RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16559
(207 letters)
>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL) and similar
proteins. This subgroup corresponds to the RRM of
U2AFBPL, a human homolog of the imprinted mouse gene
U2afbp-rs, which encodes a U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL), also termed CCCH
type zinc finger, RNA-binding motif and serine/arginine
rich protein 1 (U2AF1RS1), or U2 small nuclear RNA
auxiliary factor 1-like 1 (U2AF1L1). Although the
biological role of U2AFBPL remains unclear, it shows
high sequence homology to splicing factor U2AF 35 kDa
subunit (U2AF35 or U2AF1) that directly binds to the 3'
splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. Like U2AF35, U2AFBPL contains
two N-terminal zinc fingers, a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. .
Length = 105
Score = 147 bits (372), Expect = 8e-46
Identities = 58/105 (55%), Positives = 70/105 (66%)
Query: 94 TLLLNNFFTHLSMDNKSVREYDTDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKV 153
TLL+ N FTH ++ EYDTD LE+DE +++ F EFYDDVLPE G+V QFKV
Sbjct: 1 TLLIPNMFTHFGLEQTQRDEYDTDEGLEYDEEDLYSDFEEFYDDVLPEFEKFGEVVQFKV 60
Query: 154 CCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQFCN 198
CCN PHLRGNVYV Y +E EAL AF GR+Y GKQ+ +F
Sbjct: 61 CCNYEPHLRGNVYVQYQSEEEALAAFKMFNGRWYAGKQLTCEFSP 105
>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35) and similar proteins. This subfamily
corresponds to the RRM in U2 small nuclear
ribonucleoprotein (snRNP) auxiliary factor (U2AF) which
has been implicated in the recruitment of U2 snRNP to
pre-mRNAs. It is a highly conserved heterodimer composed
of large and small subunits; this family includes the
small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa
subunit B (U2AF35B or C3H60). U2AF35 directly binds to
the 3' splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF (U2AF65 or
U2AF2). Although the biological role of U2AF35B remains
unclear, it shows high sequence homolgy to U2AF35, which
contains two N-terminal zinc fingers, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal arginine/serine (SR) -rich segment
interrupted by glycines. In contrast to U2AF35, U2AF35B
has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 102
Score = 90.4 bits (225), Expect = 7e-24
Identities = 32/84 (38%), Positives = 44/84 (52%)
Query: 115 DTDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNERE 174
D L E E+ ++F EFY+DV EL G++ VC N HL GNVYV + E +
Sbjct: 19 DGQGVLTLSEEEIQEHFDEFYEDVFLELSRFGEIEDLVVCDNLGDHLLGNVYVKFETEED 78
Query: 175 ALRAFYALTGRFYGGKQIRGQFCN 198
A A AL GR+Y G+ + +
Sbjct: 79 AEAALQALNGRYYAGRPLYPELSP 102
>gnl|CDD|240983 cd12539, RRM_U2AF35B, RNA recognition motif in splicing factor U2AF
35 kDa subunit B (U2AF35B). This subgroup corresponds
to the RRM of U2AF35B, also termed zinc finger CCCH
domain-containing protein 60 (C3H60), which is one of
the small subunits of U2 small nuclear ribonucleoprotein
(snRNP) auxiliary factor (U2AF). It has been implicated
in the recruitment of U2 snRNP to pre-mRNAs and is a
highly conserved heterodimer composed of large and small
subunits. Members in this family are mainly found in
plant. They show high sequence homology to vertebrates
U2AF35 that directly binds to the 3' splice site of the
conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. U2AF35B contains two
N-terminal zinc fingers, a central RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. In contrast to U2AF35,
U2AF35B has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 103
Score = 75.1 bits (185), Expect = 6e-18
Identities = 35/103 (33%), Positives = 51/103 (49%), Gaps = 3/103 (2%)
Query: 94 TLLLNNFFTHLSMDNKSVREYDTDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKV 153
T+LL+N + + D E+ ++F +FY+D+ EL G+V V
Sbjct: 2 TILLSNMYQSPIA--GAPGGPRGQ-GQSLDPRELQEHFEDFYEDIFEELSKFGEVEALNV 58
Query: 154 CCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQF 196
C N H+ GNVYV + +E A A AL GRFY G+ I +F
Sbjct: 59 CDNLGDHMVGNVYVKFRDEEHAAAALKALQGRFYDGRPIIVEF 101
>gnl|CDD|240982 cd12538, RRM_U2AF35, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35). This subgroup corresponds to the RRM of
U2AF35, also termed U2AF1, which is one of the small
subunits of U2 small nuclear ribonucleoprotein (snRNP)
auxiliary factor (U2AF). It has been implicated in the
recruitment of U2 snRNP to pre-mRNAs and is a highly
conserved heterodimer composed of large and small
subunits. U2AF35 directly binds to the 3' splice site of
the conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF, U2AF65 (also
termed U2AF2). U2AF35 contains two N-terminal zinc
fingers, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich segment interrupted by
glycines. U2AF35 binds both U2AF65 and the pre-mRNA
through its RRM domain. .
Length = 104
Score = 63.9 bits (156), Expect = 1e-13
Identities = 33/107 (30%), Positives = 55/107 (51%), Gaps = 5/107 (4%)
Query: 92 SKTLLLNNFFTHLSMDNKSVREYDTDINLEFDETEMHKYFVEFYDDVLPEL-RSLGQVTQ 150
S+T+LL N + + +S ++ + E+ ++F EFY+DV EL G++ +
Sbjct: 1 SQTILLQNLYQNPQNSPQSADGLKVKVS----DVELQEHFDEFYEDVFVELEEKYGEIEE 56
Query: 151 FKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQFC 197
VC N HL GNVYV + E +A +A L R++ G+ I +
Sbjct: 57 MNVCDNLGDHLVGNVYVKFRREEDAEKAVNDLNNRWFNGQPIYAELS 103
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 47.9 bits (115), Expect = 8e-08
Identities = 25/73 (34%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 122 FDETEMHK--YFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAF 179
FD E + + E +DVL E G V KV N G VYV + A +
Sbjct: 10 FDPAEETEDEWDDEIKEDVLEECSKFGPVEHIKVDKNSP---EGVVYVKFKTVEAAQKCI 66
Query: 180 YALTGRFYGGKQI 192
AL GR++ G+QI
Sbjct: 67 QALNGRWFDGRQI 79
>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily. RRM,
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), is a highly abundant domain
in eukaryotes found in proteins involved in
post-transcriptional gene expression processes including
mRNA and rRNA processing, RNA export, and RNA stability.
This domain is 90 amino acids in length and consists of
a four-stranded beta-sheet packed against two
alpha-helices. RRM usually interacts with ssRNA, but is
also known to interact with ssDNA as well as proteins.
RRM binds a variable number of nucleotides, ranging from
two to eight. The active site includes three aromatic
side-chains located within the conserved RNP1 and RNP2
motifs of the domain. The RRM domain is found in a
variety heterogeneous nuclear ribonucleoproteins
(hnRNPs), proteins implicated in regulation of
alternative splicing, and protein components of small
nuclear ribonucleoproteins (snRNPs).
Length = 72
Score = 44.2 bits (105), Expect = 1e-06
Identities = 13/76 (17%), Positives = 35/76 (46%), Gaps = 11/76 (14%)
Query: 118 INLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALR 177
+ + E ++ + F +F G++ ++ +K +G +V + + +A +
Sbjct: 6 LPPDTTEEDLRELFSKF-----------GEIESVRIVRDKDGKSKGFAFVEFESPEDAEK 54
Query: 178 AFYALTGRFYGGKQIR 193
A AL G+ G++++
Sbjct: 55 ALEALNGKELDGRKLK 70
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 46.8 bits (111), Expect = 2e-06
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 3/75 (4%)
Query: 130 YFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGG 189
+ E DDV E G V V + + G +Y+ +S+ AL AF AL GR++GG
Sbjct: 381 FDNEILDDVKEECSKYGGVVHIYV---DTKNSAGKIYLKFSSVDAALAAFQALNGRYFGG 437
Query: 190 KQIRGQFCNVPLWSK 204
K I F ++
Sbjct: 438 KMITAAFVVNDVYDM 452
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human c-myc
gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 42.2 bits (100), Expect = 1e-05
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 133 EFYDDVLPELRSLGQVTQFKVCCNKSPHLRG--NVYVSYSNEREALRAFYALTGRFYGGK 190
+ D++ E G+V V S ++V +S+ EA++A AL GRF+GG+
Sbjct: 18 DLKDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVRALNGRFFGGR 77
Query: 191 QIRGQF 196
++ +F
Sbjct: 78 KVTARF 83
>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif.
Length = 70
Score = 40.5 bits (95), Expect = 3e-05
Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 131 FVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGK 190
++ ++ E+ + ++ V H RGNVY+++ +A RA L GR++ G+
Sbjct: 8 ELKEEEEYFGEVGKINKIYIDDV--GYENHKRGNVYITFERSEDAARAIVDLNGRYFDGR 65
Query: 191 QIR 193
++
Sbjct: 66 LVK 68
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 40.9 bits (96), Expect = 3e-04
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 11/88 (12%)
Query: 103 HLSMDNKSVREYDTDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLR 162
M + V Y +++ + ++ + F E G++T KV ++ R
Sbjct: 278 ERKMKAQGVNLYVKNLDDTVTDEKLRELFSEC-----------GEITSAKVMLDEKGVSR 326
Query: 163 GNVYVSYSNEREALRAFYALTGRFYGGK 190
G +V +SN EA RA + GR GGK
Sbjct: 327 GFGFVCFSNPEEANRAVTEMHGRMLGGK 354
Score = 28.6 bits (64), Expect = 2.4
Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 20/89 (22%)
Query: 101 FTHLSMDNKSVREYDTDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPH 160
FT+L + N D +N E ++ + F +F G++T V + S
Sbjct: 178 FTNLYVKN-----LDPSVN----EDKLRELFAKF-----------GEITSAAVMKDGSGR 217
Query: 161 LRGNVYVSYSNEREALRAFYALTGRFYGG 189
RG +V++ +A +A + G+ G
Sbjct: 218 SRGFAFVNFEKHEDAAKAVEEMNGKKIGL 246
>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT
transcription complex subunit 4 (NOT4) and similar
proteins. This subfamily corresponds to the RRM of
NOT4, also termed CCR4-associated factor 4, or E3
ubiquitin-protein ligase CNOT4, or potential
transcriptional repressor NOT4Hp, a component of the
CCR4-NOT complex, a global negative regulator of RNA
polymerase II transcription. NOT4 functions as an
ubiquitin-protein ligase (E3). It contains an N-terminal
C4C4 type RING finger motif, followed by a RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). The RING
fingers may interact with a subset of
ubiquitin-conjugating enzymes (E2s), including UbcH5B,
and mediate protein-protein interactions. T.
