RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5142
(410 letters)
>gnl|CDD|153397 cd08028, LARP_3, La RNA-binding domain of La-related protein 3.
This domain is found at the N-terminus of the La
autoantigen and similar proteins, and co-occurs with an
RNA-recognition motif (RRM). Together these domains
function to bind primary transcripts of RNA polymerase
III at their 3' terminus and protect them from
exonucleolytic degradation. Binding is specific for the
3'-terminal UUU-OH motif. The La autoantigen is also
called Lupus La protein, LARP3, or Sjoegren syndrome
type B antigen (SS-B).
Length = 82
Score = 120 bits (304), Expect = 7e-34
Identities = 50/82 (60%), Positives = 62/82 (75%)
Query: 19 VSKLENQIIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKMTTEAKVIV 78
+ LE +II QIEYYF D NL RDKFL+ +IK+DDGWV + MLKF RL ++++ +VI
Sbjct: 1 MDDLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIA 60
Query: 79 DALKKSTSKLIEVNEDGTKIRR 100
ALKKS S LIEV+ED TKIRR
Sbjct: 61 KALKKSKSGLIEVSEDKTKIRR 82
>gnl|CDD|128955 smart00715, LA, Domain in the RNA-binding Lupus La protein; unknown
function.
Length = 80
Score = 98.8 bits (247), Expect = 1e-25
Identities = 38/82 (46%), Positives = 60/82 (73%), Gaps = 2/82 (2%)
Query: 20 SKLENQIIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKMTTEAKVIVD 79
+L+ +I +Q+EYYFSD NL RDKFL+ ++ K+DG+V ++T+ F R+ +TT+ +IV+
Sbjct: 1 EELKQKIKKQVEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVE 60
Query: 80 ALKKSTSKLIEVNEDGTKIRRN 101
AL+ S +EV+EDG K+RR
Sbjct: 61 ALRSSP--KLEVSEDGLKVRRR 80
>gnl|CDD|153396 cd07323, LAM, LA motif RNA-binding domain. This domain is found at
the N-terminus of La RNA-binding proteins as well as in
other related proteins. Typically, the domain co-occurs
with an RNA-recognition motif (RRM), and together these
domains function to bind primary transcripts of RNA
polymerase III in the La autoantigen (Lupus La protein,
LARP3, or Sjoegren syndrome type B antigen, SS-B). A
variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain architecture,
appear to function as RNA-binding proteins in eukaryotic
cellular processes.
Length = 75
Score = 89.9 bits (224), Expect = 2e-22
Identities = 37/77 (48%), Positives = 58/77 (75%), Gaps = 3/77 (3%)
Query: 24 NQIIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKMTTEAKVIVDALKK 83
+I +Q+EYYFSD NL +D+FL+ + DDGWV L+ + F R+ K+TT+ ++I++AL+
Sbjct: 2 EKIKKQVEYYFSDENLCKDRFLRSLM-DDDGWVPLSLLASFNRVKKLTTDVELILEALR- 59
Query: 84 STSKLIEVNEDGTKIRR 100
S ++EV+EDGTK+RR
Sbjct: 60 -DSSVVEVSEDGTKVRR 75
>gnl|CDD|203243 pfam05383, La, La domain. This presumed domain is found at the
N-terminus of La RNA-binding proteins as well as other
proteins. The function of this region is uncertain.
Length = 59
Score = 85.3 bits (212), Expect = 6e-21
Identities = 30/59 (50%), Positives = 45/59 (76%)
Query: 26 IIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKMTTEAKVIVDALKKS 84
I +Q+EYYFSD NL RDKFL+ ++ KD G+V ++T+ F R+ K+TT+ +IV+AL+ S
Sbjct: 1 IKKQVEYYFSDENLPRDKFLRKQMDKDPGYVPISTIASFKRIKKLTTDVNLIVEALRSS 59
>gnl|CDD|153402 cd08033, LARP_6, La RNA-binding domain of La-related protein 6.
This domain is found in animal and plant proteins
related to the La autoantigen. A variety of La-related
proteins (LARPs or La ribonucleoproteins), with
differing domain architecture, appear to function as
RNA-binding proteins in eukaryotic cellular processes.
Length = 77
Score = 70.0 bits (172), Expect = 3e-15
Identities = 28/78 (35%), Positives = 53/78 (67%), Gaps = 3/78 (3%)
Query: 24 NQIIEQIEYYFSDINLARDKFLQGEIKKD-DGWVELTTMLKFARLAKMTTEAKVIVDALK 82
+I++Q+EYYFSD NL +D FL ++++ +G+V + + F ++ +T + +V+ AL+
Sbjct: 2 QKIVKQVEYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALR 61
Query: 83 KSTSKLIEVNEDGTKIRR 100
+S+ + V+EDG K+RR
Sbjct: 62 RSS--KLVVSEDGKKVRR 77
>gnl|CDD|153398 cd08029, LA_like_fungal, La-motif domain of fungal proteins similar
to the La autoantigen. This domain is found in fungal
proteins related to the La autoantigen. A variety of
La-related proteins (LARPs or La ribonucleoproteins),
with differing domain architecture, appear to function
as RNA-binding proteins in eukaryotic cellular
processes.
Length = 76
Score = 67.3 bits (165), Expect = 2e-14
Identities = 32/79 (40%), Positives = 49/79 (62%), Gaps = 4/79 (5%)
Query: 23 ENQIIEQIEYYFSDINLARDKFLQGEI-KKDDGWVELTTMLKFARLAKMTTEAKVIVDAL 81
+I +Q+E+YFSD NL DKFL ++GWV + T+ F R+ + V V+AL
Sbjct: 1 PEEIRKQVEFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRFQPLEAV-VEAL 59
Query: 82 KKSTSKLIEVNEDGTKIRR 100
++ S+L+EV+EDG +RR
Sbjct: 60 RE--SELLEVSEDGENVRR 76
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or
LARP3) and similar proteins. This subfamily corresponds
to the RRM1 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). It
also possesses a short basic motif (SBM) and a nuclear
localization signal (NLS) at the C-terminus. .
Length = 72
Score = 64.5 bits (158), Expect = 2e-13
Identities = 37/79 (46%), Positives = 50/79 (63%), Gaps = 12/79 (15%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
++YVK P DATLDDI++FF+K K+ NI MR DK KFKGS+FV F +E
Sbjct: 1 TVYVKGFPKDATLDDIQEFFEK----FGKVNNIRMRRDLDK-----KFKGSVFVEFKTEE 51
Query: 181 NAEKFLNENKDKNLKFNEN 199
+A+KFL + + LK+ E
Sbjct: 52 DAKKFLEK---EKLKYKEK 67
>gnl|CDD|153401 cd08032, LARP_7, La RNA-binding domain of La-related protein 7.
LARP7 is a component of the 7SK snRNP, a key factor in
the regulation of RNA polymerase II transcription. 7SK
functionality is dependent on the presence of LARP7,
which is thought to stabilize the 7SK RNA by interacting
with its 3' end. The release of 7SK RNA from
P-TEFb/HEXIM/7SK complexes activates the
cyclin-dependent kinase P-TEFb, which in turn
phosphorylates the C-terminal domain of RNA pol II and
mediates a transition into productive transcription
elongation.
Length = 82
Score = 63.8 bits (155), Expect = 5e-13
Identities = 32/83 (38%), Positives = 62/83 (74%), Gaps = 3/83 (3%)
Query: 19 VSKLENQIIEQIEYYFSDINLARDKFLQGEIKKD-DGWVELTTMLKFARLAKMTTEAKVI 77
V +L I +Q++++F D+NL +D+FL+ +I+K DG+++++ ++ F ++ K+TT+ K+I
Sbjct: 2 VKQLLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLI 61
Query: 78 VDALKKSTSKLIEVNEDGTKIRR 100
ALK S+ ++E+N +GT+IRR
Sbjct: 62 ARALKNSS--VVELNLEGTRIRR 82
>gnl|CDD|153399 cd08030, LA_like_plant, La-motif domain of plant proteins similar
to the La autoantigen. This domain is found in plant
proteins related to the La autoantigen. A variety of
La-related proteins (LARPs or La ribonucleoproteins),
with differing domain architecture, appear to function
as RNA-binding proteins in eukaryotic cellular
processes.
