RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16895
(93 letters)
>gnl|CDD|185400 PTZ00018, PTZ00018, histone H3; Provisional.
Length = 136
Score = 177 bits (451), Expect = 2e-59
Identities = 88/93 (94%), Positives = 92/93 (98%)
Query: 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVG 60
PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQS+A+ ALQEA+EAYLVG
Sbjct: 44 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVG 103
Query: 61 LFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 93
LFEDTNLCAIHAKRVTIMPKDIQLARRIRGER+
Sbjct: 104 LFEDTNLCAIHAKRVTIMPKDIQLARRIRGERS 136
>gnl|CDD|128705 smart00428, H3, Histone H3.
Length = 105
Score = 159 bits (405), Expect = 8e-53
Identities = 82/95 (86%), Positives = 86/95 (90%), Gaps = 2/95 (2%)
Query: 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSAAIGALQEASEAYL 58
PG VALREIR+YQKST+LLIRK PFQRLVREIAQ F T DLRFQS+AI ALQEA+EAYL
Sbjct: 11 PGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYL 70
Query: 59 VGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 93
VGLFEDTNL AIHAKRVTIMPKDIQLARRIRGER
Sbjct: 71 VGLFEDTNLLAIHAKRVTIMPKDIQLARRIRGERL 105
>gnl|CDD|177733 PLN00121, PLN00121, histone H3; Provisional.
Length = 136
Score = 158 bits (400), Expect = 9e-52
Identities = 88/93 (94%), Positives = 92/93 (98%)
Query: 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVG 60
PGTVALREIR+YQKSTELLIRKLPFQRLVREIAQDFKTDLRFQS+A+ ALQEA+EAYLVG
Sbjct: 44 PGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVG 103
Query: 61 LFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 93
LFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Sbjct: 104 LFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136
>gnl|CDD|215082 PLN00161, PLN00161, histone H3; Provisional.
Length = 135
Score = 124 bits (312), Expect = 3e-38
Identities = 68/91 (74%), Positives = 78/91 (85%), Gaps = 1/91 (1%)
Query: 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD-LRFQSAAIGALQEASEAYLV 59
PGTVALREIR+YQKSTELLIRKLPF RLVREI+ + + R+ + A+ ALQEA+E +LV
Sbjct: 37 PGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLV 96
Query: 60 GLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 90
LFED NLCAIHAKRVTIMPKD+QLARRIRG
Sbjct: 97 HLFEDCNLCAIHAKRVTIMPKDMQLARRIRG 127
>gnl|CDD|165727 PLN00160, PLN00160, histone H3; Provisional.
Length = 97
Score = 118 bits (296), Expect = 2e-36
Identities = 65/92 (70%), Positives = 78/92 (84%), Gaps = 1/92 (1%)
Query: 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSAAIGALQEASEAYLV 59
PG AL+EI+ YQKST+LLIR+LPF RLVREI + + R+Q +AI ALQEA+EA+LV
Sbjct: 3 PGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLV 62
Query: 60 GLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 91
GLFED+NLCAIH KRVTIMPKD+QLARRIRG+
Sbjct: 63 GLFEDSNLCAIHGKRVTIMPKDMQLARRIRGQ 94
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 102 bits (257), Expect = 1e-30
Identities = 41/75 (54%), Positives = 49/75 (65%)
Query: 15 STELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKR 74
S+ LLI KLPF R+VRE+ + F +LR S A ALQEA E L + ED L A HAKR
Sbjct: 1 SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60
Query: 75 VTIMPKDIQLARRIR 89
TI P+DIQLA R+
Sbjct: 61 KTITPRDIQLAVRLD 75
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 101 bits (253), Expect = 7e-30
Identities = 43/92 (46%), Positives = 58/92 (63%), Gaps = 5/92 (5%)
Query: 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVG 60
PG V L+EIRRYQ+ST+LL+ K P +R++R+ + R S+AI LQEA E YL
Sbjct: 1 PGAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGAE-----RVSSSAIEELQEALEEYLEE 55
Query: 61 LFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 92
+ ED A HAKR T+ +DI+LA + G R
Sbjct: 56 IAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 28.5 bits (64), Expect = 0.18
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 16 TELLIRKLPFQRLVREIAQDFKT 38
+++L+R +PF+ V+E+ + F T
Sbjct: 1 SKILVRNIPFEATVKELRELFST 23
>gnl|CDD|173968 cd08050, TAF6, TATA Binding Protein (TBP) Associated Factor 6
(TAF6) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 6 (TAF6) is one of several TAFs that bind TBP
and are involved in forming Transcription Factor IID
(TFIID) complex. TFIID is one of seven General
Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID,
TFIIE, TFIIF, and TFIID) that are involved in accurate
initiation of transcription by RNA polymerase II in
eukaryotes. TFIID plays an important role in the
recognition of promoter DNA and assembly of the
pre-initiation complex. TFIID complex is composed of
the TBP and at least 13 TAFs. TAFs are named after
their electrophoretic mobility in polyacrylamide gels
in different species. A new, unified nomenclature has
been suggested for the pol II TAFs to show the
relationship between TAF orthologs and paralogs.