Length = 98
Score = 37.9 bits (89), Expect = 4e-04
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 152 KVCCNKSPHLRGN------VYVSYSNEREALRAFYALTGRFYGGKQIRGQF 196
K+ N++ G+ YV+YS + +ALR A+ G + G+ ++ F
Sbjct: 37 KIVINRNTSYNGSQGPSASAYVTYSRKEDALRCIQAVDGFYLDGRLLKASF 87
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 37.2 bits (87), Expect = 5e-04
Identities = 16/77 (20%), Positives = 36/77 (46%), Gaps = 12/77 (15%)
Query: 118 INLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREAL 176
+ + E E+ + F +F G+V ++ +K + +G +V + +E +A
Sbjct: 7 LPPDTTEEELRELFSKF-----------GKVESVRLVRDKETGKSKGFAFVEFESEEDAE 55
Query: 177 RAFYALTGRFYGGKQIR 193
+A AL G+ G+ ++
Sbjct: 56 KALEALNGKELDGRPLK 72
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands and
two helices arranged in an alpha/beta sandwich, with a
third helix present during RNA binding in some cases The
C-terminal beta strand (4th strand) and final helix are
hard to align and have been omitted in the SEED
alignment The LA proteins have an N terminal rrm which
is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 34.9 bits (81), Expect = 0.003
Identities = 13/58 (22%), Positives = 31/58 (53%)
Query: 136 DDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
+D+ G + ++ +++ +G +V + +E +A +A AL G+ GG+++R
Sbjct: 13 EDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGRELR 70
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 89
Score = 34.5 bits (80), Expect = 0.005
Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 4/65 (6%)
Query: 133 EFYDDVLPELRSLGQVTQFKV----CCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYG 188
E +DV E G+V + G V+V +++ +A +A AL GR +
Sbjct: 23 EILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFD 82
Query: 189 GKQIR 193
G+ +
Sbjct: 83 GRTVV 87
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 33.6 bits (78), Expect = 0.007
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 146 GQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
G V + K+ K G +V +S E A +A L G +GG+ +R
Sbjct: 9 GNVEKIKLLKKK----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLR 52
>gnl|CDD|114855 pfam06160, EzrA, Septation ring formation regulator, EzrA. During
the bacterial cell cycle, the tubulin-like cell-division
protein FtsZ polymerises into a ring structure that
establishes the location of the nascent division site.
EzrA modulates the frequency and position of FtsZ ring
formation.
Length = 559
Score = 35.2 bits (82), Expect = 0.017
Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 10/50 (20%)
Query: 2 LIQEEWEKEQKRLRDIEEKNRQ--------EKEEREAQEK--EFKKSIED 41
+QEE E+ +K+L +IE++ + K+E EA+EK E+++ + +
Sbjct: 376 ELQEELEEIEKQLEEIEKEQEELSESLQGLRKDELEAREKLQEYRQKLHE 425
>gnl|CDD|144294 pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and
similar).
Length = 27
Score = 31.4 bits (72), Expect = 0.021
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 62 PDKELCPFYSKVGACRFFDHCSRNH 86
ELC F+S+ G C++ D C H
Sbjct: 1 YKTELCRFFSRTGTCKYGDRCKFAH 25
>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM4 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in theThe CD
corresponds to the RRM. regulation of poly(A) tail
length during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping. The
family represents type I polyadenylate-binding proteins
(PABPs), including polyadenylate-binding protein 1
(PABP-1 or PABPC1), polyadenylate-binding protein 3
(PABP-3 or PABPC3), polyadenylate-binding protein 4
(PABP-4 or APP-1 or iPABP), polyadenylate-binding
protein 5 (PABP-5 or PABPC5), polyadenylate-binding
protein 1-like (PABP-1-like or PABPC1L),
polyadenylate-binding protein 1-like 2 (PABPC1L2 or
RBM32), polyadenylate-binding protein 4-like
(PABP-4-like or PABPC4L), yeast polyadenylate-binding
protein, cytoplasmic and nuclear (PABP or ACBP-67), and
similar proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found in
the nucleus. PABP-1 may be involved in nucleocytoplasmic
trafficking and utilization of mRNP particles. PABP-1
contains four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a less well conserved
linker region, and a proline-rich C-terminal conserved
domain (CTD). PABP-3 is a testis-specific
poly(A)-binding protein specifically expressed in round
spermatids. It is mainly found in mammalian and may play
an important role in the testis-specific regulation of
mRNA homeostasis. PABP-3 shows significant sequence
similarity to PABP-1. However, it binds to poly(A) with
a lower affinity than PABP-1. Moreover, PABP-1 possesses
an A-rich sequence in its 5'-UTR and allows binding of
PABP and blockage of translation of its own mRNA. In
contrast, PABP-3 lacks the A-rich sequence in its
5'-UTR. PABP-4 is an inducible poly(A)-binding protein
(iPABP) that is primarily localized to the cytoplasm. It
shows significant sequence similarity to PABP-1 as well.
The RNA binding properties of PABP-1 and PABP-4 appear
to be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal brain
and in a range of adult tissues in mammalian, such as
ovary and testis. It may play an important role in germ
cell development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 79
Score = 32.6 bits (75), Expect = 0.026
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 136 DDVLPELRS-LGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGK 190
D+ L E S G +T KV ++ +G +V +S+ EA +A + GR GGK
Sbjct: 15 DERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGK 70
>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45
kDa-splicing factor (SPF45) and similar proteins. This
subgroup corresponds to the RRM of SPF45, also termed
RNA-binding motif protein 17 (RBM17), an RNA-binding
protein consisting of an unstructured N-terminal region,
followed by a G-patch motif and a C-terminal U2AF (U2
auxiliary factor) homology motifs (UHM) that harbors a
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain) and an
Arg-Xaa-Phe sequence motif. SPF45 regulates alternative
splicing of the apoptosis regulatory gene FAS (also
known as CD95). It induces exon 6 skipping in FAS
pre-mRNA through the UHM domain that binds to
tryptophan-containing linear peptide motifs (UHM ligand
motifs, ULMs) present in the 3' splice site-recognizing
factors U2AF65, SF1 and SF3b155. .
Length = 96
Score = 32.6 bits (75), Expect = 0.028
Identities = 10/40 (25%), Positives = 22/40 (55%)
Query: 165 VYVSYSNEREALRAFYALTGRFYGGKQIRGQFCNVPLWSK 204
++V + A++A L GRF+GG+ ++ F + + +
Sbjct: 54 IFVEFERVESAIKAVVDLNGRFFGGRTVKASFYDEERFRR 93
>gnl|CDD|179877 PRK04778, PRK04778, septation ring formation regulator EzrA;
Provisional.
Length = 569
Score = 34.4 bits (80), Expect = 0.028
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 10/50 (20%)
Query: 2 LIQEEWEKEQKRLRDIEEK--------NRQEKEEREAQEK--EFKKSIED 41
+QEE E+ K+L +IE++ K+E EA+EK ++ + +
Sbjct: 380 ELQEELEEILKQLEEIEKEQEKLSEMLQGLRKDELEAREKLERYRNKLHE 429
>gnl|CDD|217286 pfam02919, Topoisom_I_N, Eukaryotic DNA topoisomerase I, DNA
binding fragment. Topoisomerase I promotes the
relaxation of DNA superhelical tension by introducing a
transient single-stranded break in duplex DNA and are
vital for the processes of replication, transcription,
and recombination. This family may be more than one
structural domain.
Length = 215
Score = 34.1 bits (79), Expect = 0.029
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 8 EKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFI-EGVCN---ELPDGFR 55
EKE+K+ EEK + KEE++ E+ + + D E V N E P FR
Sbjct: 98 EKEKKKAMSKEEK-KAIKEEKDKLEEPYGYCLVDGRKEKVGNFRVEPPGLFR 148
>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate
dead end protein homolog 1 (DND1). This subgroup
corresponds to the RRM1 of DND1, also termed RNA-binding
motif, single-stranded-interacting protein 4, an
RNA-binding protein that is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. For instance, DND1 binds cell cycle
inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle
regulator and tumor suppressor, LATS2 (large tumor
suppressor, homolog 2 of Drosophila). It helps maintain
their protein expression through blocking the inhibitory
function of microRNAs (miRNA) from these transcripts.
DND1 may also impose another level of translational
regulation to modulate expression of critical factors in
embryonic stem (ES) cells. DND1 interacts specifically
with apolipoprotein B editing complex 3 (APOBEC3), a
multi-functional protein inhibiting retroviral
replication. The DND1-APOBEC3 interaction may play a
role in maintaining viability of germ cells and for
preventing germ cell tumor development. DND1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 32.1 bits (73), Expect = 0.036
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 133 EFYDDVL-PELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTG 184
+ Y+D L P +S+G + +F++ S RG Y YS+ R A A L
Sbjct: 12 DVYEDRLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAIATLHN 64
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 34.0 bits (78), Expect = 0.041
Identities = 9/38 (23%), Positives = 24/38 (63%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIE 40
+Q++ EQ+RL+ +E++ +E+++ E+ K++
Sbjct: 92 LQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAAL 129
Score = 30.5 bits (69), Expect = 0.51
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 4 QEEWEKEQKRLRDIEEKNRQEKEEREAQEKE 34
+ + E++RL E+K + E+ ++A K+
Sbjct: 101 ERLKQLEKERLAAQEQKKQAEEAAKQAALKQ 131
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 34.3 bits (78), Expect = 0.043
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 165 VYVSYSNEREALRAFYALTGRFYGGKQIRGQ 195
++V +S+ E RA AL GRF+GG+ + +
Sbjct: 568 IFVEFSDSMEVDRAKAALDGRFFGGRTVVAE 598
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM2
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal, highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 30.8 bits (69), Expect = 0.092
Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 136 DDVLPELRSLGQVTQFKVCCNKSP-HLRGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
+D+ G+++ +V + + +G +VS+ N+ +A A + G++ GG+QIR
Sbjct: 16 EDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIR 74
>gnl|CDD|238356 cd00660, Topoisomer_IB_N, Topoisomer_IB_N: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the monomeric yeast and human topo I
and heterodimeric topo I from Leishmania donvanni. Topo
I enzymes are divided into: topo type IA (bacterial)
and type IB (eukaryotic). Topo I relaxes superhelical
tension in duplex DNA by creating a single-strand nick,
the broken strand can then rotate around the unbroken
strand to remove DNA supercoils and, the nick is
religated, liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit re-ligation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topos I play putative roles
in organizing the kinetoplast DNA network unique to
these parasites. This family may represent more than
one structural domain.
Length = 215
Score = 32.6 bits (75), Expect = 0.094
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 8 EKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFI-EGVCN---ELPDGFR 55
EKE+K+ EEK + KEE+E E+ + + D E V N E P FR
Sbjct: 97 EKEKKKAMSKEEK-KAIKEEKEKLEEPYGYCLVDGHKEKVGNFRIEPPGLFR 147
>gnl|CDD|216292 pfam01086, Clathrin_lg_ch, Clathrin light chain.
Length = 225
Score = 32.0 bits (73), Expect = 0.14
Identities = 13/40 (32%), Positives = 27/40 (67%), Gaps = 2/40 (5%)
Query: 5 EEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIE 44
+W +E++ LR IEE++ ++++E ++ +K I+DF E
Sbjct: 115 RKW-RERRDLR-IEERDEASEKKKEELIEKAQKEIDDFYE 152
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM2
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA). However, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 75
Score = 30.2 bits (68), Expect = 0.16
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 157 KSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQFCN 198
KS RG +VS+ ++++A A + G++ G + IR CN
Sbjct: 36 KSGRSRGYGFVSFRSQQDAENAINEMNGKWLGSRPIR---CN 74
>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of
poly(U)-binding-splicing factor PUF60 and similar
proteins. This subgroup corresponds to the RRM3 of
PUF60, also termed FUSE-binding protein-interacting
repressor (FBP-interacting repressor or FIR), or
Ro-binding protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1), an essential splicing factor that functions
as a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins. The
research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 98
Score = 30.5 bits (69), Expect = 0.16
Identities = 11/31 (35%), Positives = 22/31 (70%)
Query: 165 VYVSYSNEREALRAFYALTGRFYGGKQIRGQ 195
++V +S EA +A AL GR++GG++++ +
Sbjct: 55 IFVEFSLPSEAEKAIQALNGRWFGGRKVKAE 85
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis. TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 30.0 bits (68), Expect = 0.19
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 18/81 (22%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVC----CNKSPHLRGNVYVSYSNE 172
D++ E D + F F G+++ +V KS +G +VS+ +
Sbjct: 6 DLSPEIDTETLRAAFAPF-----------GEISDARVVKDMQTGKS---KGYGFVSFVKK 51
Query: 173 REALRAFYALTGRFYGGKQIR 193
+A A ++ G++ GG+ IR
Sbjct: 52 EDAENAIQSMNGQWLGGRAIR 72
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This subgroup
corresponds to the RRM3 of the CUGBP1 and ETR-3-like
factors (CELF) or BRUNOL (Bruno-like) proteins, a family
of structurally related RNA-binding proteins involved in
the regulation of pre-mRNA splicing in the nucleus and
in the control of mRNA translation and deadenylation in
the cytoplasm. The family contains six members: CELF-1
(also termed BRUNOL-2, or CUG-BP1, or NAPOR, or
EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or
CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or
TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also
termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6
(also termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region and
the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and function,
the CELF family can be divided into two subfamilies, the
first containing CELFs 1 and 2, and the second
containing CELFs 3, 4, 5, and 6. The different CELF
proteins may act through different sites on at least
some substrates. Furthermore, CELF proteins may interact
with each other in varying combinations to influence
alternative splicing in different contexts. .