Length = 90
Score = 58.6 bits (142), Expect = 4e-11
Identities = 32/86 (37%), Positives = 48/86 (55%), Gaps = 11/86 (12%)
Query: 26 IIEQIEYYFSDINLARDKFLQGEIKKD-DGWVELTTMLKFARLAKM-----TTEAKVIVD 79
++ Q+E+YFSD NL RD FL E+++D DG V L + F+R+ + V D
Sbjct: 5 VLRQVEFYFSDSNLPRDDFLLEEVEEDPDGMVSLALICSFSRMRSLLGLGGGKPEDVPED 64
Query: 80 ALKK-----STSKLIEVNEDGTKIRR 100
LK TS L++V+EDG ++ R
Sbjct: 65 TLKAVAEALRTSTLLKVSEDGKRVGR 90
>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or
LARP3) and similar proteins. This subgroup corresponds
to the RRM2 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition, it possesses a short basic motif (SBM) and a
nuclear localization signal (NLS) at the C-terminus. .
Length = 76
Score = 57.6 bits (140), Expect = 6e-11
Identities = 25/78 (32%), Positives = 47/78 (60%), Gaps = 5/78 (6%)
Query: 275 GALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKA 334
G +L S + E SRED++E E+ E+ +++F G+ +VR+K+EN A+ L+
Sbjct: 1 GCVLHFSGVGEQTSREDLKEAFEEFG----EVAWVDFARGQTEGYVRFKEENAAKEALEK 56
Query: 335 LG-SKEIVIKDVKVSIEV 351
L +K + IK +V++++
Sbjct: 57 LKEAKNLKIKGSEVTVKL 74
>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif. This domain is found in
protein La which functions as an RNA chaperone during
RNA polymerase III transcription, and can also stimulate
translation initiation. It contains a five stranded beta
sheet which forms an atypical RNA recognition motif.
Length = 102
Score = 57.4 bits (139), Expect = 2e-10
Identities = 30/108 (27%), Positives = 58/108 (53%), Gaps = 8/108 (7%)
Query: 275 GALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKA 334
G +LK S + +P SREDI+E + E+ +++F G+ +VR+K A+ L+
Sbjct: 1 GVILKFSGLNKPTSREDIKEAFSQHG----EVKYVDFLEGDKEGYVRFKTPEAAKKALEK 56
Query: 335 LGSKEIVIKDVKVSIEVVTGEEEQTVLDRMKIDIFKRRQKLMNEKKSG 382
++ IK+ +V++E++ GEEE+ + I + +Q +N +
Sbjct: 57 ATEAKLKIKEAEVTLELLEGEEEKEYWKK----IIEDQQAKLNNPREK 100
>gnl|CDD|153403 cd08034, LARP_1_2, La RNA-binding domain proteins similar to
La-related proteins 1 and 2. This domain is found in
proteins similar to vertebrate La-related proteins 1 and
2 (LARP1, LARP2). A variety of La-related proteins
(LARPs or La ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding proteins
in eukaryotic cellular processes.
Length = 73
Score = 53.6 bits (129), Expect = 2e-09
Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 5/75 (6%)
Query: 26 IIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKMTTEAKVIVDALKKST 85
I +QIEYYFS NL +D FL+ ++ +G++ + + F R+ +TT+ +I++ALK ST
Sbjct: 4 IKKQIEYYFSVDNLEKDFFLRRKM-DPEGYLPIALIASFHRVQALTTDVNLILEALKDST 62
Query: 86 SKLIEVNEDGTKIRR 100
V K+R
Sbjct: 63 ----VVELVDEKVRC 73
>gnl|CDD|153400 cd08031, LARP_4_5_like, La RNA-binding domain of proteins similar
to La-related proteins 4 and 5. This domain is found
in proteins similar to La-related proteins 4 and 5
(LARP4, LARP5). A variety of La-related proteins (LARPs
or La ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding
proteins in eukaryotic cellular processes.
Length = 75
Score = 52.4 bits (126), Expect = 4e-09
Identities = 28/76 (36%), Positives = 48/76 (63%), Gaps = 3/76 (3%)
Query: 24 NQIIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKMTTEAKVIVDALKK 83
+ Q+EYYFS NLA D +L ++ D +V + T+ F ++ K+TT+ +IV+AL++
Sbjct: 2 ELLKRQLEYYFSRENLANDAYLLSQMDSDQ-YVPIWTIANFNKIKKLTTDIDLIVEALRE 60
Query: 84 STSKLIEVNEDGTKIR 99
S ++V+E G K+R
Sbjct: 61 SP--NVQVDEKGEKVR 74
>gnl|CDD|153406 cd08037, LARP_1, La RNA-binding domain of La-related protein 1.
This domain is found in vertebrate La-related protein 1
(LARP1). A variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain architecture,
appear to function as RNA-binding proteins in eukaryotic
cellular processes.
Length = 73
Score = 46.0 bits (109), Expect = 8e-07
Identities = 32/78 (41%), Positives = 51/78 (65%), Gaps = 5/78 (6%)
Query: 23 ENQIIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKMTTEAKVIVDALK 82
++ I QIEYYFS NL RD FL+ ++ +DG++ +T + F R+ +TT+ +I+ ALK
Sbjct: 1 KDYIKRQIEYYFSVDNLERDFFLRRKM-DEDGFLPVTLIASFHRVQALTTDISLIIKALK 59
Query: 83 KSTSKLIEVNEDGTKIRR 100
SK++E+ + KIRR
Sbjct: 60 D--SKVVEIIDM--KIRR 73
>gnl|CDD|153407 cd08038, LARP_2, La RNA-binding domain of La-related protein 2.
This domain is found in vertebrate La-related protein 2
(LARP2). A variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain architecture,
appear to function as RNA-binding proteins in eukaryotic
cellular processes.
Length = 73
Score = 45.3 bits (107), Expect = 1e-06
Identities = 31/75 (41%), Positives = 44/75 (58%), Gaps = 5/75 (6%)
Query: 26 IIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKMTTEAKVIVDALKKST 85
I QIEYYFS NL RD FL+ ++ G++ ++ + F R+ +TT +I++ALK ST
Sbjct: 4 IKRQIEYYFSTENLERDFFLRRKMDL-QGFLPISLIAGFYRVQALTTNVDLILEALKDST 62
Query: 86 SKLIEVNEDGTKIRR 100
EV KIRR
Sbjct: 63 ----EVEIVDQKIRR 73
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 44.1 bits (105), Expect = 4e-06
Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 8/75 (10%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+L+V +P D T +++++ F K K+ ++ + ++ K KG FV F+++E
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFG----KVESVRLVRDKET----GKSKGFAFVEFESEE 52
Query: 181 NAEKFLNENKDKNLK 195
+AEK L K L
Sbjct: 53 DAEKALEALNGKELD 67
Score = 29.9 bits (68), Expect = 0.34
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 278 LKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPT--AFVRYKKENNAEAVLKAL 335
L + ++ + E++RE+ K + + + G+ AFV ++ E +AE L+AL
Sbjct: 2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61
Query: 336 GSKEIVIKDVKV 347
KE+ + +KV
Sbjct: 62 NGKELDGRPLKV 73
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 43.7 bits (104), Expect = 5e-06
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 10/74 (13%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
LYV+ +P T +D+++FF S K+ + + N+ + +G FV F + E+
Sbjct: 1 LYVRNLPPSVTEEDLREFF----SPYGKVEGVRLVR------NKDRPRGFAFVEFASPED 50
Query: 182 AEKFLNENKDKNLK 195
AE L + L
Sbjct: 51 AEAALKKLNGLVLD 64
Score = 27.9 bits (63), Expect = 1.9
Identities = 15/63 (23%), Positives = 26/63 (41%)
Query: 278 LKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKALGS 337
L + ++ V+ ED+RE + + + AFV + +AEA LK L
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 338 KEI 340
+
Sbjct: 61 LVL 63
>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 = 42.2 bits (100), Expect = 2e-05
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 11/68 (16%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNKE 180
L+V +P D T +D+KD F K I +I I+R+ + KG FV F+++E
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFG----PIESIRIVRD------ETGRSKGFAFVEFEDEE 50
Query: 181 NAEKFLNE 188
+AEK L
Sbjct: 51 DAEKALEA 58
Score = 27.2 bits (61), Expect = 3.1
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 278 LKISDIKEPVSREDIREVLEKV-QTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKALG 336
L + ++ + ED++++ K + IV E + AFV ++ E +AE L+AL
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 337 SKEI 340
KE+
Sbjct: 61 GKEL 64
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9),
which represent a group of nuclear RNA binding proteins
that are involved in pre-mRNA processing. GRSF-1 is a
cytoplasmic poly(A)+ mRNA binding protein which
interacts with RNA in a G-rich element-dependent manner.