Several hypotheses are proposed for TAFs functions such
as serving as activator-binding sites, core-promoter
recognition or a role in essential catalytic activity.
These TAFs, with the help of specific activators, are
required only for expression of a subset of genes and
are not universally involved for transcription as are
GTFs. In yeast and human cells, TAFs have been found as
components of other complexes besides TFIID. Several
TAFs interact via histone-fold (HFD) motifs; the HFD is
the interaction motif involved in heterodimerization of
the core histones and their assembly into nucleosome
octamers. The minimal HFD contains three alpha-helices
linked by two loops and is found in core histones, TAFs
and many other transcription factors. TFIID has a
histone octamer-like substructure. TAF6 is a shared
subunit of histone acetyltransferase complex SAGA and
TFIID complexes. TAF6 domain interacts with TAF9 and
makes a novel histone-like heterodimer that is
structurally related to histones H4 and H3. TAF6 may
also interact with the downstream core promoter element
(DPE).
Length = 343
Score = 28.1 bits (63), Expect = 0.61
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 18/62 (29%)
Query: 29 VREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 88
+ +A+D + LR I +QEA++ H+KR + D+ A R+
Sbjct: 22 AQLLAEDVEYRLR----EI--IQEAAK------------FMRHSKRRKLTTSDVNHALRL 63
Query: 89 RG 90
R
Sbjct: 64 RN 65
>gnl|CDD|237585 PRK14015, pepN, aminopeptidase N; Provisional.
Length = 875
Score = 27.4 bits (62), Expect = 1.0
Identities = 22/95 (23%), Positives = 29/95 (30%), Gaps = 19/95 (20%)
Query: 11 RYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEA--------------SEA 56
R++ L R L V Q D A L + SEA
Sbjct: 569 RWEAGQRLATRLL--LANVARHGQPLSLDEALIDAFRAVLLDESLDPAFAAELLTLPSEA 626
Query: 57 YLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 91
L E + AIHA R + LA ++ E
Sbjct: 627 ELAEQMEVIDPDAIHAAREALR---RALATALKDE 658
>gnl|CDD|173964 cd07981, TAF12, TATA Binding Protein (TBP) Associated Factor 12
(TAF12) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 12 (TAF12) is one of several TAFs that bind TBP
and are involved in forming the TFIID complex. TFIID is
one of the seven General Transcription Factors (GTFs)
(TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are
involved in accurate initiation of transcription by RNA
polymerase II in eukaryotes. TFIID plays an important
role in the recognition of promoter DNA and assembly of
the pre-initiation complex. TFIID complex is composed
of the TBP and at least 13 TAFs. TAFs are named after
their electrophoretic mobility in polyacrylamide gels
in different species. A new, unified nomenclature has
been suggested for the pol II TAFs to show the
relationship between TAF orthologs and paralogs.
Several hypotheses are proposed for TAFs function such
as serving as activator-binding sites, core-promoter
recognition or a role in essential catalytic activity.