Length = 73
Score = 29.5 bits (67), Expect = 0.22
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 12/76 (15%)
Query: 121 EFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHL-RGNVYVSYSNEREALRAF 179
EF + ++++ F F G V KV +K+ + +VSY N A A
Sbjct: 9 EFTDQDLYQLFAPF-----------GNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAI 57
Query: 180 YALTGRFYGGKQIRGQ 195
A+ G GGK+++ Q
Sbjct: 58 KAMNGFQVGGKRLKVQ 73
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 29.4 bits (67), Expect = 0.23
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 136 DDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
+D+ G+V ++ NK RG +V +++ +A A L G G+ +R
Sbjct: 13 EDLREFFSPYGKVEGVRLVRNKDRP-RGFAFVEFASPEDAEAALKKLNGLVLDGRTLR 69
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 31.8 bits (72), Expect = 0.25
Identities = 9/35 (25%), Positives = 18/35 (51%)
Query: 163 GNVYVSYSNEREALRAFYALTGRFYGGKQIRGQFC 197
G V++ Y++ R A +A + GR + + + F
Sbjct: 465 GKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFY 499
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 140
Score = 30.6 bits (70), Expect = 0.26
Identities = 13/71 (18%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIEGVCNELPDGFRTNVETKP 62
+++E +K +++L+ + + RE +EKE +K +++F + +++ +
Sbjct: 37 LEKELQKLKEKLQK--DAATLSEAAREKKEKELQKKVQEF-----QRKQQKLQQDLQKRQ 89
Query: 63 DKELCPFYSKV 73
+EL K+
Sbjct: 90 QEELQKILDKI 100
>gnl|CDD|107157 PHA02244, PHA02244, ATPase-like protein.
Length = 383
Score = 31.6 bits (71), Expect = 0.29
Identities = 39/162 (24%), Positives = 62/162 (38%), Gaps = 33/162 (20%)
Query: 10 EQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIEGVCNELPDGFRTNVETKPDKELCPF 69
EQ + I EK E E +E + KK IED E ELP E KP ++
Sbjct: 37 EQAIIDAIREK--AETEGKEIAIDDIKKEIEDSPEEQFFELPVKIELQQEGKPAGDISGI 94
Query: 70 YSKVGACRFFDH-----------------------CSRNHIKPSVSKTLLLNNFFTHLSM 106
+ A H +NHI +++ L L+ +F + M
Sbjct: 95 DTTKIASNPTFHYETADIAKIVNANIPVFLKGGAGSGKNHIAEQIAEALDLDFYFMNAIM 154
Query: 107 DNKSVREYDTDINLEFDETEMHK-------YFVEFYDDVLPE 141
D ++ + D N +F ET ++ +F++ D +PE
Sbjct: 155 DEFELKGF-IDANGKFHETPFYEAFKKGGLFFIDEIDASIPE 195
>gnl|CDD|239570 cd03488, Topoisomer_IB_N_htopoI_like, Topoisomer_IB_N_htopoI_like :
N-terminal DNA binding fragment found in eukaryotic DNA
topoisomerase (topo) IB proteins similar to the
monomeric yeast and human topo I. Topo I enzymes are
divided into: topo type IA (bacterial) and type IB
(eukaryotic). Topo I relaxes superhelical tension in
duplex DNA by creating a single-strand nick, the broken
strand can then rotate around the unbroken strand to
remove DNA supercoils and, the nick is religated,
liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit religation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. This family may represent more than
one structural domain.
Length = 215
Score = 31.2 bits (71), Expect = 0.30
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 8 EKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIED-FIEGVCN---ELPDGFR 55
+KE+K+ EEK + K E+E E+E+ I D E V N E P FR
Sbjct: 97 QKEEKKAMSKEEK-KAIKAEKEKLEEEYGFCILDGHKEKVGNFRIEPPGLFR 147
>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
eukaryotic snRNP [Transcription].
Length = 564
Score = 31.2 bits (71), Expect = 0.32
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEE-REAQEKEFKK 37
++++ EKE K+L + EK E EE +A E+ +K
Sbjct: 287 LEKKLEKELKKLENKLEKQEDELEELEKAAEELRQK 322
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 29.3 bits (65), Expect = 0.33
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 10/74 (13%)
Query: 130 YFVEFYDDVLPELRS---------LGQVTQFKVCCNKSP-HLRGNVYVSYSNEREALRAF 179
+F F D+ PE+ + G+++ +V + + +G +VS+ N+ +A A
Sbjct: 1 HFHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 60
Query: 180 YALTGRFYGGKQIR 193
+ G++ GG+QIR
Sbjct: 61 QQMGGQWLGGRQIR 74
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich
splicing factor 12 (SRSF12) and similar proteins. This
subgroup corresponds to the RRM of SRSF12, also termed
35 kDa SR repressor protein (SRrp35), or splicing
factor, arginine/serine-rich 13B (SFRS13B), or splicing
factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a
serine/arginine (SR) protein-like alternative splicing
regulator that antagonizes authentic SR proteins in the
modulation of alternative 5' splice site choice. For
instance, it activates distal alternative 5' splice site
of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains
a single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 29.2 bits (65), Expect = 0.41
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQF 196
RG Y+ + + R+A A Y L ++ G+QI QF
Sbjct: 42 RGFAYIQFEDVRDAEDALYNLNRKWVCGRQIEIQF 76
>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM1 of RBM46, also termed
cancer/testis antigen 68 (CT68), a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 29.1 bits (65), Expect = 0.42
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 134 FYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALT------GRFY 187
+ D+++P G++ +F++ S RG +V Y+ + EA A L G+F
Sbjct: 14 YEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRILNNYEIRPGKFI 73
Query: 188 G 188
G
Sbjct: 74 G 74
>gnl|CDD|240911 cd12465, RRM_UHMK1, RNA recognition motif found in U2AF homology
motif kinase 1 (UHMK1) and similar proteins. This
subgroup corresponds to the RRM of UHMK1. UHMK1, also
termed kinase interacting with stathmin (KIS) or P-CIP2,
is a serine/threonine protein kinase functionally
related to RNA metabolism and neurite outgrowth. It
contains an N-terminal kinase domain and a C-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), with
high homology to the corresponding motif of the
mammalian U2 small nuclear ribonucleoprotein auxiliary
factor U2AF 65 kDa subunit (U2AF65 or U2AF2). UHMK1
targets two key regulators of cell proliferation and
migration, the cyclin-dependent kinase (CDK) inhibitor
p27Kip1 and the microtubule-destabilizing protein
stathmin. It plays a critical role during vascular wound
repair by preventing excessive vascular smooth muscle
cell (VSMC) migration into the vascular lesion.
Moreover, UHMK1 may control cell migration and neurite
outgrowth by interacting with and phosphorylating the
splicing factor SF1, thereby probably contributing to
the control of protein expression. Furthermore, UHMK1
may be functionally related to microtubule dynamics and
axon development. It localizes to RNA granules,
interacts with three proteins found in RNA granules
(KIF3A, NonO, and eEF1A), and further enhances the local
translation. UHMK1 is highly expressed in regions of the
brain implicated in schizophrenia and may play a role in
susceptibility to schizophrenia.
Length = 88
Score = 29.2 bits (65), Expect = 0.53
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 128 HKYFVEFYDDVLPELRSLGQV--TQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGR 185
H E Y+D++ +++ Q + K +G V+V Y+N ++ A LTGR
Sbjct: 16 HLQNEEEYEDIIEDIKEECQKYGPVVSLLIPKENPGKGQVFVEYANAGDSKAAQKLLTGR 75
Query: 186 FYGGKQIRGQF 196
+ GK + F
Sbjct: 76 IFDGKFVVATF 86
>gnl|CDD|241132 cd12688, RRM1_PTBP1_like, RNA recognition motif 1 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM1 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), and similar
proteins found in Metazoa. PTB is an important negative
regulator of alternative splicing in mammalian cells and
functions at several aspects of mRNA metabolism,
including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 also contains four RRMs. ROD1 coding
protein Rod1 is a mammalian PTB homolog of a regulator
of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein and negatively regulates the
onset of differentiation. ROD1 is predominantly
expressed in hematopoietic cells or organs. It may play
a role controlling differentiation in mammals. All
members in this family contain four RNA recognition
motifs (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 81
Score = 28.5 bits (64), Expect = 0.61
Identities = 12/18 (66%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 158 SPHLRG-NVYVSYSNERE 174
+P+LRG VYV YSN RE
Sbjct: 60 TPNLRGRPVYVQYSNHRE 77
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 28.4 bits (64), Expect = 0.76
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 11/78 (14%)
Query: 117 DINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
D+ + D+ +++++F + Y P + KV +++ + RG +V +S+E E
Sbjct: 8 DLTPDVDDYQLYEFFSKRY----PSCKGA------KVVLDQNGNSRGYGFVRFSDESEQK 57
Query: 177 RAFYALTG-RFYGGKQIR 193
RA + G GGK IR
Sbjct: 58 RALTEMQGASGLGGKPIR 75
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM1
of U1A/U2B"/SNF protein family which contains Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs), connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. Moreover,
U2B" does not require an auxiliary protein for binding
to RNA, and its nuclear transport is independent of U2
snRNA binding. .
Length = 78
Score = 28.3 bits (64), Expect = 0.78
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 144 SLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGR-FYGGKQIRGQFC 197
G V + +K+ +RG +V + + A A AL G FY K +R Q+
Sbjct: 26 QFGPVLD--IVASKTLKMRGQAFVVFKDVESATNALRALQGFPFY-DKPMRIQYA 77
>gnl|CDD|173965 cd08045, TAF4, TATA Binding Protein (TBP) Associated Factor 4
(TAF4) 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 4 (TAF4) is one of several TAFs that bind TBP and
are involved in forming the Transcription Factor IID
(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
eukaryote. 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 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 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. Each TAF, with the help of a
specific activator, is required only for the expression
of subset of genes and is 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; 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. TAF4 domain interacts with TAF12 and makes
a novel histone-like heterodimer that binds DNA and has
a core promoter function of a subset of genes.
Length = 212
Score = 29.6 bits (67), Expect = 0.88
Identities = 10/26 (38%), Positives = 19/26 (73%)
Query: 12 KRLRDIEEKNRQEKEEREAQEKEFKK 37
K+LR +E+ R+E+E+R+ +E+E
Sbjct: 114 KQLRFLEQLEREEEEKRDEEERERLL 139
>gnl|CDD|224253 COG1334, FlaG, Uncharacterized flagellar protein FlaG [Cell
motility and secretion].
Length = 120
Score = 28.9 bits (65), Expect = 0.88
Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 3/66 (4%)
Query: 8 EKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIEGVCNELPDGFRTNVETKPDKELC 67
EQ+ E ++E +E +E+ K+ + +E + N+L T++ D EL
Sbjct: 22 ILEQQSTNIQEV--KEESKETIKKEQRSKEKLALIVEDI-NKLLKSLNTHLNFSYDDELG 78
Query: 68 PFYSKV 73
K+
Sbjct: 79 ELVVKI 84
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is a
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence in
its 5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Unlike other PABPs, PABP-5 contains only
four RRMs, but lacks both the linker region and the CTD.