It may function in RNA packaging, stabilization of RNA
secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2 (also
termed RBM35B) are epithelial-specific RNA binding
proteins that promote splicing of the epithelial variant
of fibroblast growth factor receptor 2 (FGFR2), ENAH
(also termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. Fusilli shows high sequence
homology to ESRPs. It can regulate endogenous FGFR2
splicing and functions as a splicing factor. The
biological roles of both, RBM12 and RBM12B, remain
unclear. RBM19 is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 41.4 bits (98), Expect = 4e-05
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 8/71 (11%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+ ++ +P AT +DI+DFF D+ I + D + G +V F + E+
Sbjct: 2 VRLRGLPFSATEEDIRDFFS---GLDIPPDGIHIVYDDDG-----RPTGEAYVEFASPED 53
Query: 182 AEKFLNENKDK 192
A + L ++ +K
Sbjct: 54 ARRALRKHNNK 64
>gnl|CDD|227520 COG5193, LHP1, La protein, small RNA-binding pol III transcript
stabilizing protein and related La-motif-containing
proteins involved in translation [Posttranslational
modification, protein turnover, chaperones /
Translation, ribosomal structure and biogenesis].
Length = 438
Score = 45.0 bits (106), Expect = 5e-05
Identities = 45/200 (22%), Positives = 89/200 (44%), Gaps = 18/200 (9%)
Query: 3 ETDSSATNGNSGAEAEVSKLENQIIEQIEYYFS-----DINLARDKFLQGEIKKD---DG 54
T+SS + ++++ ++Q+E+YFS D N +DKFL+ K+ D
Sbjct: 52 LTESSKSKKEDKNPSKLTSNTKWTLKQVEFYFSGSKDTDSNFPKDKFLKTTAPKNKKRDK 111
Query: 55 WVELTTMLKFARLAKMTTEAKVIVDALKKS-TSKLIEVNEDGTKIRRNPEKELPTFDIDF 113
WV + T+ F R+ + + AL+KS ++++EV+ G+ R ++L + +
Sbjct: 112 WVPIKTIATFNRMKNSGSPVSAVSGALRKSLDARVLEVSSSGSNKNRT--EKLISNNNK- 168
Query: 114 VKDLIAQSLYVKYIPVDATLDDIKDFFKKNTSEDVK----ITNIIMRNYQDKLANQKKFK 169
+ + +Y + + + +++ +RN +D L K F+
Sbjct: 169 STSQMQRDVYQNGFGKEDVNNASRPEQQEDLEIQFPPHYHAPPSQIRNRRDWL--NKNFR 226
Query: 170 GSIFVTFDNKENAEKFLNEN 189
GS+FV F A++F N
Sbjct: 227 GSVFVEFKYFREAQRFNNGF 246
Score = 30.8 bits (69), Expect = 1.4
Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 24 NQIIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKMTTEAKVIVDALKK 83
EQIEYYFS+ NL D+FL+ + KK G++ L+ + KF R + +I+ A+K+
Sbjct: 272 MAKKEQIEYYFSEENLKSDEFLRKKFKK-AGFIPLSFIGKFYRNLSFGGDKNLILAAMKE 330
Query: 84 S 84
Sbjct: 331 V 331
>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 = 40.4 bits (95), Expect = 8e-05
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
L+V +P D T +D+++ F K +I ++ + +D K KG FV F++ E+
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFG----EIESVRIVRDKDG-----KSKGFAFVEFESPED 51
Query: 182 AEKFLNENKDKNLK 195
AEK L K L
Sbjct: 52 AEKALEALNGKELD 65
Score = 34.2 bits (79), Expect = 0.012
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 278 LKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPT--AFVRYKKENNAEAVLKAL 335
L + ++ + ED+RE+ K + + + + G+ AFV ++ +AE L+AL
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKF-GEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEAL 59
Query: 336 GSKEIVIKDVKVS 348
KE+ + +KVS
Sbjct: 60 NGKELDGRKLKVS 72
>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen
(La or SS-B or LARP3), La-related protein 7 (LARP7 or
PIP7S) and similar proteins. This subfamily corresponds
to the RRM2 of La and LARP7. La is a highly abundant
nuclear phosphoprotein and well conserved in eukaryotes.
It specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. LARP7
is an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3' -UUU-OH)
of 7SK RNA. It is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP), intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. LARP7 plays an essential role in the inhibition
of positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
Both La and LARP7 contain an N-terminal La motif (LAM),
followed by two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 40.0 bits (94), Expect = 1e-04
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 275 GALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKA 334
G +LKI+ I V+REDI+ V + E+ +++F G T ++R+K A+ +A
Sbjct: 1 GVILKITSIGPGVTREDIKAVFAQFG----EVKYVDFTEGADTGYIRFKTPEAAQKAREA 56
Query: 335 LGSKEIVIKDVKVSIEVVT 353
K + ++ + +
Sbjct: 57 FVEKGEGLLGKEIKLSALE 75
>gnl|CDD|153405 cd08036, LARP_5, La RNA-binding domain of La-related protein 5.
This domain is found in vertebrate La-related protein 5
(LARP5). A variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding
proteins in eukaryotic cellular processes.
Length = 75
Score = 38.8 bits (90), Expect = 3e-04
Identities = 22/75 (29%), Positives = 43/75 (57%), Gaps = 3/75 (4%)
Query: 25 QIIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKMTTEAKVIVDALKKS 84
+ + +E+ S NLA D +L ++ D +V + T+ + K++T+ +IVD L+
Sbjct: 3 LLKKTLEFCLSRENLASDMYLISQMDSDQ-YVPIMTVANLDHIKKLSTDVDLIVDVLR-- 59
Query: 85 TSKLIEVNEDGTKIR 99
+ L++V+E G K+R
Sbjct: 60 SLPLVQVDEKGEKVR 74
>gnl|CDD|153404 cd08035, LARP_4, La RNA-binding domain of La-related protein 4.
This domain is found in vertebrate La-related protein 4
(LARP4), also known as c-MPL binding protein. La-type
domains often co-occur with RNA-recognition motifs
(RRMs). A variety of La-related proteins (LARPs or La
ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding
proteins in eukaryotic cellular processes.
Length = 75
Score = 38.5 bits (89), Expect = 3e-04
Identities = 23/72 (31%), Positives = 46/72 (63%), Gaps = 3/72 (4%)
Query: 28 EQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKMTTEAKVIVDALKKSTSK 87
+Q+E+ FS NL++D +L ++ D +V + T+ + K+TT+ +I+D L+ +S
Sbjct: 6 KQLEFCFSRENLSKDLYLISQMDSDQ-FVPIWTVANMEGIKKLTTDMDLILDVLR--SSP 62
Query: 88 LIEVNEDGTKIR 99
+++V+E G K+R
Sbjct: 63 MVQVDETGEKVR 74
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair
protein alkB homolog 8 (ALKBH8) and similar proteins.
This subfamily corresponds to the RRM of ALKBH8, also
termed alpha-ketoglutarate-dependent dioxygenase ABH8,
or S-adenosyl-L-methionine-dependent tRNA
methyltransferase ABH8, expressed in various types of
human cancers. It is essential in urothelial carcinoma
cell survival mediated by NOX-1-dependent ROS signals.
ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation of
tRNA modification. ALKBH8 localizes to the cytoplasm. It
contains the characteristic AlkB domain that is composed
of a tRNA methyltransferase motif, a motif homologous to
the bacterial AlkB DNA/RNA repair enzyme, and a
dioxygenase catalytic core domain encompassing
cofactor-binding sites for iron and 2-oxoglutarate. In
addition, unlike other AlkB homologs, ALKBH8 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal S-adenosylmethionine (SAM)-dependent
methyltransferase (MT) domain. .