These TAFs, with the help of specific activators, are
required only for expression of a subset of genes and
are not universally involved for transcription as are
GTFs. In yeast and human cells, TAFs have been found as
components of other complexes besides TFIID. Several
TAFs interact via histone-fold (HFD) motifs; the HFD is
the interaction motif involved in heterodimerization of
the core histones and their assembly into nucleosome
octamers. The minimal HFD contains three alpha-helices
linked by two loops and is found in core histones, TAFs
and many other transcription factors. TFIID has a
histone octamer-like substructure. TAF12 domain
interacts with TAF4 and makes a novel histone-like
heterodimer that binds DNA and has a core promoter
function of a subset of genes.
Length = 72
Score = 25.6 bits (57), Expect = 1.7
Identities = 14/60 (23%), Positives = 28/60 (46%)
Query: 26 QRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85
+R ++E+ ++ + L E ++ ++ + ED A H K T+ KD+QL
Sbjct: 4 KRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLH 63
>gnl|CDD|202084 pfam01997, Translin, Translin family. Members of this family
include Translin that interacts with DNA and forms a
ring around the DNA. This family also includes human
translin-associated protein X, which was found to
interact with translin with yeast two-hybrid screen.
Length = 187
Score = 26.8 bits (60), Expect = 1.7
Identities = 14/64 (21%), Positives = 23/64 (35%), Gaps = 12/64 (18%)
Query: 7 REIRRYQKSTELLIRKLPF----------QRLVREIAQDFKT--DLRFQSAAIGALQEAS 54
R+I R K + + + L+ ++ + K R+ A ALQE
Sbjct: 12 RDITRLSKKAIFALHRGDAEEAEELLKEAKELLAKLKELLKGHPYYRYSGAWSNALQEYV 71
Query: 55 EAYL 58
EA
Sbjct: 72 EALT 75
>gnl|CDD|132031 TIGR02986, restrict_Alw26I, type II restriction endonuclease,
Alw26I/Eco31I/Esp3I family. Members of this family are
type II restriction endonucleases of the
Alw26I/Eco31I/Esp3I family. Characterized specificities
of three members are GGTCTC, CGTCTC, and the shared
subsequence GTCTC [DNA metabolism,
Restriction/modification].
Length = 424
Score = 26.3 bits (58), Expect = 2.3
Identities = 16/87 (18%), Positives = 33/87 (37%), Gaps = 17/87 (19%)
Query: 10 RRYQKSTELLIRKLP--FQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNL 67
+R +R + R++ I + F + + + A Y FE ++
Sbjct: 332 KRLSNI----LRSNQDTYMRILWYILSN--GGAEFLATLLK-PEYAEYNYT---FEGLDI 381
Query: 68 CAIHAKRVTIMPK-----DIQLARRIR 89
+ + V+ P+ D + ARR+R
Sbjct: 382 GTLFGEIVSKTPRNTKRADSEAARRVR 408
>gnl|CDD|173963 cd07979, TAF9, TATA Binding Protein (TBP) Associated Factor 9
(TAF9) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 9 (TAF9) is one of several TAFs that bind TBP
and are involved in forming the TFIID complex. TFIID is
one of seven General Transcription Factors (GTF)
(TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are
involved in accurate initiation of transcription by RNA
polymerase II in eukaryotes. TFIID plays an important
role in the recognition of promoter DNA and assembly of
the pre-initiation complex. The TFIID complex is
composed of the TBP and at least 13 TAFs. TAFs from
various species were originally named by their
predicted molecular weight or their electrophoretic
mobility in polyacrylamide gels. A new, unified
nomenclature for the pol II TAFs has been suggested to
show the relationship between TAFs orthologs and
paralogs. Human TAF9 has a paralogue gene (TAF9L) which
has a redundant function. Several hypotheses are
proposed for TAF function such as serving as
activator-binding sites, in core-promoter recognition
or a role in essential catalytic activity. It has been
shown that TAF9 interacts directly with different
transcription factors such as p53, herpes simplex virus
activator vp16 and the basal transcription factor
TFIIB. Each TAF, with the help of a specific activator,
is required only for expression of subset of genes and
are not universally involved for transcription as are
GTFs. In yeast and human cells, TAFs have been found as
components of other complexes besides TFIID. TAF9 is a
component of TFIID in multiple organisms as well as
different TBP-free TAF complexes containing the
GCN5-type histone acetyltransferase. Several TAFs
interact via histone-fold (HFD) motifs; HFD is the
interaction motif involved in heterodimerization of the
core histones and their assembly into nucleosome
octamers. The minimal HFD contains three alpha-helices
linked by two loops and is found in core histones, TAFS
and many other transcription factors. TFIID has a
histone octamer-like substructure. TFIID has a histone
octamer-like substructure. TAF9 is a shared subunit of
both, histone acetyltransferase complex (SAGA) and
TFIID complexes. TAF9 domain interacts with TAF6 to
form a novel histone-like heterodimer that is
structurally related to the histone H3 and H4 oligomer.