PABP-1-like and PABP-1-like 2 are the orthologs of
PABP-1. PABP-4-like is the ortholog of PABP-5. Their
cellular functions remain unclear. The family also
includes the yeast PABP, a conserved poly(A) binding
protein containing poly(A) tails that can be attached to
the 3'-ends of mRNAs. The yeast PABP and its homologs
may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 77
Score = 27.9 bits (63), Expect = 0.88
Identities = 10/41 (24%), Positives = 20/41 (48%)
Query: 152 KVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQI 192
KV +++ +G +V + E A+RA + G K++
Sbjct: 33 KVATDENGGSKGYGFVHFETEEAAVRAIEKVNGMLLNDKKV 73
>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
2 found in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes 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 = 74
Score = 28.0 bits (63), Expect = 0.89
Identities = 15/76 (19%), Positives = 34/76 (44%), Gaps = 10/76 (13%)
Query: 119 NLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSP-HLRGNVYVSYSNEREALR 177
NL F TE +++ + G++++ + +K +G +VS+ A++
Sbjct: 6 NLPFTTTE---------EELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVK 56
Query: 178 AFYALTGRFYGGKQIR 193
A+ L G + G+ +
Sbjct: 57 AYSELDGSIFQGRLLH 72
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 29.2 bits (65), Expect = 0.91
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 144 SLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
G V KV ++ + RG +V++++E A A + G+ G+ IR
Sbjct: 57 HFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIR 107
>gnl|CDD|119255 pfam10735, DUF2526, Protein of unknown function (DUF2526). This
family of proteins with unknown function is restricted
to Enterobacteriaceae. The family has a highly
conserved sequence.
Length = 77
Score = 28.0 bits (62), Expect = 0.91
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 2 LIQEEWEKEQKRLRD-IEEKNRQEKEEREAQEKEFKK 37
L +EE +Q+RLR I RQ KE+REA+ ++ K
Sbjct: 36 LSREERYDQQQRLRTAIAHHGRQHKEDREARREQLTK 72
>gnl|CDD|236057 PRK07578, PRK07578, short chain dehydrogenase; Provisional.
Length = 199
Score = 29.4 bits (67), Expect = 0.97
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 39 IEDFIEGVCNELPDGFRTNV 58
+E F++ ELP G R NV
Sbjct: 132 LEGFVKAAALELPRGIRINV 151
>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein. TolA couples the inner
membrane complex of itself with TolQ and TolR to the
outer membrane complex of TolB and OprL (also called
Pal). Most of the length of the protein consists of
low-complexity sequence that may differ in both length
and composition from one species to another,
complicating efforts to discriminate TolA (the most
divergent gene in the tol-pal system) from paralogs such
as TonB. Selection of members of the seed alignment and
criteria for setting scoring cutoffs are based largely
conserved operon struction. //The Tol-Pal complex is
required for maintaining outer membrane integrity. Also
involved in transport (uptake) of colicins and
filamentous DNA, and implicated in pathogenesis.
Transport is energized by the proton motive force. TolA
is an inner membrane protein that interacts with
periplasmic TolB and with outer membrane porins ompC,
phoE and lamB [Transport and binding proteins, Other,
Cellular processes, Pathogenesis].
Length = 346
Score = 29.8 bits (67), Expect = 0.97
Identities = 9/39 (23%), Positives = 19/39 (48%)
Query: 2 LIQEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIE 40
+ E + E+ + E+ RQ++ E+ A ++ K E
Sbjct: 70 QKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKAAKQAE 108
Score = 29.0 bits (65), Expect = 1.6
Identities = 7/29 (24%), Positives = 19/29 (65%)
Query: 4 QEEWEKEQKRLRDIEEKNRQEKEEREAQE 32
+++ EQ R +++E++ EK ++A++
Sbjct: 81 EKQRAAEQARQKELEQRAAAEKAAKQAEQ 109
Score = 28.3 bits (63), Expect = 3.4
Identities = 8/34 (23%), Positives = 18/34 (52%)
Query: 4 QEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKK 37
++ ++ ++ + EEK +Q +E + Q E K
Sbjct: 101 EKAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKA 134
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the RRM
of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19), is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates distal
alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 28.1 bits (63), Expect = 1.0
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 160 HLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQF 196
RG YV + + R+A A Y L + G++I QF
Sbjct: 40 RPRGFAYVQFEDVRDAEDALYYLDRTRFLGREIEIQF 76
>gnl|CDD|219978 pfam08701, GN3L_Grn1, GNL3L/Grn1 putative GTPase. Grn1 (yeast)
and GNL3L (human) are putative GTPases which are
required for growth and play a role in processing of
nucleolar pre-rRNA. This family contains a potential
nuclear localisation signal.
Length = 80
Score = 28.0 bits (63), Expect = 1.1
Identities = 10/24 (41%), Positives = 18/24 (75%)
Query: 14 LRDIEEKNRQEKEEREAQEKEFKK 37
L +IEEK R+++EE+E +++ K
Sbjct: 48 LEEIEEKKRKQEEEKERRKEARKA 71
>gnl|CDD|221756 pfam12757, DUF3812, Protein of unknown function (DUF3812). This is
a family of fungal proteins whose function is not known.
Length = 126
Score = 28.8 bits (65), Expect = 1.1
Identities = 11/33 (33%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 10 EQKRLRDIEEKNRQEKEEREAQE-KEFKKSIED 41
E +R RD E+K +E+ +R+ +E KE ++ +
Sbjct: 94 EAQRARDEEKKLDEEEAKRQHEEAKEREREKKK 126
Score = 26.5 bits (59), Expect = 5.9
Identities = 10/28 (35%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 8 EKEQKRLRDIEEKNRQEKE-EREAQEKE 34
E+K+L + E K + E+ ERE ++K+
Sbjct: 99 RDEEKKLDEEEAKRQHEEAKEREREKKK 126
>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 = 29.5 bits (67), Expect = 1.2
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 9 KEQKRLRDIEEKNRQEKEEREAQEKEFKK 37
K +K+ E + K++ EA K+ K
Sbjct: 420 KAEKKAEKEEAEKAAAKKKAEAAAKKAKG 448
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 29.5 bits (67), Expect = 1.2
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 4/34 (11%)
Query: 5 EEWEKEQKRLRDIEEKNR----QEKEEREAQEKE 34
E EQ++ + E K R Q + ERE +E
Sbjct: 437 EIRAIEQEKKKAEEAKARFEARQARLEREKAARE 470
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), 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 = 76
Score = 27.7 bits (62), Expect = 1.3
Identities = 13/52 (25%), Positives = 20/52 (38%)
Query: 146 GQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQFC 197
G +T ++ K R +V Y E EA +A F +I + C
Sbjct: 25 GTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNSFIDTSKITVEIC 76
>gnl|CDD|220431 pfam09831, DUF2058, Uncharacterized protein conserved in bacteria
(DUF2058). This domain, found in various prokaryotic
proteins, has no known function.
Length = 177
Score = 28.7 bits (65), Expect = 1.3
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 9 KEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIEGVCNELPDG 53
K +K RD E NRQ + E A++K I+ IE + DG
Sbjct: 50 KAEKAERD-RELNRQRQAE--AEQKAIVAQIKQLIEQNRIDRKDG 91
>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter
subunit G; Reviewed.
Length = 197
Score = 28.9 bits (64), Expect = 1.3
Identities = 12/36 (33%), Positives = 25/36 (69%), Gaps = 3/36 (8%)
Query: 6 EWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIED 41
EWE+ +++ I+E+ QE++ERE +E+ ++ +D
Sbjct: 143 EWERREEK---IDEREDQEEQEREREEQTIEEQSDD 175
Score = 27.0 bits (59), Expect = 5.9
Identities = 17/46 (36%), Positives = 29/46 (63%), Gaps = 5/46 (10%)
Query: 4 QEEWEKEQKRLRDIEEK----NRQEK-EEREAQEKEFKKSIEDFIE 44
QE+ EK ++ ++EE+ R+EK +ERE QE++ ++ E IE
Sbjct: 125 QEQIEKARQEREELEERMEWERREEKIDEREDQEEQEREREEQTIE 170
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 28.5 bits (64), Expect = 1.3
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 9 KEQKRLRDIEEKNRQEKEEREAQEK 33
+E +RL ++EK ++E E+ E Q+K
Sbjct: 47 REYERLELMDEKWKKETEDEEFQQK 71
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 28.9 bits (65), Expect = 1.5
Identities = 10/40 (25%), Positives = 24/40 (60%), Gaps = 5/40 (12%)
Query: 5 EEW-----EKEQKRLRDIEEKNRQEKEEREAQEKEFKKSI 39
E W + QK+L+ + E+ ++++ E+E +E E ++ +
Sbjct: 90 ENWLSAKQAQRQKKLQKLLEEKQKQEREKEREEAELRQRL 129
Score = 28.5 bits (64), Expect = 2.5
Identities = 8/35 (22%), Positives = 21/35 (60%)
Query: 5 EEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSI 39
+EWE ++ + + + + + K+ ++ QE+E +K
Sbjct: 185 QEWELKKLKQQQQKREEERRKQRKKQQEEEERKQK 219
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to the
RRM domain of hnRNP G, also termed glycoprotein p43 or
RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several pre-mRNAs.
Moreover, hnRNP G may function as a regulator of
transcription for SREBP-1c and GnRH1. Research has shown
that hnRNP G may also act as a tumor-suppressor since it
upregulates the Txnip gene and promotes the fidelity of
DNA end-joining activity. In addition, hnRNP G appears
to play a critical role in proper neural development of
zebrafish and frog embryos. The family also includes
several paralogs of hnRNP G, such as hRBMY and hnRNP G-T
(also termed RNA-binding motif protein,
X-linked-like-2). Both, hRBMY and hnRNP G-T, are
exclusively expressed in testis and critical for male
fertility. Like hnRNP G, hRBMY and hnRNP G-T interact
with factors implicated in the regulation of pre-mRNA
splicing, such as hTra2-beta1 and T-STAR. Although
members in this family share a high conserved N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), they
appear to recognize different RNA targets. For instance,
hRBMY interacts specifically with a stem-loop structure
in which the loop is formed by the sequence CA/UCAA. In
contrast, hnRNP G associates with single stranded RNA
sequences containing a CCA/C motif. In addition to the
RRM, hnRNP G contains a nascent transcripts targeting
domain (NTD) in the middle region and a novel auxiliary
RNA-binding domain (RBD) in its C-terminal region. The
C-terminal RBD exhibits distinct RNA binding
specificity, and would play a critical role in the
regulation of alternative splicing by hnRNP G. .
Length = 80
Score = 27.6 bits (62), Expect = 1.6
Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 16/83 (19%)
Query: 114 YDTDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHL---RGNVYVSYS 170
+ + ++ E E+ F +F G+V +V K P RG +V++
Sbjct: 5 FVSGLSTRTTEKELEALFSKF-----------GRVE--EVLLMKDPETGESRGFGFVTFE 51
Query: 171 NEREALRAFYALTGRFYGGKQIR 193
+ +A A L G+ G+ I+
Sbjct: 52 SVEDADAAIRDLNGKELEGRVIK 74
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 29.2 bits (66), Expect = 1.7
Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 3/93 (3%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIEGVCNELPDGFRTNVETKP 62
I+ + E+ +K L+ +EEK Q + E E +E+E +K+ F++ +L + +N+
Sbjct: 93 IEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYDSNLSEAL 152
Query: 63 DKELCPFYSKVGACRFFDHCSRNHIKPSVSKTL 95
Y K + + S +L
Sbjct: 153 KGLN---YKKNFKEKLLKELKSVILNASSLLSL 182
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in yeast.