Length = 80
Score = 35.7 bits (83), Expect = 0.004
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 4/63 (6%)
Query: 287 VSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKALGSKEIVIKDVK 346
VSRE++ V EK T + +V G+P FV Y +A A AL KE+ +
Sbjct: 15 VSREELLRVFEKYGTVED-LVMPP---GKPYCFVSYSSIEDAAAAYDALNGKELELPQQN 70
Query: 347 VSI 349
+
Sbjct: 71 KPL 73
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 35.0 bits (81), Expect = 0.007
Identities = 22/66 (33%), Positives = 27/66 (40%), Gaps = 8/66 (12%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
L+V +P D T +D+ F KN + R DK K KG FV FD E
Sbjct: 3 LFVGNLPYDTTAEDLLAHF-KNAGAPPSV-----RLLTDK--KTGKSKGCAFVEFDTAEA 54
Query: 182 AEKFLN 187
K L
Sbjct: 55 MTKALK 60
>gnl|CDD|178006 PLN02380, PLN02380, 1-acyl-sn-glycerol-3-phosphate acyltransferase.
Length = 376
Score = 35.9 bits (83), Expect = 0.033
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 8/56 (14%)
Query: 98 IRRNPEKELPTFDIDFVKDLIAQSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNI 153
I+R+ KELP D D IAQ ++ DA LD F ++T D + +I
Sbjct: 252 IKRHSMKELPETD-----DGIAQWCKDVFVAKDALLD---KHFAEDTFGDQEYQDI 299
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch
site protein p14 (SF3B14) and similar proteins. This
subfamily corresponds to the RRM of SF3B14 (also termed
p14), a 14 kDa protein subunit of SF3B which is a
multiprotein complex that is an integral part of the U2
small nuclear ribonucleoprotein (snRNP) and the U11/U12
di-snRNP. SF3B is essential for the accurate excision of
introns from pre-messenger RNA and has been involved in
the recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B14 associates directly
with another SF3B subunit called SF3B155. It is also
present in both U2- and U12-dependent spliceosomes and
may contribute to branch site positioning in both the
major and minor spliceosome. Moreover, SF3B14 interacts
directly with the pre-mRNA branch adenosine early in
spliceosome assembly and within the fully assembled
spliceosome. SF3B14 contains one well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 33.0 bits (76), Expect = 0.036
Identities = 14/63 (22%), Positives = 31/63 (49%), Gaps = 11/63 (17%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
LYV+ +P + +++ D F K + Q ++ N K+ +G+ FV +++ +
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAI-----------RQIRIGNTKETRGTAFVVYEDIYD 53
Query: 182 AEK 184
A+
Sbjct: 54 AKN 56
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ)
autosomal homologs, DAZL (DAZ-like) and BOULE. This
subfamily corresponds to the RRM domain of two Deleted
in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like)
and BOULE. BOULE is the founder member of the family and
DAZL arose from BOULE in an ancestor of vertebrates. The
DAZ gene subsequently originated from a duplication
transposition of the DAZL gene. Invertebrates contain a
single DAZ homolog, BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. The family members encode closely related
RNA-binding proteins that are required for fertility in
numerous organisms. These proteins contain an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a varying
number of copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 33.0 bits (76), Expect = 0.041
Identities = 28/81 (34%), Positives = 41/81 (50%), Gaps = 14/81 (17%)
Query: 118 IAQSLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTF 176
I ++V IP D T ++++DFF + + +DVKI D+ K G FVTF
Sbjct: 1 IPNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIIT-------DRAGVSK---GYGFVTF 50
Query: 177 DNKENAEKFLNENKDKNLKFN 197
+ +E+AEK L NL F
Sbjct: 51 ETQEDAEKIL---AMGNLNFR 68
>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing
factor Cwc2 and similar proteins. This subfamily
corresponds to the RRM of yeast protein Cwc2, also
termed Complexed with CEF1 protein 2, or
PRP19-associated complex protein 40 (Ntc40), or
synthetic lethal with CLF1 protein 3, one of the
components of the Prp19-associated complex [nineteen
complex (NTC)] that can bind to RNA. NTC is composed of
the scaffold protein Prp19 and a number of associated
splicing factors, and plays a crucial role in intron
removal during premature mRNA splicing in eukaryotes.
Cwc2 functions as an RNA-binding protein that can bind
both small nuclear RNAs (snRNAs) and pre-mRNA in vitro.
It interacts directly with the U6 snRNA to link the NTC
to the spliceosome during pre-mRNA splicing. In the
N-terminal half, Cwc2 contains a CCCH-type zinc finger
(ZnF domain), a RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and an intervening loop, also termed
RNA-binding loop or RB loop, between ZnF and RRM, all of
which are necessary and sufficient for RNA binding. The
ZnF is also responsible for mediating protein-protein
interaction. The C-terminal flexible region of Cwc2
interacts with the WD40 domain of Prp19.
Length = 78
Score = 32.6 bits (75), Expect = 0.042
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 278 LKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAE 329
L + IK + + I E+L + + +I I + AFVRYK +AE
Sbjct: 4 LYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSKGIAFVRYKYRASAE 55
>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation
initiation factor 4B (eIF-4B) and similar proteins.
This subfamily corresponds to the RRM of eIF-4B, a
multi-domain RNA-binding protein that has been primarily
implicated in promoting the binding of 40S ribosomal
subunits to mRNA during translation initiation. It
contains two RNA-binding domains; the N-terminal
well-conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), binds the 18S rRNA of the 40S ribosomal subunit
and the C-terminal basic domain (BD), including two
arginine-rich motifs (ARMs), binds mRNA during
initiation, and is primarily responsible for the
stimulation of the helicase activity of eIF-4A. eIF-4B
also contains a DRYG domain (a region rich in Asp, Arg,
Tyr, and Gly amino acids) in the middle, which is
responsible for both, self-association of eIF-4B and
binding to the p170 subunit of eIF3. Additional research
indicates that eIF-4B can interact with the poly(A)
binding protein (PABP) in mammalian cells, which can
stimulate both, the eIF-4B-mediated activation of the
helicase activity of eIF-4A and binding of poly(A) by
PABP. eIF-4B has also been shown to interact
specifically with the internal ribosome entry sites
(IRES) of several picornaviruses which facilitate
cap-independent translation initiation. .
Length = 77
Score = 32.0 bits (73), Expect = 0.084
Identities = 13/70 (18%), Positives = 36/70 (51%), Gaps = 8/70 (11%)
Query: 123 YVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKENA 182
Y+ +P D T +DIK+FF+ + ++++ + + + +G + F+++++
Sbjct: 5 YLGNLPYDVTEEDIKEFFR-----GLNVSSV---RLPREPGDPGRLRGFGYAEFEDRDSL 56
Query: 183 EKFLNENKDK 192
+ L+ N +
Sbjct: 57 LQALSLNDES 66
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM2 of RBM40 and the RRM of RBM41.
RBM40, also known as RNA-binding region-containing
protein 3 (RNPC3) or U11/U12 small nuclear
ribonucleoprotein 65 kDa protein (U11/U12-65K protein).
It serves as a bridging factor between the U11 and U12
snRNPs. It contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), connected by a linker that
includes a proline-rich region. It binds to the
U11-associated 59K protein via its RRM1 and employs the
RRM2 to bind hairpin III of the U12 small nuclear RNA
(snRNA). The proline-rich region might be involved in
protein-protein interactions. RBM41 contains only one
RRM. Its biological function remains unclear. .
Length = 82
Score = 31.8 bits (73), Expect = 0.099
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 8/71 (11%)
Query: 120 QSLYVKYIPVDATLDDIKDFFKK--NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFD 177
+ LYVK + T +D+ F + ++S + K I +L + + KG FVTF
Sbjct: 2 KRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDI------RLMTEGRMKGQAFVTFP 55
Query: 178 NKENAEKFLNE 188
++E A K LN
Sbjct: 56 SEEIATKALNL 66
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM1 of RBM40, also known as
RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of the
U12 small nuclear RNA (snRNA). The proline-rich region
might be involved in protein-protein interactions. .