Length = 117
Score = 26.0 bits (58), Expect = 2.4
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 56 AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 90
Y + +D + + HA + I D++LA + R
Sbjct: 33 RYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRV 67
>gnl|CDD|234474 TIGR04113, cas_csx17, CRISPR-associated protein Csx17, subtype
Dpsyc. Members of this protein family are found
exclusively in CRISPR-associated (cas) type I system
gene clusters of the Dpsyc subtype. Markers for that
type include a variant form of cas3 (model TIGR02621)
and the GSU0054-like protein family (model TIGR02165).
This family occurs in less than half of known Dpsyc
clusters.
Length = 704
Score = 26.2 bits (58), Expect = 2.9
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 1/49 (2%)
Query: 11 RYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLV 59
R Q +L+ + R +D K F SA ++EA A
Sbjct: 371 RRQPRADLINELDGWLNRFRSFPRDGKAPASFLSAR-RRIEEAIFAAAT 418
>gnl|CDD|225055 COG2144, COG2144, Selenophosphate synthetase-related proteins
[General function prediction only].
Length = 324
Score = 26.2 bits (58), Expect = 2.9
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 6 LREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD 39
L ++ + E ++RK P + VRE +F
Sbjct: 3 LEDLISELRLFEGILRKNPIKDAVREFLDEFYGA 36
>gnl|CDD|237549 PRK13897, PRK13897, type IV secretion system component VirD4;
Provisional.
Length = 606
Score = 25.9 bits (57), Expect = 3.1
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 12 YQKSTELLIRKLP 24
YQ++TE L RKLP
Sbjct: 388 YQQATEFLCRKLP 400
>gnl|CDD|212542 cd11600, HDAC_Clr3, Class II Histone deacetylase Clr3 and similar
proteins. Clr3 is a class II Histone deacetylase
Zn-dependent enzyme that catalyzes hydrolysis of an
N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Clr3 is the homolog
of the class-II HDAC HdaI in S. cerevisiae, and is
essential for silencing in heterochromatin regions, such
as centromeric regions, ribosomal DNA, the mating-type
region and telomeric loci. Clr3 has also been implicated
in the regulation of stress-related genes; the histone
acetyltransferase, Gcn5, in S. cerevisiae,
preferentially acetylates global histone H3K14 while
Clr3 preferentially deacetylates H3K14ac, and therefore,
interplay between Gcn5 and Clr3 is crucial for the
regulation of many stress-response genes.