Yra1p is associated with Pse1p and Kap123p, two members
of the beta-importin family, further mediating transport
of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission yeast
as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 27.4 bits (61), Expect = 1.7
Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 12/74 (16%)
Query: 119 NLEFDETE--MHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREAL 176
NL D TE + +YFV +G + + + N+ G +++ +A
Sbjct: 6 NLPKDVTEAQIREYFVS----------QIGPIKRVLLSYNEGGKSTGIANITFKRAGDAT 55
Query: 177 RAFYALTGRFYGGK 190
+A+ GR G
Sbjct: 56 KAYDKFNGRIDDGN 69
>gnl|CDD|221533 pfam12329, TMF_DNA_bd, TATA element modulatory factor 1 DNA
binding. This is the middle region of a family of TATA
element modulatory factor 1 proteins conserved in
eukaryotes that contains at its N-terminal section a
number of leucine zippers that could potentially form
coiled coil structures. The whole proteins bind to the
TATA element of some RNA polymerase II promoters and
repress their activity. by competing with the binding
of TATA binding protein. TMFs are evolutionarily
conserved golgins that bind Rab6, a ubiquitous ras-like
GTP-binding Golgi protein, and contribute to Golgi
organisation in animal and plant cells.
Length = 74
Score = 27.3 bits (61), Expect = 1.7
Identities = 10/37 (27%), Positives = 20/37 (54%)
Query: 5 EEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIED 41
E+ K++ + + +K R + +E E + E KK +E
Sbjct: 22 EKLSKKELKHNNTIKKLRAKNKELEKEIAELKKKLEK 58
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 81
Score = 27.4 bits (61), Expect = 1.8
Identities = 25/81 (30%), Positives = 32/81 (39%), Gaps = 6/81 (7%)
Query: 126 EMHKYFVEF--YDDVLPELRSL----GQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAF 179
E HK FV + EL L G V ++ N+S +G YV Y NE A +A
Sbjct: 1 EKHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAV 60
Query: 180 YALTGRFYGGKQIRGQFCNVP 200
+ G K I N P
Sbjct: 61 LKMDGTEIKEKTISVAISNPP 81
>gnl|CDD|240881 cd12435, RRM_GW182_like, RNA recognition motif in the GW182 family
proteins. This subfamily corresponds to the RRM of the
GW182 family which includes three paralogs of TNRC6
(GW182-related) proteins comprising GW182/TNGW1, TNRC6B
(containing three isoforms) and TNRC6C in mammal, a
single Drosophila ortholog (dGW182, also called Gawky)
and two Caenorhabditis elegans orthologs AIN-1 and
AIN-2, which contain multiple miRNA-binding sites and
have important functions in miRNA-mediated translational
repression, as well as mRNA degradation in Metazoa. The
GW182 family proteins directly interact with Argonaute
(Ago) proteins, and thus function as downstream
effectors in the miRNA pathway, responsible for
inhibition of translation and acceleration of mRNA
decay. Members in this family are characterized by an
abnormally high content of glycine/tryptophan (G/W)
repeats, one or more glutamine (Q)-rich motifs, and a
C-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
The only exception is the worm protein that does not
contain a recognizable RRM domain. The GW182 family
proteins are recruited to miRNA targets through an
interaction between their N-terminal domain and an
Argonaute protein. Then they promote translational
repression and/or degradation of miRNA targets through
their C-terminal silencing domain. .
Length = 71
Score = 26.9 bits (60), Expect = 1.9
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 159 PHLR-GNVYVSYSNEREALRAFYALTGRFYGGKQIRGQF 196
+LR GN + YS++ EA +A AL G + +F
Sbjct: 33 LNLRHGNALIRYSSKEEAAKAQSALNNCVLGNTTLLAEF 71
>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding
protein Raly. This subgroup corresponds to the RRM of
Raly, also termed autoantigen p542, or heterogeneous
nuclear ribonucleoprotein C-like 2, or hnRNP core
protein C-like 2, or hnRNP associated with lethal yellow
protein homolog, an RNA-binding protein that may play a
critical role in embryonic development. It is encoded by
Raly, a ubiquitously expressed gene of unknown function.
Raly shows a high degree of identity with the 5'
sequences of p542 gene encoding autoantigen, which can
cross-react with EBNA-1 of the Epstein Barr virus. Raly
contains two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes a unique
glycine/serine-rich stretch. .
Length = 76
Score = 26.9 bits (59), Expect = 2.4
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQI 192
+G +V YSNER A A GR G+ +
Sbjct: 36 KGYAFVQYSNERHARGAVIGENGRVLAGQTL 66
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis.TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 26.9 bits (60), Expect = 2.4
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 166 YVSYSNEREALRAFYALTGRFYGGKQIR 193
+V Y + R A A + GR G++I+
Sbjct: 41 FVEYYDHRSAAAALQTMNGRLILGQEIK 68
>gnl|CDD|215246 PLN02447, PLN02447, 1,4-alpha-glucan-branching enzyme.
Length = 758
Score = 28.9 bits (65), Expect = 2.5
Identities = 13/38 (34%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 109 KSVREYDTDINLEFDETEMHKYFVEFYDDVLPELRSLG 146
++R Y+ + + +E +++ Y EF DDVLP +++LG
Sbjct: 228 AALRIYEAHVGMSSEEPKVNSY-REFADDVLPRIKALG 264
>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 28.4 bits (64), Expect = 2.5
Identities = 15/40 (37%), Positives = 26/40 (65%), Gaps = 3/40 (7%)
Query: 5 EEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIE 44
E E EQ+ LR EK ++E++ EAQE+ +++ ++ IE
Sbjct: 214 EAAEAEQELLR---EKQKEEEQMMEAQERSYQEHVKQLIE 250
>gnl|CDD|221371 pfam12004, DUF3498, Domain of unknown function (DUF3498). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 433 to 538 amino acids in length. This domain is
found associated with pfam00616, pfam00168. This domain
has two conserved sequence motifs: DLQ and PLSFQNP.
Length = 489
Score = 28.5 bits (63), Expect = 2.5
Identities = 15/38 (39%), Positives = 25/38 (65%), Gaps = 5/38 (13%)
Query: 1 LLIQEEWEKE-----QKRLRDIEEKNRQEKEEREAQEK 33
LL QE+ ++ Q RL D EE+ R+++EE+++Q K
Sbjct: 393 LLGQEQQMQKLLQEYQARLEDSEERLRRQQEEKDSQMK 430
>gnl|CDD|206756 cd10019, 14-3-3_sigma, 14-3-3 sigma, an isoform of 14-3-3
protein. 14-3-3 protein sigma isoform, also known as
stratifin or human mammary epithelial marker (HME) 1,
has been most directly linked to tumor development. In
humans, it is expressed by the SFN gene, strictly in
stratified squamous epithelial cells in response to DNA
damage where it is transcriptionally induced in a
p53-dependent manner, subsequently causing cell-cycle
arrest at the G2/M checkpoint. Up-regulation and
down-regulation of 14-3-3 sigma expression have both
been described in tumors. For example, in human breast
cancer, 14-3-3 sigma is predominantly down-regulated by
CpG methylation, acting as both a tumor suppressor and
a prognostic indicator, while in human scirrhous-type
gastric carcinoma (SGC), it is up-regulated and may
play an important role in SGC carcinogenesis and
progression. Loss of 14-3-3 sigma expression sensitizes
tumor cells to treatment with conventional cytostatic
drugs, making this protein an attractive therapeutic
target. 14-3-3 domains are an essential part of 14-3-3
proteins, a ubiquitous class of regulatory,
phosphoserine/threonine-binding proteins found in all
eukaryotic cells, including yeast, protozoa and
mammalian cells.
Length = 242
Score = 28.5 bits (63), Expect = 2.5
Identities = 12/36 (33%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 14 LRDIEEKNRQEKEEREAQE-KEFKKSIEDFIEGVCN 48
L IE+K+ +E E + E +E+++ +E ++GVC+
Sbjct: 62 LSSIEQKSNEEGSEEKGPEVREYREKVETELQGVCD 97
>gnl|CDD|198139 smart01071, CDC37_N, Cdc37 N terminal kinase binding. Cdc37 is a
molecular chaperone required for the activity of
numerous eukaryotic protein kinases. This domain
corresponds to the N terminal domain which binds
predominantly to protein kinases.and is found N terminal
to the Hsp (Heat shocked protein) 90-binding domain.
Expression of a construct consisting of only the
N-terminal domain of Saccharomyces pombe Cdc37 results
in cellular viability. This indicates that interactions
with the cochaperone Hsp90 may not be essential for
Cdc37 function.
Length = 154
Score = 27.8 bits (62), Expect = 2.8
Identities = 9/31 (29%), Positives = 21/31 (67%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEEREAQEK 33
+ EE +K + +L+ +++ R++ +E E +EK
Sbjct: 109 LLEELKKHRDKLKKEQKELRKKLDELEKEEK 139
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM2 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 26.4 bits (59), Expect = 2.9
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 158 SPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
+P +V + + R A A AL GR + G +++
Sbjct: 34 TPLRPSQKFVEFYDIRAAEAALDALNGRPFLGGRLK 69
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 28.3 bits (64), Expect = 2.9
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEEREA 30
+EE E+E RLR +E+ E+EE +
Sbjct: 176 RKEEKEREVARLRAQQEEAEDEREELDE 203
>gnl|CDD|204614 pfam11221, Med21, Subunit 21 of Mediator complex. Med21 has been
known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in
Drosophila. The heterodimer of the two subunits Med7 and
Med21 appears to act as a hinge between the middle and
the tail regions of Mediator.
Length = 132
Score = 27.6 bits (62), Expect = 3.0
Identities = 12/28 (42%), Positives = 21/28 (75%), Gaps = 1/28 (3%)
Query: 8 EKEQ-KRLRDIEEKNRQEKEEREAQEKE 34
E+EQ +R++++EE+ R+ + ERE KE
Sbjct: 87 EEEQLRRIKELEEELREVEAEREEAVKE 114
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM1 in
hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF),
and dead end protein homolog 1 (DND1). hnRNP R is a
ubiquitously expressed nuclear RNA-binding protein that
specifically binds mRNAs with a preference for poly(U)
stretches. It has been implicated in mRNA processing and
mRNA transport, and also acts as a regulator to modify
binding to ribosomes and RNA translation. hnRNP Q is
also a ubiquitously expressed nuclear RNA-binding
protein. It has been identified as a component of the
spliceosome complex, as well as a component of the
apobec-1 editosome, and has been implicated in the
regulation of specific mRNA transport. ACF is an
RNA-binding subunit of a core complex that interacts
with apoB mRNA to facilitate C to U RNA editing. It may
also act as an apoB mRNA recognition factor and
chaperone, and play a key role in cell growth and
differentiation. DND1 is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members in this family, except for DND1,
contain three conserved RNA recognition motifs (RRMs);
DND1 harbors only two RRMs. .
Length = 78
Score = 26.8 bits (60), Expect = 3.1
Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 5/64 (7%)
Query: 134 FYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
F D+++P G + + ++ + S RG +V+Y+N+ A RA + +IR
Sbjct: 14 FEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAV-----KQLHNYEIR 68
Query: 194 GQFC 197
Sbjct: 69 PGKR 72
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone, and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living cells.
RRM2/3 are implicated in ACF interaction with APOBEC-1.
.
Length = 78
Score = 26.5 bits (58), Expect = 3.3
Identities = 13/49 (26%), Positives = 30/49 (61%)
Query: 134 FYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYAL 182
F D+++P +G++ + ++ + + + RG +V++SN++EA A L
Sbjct: 14 FEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQL 62
>gnl|CDD|150747 pfam10107, Endonuc_Holl, Endonuclease related to archaeal
Holliday junction resolvase. This domain is found in
various predicted bacterial endonucleases which are
distantly related to archaeal Holliday junction
resolvases.