Length = 73
Score = 31.1 bits (71), Expect = 0.14
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 11/66 (16%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+L V+++P + + DD +D K + V++ ++ + K K + F TFDN++
Sbjct: 1 TLLVRHLPPELSEDDKEDLLKHFGASSVRV-----------MSRRGKLKNTAFATFDNEQ 49
Query: 181 NAEKFL 186
A + L
Sbjct: 50 AASQAL 55
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 31.0 bits (71), Expect = 0.19
Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 8/74 (10%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
LYV +P + T +D+KD F + +V +I D+ + +G FV + E
Sbjct: 2 LYVGNLPYNVTEEDLKDLFGQ--FGEVTSARVIT----DRET--GRSRGFGFVEMETAEE 53
Query: 182 AEKFLNENKDKNLK 195
A + + +
Sbjct: 54 ANAAIEKLNGTDFG 67
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 33.8 bits (77), Expect = 0.19
Identities = 37/163 (22%), Positives = 64/163 (39%), Gaps = 22/163 (13%)
Query: 228 LIKWQQEYHEEKKQE------VRSKRDKSKKSTEGDGEGNTEGSKQ--VVLELPTGALLK 279
LI+ + ++ + RD+ K + E G+ Q + E PT + K
Sbjct: 119 LIEEAHAAARDIPEKRIDDEIIEEVRDQVKVYAKKAKECPHCGAPQHELEFEEPTIFIEK 178
Query: 280 ISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKALGSKE 339
+ + +IR++ EK+ DD E++ + P V L+A
Sbjct: 179 TEIEEHRLLPIEIRDIFEKIIDDDLELIGFDPKKARPEWAV-----------LQAFLVPP 227
Query: 340 IVIKDVKVSIEVVTGEEEQTVLDRMKIDIFKRRQKLMNEKKSG 382
+ + SI + TGE + L + +DI K QKL K +G
Sbjct: 228 LT---ARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAG 267
>gnl|CDD|233678 TIGR01998, PTS-II-BC-nag, PTS system, N-acetylglucosamine-specific
IIBC component. This model represents the combined B
and C domains of the PTS transport system enzyme II
specific for N-acetylglucosamine transport. Many of the
genes in this family also include an A domain as part of
the same polypeptide and thus should be given the name
"PTS system, N-acetylglucosamine-specific IIABC
component". This family is most closely related to the
glucose-specific PTS enzymes [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 476
Score = 33.6 bits (77), Expect = 0.21
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 329 EAVLKALGSKEIVIKDVKVSIEVVTGEEEQTVLDRMK 365
E LKALG++ +V +++V+ G + V MK
Sbjct: 441 EPALKALGARGVVKLGKH-NLQVILGPLAEIVAGEMK 476
>gnl|CDD|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subfamily
corresponds to the RRM2 of GRSF-1, a cytoplasmic
poly(A)+ mRNA binding protein which interacts with RNA
in a G-rich element-dependent manner. It may function in
RNA packaging, stabilization of RNA secondary structure,
or other macromolecular interactions. GRSF-1 contains
three potential RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 30.9 bits (70), Expect = 0.21
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 8/65 (12%)
Query: 127 IPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKENAEKFL 186
+P T DDI DFF+ D + ++ R + + G +V F E A K L
Sbjct: 9 LPYSCTEDDIIDFFRGLDIVDDGVVIVLNR--------RGRKTGEAYVQFATPEMANKAL 60
Query: 187 NENKD 191
++++
Sbjct: 61 LKHRE 65
>gnl|CDD|240842 cd12396, RRM1_Nop13p_fungi, RNA recognition motif 1 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM1 of Nop13p encoded
by YNL175c from Saccharomyces cerevisiae. It shares high
sequence similarity with nucleolar protein 12 (Nop12p).
Both, Nop12p and Nop13p, are not essential for growth.
However, unlike Nop12p that is localized to the
nucleolus, Nop13p localizes primarily to the nucleolus
but is also present in the nucleoplasm to a lesser
extent. Nop13p contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 85
Score = 30.6 bits (69), Expect = 0.34
Identities = 13/62 (20%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDV---KITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
+++ + T + ++ FF + + + +IT + M + + K K+ KG +V F +
Sbjct: 1 VWIGNLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYVDFTS 60
Query: 179 KE 180
+E
Sbjct: 61 QE 62
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein
7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S), an
oligopyrimidine-binding protein that binds to the highly
conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK
RNA. LARP7 is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP). It intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. It plays an essential role in the inhibition of
positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
LARP7 contains a La motif (LAM) and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the N-terminal region,
which mediates binding to the U-rich 3' terminus of 7SK
RNA. LARP7 also carries another putative RRM domain at
its C-terminus. .
Length = 80
Score = 29.6 bits (67), Expect = 0.56
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 8/63 (12%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+YV+ +P +AT + +K F K + + + + Y+ KG F+ F+ E
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGT----VVYVSLPRYKHT----GDIKGFAFIEFETPEE 53
Query: 182 AEK 184
A+K
Sbjct: 54 AQK 56
>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM1 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 mammals, 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 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 = 29.4 bits (67), Expect = 0.62
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 8/75 (10%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
SLYV + D T + + F S + +I R +D ++ G +V F N
Sbjct: 1 SLYVGDLHPDVTEAMLYEIF----SPAGPVLSI--RVCRD--LITRRSLGYAYVNFQNPA 52
Query: 181 NAEKFLNENKDKNLK 195
+AE+ L+ +K
Sbjct: 53 DAERALDTLNFDVIK 67
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 71
Score = 29.2 bits (66), Expect = 0.77
Identities = 15/68 (22%), Positives = 31/68 (45%), Gaps = 13/68 (19%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
++V + D T +D++ +F + +T++ + K F+ FVTF + E
Sbjct: 3 VFVGRLTEDMTEEDLRQYFSQFGE----VTDVYI---------PKPFRAFAFVTFADPEV 49
Query: 182 AEKFLNEN 189
A+ E+
Sbjct: 50 AQSLCGED 57
>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. This subfamily corresponds to the
RRM1 of PHIP1. A. thaliana PHIP1 and its homologs
represent a novel class of plant-specific RNA-binding
proteins that may play a unique role in the polarized
mRNA transport to the vicinity of the cell plate. The
family members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein and
is localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 28.9 bits (65), Expect = 0.83
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 8/66 (12%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+YV IP +T D+I+ +F S +I + + + D +F+G F+TF +E
Sbjct: 1 VYVGGIPYYSTEDEIRSYF----SYCGEIEELDLMTFPD----TGRFRGIAFITFKTEEA 52
Query: 182 AEKFLN 187
A++ L
Sbjct: 53 AKRALA 58
>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 = 28.9 bits (65), Expect = 0.87
Identities = 14/68 (20%), Positives = 28/68 (41%), Gaps = 8/68 (11%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
L+V + DA D I + F + ++ + + + KG +V F ++E
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYG--EISSVRLPTD------PDSGRPKGFGYVEFSSQEA 52
Query: 182 AEKFLNEN 189
A+ L+
Sbjct: 53 AQAALDAL 60
>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen;
Provisional.
Length = 1136
Score = 31.3 bits (70), Expect = 1.0
Identities = 44/192 (22%), Positives = 89/192 (46%), Gaps = 8/192 (4%)
Query: 143 NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKENAEKFLNENKDKNLKFN--ENC 200
N + ++ + N ++N + + K + D +EN E+ EN ++N++ N EN
Sbjct: 916 NIAHEINLINKELKNQNENVPEHLKEHAEANIEEDAEENVEEDAEENVEENVEENVEENV 975
Query: 201 EHKNAEKFLNENKDKNLKFN--ENCEHSLLIKWQQEYHEEKKQEVRSKRDKSKKSTEGDG 258
E +N E+ + EN ++N++ N EN E ++ ++ E ++ V +++ + E +
Sbjct: 976 E-ENVEENVEENVEENVEENVEENVEENIEENVEENVEENIEENVEEYDEENVEEVEENV 1034
Query: 259 EGNTEGSKQVVLE-LPTGALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPT 317
E E + + + E I + E E++ E+ E ++ + +E V E NV E
Sbjct: 1035 EEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEIEENIEENIEENV--EENVEENV 1092
Query: 318 AFVRYKKENNAE 329
+ E N E
Sbjct: 1093 EEIEENVEENVE 1104
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins. This
subfamily includes the RRM1 and RRM2 of RNA-binding
protein 5 (RBM5 or LUCA15 or H37) and RNA-binding
protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding
protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs
share high sequence homology and may play an important
role in regulating apoptosis. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor. RBM6 has been predicted to be a
nuclear factor based on its nuclear localization signal.
Both, RBM6 and RBM5, specifically bind poly(G) RNA.