Length = 313
Score = 25.8 bits (57), Expect = 3.7
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 25 FQRLVREIAQDFKTDLRFQSAAIGA 49
FQR+V IA +F DL SA A
Sbjct: 225 FQRIVMPIAYEFDPDLVIISAGFDA 249
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 25.6 bits (57), Expect = 3.8
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEA 56
E LI K+ F R+ ++A+ K R+Q A+ AL A
Sbjct: 368 EPLIGKVRFSRIGIKLAETHKKGYRWQHEAVIALASPDNA 407
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 25.7 bits (56), Expect = 3.9
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 15 STELLIRKLPFQRLVR 30
STE +++ LPFQRL R
Sbjct: 437 STEKVLKSLPFQRLKR 452
Score = 24.6 bits (53), Expect = 9.7
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 15 STELLIRKLPFQRLVR 30
STE +++ LP QRL R
Sbjct: 120 STENVLKSLPLQRLKR 135
>gnl|CDD|163654 cd07411, MPP_SoxB_N, Thermus thermophilus SoxB and related
proteins, N-terminal metallophosphatase domain. SoxB
(sulfur oxidation protein B) is a periplasmic
thiosulfohydrolase and an essential component of the
sulfur oxidation pathway in archaea and bacteria. SoxB
has a dinuclear manganese cluster and is thought to
catalyze the release of sulfate from a protein-bound
cysteine S-thiosulfonate. SoxB is expressed from the
sox (sulfur oxidation) gene cluster, which encodes 15
other sox genes, and has two domains, an N-terminal
metallophosphatase domain and a C-terminal
5'-nucleotidase domain. SoxB binds the SoxYZ complex
and is thought to function as a sulfate-thiohydrolase.
SoxB is closely related to the UshA, YchR, and CpdB
proteins, all of which have the same two-domain
architecture. The N-terminal metallophosphatase domain
belongs to a large superfamily of distantly related
metallophosphatases (MPPs) that includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 264
Score = 24.9 bits (55), Expect = 7.0
Identities = 6/13 (46%), Positives = 10/13 (76%)
Query: 78 MPKDIQLARRIRG 90
+P D++LA R+ G
Sbjct: 195 LPVDVELAERVPG 207
>gnl|CDD|219450 pfam07524, Bromo_TP, Bromodomain associated. This domain is
predicted to bind DNA and is often found associated
with pfam00439 and in transcription factors. It has a
histone-like fold.
Length = 77
Score = 24.2 bits (53), Expect = 7.0
Identities = 10/45 (22%), Positives = 19/45 (42%)
Query: 41 RFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85
+ +A+ L + +++Y+ L A HA R D+ L
Sbjct: 23 SAEESALETLTDIAQSYIQELGRQAKRFAEHAGRSEPTLFDVVLT 67
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
MRD1 is encoded by a novel yeast gene MRD1 (multiple
RNA-binding domain). It is well-conserved in yeast and
its homologs exist in all eukaryotes. MRD1 is present
in the nucleolus and the nucleoplasm. It interacts with
the 35 S precursor rRNA (pre-rRNA) and U3 small
nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the
35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 76
Score = 24.1 bits (53), Expect = 7.1
Identities = 7/23 (30%), Positives = 15/23 (65%)
Query: 16 TELLIRKLPFQRLVREIAQDFKT 38
T+L++R +PF+ +E+ + F
Sbjct: 1 TKLIVRNVPFEATKKELRELFSP 23
>gnl|CDD|162338 TIGR01398, FlhA, flagellar biosynthesis protein FlhA. This model
describes flagellar biosynthesis protein FlhA, one of a
large number of genes associated with the biosynthesis
of functional bacterial flagella. Homologs of many such
proteins, including FlhA, function in type III protein
secretion systems. A separate model describes InvA
(Salmonella enterica), LcrD (Yersinia enterocolitica),
HrcV (Xanthomonas), etc., all of which score below the
noise cutoff for this model [Cellular processes,
Chemotaxis and motility].
Length = 678
Score = 24.9 bits (55), Expect = 8.7
Identities = 10/35 (28%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 5 ALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD 39
L + K +LL+ + QRL R+I Q + +
Sbjct: 544 TLADYAPITKDPDLLVEHVR-QRLGRQITQQYLDE 577
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 0.138 0.381
Gapped
Lambda K H
0.267 0.0663 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,871,843
Number of extensions: 401614
Number of successful extensions: 502
Number of sequences better than 10.0: 1
Number of HSP's gapped: 498
Number of HSP's successfully gapped: 45
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
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 (24.3 bits)