Length = 153
Score = 27.7 bits (62), Expect = 3.3
Identities = 10/37 (27%), Positives = 18/37 (48%)
Query: 4 QEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIE 40
E E + R + + + Q+KEE+E ++ KS
Sbjct: 33 NAEREAQAMREAEAKFEEWQKKEEKEIRKDAVNKSRA 69
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 28.2 bits (64), Expect = 3.6
Identities = 12/41 (29%), Positives = 26/41 (63%)
Query: 4 QEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIE 44
E EK ++ L E++ Q+++E E +E+E ++ IE+ ++
Sbjct: 102 LELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQ 142
>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family. This family of
proteins contain a band 4.1 domain (pfam00373), at
their amino terminus. This family represents the rest
of these proteins.
Length = 244
Score = 27.8 bits (62), Expect = 3.6
Identities = 12/31 (38%), Positives = 22/31 (70%)
Query: 4 QEEWEKEQKRLRDIEEKNRQEKEEREAQEKE 34
Q+E E+ ++ ++EEK +QE+EE + EK+
Sbjct: 25 QKELEEYEETALELEEKLKQEEEEAQLLEKK 55
>gnl|CDD|191634 pfam06886, TPX2, Targeting protein for Xklp2 (TPX2). This family
represents a conserved region approximately 60 residues
long within the eukaryotic targeting protein for Xklp2
(TPX2). Xklp2 is a kinesin-like protein localised on
centrosomes throughout the cell cycle and on spindle
pole microtubules during metaphase. In Xenopus, it has
been shown that Xklp2 protein is required for
centrosome separation and maintenance of spindle
bi-polarity. TPX2 is a microtubule-associated protein
that mediates the binding of the C-terminal domain of
Xklp2 to microtubules. It is phosphorylated during
mitosis in a microtubule-dependent way.
Length = 57
Score = 25.8 bits (57), Expect = 3.7
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 8 EKEQKRLRDIEEKNRQEKEEREAQEKEFKKSI 39
EKE+ + EE ++KEE E K+ +K +
Sbjct: 19 EKEKALEAEKEEAEARQKEEEEEAIKQLRKEL 50
>gnl|CDD|216295 pfam01093, Clusterin, Clusterin.
Length = 434
Score = 28.1 bits (63), Expect = 3.8
Identities = 21/49 (42%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEE--REAQEKEFKKSIEDFIEGVCNE 49
+ E E+E K L EK ++EKEE + A E E K E E VCNE
Sbjct: 31 LMERTEEEHKNLMSTLEKTKKEKEEALKLANEVEEKLEEE---EEVCNE 76
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 27.2 bits (61), Expect = 3.8
Identities = 16/78 (20%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEK-----EEREAQEKEFKKSIEDFIEGVCNELPDGFRTN 57
+Q E +K++K L+ E+K +++ E R+A+++E ++ ++ + +
Sbjct: 47 LQAELQKKEKELQKEEQKLQKQAATLSEEARKAKQQELQQKQQEL-----QQKQQAAQQE 101
Query: 58 VETKPDKELCPFYSKVGA 75
++ K + L P Y K+
Sbjct: 102 LQQKQQELLQPIYDKIDK 119
>gnl|CDD|235366 PRK05218, PRK05218, heat shock protein 90; Provisional.
Length = 613
Score = 28.2 bits (64), Expect = 3.9
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 7/44 (15%)
Query: 8 EKEQKRLR-------DIEEKNRQEKEEREAQEKEFKKSIEDFIE 44
E + K + D+ +++ +EKEE+E E+EFK +E E
Sbjct: 460 EFDGKPFKSVARGDLDLGKEDEEEKEEKEEAEEEFKPLLERLKE 503
>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM1 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. This family also includes the sex-lethal
protein (SXL) from Drosophila melanogaster. SXL governs
sexual differentiation and X chromosome dosage
compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds to its own pre-mRNA
and promotes female-specific alternative splicing. It
contains an N-terminal Gly/Asn-rich domain that may be
responsible for the protein-protein interaction, and
tandem RRMs that show high preference to bind
single-stranded, uridine-rich target RNA transcripts. .
Length = 77
Score = 26.2 bits (58), Expect = 4.2
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 141 ELRSL----GQVTQFKVCCNK-SPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
ELRSL G + K+ ++ + G +V Y +E +A +A L G K+++
Sbjct: 16 ELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLK 73
>gnl|CDD|215581 PLN03109, PLN03109, ETHYLENE-INSENSITIVE3-like3 protein;
Provisional.
Length = 599
Score = 27.9 bits (62), Expect = 4.4
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 9 KEQKRLRDIEEKNRQEKEEREAQEKEFKKSIED 41
K++ +L+ I+E RQ+K ++ A EK K I D
Sbjct: 48 KDRIKLKRIKE--RQKKLQQAALEKSKPKKISD 78
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like
proteins. This subgroup corresponds to the RRM1 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and it is highly
conserved between plants and fungi. Up to date, the
intracellular localization, RNA target(s), cellular
interactions and phosphorylation states of Mei2-like
proteins in plants remain unclear. .
Length = 77
Score = 26.1 bits (58), Expect = 4.4
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQFC 197
RG + VSY + R A RA AL G GG+++ F
Sbjct: 38 RGFIMVSYYDIRAARRAKRALQGTELGGRKLDIHFS 73
>gnl|CDD|216134 pfam00816, Histone_HNS, H-NS histone family.
Length = 92
Score = 26.4 bits (59), Expect = 4.6
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 5 EEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDF 42
EE E ++L +E K ER A E ++ ++
Sbjct: 1 EELEALIEKLE--KEIEAARKAERAAALAEIRELAAEY 36
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 27.7 bits (62), Expect = 4.6
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 2 LIQEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIED 41
+++E EK ++RL ++EE ++E E + E K+
Sbjct: 727 QLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEAR 766
Score = 27.3 bits (61), Expect = 7.0
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 8/40 (20%)
Query: 5 EEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIE 44
+E+E+ KRL +++EK + K E E +K+I + IE
Sbjct: 979 QEYEEVLKRLDELKEK--RAKLEEE------RKAILERIE 1010
>gnl|CDD|225664 COG3122, COG3122, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 215
Score = 27.2 bits (60), Expect = 4.8
Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 10 EQKRLRDIE-EKNRQEKEEREAQEKEFKKSIEDFIEGVCNELPDG 53
E+ + +E +K E++++ A KE+K ++ IE +PDG
Sbjct: 83 EENKAEQLERDKQLSEQQKQAALAKEYKAQVKQLIEMNRLNIPDG 127
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM5
of MRD1 which 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). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 25.9 bits (57), Expect = 4.8
Identities = 22/78 (28%), Positives = 33/78 (42%), Gaps = 9/78 (11%)
Query: 119 NLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRA 178
NL F+ T+ DV S GQ+ +V RG +V +S +EAL A
Sbjct: 7 NLPFEATK---------KDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNA 57
Query: 179 FYALTGRFYGGKQIRGQF 196
AL G+++ Q+
Sbjct: 58 MNALKDTHLLGRRLVLQY 75
>gnl|CDD|219180 pfam06798, PrkA, PrkA serine protein kinase C-terminal domain.
This is a family of PrkA bacterial and archaeal serine
kinases approximately 630 residues long. This family
corresponds to the C-terminal domain.
Length = 254
Score = 27.5 bits (62), Expect = 4.9
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 20 KNRQEKEEREAQEKEFKKSIEDFIEGVCNELPDGFRTNV 58
K+ EE E E+ F +SIE+ I G+ E FR +
Sbjct: 138 KDPLTGEELEPDER-FLRSIEEQI-GISEERKKDFRREI 174
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 27.6 bits (61), Expect = 5.1
Identities = 7/31 (22%), Positives = 20/31 (64%)
Query: 4 QEEWEKEQKRLRDIEEKNRQEKEEREAQEKE 34
Q++ +E ++ +E+K ++E+ + A E++
Sbjct: 116 QQKQAEEAEKQAQLEQKQQEEQARKAAAEQK 146
>gnl|CDD|219911 pfam08572, PRP3, pre-mRNA processing factor 3 (PRP3). Pre-mRNA
processing factor 3 (PRP3) is a U4/U6-associated
splicing factor. The human PRP3 has been implicated in
autosomal retinitis pigmentosa.
Length = 222
Score = 27.3 bits (61), Expect = 5.5
Identities = 10/25 (40%), Positives = 18/25 (72%), Gaps = 4/25 (16%)
Query: 9 KEQKRLRDIEEKNRQEKEEREAQEK 33
KEQK+LR + R++++ +E QE+
Sbjct: 143 KEQKKLR----RQRRKEKRKEKQER 163
>gnl|CDD|221250 pfam11831, Myb_Cef, pre-mRNA splicing factor component. This
family is a region of the Myb-Related Cdc5p/Cef1
proteins, in fungi, and is part of the pre-mRNA splicing
factor complex.
Length = 363
Score = 27.3 bits (61), Expect = 5.5
Identities = 8/34 (23%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 5 EEWEKEQKRLRDIEEKNRQEKEEREAQE-KEFKK 37
E E E++ D +++ +++ EA+E +E ++
Sbjct: 156 EPEEMEEELEEDAADRDARKRAAEEAKEQEELRR 189
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 27.7 bits (62), Expect = 5.5
Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFI 43
++E KEQKRLR ++++ ++K+E E EK K +F
Sbjct: 558 EEKEALKEQKRLRKLKKQEEKKKKELEKLEK-AKIPPAEFF 597
>gnl|CDD|233890 TIGR02486, RDH, reductive dehalogenase. This model represents a
family of corrin and 8-iron Fe-S cluster-containing
reductive dehalogenases found primarily in halorespiring
microorganisms such as dehalococcoides ethenogenes which
contains as many as 17 enzymes of this type with varying
substrate ranges. One example of a characterized species
is the tetrachloroethene reductive dehalogenase
(1.97.1.8) which also acts on trichloroethene converting
it to dichloroethene.
Length = 314
Score = 27.4 bits (61), Expect = 5.7
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 8/42 (19%)
Query: 67 CPFYSKVGACRFFDHCSRNHIKPSVSKTLLLNNFFTHLSMDN 108
CPF K + + H + ++ +VS T + N+FFT +MD
Sbjct: 276 CPFNKKPNS---WIH---DVVRSTVSTTSVFNSFFT--NMDK 309
>gnl|CDD|238252 cd00446, GrpE, GrpE is the adenine nucleotide exchange factor of
DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the
ATPase domain of Hsp70 catalyzing the dissociation of
ADP, which enables rebinding of ATP, one step in the
Hsp70 reaction cycle in protein folding. In eukaryotes,
only the mitochondrial Hsp70, not the cytosolic form,
is GrpE dependent.
Length = 137
Score = 26.7 bits (60), Expect = 5.8
Identities = 11/43 (25%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 3 IQEEWEKEQKRLRDIEE-KNRQEKEEREAQEKEFKKSIEDFIE 44
++E +K + L + E + R E+E EA++ +K +D +
Sbjct: 1 LEELKDKLLRALAEFENYRKRTEREREEARKYAIEKFAKDLLP 43
>gnl|CDD|213216 cd03249, ABC_MTABC3_MDL1_MDL2, ATP-binding cassette domain of a
mitochondrial protein MTABC3 and related proteins.
MTABC3 (also known as ABCB6) is a mitochondrial
ATP-binding cassette protein involved in iron
homeostasis and one of four ABC transporters expressed
in the mitochondrial inner membrane, the other three
being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast
MDL1 (multidrug resistance-like protein 1) and MDL2
(multidrug resistance-like protein 2) transporters are
also included in this CD. MDL1 is an ATP-dependent
permease that acts as a high-copy suppressor of ATM1 and
is thought to have a role in resistance to oxidative
stress. Interestingly, subfamily B is more closely
related to the carboxyl-terminal component of subfamily
C than the two halves of ABCC molecules are with one
another.