RBM10 is a paralog of RBM5. It may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. All family
members contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 84
Score = 29.1 bits (66), Expect = 1.1
Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 120 QSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDN 178
+L ++ + + T +DI S V I ++ ++R DKL + G FV F +
Sbjct: 3 NTLILRGLDLLTTEEDILQALSAIAS--VPIKDVRLIR---DKLTGTSR--GFAFVEFPS 55
Query: 179 KENAEKFLNENK 190
E+A ++++
Sbjct: 56 LEDATQWMDALN 67
>gnl|CDD|237275 PRK13022, secF, preprotein translocase subunit SecF; Reviewed.
Length = 289
Score = 30.9 bits (71), Expect = 1.1
Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 8/81 (9%)
Query: 275 GALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAF-VR--YKKENNAEAV 331
G ++++ ++P E +RE LEK +D ++ N G +R E +E V
Sbjct: 42 GTVIEVR-FEQPADLEQVREALEKAGFEDAQVQ----NFGSSRDVLIRLPPASEELSEKV 96
Query: 332 LKALGSKEIVIKDVKVSIEVV 352
KAL +E V
Sbjct: 97 KKALNKAYGPNDAEVRRVEFV 117
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation
initiation factor 3 subunit B (eIF-3B) and similar
proteins. This subfamily corresponds to the RRM domain
in eukaryotic translation initiation factor 3 (eIF-3), a
large multisubunit complex that plays a central role in
the initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3
subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or
eIF-3 p116, is the major scaffolding subunit of eIF-3.
It interacts with eIF-3 subunits A, G, I, and J. eIF-3B
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is involved in the
interaction with eIF-3J. The interaction between eIF-3B
and eIF-3J is crucial for the eIF-3 recruitment to the
40 S ribosomal subunit. eIF-3B also binds directly to
domain III of the internal ribosome-entry site (IRES)
element of hepatitis-C virus (HCV) RNA through its
N-terminal RRM, which may play a critical role in both
cap-dependent and cap-independent translation.
Additional research has shown that eIF-3B may function
as an oncogene in glioma cells and can be served as a
potential therapeutic target for anti-glioma therapy.
This family also includes the yeast homolog of eIF-3
subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that
interacts with the yeast homologs of eIF-3 subunits
A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In
yeast, eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A (TIF32)
and eIF-3J (HCR1). In contrast to its human homolog,
yeast eIF-3B (PRT1) may have potential to bind its total
RNA through its RRM domain. .
Length = 84
Score = 28.7 bits (65), Expect = 1.2
Identities = 24/78 (30%), Positives = 32/78 (41%), Gaps = 13/78 (16%)
Query: 127 IPV--DATLDDIKDFFKK--NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKENA 182
+PV + L+ +K +K + KI I M + K KG FV F E A
Sbjct: 9 LPVVGEEKLEKLKKVLRKIFSKFGVGKIVGIYM-----PVDETGKTKGYAFVEFATPEEA 63
Query: 183 E---KFLNENK-DKNLKF 196
+ K LN K DK F
Sbjct: 64 KEAVKALNGYKLDKKHTF 81
>gnl|CDD|132527 TIGR03488, cas_Cas5p, CRISPR-associated protein Cas5, subtype
PGING. CC Members of this protein family are cas, or
CRISPR-associated, proteins. The two sequences in the
alignment seed are found within cas gene clusters that
are adjacent to CRISPR DNA repeats in two members of the
order Bacteroidales, Porphyromonas gingivalis W83 and
Bacteroides forsythus ATCC 43037. This cas protein
family is unique to the Pgingi (Porphyromonas
gingivalis) subtype, but shows some sequence similarity
to genes of the Cas5 type (see TIGR02593).
Length = 237
Score = 30.7 bits (69), Expect = 1.3
Identities = 24/119 (20%), Positives = 50/119 (42%), Gaps = 1/119 (0%)
Query: 97 KIRRNPEKELPTFDIDFVKDLIAQSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMR 156
K R +K++ K I ++ +IP+ D+ D + E ++ R
Sbjct: 63 KDREAIQKDIEKIRKKQKKGHIPNTIGSIFIPLLMDFFDLDDQPIIDFDEPCFFNDLWKR 122
Query: 157 NYQDKLANQKKFKGSIFVTFDNKENAEKFLNENKDKNLKFNENCEHKNAEKFLNENKDK 215
++ A + F G+ + + + KF+ EN+ ++ + + ++ EKF EN D
Sbjct: 123 AFRRADAGKIHFGGTENIDYRLIMDKFKFMCENE-RDEENEDKIDNHALEKFFKENIDF 180
>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras
GTPase-activating protein-binding protein G3BP1, G3BP2
and similar proteins. This subfamily corresponds to the
RRM domain in the G3BP family of RNA-binding and SH3
domain-binding proteins. G3BP acts at the level of RNA
metabolism in response to cell signaling, possibly as
RNA transcript stabilizing factors or an RNase. Members
include G3BP1, G3BP2 and similar proteins. These
proteins associate directly with the SH3 domain of
GTPase-activating protein (GAP), which functions as an
inhibitor of Ras. They all contain an N-terminal nuclear
transfer factor 2 (NTF2)-like domain, an acidic domain,
a domain containing PXXP motif(s), an RNA recognition
motif (RRM), and an Arg-Gly-rich region (RGG-rich
region, or arginine methylation motif).
Length = 81
Score = 28.5 bits (64), Expect = 1.3
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 10/68 (14%)
Query: 120 QSLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
L+V +P D T D++K+FFK+ +V+I + + FV FD+
Sbjct: 4 HQLFVGNLPHDITEDELKEFFKEFGNVLEVRI---------NSKGGGGRLPNFGFVVFDD 54
Query: 179 KENAEKFL 186
E +K L
Sbjct: 55 PEAVQKIL 62
>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit G (eIF-3G) and
similar proteins. This subfamily corresponds to the RRM
of eIF-3G and similar proteins. eIF-3G, also termed
eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or
eIF3-p44, is the RNA-binding subunit of eIF3, a large
multisubunit complex that plays a central role in the
initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and
beta-globin mRNA, and therefore appears to be a
nonspecific RNA-binding protein. eIF-3G is one of the
cytosolic targets and interacts with mature
apoptosis-inducing factor (AIF). eIF-3G contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). This family
also includes yeast eIF3-p33, a homolog of vertebrate
eIF-3G, plays an important role in the initiation phase
of protein synthesis in yeast. It binds both, mRNA and
rRNA, fragments due to an RRM near its C-terminus. .
Length = 77
Score = 28.3 bits (64), Expect = 1.4
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 12/66 (18%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNY--QDKLANQKKFKGSIFVTFDN 178
++ V + DA DD+++ F+ I R Y +DK Q + G FVTF
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGP--------ISRVYLAKDKETGQSR--GFAFVTFHT 50
Query: 179 KENAEK 184
+E+AE+
Sbjct: 51 REDAER 56
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 28.5 bits (64), Expect = 1.5
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
L+++ + T +D++ F K ++ + + DKL KK KG FVT+ E+
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGP----LSEVHLP--IDKLT--KKPKGFAFVTYMIPEH 56
Query: 182 AEKFLNE 188
A K E
Sbjct: 57 AVKAFAE 63
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic
RNA-binding protein RBM24, RBM38 and similar proteins.
