIGKGGETIAQIQKDTG 44
G +IGKGG T+ +I ++TG
Sbjct: 88 GLVIGKGGSTLREITRETG 106
>gnl|CDD|237205 PRK12792, flhA, flagellar biosynthesis protein FlhA; Reviewed.
Length = 694
Score = 25.1 bits (55), Expect = 5.2
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 11 DG-VCQIKILVPSYAAGAIIGKGG 33
DG V QI L+ S AAG ++ KGG
Sbjct: 245 DGLVSQIPALIVSLAAGLLVSKGG 268
>gnl|CDD|220400 pfam09785, Prp31_C, Prp31 C terminal domain. This is the C
terminal domain of the pre-mRNA processing factor
Prp31. Prp31 is required for U4/U6.U5 tri-snRNP
formation. In humans this protein has been linked to
autosomal dominant retinitis pigmentosa.
Length = 124
Score = 24.6 bits (54), Expect = 5.3
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 29 IGKGGET-IAQIQKDTGSKIKMSKAN 53
+G GG I QKD +K K+SK
Sbjct: 65 LGSGGGGRIRLSQKDAKTKAKLSKKM 90
>gnl|CDD|236971 PRK11760, PRK11760, putative 23S rRNA C2498 ribose 2'-O-ribose
methyltransferase; Provisional.
Length = 357
Score = 24.8 bits (55), Expect = 5.4
Identities = 7/13 (53%), Positives = 7/13 (53%)
Query: 62 ITLFLLSRPGFEP 74
L L RPGFE
Sbjct: 2 NKLLLYCRPGFEK 14
>gnl|CDD|224696 COG1782, COG1782, Predicted metal-dependent RNase, consists of a
metallo-beta-lactamase domain and an RNA-binding KH
domain [General function prediction only].
Length = 637
Score = 24.6 bits (54), Expect = 5.7
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 26 GAIIGKGGETIAQIQKDTG 44
G +IGKGG T+ +I +TG
Sbjct: 111 GLVIGKGGSTLREITAETG 129
>gnl|CDD|182960 PRK11098, PRK11098, microcin B17 transporter; Reviewed.
Length = 409
Score = 24.6 bits (54), Expect = 5.9
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 7 FIRADGVCQIKILVPSYAAGAI 28
+++ D V + +L PS AG I
Sbjct: 329 YLQVDNVFGLFLLFPSIVAGTI 350
>gnl|CDD|221909 pfam13083, KH_4, KH domain.
Length = 71
Score = 24.0 bits (53), Expect = 6.4
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQ 40
+ I++ V G +IGK G T+ +Q
Sbjct: 25 ENTVVIELNVAGEDLGKLIGKRGRTLDALQ 54
>gnl|CDD|184236 PRK13679, PRK13679, hypothetical protein; Provisional.
Length = 168
Score = 24.1 bits (53), Expect = 7.1
Identities = 8/30 (26%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 34 ETIAQIQKDTGS-KIKMSKANDFYPVYQVI 62
E + I +T + ++K + F P VI
Sbjct: 53 EELRAIASETKPFTLHVTKVSSFAPTNNVI 82
>gnl|CDD|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase;
Provisional.
Length = 891
Score = 24.5 bits (53), Expect = 7.2
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 28 IIGKGGETIAQIQKDTG 44
IIG GG+ + I ++TG
Sbjct: 699 IIGSGGKKVKSIIEETG 715
>gnl|CDD|235233 PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4;
Provisional.
Length = 235
Score = 24.1 bits (53), Expect = 8.3
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 28 IIGKGGETIAQIQKDTGSKI 47
+IGK G I ++++TG I
Sbjct: 159 VIGKKGSMINMLKEETGCDI 178
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
0.320 0.138 0.395
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,866,906
Number of extensions: 288947
Number of successful extensions: 280
Number of sequences better than 10.0: 1
Number of HSP's gapped: 280
Number of HSP's successfully gapped: 52
Length of query: 78
Length of database: 10,937,602
Length adjustment: 47
Effective length of query: 31
Effective length of database: 8,852,964
Effective search space: 274441884
Effective search space used: 274441884
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 (21.8 bits)
S2: 53 (24.2 bits)