Length = 238
Score = 27.1 bits (61), Expect = 5.8
Identities = 16/39 (41%), Positives = 18/39 (46%), Gaps = 6/39 (15%)
Query: 20 KNRQEKEEREAQEKEFKKSIEDFIEGVCNELPDGFRTNV 58
K EE E K K +I DFI LPDG+ T V
Sbjct: 101 KPDATDEEVEEAAK--KANIHDFIMS----LPDGYDTLV 133
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding
protein 18 and similar proteins. This subfamily
corresponds to the RRM of RBM18, a putative RNA-binding
protein containing a well-conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The biological role of RBM18
remains unclear. .
Length = 80
Score = 25.7 bits (57), Expect = 6.0
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 137 DVLPELRSLGQVTQFKVCCNKSPHLRGN----VYVSYSNEREALRAFYALTGRFYGGKQI 192
+L G++ +F +KS L+G +V++ + EA +A +L G+ GK++
Sbjct: 15 HLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTALGKKL 74
>gnl|CDD|216840 pfam02005, TRM, N2,N2-dimethylguanosine tRNA methyltransferase.
This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA.
The TRM1 gene of Saccharomyces cerevisiae is necessary
for the N2,N2-dimethylguanosine modification of both
mitochondrial and cytoplasmic tRNAs. The enzyme is found
in both eukaryotes and archaebacteria.
Length = 375
Score = 27.3 bits (61), Expect = 6.1
Identities = 18/79 (22%), Positives = 28/79 (35%), Gaps = 15/79 (18%)
Query: 26 EEREAQEKEFKKSIEDFIEGVCNELPD----------GFRTNVETKPDKELCPFYSKVGA 75
E E+ +EF K I ++ + EL D + P ++ S +
Sbjct: 290 EIAESPPEEFSKRILGLLKLIKEELLDVPLYYDLHQLASVLKLSVPPLQD---VVSALLN 346
Query: 76 CRFFDHCSRNHIKPSVSKT 94
F SR H P+ KT
Sbjct: 347 AGF--EVSRTHANPTGIKT 363
>gnl|CDD|132845 cd07206, Pat_TGL3-4-5_SDP1, Triacylglycerol lipase 3, 4, and 5
and Sugar-Dependent 1 lipase. Triacylglycerol lipases
are involved in triacylglycerol mobilization and
degradation; they are found in lipid particles. TGL4 is
30% homologus to TGL3, whereas TGL5 is 26% homologus to
TGL3. Sugar-Dependent 1 (SDP1) lipase has a
patatin-like acyl-hydrolase domain that initiates the
breakdown of storage oil in germinating Arabidopsis
seeds. This family includes subfamilies of proteins:
TGL3, TGL4, TGL5, and SDP1.
Length = 298
Score = 27.2 bits (61), Expect = 6.3
Identities = 10/41 (24%), Positives = 16/41 (39%)
Query: 36 KKSIEDFIEGVCNELPDGFRTNVETKPDKELCPFYSKVGAC 76
K IED+IE V L + + +E F+ +
Sbjct: 26 KHLIEDYIEEVDLSLEYLALLDTKELSVEEKLDFFRRARHA 66
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 25.7 bits (56), Expect = 6.3
Identities = 13/49 (26%), Positives = 27/49 (55%)
Query: 134 FYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYAL 182
+ D+++P S+G++ + ++ + RG +V Y+ + EA RA L
Sbjct: 14 YEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVREL 62
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 25.6 bits (56), Expect = 6.4
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 141 ELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQI 192
ELR L + V C+K ++ +V E EAL A AL G+ G++I
Sbjct: 16 ELRGLFEEFGRVVECDK---VKDYAFVHMEREEEALAAIEALNGKEVKGRRI 64
>gnl|CDD|129833 TIGR00750, lao, LAO/AO transport system ATPase. In E. coli,
mutation of this kinase blocks phosphorylation of two
transporter system periplasmic binding proteins and
consequently inhibits those transporters. This kinase is
also found in Gram-positive bacteria, archaea, and the
roundworm C. elegans. It may have a more general, but
still unknown function. Mutations have also been found
that do not phosphorylate the periplasmic binding
proteins, yet still allow transport. The ATPase activity
of this protein seems to be necessary, however
[Transport and binding proteins, Amino acids, peptides
and amines, Regulatory functions, Protein interactions].
Length = 300
Score = 27.0 bits (60), Expect = 6.6
Identities = 12/67 (17%), Positives = 26/67 (38%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIEGVCNELPDGFRTNVETKP 62
I E W+ ++ + ++ R+ + KK +E+ + D +R +
Sbjct: 226 IDELWDAIEEHKTFLTASGLLQERRRQRSVEWLKKLVEEEVLKKVFANEDVYRDLLLAVL 285
Query: 63 DKELCPF 69
EL P+
Sbjct: 286 AGELDPY 292
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich
splicing factor 10 (SRSF10) and similar proteins. This
subgroup corresponds to the RRM of SRSF10, also termed
40 kDa SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). SRSF10 is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 25.7 bits (56), Expect = 6.7
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQF 196
RG YV + + R+A A + L ++ G+QI QF
Sbjct: 42 RGFAYVQFEDVRDAEDALHNLDRKWICGRQIEIQF 76
>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2
and similar proteins. This subfamily corresponds to the
RRM2 of yeast protein gar2, a novel nucleolar protein
required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture with
nucleolin from vertebrates and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of gar2 is made up of highly acidic regions separated
from each other by basic sequences, and contains
multiple phosphorylation sites. The central domain of
gar2 contains two closely adjacent N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
C-terminal RGG (or GAR) domain of gar2 is rich in
glycine, arginine and phenylalanine residues. .
Length = 73
Score = 25.4 bits (56), Expect = 6.8
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 10/76 (13%)
Query: 119 NLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNEREALR 177
NL FD E D + G+++ ++ + S +G YV +S++ A
Sbjct: 5 NLSFDADE---------DSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQA 55
Query: 178 AFYALTGRFYGGKQIR 193
A AL G G+ +R
Sbjct: 56 ALDALGGTDLLGRPVR 71
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 92
Score = 25.7 bits (57), Expect = 6.9
Identities = 16/55 (29%), Positives = 24/55 (43%)
Query: 144 SLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQFCN 198
+G+ T ++ + RG +V Y+ +A A AL G G IR F N
Sbjct: 26 QVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRVSFGN 80
>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain,
potential nuclease [General function prediction only].
Length = 290
Score = 27.2 bits (60), Expect = 7.0
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEEREAQEKEF---KKSIEDFIEGVCNELPDGFRTNVE 59
++ E+E+ Q+RL+ +E +N + +E + E KK ++ GV ELP+ +
Sbjct: 161 LEAEYEEVQERLKRLEVENSRLEEMLKKLPGEVYDLKKRWDELEPGV--ELPEEELISDL 218
Query: 60 TKPDKELCP 68
K L P
Sbjct: 219 VKETLNLAP 227
>gnl|CDD|217206 pfam02731, SKIP_SNW, SKIP/SNW domain. This domain is found in
chromatin proteins.
Length = 158
Score = 26.5 bits (59), Expect = 7.1
Identities = 10/25 (40%), Positives = 19/25 (76%), Gaps = 1/25 (4%)
Query: 1 LLIQEEWEKEQKRLRDIEEKNRQEK 25
L +E+ EKE+K LR++ ++ R+E+
Sbjct: 135 LAEKEKQEKEEK-LRELAQRAREER 158
>gnl|CDD|223649 COG0576, GrpE, Molecular chaperone GrpE (heat shock protein)
[Posttranslational modification, protein turnover,
chaperones].
Length = 193
Score = 26.9 bits (60), Expect = 7.3
Identities = 11/42 (26%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 5 EEWEKEQKRLR-DIEE-KNRQEKEEREAQEKEFKKSIEDFIE 44
EE + + R + + E + R E+E EA++ +K +D +
Sbjct: 53 EELKDKYLRAQAEFENLRKRTEREREEAKKYAIEKFAKDLLP 94
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are putative
RNA-binding proteins carrying three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and TEL characteristic
motifs that allow sequence and putative functional
discrimination between the terminal EAR1-like proteins
and Mei2-like proteins. .
Length = 71
Score = 25.6 bits (56), Expect = 7.4
Identities = 10/37 (27%), Positives = 20/37 (54%)
Query: 157 KSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
++P R +V + + R+A +A A+ G+ GK +
Sbjct: 33 ETPCKREQRFVEFFDVRDAAKALRAMNGKEISGKPVV 69
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein 3
(RBM3) and similar proteins. This subfamily corresponds
to the RRM domain of two structurally related
heterogenous nuclear ribonucleoproteins, CIRBP (also
termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL),
both of which belong to a highly conserved cold shock
proteins family. The cold shock proteins can be induced
after exposure to a moderate cold-shock and other
cellular stresses such as UV radiation and hypoxia.
CIRBP and RBM3 may function in posttranscriptional
regulation of gene expression by binding to different
transcripts, thus allowing the cell to response rapidly
to environmental signals. However, the kinetics and
degree of cold induction are different between CIRBP and
RBM3. Tissue distribution of their expression is
different. CIRBP and RBM3 may be differentially
regulated under physiological and stress conditions and
may play distinct roles in cold responses of cells.
CIRBP, also termed glycine-rich RNA-binding protein
CIRP, is localized in the nucleus and mediates the
cold-induced suppression of cell cycle progression.
CIRBP also binds DNA and possibly serves as a chaperone
that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore, RBM3
may be essential for cell proliferation and mitosis.
Both, CIRBP and RBM3, contain an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), that is
involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 25.6 bits (56), Expect = 7.5
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 162 RGNVYVSYSNEREALRAFYALTGRFYGGKQIR 193
RG +V++ N +A A A+ G+ G+QIR
Sbjct: 42 RGFGFVTFENPDDAKDAMMAMNGKSVDGRQIR 73
>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase.
Length = 1066
Score = 27.2 bits (60), Expect = 7.6
Identities = 12/27 (44%), Positives = 20/27 (74%)
Query: 11 QKRLRDIEEKNRQEKEEREAQEKEFKK 37
+K++ EE R++K+E +A+EKE KK
Sbjct: 9 EKKILTEEELERKKKKEEKAKEKELKK 35
>gnl|CDD|213341 cd05392, RasGAP_Neurofibromin_like, Ras-GTPase Activating Domain of
proteins similar to neurofibromin. Neurofibromin-like
proteins include the Saccharomyces cerevisiae RasGAP
proteins Ira1 and Ira2, the closest homolog of
neurofibromin, which is responsible for the human
autosomal dominant disease neurofibromatosis type I
(NF1). The RasGAP Ira1/2 proteins are negative
regulators of the Ras-cAMP signaling pathway and
conserved from yeast to human. In yeast Ras proteins are
activated by GEFs, and inhibited by two GAPs, Ira1 and
Ira2. Ras proteins activate the cAMP/protein kinase A
(PKA) pathway, which controls metabolism, stress
resistance, growth, and meiosis. Recent studies showed
that the kelch proteins Gpb1 and Gpb2 inhibit Ras
activity via association with Ira1 and Ira2. Gpb1/2 bind
to a conserved C-terminal domain of Ira1/2, and loss of
Gpb1/2 results in a destabilization of Ira1 and Ira2,
leading to elevated levels of Ras2-GTP and uninhibited
cAMP-PKA signaling. Since the Gpb1/2 binding domain on
Ira1/2 is conserved in the human neurofibromin protein,
the studies suggest that an analogous signaling
mechanism may contribute to the neoplastic development
of NF1.
Length = 317
Score = 26.9 bits (60), Expect = 7.7
Identities = 9/42 (21%), Positives = 17/42 (40%), Gaps = 3/42 (7%)
Query: 18 EEKNRQEKEEREAQEKEFKKSIEDFIEGVCN---ELPDGFRT 56
EK + + E E K + ++ + + +LP FR
Sbjct: 113 VEKIKPDDENLEENADLLMKYAQMLLDSITDSVDQLPPSFRY 154
>gnl|CDD|204831 pfam12137, RapA_C, RNA polymerase recycling family C-terminal.