This subfamily corresponds to the RRM of RBM24 and RBM38
from vertebrate, SUPpressor family member SUP-12 from
Caenorhabditis elegans and similar proteins. Both, RBM24
and RBM38, are preferentially expressed in cardiac and
skeletal muscle tissues. They regulate myogenic
differentiation by controlling the cell cycle in a
p21-dependent or -independent manner. RBM24, also termed
RNA-binding region-containing protein 6, interacts with
the 3'-untranslated region (UTR) of myogenin mRNA and
regulates its stability in C2C12 cells. RBM38, also
termed CLL-associated antigen KW-5, or HSRNASEB, or
RNA-binding region-containing protein 1(RNPC1), or
ssDNA-binding protein SEB4, is a direct target of the
p53 family. It is required for maintaining the stability
of the basal and stress-induced p21 mRNA by binding to
their 3'-UTRs. It also binds the AU-/U-rich elements in
p63 3'-UTR and regulates p63 mRNA stability and
activity. SUP-12 is a novel tissue-specific splicing
factor that controls muscle-specific splicing of the
ADF/cofilin pre-mRNA in C. elegans. All family members
contain a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 28.3 bits (64), Expect = 1.5
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 12/69 (17%)
Query: 122 LYVKYIPVDATLDDIKDFFKK--NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
++V +P T D ++ +F + E V IT+ K +G FVTF +K
Sbjct: 3 IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITD----------RQTGKSRGYGFVTFKDK 52
Query: 180 ENAEKFLNE 188
E+AE+ +
Sbjct: 53 ESAERACKD 61
>gnl|CDD|232982 TIGR00457, asnS, asparaginyl-tRNA synthetase. In a multiple
sequence alignment of representative asparaginyl-tRNA
synthetases (asnS), archaeal/eukaryotic type
aspartyl-tRNA synthetases (aspS_arch), and bacterial
type aspartyl-tRNA synthetases (aspS_bact), there is a
striking similarity between asnS and aspS_arch in gap
pattern and in sequence, and a striking divergence of
aspS_bact. Consequently, a separate model was built for
each of the three groups. This model, asnS, represents
asparaginyl-tRNA synthetases from the three domains of
life. Some species lack this enzyme and charge tRNA(asn)
by misacylation with Asp, followed by transamidation of
Asp to Asn [Protein synthesis, tRNA aminoacylation].
Length = 453
Score = 30.4 bits (69), Expect = 1.6
Identities = 26/98 (26%), Positives = 40/98 (40%), Gaps = 16/98 (16%)
Query: 114 VKDLIA-QSLYVKYIPVDATLDDIKD---FFKKNTSEDVKIT--NIIMRN-----YQDKL 162
+ DL+ +KYI + A L++ F +KN +D+ NII Y D +
Sbjct: 246 LNDLLQLAETLIKYI-IKAVLENCSQELKFLEKNFDKDLIKRLENIINNKFARITYTDAI 304
Query: 163 A----NQKKFKGSIFVTFDNKENAEKFLNENKDKNLKF 196
+ K F+ F D + E+FL E K F
Sbjct: 305 EILKESDKNFEYEDFWGDDLQTEHERFLAEEYFKPPVF 342
>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 82
Score = 28.3 bits (64), Expect = 1.7
Identities = 21/64 (32%), Positives = 37/64 (57%), Gaps = 8/64 (12%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+++++ +P DAT +++K+ F + +VK I+ DKL KG+ FV F KE
Sbjct: 2 TVFIRNLPFDATEEELKELFSQ--FGEVKYARIVK----DKLT--GHSKGTAFVKFKTKE 53
Query: 181 NAEK 184
+A+K
Sbjct: 54 SAQK 57
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and plant
flowering time control protein FCA. This subfamily
corresponds to the RRM1 and RRM2 domains of the CUGBP1
and ETR-3-like factors (CELF) as well as plant flowering
time control protein FCA. CELF, also termed BRUNOL
(Bruno-like) proteins, is a family of structurally
related RNA-binding proteins involved in regulation of
pre-mRNA splicing in the nucleus, and control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also known as
BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known
as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also
known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4
(BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (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.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 28.3 bits (64), Expect = 1.7
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 10/64 (15%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L+V +P AT +D++ F++ E+V I +R DK Q K G FV F ++E
Sbjct: 2 LFVGQLPKTATEEDVRALFEEYGNIEEVTI----IR---DKDTGQSK--GCAFVKFSSRE 52
Query: 181 NAEK 184
A+K
Sbjct: 53 EAQK 56
>gnl|CDD|220945 pfam11019, DUF2608, Protein of unknown function (DUF2608). This
family is conserved in Bacteria. The function is not
known.
Length = 251
Score = 30.3 bits (69), Expect = 1.7
Identities = 36/189 (19%), Positives = 64/189 (33%), Gaps = 25/189 (13%)
Query: 22 LENQIIEQIEYYFSDINL--ARDKFLQGEIKKDDGW--VELTTMLKFARLAKMTTEAKV- 76
L++ ++ E S I K + + + +L E+ V
Sbjct: 27 LDDTLLTPKEPLGSSIWYQWRLGKLQKLLASESKAVEKIFEEWILISELRKMELIESDVP 86
Query: 77 -IVDALKKSTSKLIEVNEDGTKIRRNPEKELPTFDIDFVKDLIAQSLYVKYIPVDATLDD 135
+++ L+ ++ + E + +EL IDF + ++K+ D+ L
Sbjct: 87 SLINKLQNKGITVLGLTERPPNMESWTLRELKRLGIDFSSSSFPEDGFIKFPVTDSALSR 146
Query: 136 IKDFFKKNTSEDVKITNIIMRNYQDK-------LAN-QKKFKGSIFVTFDNKENAEKFLN 187
F+K I+ +K L + K IFV DNKEN E
Sbjct: 147 APVFYK----------GILFTGGLNKGEMLKYFLDKTNQSPKKIIFVD-DNKENLESMGE 195
Query: 188 ENKDKNLKF 196
K N+ F
Sbjct: 196 ACKKANILF 204
>gnl|CDD|202558 pfam03159, XRN_N, XRN 5'-3' exonuclease N-terminus. This family
aligns residues towards the N-terminus of several
proteins with multiple functions. The members of this
family all appear to possess 5'-3' exonuclease activity
EC:3.1.11.-. Thus, the aligned region may be necessary
for 5' to 3' exonuclease function. The family also
contains several Xrn1 and Xrn2 proteins. The 5'-3'
exoribonucleases Xrn1p and Xrn2p/Rat1p function in the
degradation and processing of several classes of RNA in
Saccharomyces cerevisiae. Xrn1p is the main enzyme
catalyzing cytoplasmic mRNA degradation in multiple
decay pathways, whereas Xrn2p/Rat1p functions in the
processing of rRNAs and small nucleolar RNAs (snoRNAs)
in the nucleus.
Length = 237
Score = 30.0 bits (68), Expect = 2.1
Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 10/77 (12%)
Query: 157 NYQDKLANQKKFKGSIFVTFD--------NKENAEKFLN--ENKDKNLKFNENCEHKNAE 206
Y D+L N + + +++ D N++ + +F + K+K + EN E E
Sbjct: 65 EYIDRLFNIVRPRKLLYMAIDGVAPRAKMNQQRSRRFRAAKDAKEKEAEAEENREELETE 124
Query: 207 KFLNENKDKNLKFNENC 223
K + KF+ NC
Sbjct: 125 GIKLPEKVEKEKFDSNC 141
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'.
This family consists of the archaeal A' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein.
Length = 867
Score = 30.5 bits (69), Expect = 2.2
Identities = 30/117 (25%), Positives = 50/117 (42%), Gaps = 14/117 (11%)
Query: 266 KQVVLELPTGALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKE 325
K++ E PT + + ++ +IRE LEK+ +D E++ I V P
Sbjct: 152 KKIKFEKPTYFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEW------- 204
Query: 326 NNAEAVLKALGSKEIVIKDVKVSIEVVTGEEEQTVLDRMKIDIFKRRQKLMNEKKSG 382
VL L + V+ SI + TGE + L +DI + Q+L ++G
Sbjct: 205 ----MVLTVLPVPPVT---VRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAG 254
>gnl|CDD|241107 cd12663, RRM1_RAVER1, RNA recognition motif 1 in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM1 of raver-1, 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-1 contains 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
PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB
through the PTB-binding motifs at its C-terminal half,
and binds to other partners, such as RNA having the
sequence UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the sequence
UCAUGCAGUCUG with micromolar affinity is found in
vinculin mRNA. Additional research indicates that the
RRM1 of raver-1 directs its interaction with the tail
domain of activated vinculin. Then the raver1/vinculin
tail (Vt) complex binds to vinculin mRNA, which is
permissive for vinculin binding to F-actin. .