This domain is found in bacteria. This domain is about
360 amino acids in length. This domain is found
associated with pfam00271, pfam00176. The function of
this domain is not known, but structurally it forms an
alpha-beta fold in nature with a central beta-sheet
flanked by helices and loops, the beta-sheet being
mainly antiparallel and flanked by four alpha helices,
among which the two longer helices exhibit a coiled-coil
arrangement.
Length = 362
Score = 27.1 bits (61), Expect = 7.8
Identities = 11/43 (25%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 3 IQEEWEKEQKRLRDIEEKN---RQEKEER-EAQEKEFKKSIED 41
+Q++ E RL+ ++ N R E+ E E Q +E +++
Sbjct: 306 MQQQLSAELARLKALKAVNPNIRDEEIEALEQQREELLTALDK 348
>gnl|CDD|216249 pfam01025, GrpE, GrpE.
Length = 165
Score = 26.4 bits (59), Expect = 8.0
Identities = 10/52 (19%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 3 IQEEWEKEQKRLRDIEEKNRQEKEE----REAQEKEFKKSIEDFIEGVCNEL 50
++EE E+ ++ + +++++ + E R+ E+E +++ + IE +L
Sbjct: 16 LEEELEELEEEIEELKDRLLRLLAEFENYRKRTEREREEAKKYAIEKFAKDL 67
>gnl|CDD|206755 cd08774, 14-3-3, 14-3-3 domain. 14-3-3 domain is an essential
part of 14-3-3 proteins, a ubiquitous class of
regulatory, phosphoserine/threonine-binding proteins
found in all eukaryotic cells, including yeast,
protozoa and mammalian cells. 14-3-3 proteins play
important roles in many biological processes that are
regulated by phosphorylation, including cell cycle
regulation, cell proliferation, protein trafficking,
metabolic regulation and apoptosis. More than 300
binding partners of the 14-3-3 domain have been
identified in all subcellular compartments and include
transcription factors, signaling molecules, tumor
suppressors, biosynthetic enzymes, cytoskeletal
proteins and apoptosis factors. 14-3-3 binding can
alter the conformation, localization, stability,
phosphorylation state, activity as well as molecular
interactions of a target protein. They function only as
dimers, some preferring strictly homodimeric
interaction, while others form heterodimers. Binding of
the 14-3-3 domain to its target occurs in a
phosphospecific manner where it binds to one of two
consensus sequences of their target proteins; RSXpSXP
(mode-1) and RXXXpSXP (mode-2). In some instances,
14-3-3 domain containing proteins are involved in
regulation and signaling of a number of cellular
processes in phosphorylation-independent manner. Many
organisms express multiple isoforms: there are seven
mammalian 14-3-3 family members (beta, gamma, eta,
theta, epsilon, sigma, zeta), each encoded by a
distinct gene, while plants contain up to 13 isoforms.
The flexible C-terminal segment of 14-3-3 isoforms
shows the highest sequence variability and may
significantly contribute to individual isoform
uniqueness by playing an important regulatory role by
occupying the ligand binding groove and blocking the
binding of inappropriate ligands in a distinct manner.
Elevated amounts of 14-3-3 proteins are found in the
cerebrospinal fluid of patients with Creutzfeldt-Jakob
disease. In protozoa, like Plasmodium or
Cryptosporidium parvum 14-3-3 proteins play an
important role in key steps of parasite development.
Length = 225
Score = 26.8 bits (60), Expect = 8.1
Identities = 12/40 (30%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 12 KRLRDIEEKNRQEKEEREAQE-KEFKKSIEDFIEGVCNEL 50
+ L IE+K + E + + KE+K+ IE ++ +CN++
Sbjct: 57 RILSSIEQKESSKGNEEKLKLIKEYKEKIEKELKDICNDI 96
>gnl|CDD|233193 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 27.3 bits (61), Expect = 8.2
Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 11 QKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIEGVCNELPDGFRTNVE--TKPD---KE 65
+K + + +K R+E ++ + E K++ED + L + ++ K E
Sbjct: 129 EKFKKSLTKKTREEFQDNYRETLESIKALEDIKRNLLELLREYGAELLKEYDKTGHIYSE 188
Query: 66 LCPFYS 71
L F +
Sbjct: 189 LLEFLA 194
>gnl|CDD|221805 pfam12848, ABC_tran_2, ABC transporter. This domain is related
to pfam00005.
Length = 85
Score = 25.6 bits (57), Expect = 8.3
Identities = 12/27 (44%), Positives = 20/27 (74%), Gaps = 1/27 (3%)
Query: 18 EEKNRQEKEEREAQEKEFKKSIEDFIE 44
EE+ Q+++ E Q+KE KK +E+FI+
Sbjct: 23 EERLEQQEKAYEKQQKEIKK-LEEFID 48
>gnl|CDD|128345 smart00030, CLb, CLUSTERIN Beta chain.
Length = 206
Score = 26.7 bits (59), Expect = 8.4
Identities = 15/45 (33%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 5 EEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIEGVCNE 49
E+ KE+K L E+ +++KEE +E ++ +++ +GVCNE
Sbjct: 39 EKTNKERKSLLSTLEEAKKKKEEALKDTRESEEKLKES-QGVCNE 82
>gnl|CDD|178772 PLN03233, PLN03233, putative glutamate-tRNA ligase; Provisional.
Length = 523
Score = 26.9 bits (59), Expect = 8.6
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 9/55 (16%)
Query: 92 SKTLLLNNFFTHLSMDNKSVREYDTDINLEFDETEMHKYFVEFYDDVLPELRSLG 146
+K LLN+++ R Y + L FD+T K EF + ++ +L +
Sbjct: 29 AKAALLNDYYA---------RRYKGRLILRFDDTNPSKEKAEFEESIIEDLGKIE 74
>gnl|CDD|217933 pfam04156, IncA, IncA protein. Chlamydia trachomatis is an
obligate intracellular bacterium that develops within a
parasitophorous vacuole termed an inclusion. The
inclusion is non-fusogenic with lysosomes but intercepts
lipids from a host cell exocytic pathway. Initiation of
chlamydial development is concurrent with modification
of the inclusion membrane by a set of C.
trachomatis-encoded proteins collectively designated
Incs. One of these Incs, IncA, is functionally
associated with the homotypic fusion of inclusions. This
family probably includes members of the wider Inc family
rather than just IncA.
Length = 186
Score = 26.7 bits (59), Expect = 8.9
Identities = 9/41 (21%), Positives = 19/41 (46%)
Query: 4 QEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIE 44
Q E + +++L +++E+ +E E E + ED
Sbjct: 78 QGELSELKQQLSELQEELEDLEERIAELESELEDLKEDLQL 118
>gnl|CDD|218308 pfam04882, Peroxin-3, Peroxin-3. Peroxin-3 is a peroxisomal
protein. It is thought to be involve in membrane
vesicle assembly prior to the translocation of matrix
proteins.
Length = 399
Score = 26.9 bits (60), Expect = 9.0
Identities = 7/19 (36%), Positives = 14/19 (73%)
Query: 11 QKRLRDIEEKNRQEKEERE 29
QK+LR+ +E+ +E+ +E
Sbjct: 33 QKKLREFQERLAEERFAKE 51
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is an
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 80
Score = 25.2 bits (56), Expect = 9.1
Identities = 15/72 (20%), Positives = 33/72 (45%), Gaps = 11/72 (15%)
Query: 121 EFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFY 180
+ D+ ++ + F ++ G++T KV + +G +V++ N A +A
Sbjct: 12 DMDDEKLKELFGKY-----------GKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVE 60
Query: 181 ALTGRFYGGKQI 192
L G+ GK++
Sbjct: 61 ELNGKEVNGKKL 72
>gnl|CDD|232913 TIGR00308, TRM1, tRNA(guanine-26,N2-N2) methyltransferase. This
enzyme is responsible for two methylations of a
characteristic guanine of most tRNA molecules. The
activity has been demonstrated for eukaryotic and
archaeal proteins, which are active when expressed in E.
coli, a species that lacks this enzyme. At least one
Eubacterium, Aquifex aeolicus, has an ortholog, as do
all completed archaeal genomes [Protein synthesis, tRNA
and rRNA base modification].
Length = 374
Score = 26.7 bits (59), Expect = 9.3
Identities = 23/88 (26%), Positives = 36/88 (40%), Gaps = 11/88 (12%)
Query: 16 DIEEKNRQEKEEREAQEKEF--KKSIEDFIEGVCNEL---PDGFRTNVETKPDKELCPFY 70
+ +K E+ R A+EKE+ +K + + + NEL P + + K P
Sbjct: 272 PLHDKEFIEEVLRIAEEKEYGTRKRVLKMLSLIKNELSDPPGYYSPHHIASVLKLSVPPL 331
Query: 71 SKV----GACRFFDHCSRNHIKPSVSKT 94
V + F SR H +PS KT
Sbjct: 332 KDVVAGLKSLGF--EASRTHYQPSGIKT 357
>gnl|CDD|215492 PLN02907, PLN02907, glutamate-tRNA ligase.
Length = 722
Score = 27.0 bits (60), Expect = 9.4
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 9/55 (16%)
Query: 92 SKTLLLNNFFTHLSMDNKSVREYDTDINLEFDETEMHKYFVEFYDDVLPELRSLG 146
+K LLN +F R Y + + FD+T K EF +++L ++ +LG
Sbjct: 231 AKAALLNQYFA---------RRYKGKLIVRFDDTNPSKESDEFVENILKDIETLG 276
>gnl|CDD|237256 PRK12901, secA, preprotein translocase subunit SecA; Reviewed.
Length = 1112
Score = 26.9 bits (60), Expect = 9.4
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 5 EEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIEDFIEGVCNE-LPDGFRTNVET 60
+ + E+ + IE + E+E+ AQ + +K + +E V +E LP+ F ET
Sbjct: 60 IDAKIEELKAEAIESLDIDEREDIYAQIDKLEKEAYEILEKVLDEILPEAFAIVKET 116
>gnl|CDD|227478 COG5149, TOA1, Transcription initiation factor IIA, large chain
[Transcription].
Length = 293
Score = 26.6 bits (58), Expect = 9.4
Identities = 23/78 (29%), Positives = 31/78 (39%), Gaps = 9/78 (11%)
Query: 4 QEEWEKEQKRLRDIEEKNRQEKEEREAQEKEFKKSIE-DFIEGVCNELPD-----GFRTN 57
Q EW+ E+ R RD ++ Q + E FK EG+ ++L D G
Sbjct: 182 QSEWDGERMRRRDGKQGIHQYERLSEGPAHAFKGKPTTAKDEGMFSDLDDSDVDSGDSEI 241
Query: 58 VETKPDKE--LCPFYSKV 73
TK LC Y KV
Sbjct: 242 EGTKGSTNCMLC-LYDKV 258
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein
interacting with the FHA domain of pKI-67 (NIFK) and
similar proteins. This subgroup corresponds to the RRM
of NIFK and Nop15p. NIFK, also termed MKI67 FHA
domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also includes
Saccharomyces cerevisiae YNL110C gene encoding ribosome
biogenesis protein 15 (Nop15p), also termed nucleolar
protein 15. Both, NIFK and Nop15p, contain an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 25.2 bits (56), Expect = 9.7
Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 12/52 (23%)
Query: 122 FDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNE 172
F E E+ KYF +F G VT+ ++ +K + +G +V + +
Sbjct: 11 FYEPELRKYFSQF-----------GTVTRLRLSRSKKTGKSKGYAFVEFESP 51
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 0.136 0.416
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,580,182
Number of extensions: 969897
Number of successful extensions: 3108
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2930
Number of HSP's successfully gapped: 355
Length of query: 207
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 115
Effective length of database: 6,857,034
Effective search space: 788558910
Effective search space used: 788558910
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: 57 (25.6 bits)