Length = 71
Score = 27.6 bits (61), Expect = 2.4
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 154 IMRNYQDKLANQKKFKGSIFVTFDNKENAEKFLNE 188
++ +Y+ K K+KG+ FVT N E AE + E
Sbjct: 20 LLGDYELKYCFVDKYKGTAFVTLLNGEQAESAIKE 54
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of 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 functions 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 = 74
Score = 27.7 bits (61), Expect = 2.5
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 315 EPTAFVRYKKENNAEAVLKALGSKEIVIKDVKVS 348
+P FV + + +A A L A+ ++I+ K+VKV+
Sbjct: 39 DPYCFVEFFEHRHAAASLAAMNGRKIMGKEVKVN 72
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 28.3 bits (64), Expect = 2.5
Identities = 23/75 (30%), Positives = 31/75 (41%), Gaps = 10/75 (13%)
Query: 127 IPVDATLDDIKDFFKKNTSEDVKITNI------IMRNYQDKLAN-QKKFKGSIFVTFDNK 179
+P +K+ F K SE IMR+ + N + K KG FV F N
Sbjct: 8 LPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTNH 67
Query: 180 ENAEKFL---NENKD 191
E+A K L N N +
Sbjct: 68 EHALKALRALNNNPE 82
>gnl|CDD|224397 COG1480, COG1480, Predicted membrane-associated HD superfamily
hydrolase [General function prediction only].
Length = 700
Score = 30.0 bits (68), Expect = 2.5
Identities = 32/164 (19%), Positives = 66/164 (40%), Gaps = 11/164 (6%)
Query: 20 SKLENQIIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKMTTEAKV--- 76
+++ I++ + +F IN + + E + + ++ LK RL + T +
Sbjct: 87 AEITQNIVQLYQNFFDAINEVKRSLEENEDENTEYSLKQVKQLK-DRLLRDTNTVDISEE 145
Query: 77 -IVDALKKSTSKLIEVNEDG--TKIRRNPEKELPTFDIDFVKDLIAQSLYVKYIP---VD 130
I+ L+ S+ + + +D T++ +P + K I L + +P +D
Sbjct: 146 RILTLLELD-SEDLNLTQDTIITEVENAMGNGIPAGILSKAKSSIVILLVQETVPSQALD 204
Query: 131 ATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFV 174
A + + K N D + T + + K+ K KG I V
Sbjct: 205 AATEILNSALKPNYVYDEEQTENLRQEALSKVEPVKISKGQIIV 248
>gnl|CDD|130782 TIGR01721, AMN-like, AMP nucleosidase, putative. The sequences in
the clade represented by this model are most closely
related to the AMP nucleosidase found in TIGR01717.
These sequences are found only in Chlamydia and
Porphyromonas and differ sufficiently from the
characterized AMP nucleosidase to put some doubt on
assignment of this name.
Length = 266
Score = 29.5 bits (66), Expect = 2.9
Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 15/95 (15%)
Query: 213 KDKNLKFNENCEHSLLIK-WQQEYHEEKKQEVRSKRDKSKKSTEGDGEGNTEGSKQVVLE 271
++K ++ H+ I+ W E++++ + ++ K+ + E T +
Sbjct: 146 ENKGKDYHIGITHTTNIRFW--EFNKKFRDKLYET-----KAQGVEMECATLFTAGYRRN 198
Query: 272 LPTGALLKISDIKEPVSREDIREVLEKVQTDDQEI 306
LP GALL ISD+ P+ E I K + DQ +
Sbjct: 199 LPXGALLLISDL--PLRPEGI-----KTKESDQLV 226
>gnl|CDD|235270 PRK04286, PRK04286, hypothetical protein; Provisional.
Length = 298
Score = 29.6 bits (67), Expect = 2.9
Identities = 23/94 (24%), Positives = 42/94 (44%), Gaps = 15/94 (15%)
Query: 262 TEGSK-----QVVLELPTGALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEP 316
+GSK V + + + SD++ P++ E + +LEK ++V I G P
Sbjct: 160 ADGSKLGYVIMVRISDGDESFVFASDVQGPLNDEAVEFILEK----KPDVVIIG---GPP 212
Query: 317 TAFVRYK-KENNAEAVLKALGSKEIVIKDVKVSI 349
T + + E + E ++ L +EIV + I
Sbjct: 213 TYLLGRRLSEEDLEKGIENL--EEIVKNTPETLI 244
>gnl|CDD|179427 PRK02471, PRK02471, bifunctional glutamate--cysteine
ligase/glutathione synthetase; Provisional.
Length = 752
Score = 29.9 bits (68), Expect = 3.2
Identities = 16/37 (43%), Positives = 20/37 (54%)
Query: 278 LKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVG 314
L IS KEP S ED + LE +D ++ EF VG
Sbjct: 538 LGISIFKEPASLEDYEKALEIAFREDSSVLVEEFIVG 574
>gnl|CDD|240952 cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif 2 in epithelial
splicing regulatory protein ESRP1, ESRP2, Drosophila
RNA-binding protein Fusilli and similar proteins. This
subfamily corresponds to the RRM2 of ESRPs and Fusilli.
ESRP1 (also termed RBM35A) and ESRP2 (also termed
RBM35B) are epithelial-specific RNA binding proteins
that promote splicing of the epithelial variant of the
fibroblast growth factor receptor 2 (FGFR2), ENAH (also
termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. They are highly conserved
paralogs and specifically bind to GU-rich binding site.
ESRP1 and ESRP2 contain three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes
Drosophila fusilli (fus) gene encoding RNA-binding
protein Fusilli.Loss of fusilli activity causes
lethality during embryogenesis in flies. Drosophila
Fusilli can regulate endogenous FGFR2 splicing and
functions as a splicing factor. It shows high sequence
homology to ESRPs and contains three RRMs as well. It
also has an N-terminal domain with unknown function and
a C-terminal domain particularly rich in alanine,
glutamine, and serine. .
Length = 80
Score = 27.3 bits (61), Expect = 3.4
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 13/69 (18%)
Query: 127 IPVDATLDDIKDFFKKNTSEDVKITN----IIMRNYQDKLANQKKFKGSIFVTFDNKENA 182
+P AT DI FF + I+ D G FV F+ +E+A
Sbjct: 9 LPYSATAADILAFFG----GLCPVVGGPDGILFVTGPDGRPT-----GDAFVLFETEEDA 59
Query: 183 EKFLNENKD 191
++ L ++K+
Sbjct: 60 QRALGKHKE 68
>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional.
Length = 1832
Score = 29.7 bits (67), Expect = 3.6
Identities = 21/89 (23%), Positives = 35/89 (39%), Gaps = 1/89 (1%)
Query: 168 FKGSIFVTFDNKENAEKFLNENKDKNLKF-NENCEHKNAEKFLNENKDKNLKFNENCEHS 226
G+ V + + F+ N+ K+++ N N E K DK K N S
Sbjct: 1492 LNGNENVNKKINQKKKGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNLESVLS 1551
Query: 227 LLIKWQQEYHEEKKQEVRSKRDKSKKSTE 255
K +E + E + R + + K +TE
Sbjct: 1552 NQEKNIEEDYAESDIKKRKNKKQYKSNTE 1580
>gnl|CDD|241190 cd12746, RRM2_RBM12B, RNA recognition motif 2 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM2 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role remains
unclear. .
Length = 78
Score = 27.4 bits (61), Expect = 3.6
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 10/61 (16%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
L+++ +P T D+++DFF + V I ++N + G+ V F KE+
Sbjct: 2 LFLRGLPFSVTEDNVRDFFSGLKVDGV----IFLKNRRG------LNNGNSMVKFATKED 51
Query: 182 A 182
A
Sbjct: 52 A 52
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM1
of nucleolysin TIAR, also termed TIA-1-related protein,
and 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 = 81
Score = 27.4 bits (60), Expect = 4.0
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 310 EFNVGEPTAFVRYKKENNAEAVLKALGSKEIVIKDVKVS 348
E +P FV + + +A A L A+ ++I+ K+VKV+
Sbjct: 34 EHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN 72
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the RRM
of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or
splicing component, 35 kDa (splicing factor SC35 or
SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of pre-mRNA.
It is also involved in transcription elongation by
directly or indirectly mediating the recruitment of
elongation factors to the C-terminal domain of
polymerase II. SRSF2 is exclusively localized in the
nucleus and is restricted to nuclear processes. 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. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory elements
on the pre-mRNA. The RS domain modulates SRSF2 activity
through phosphorylation, directly contacts RNA, and
promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 26.9 bits (60), Expect = 4.0
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 10/76 (13%)
Query: 278 LKISDIKEPVSREDIREVLEKVQTDDQEI--VFI--EFNVGEPT--AFVRYKKENNAEAV 331
LK+ ++ + +D+R V EK E+ V+I + E AFVR+ + +AE
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYG----EVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDA 56
Query: 332 LKALGSKEIVIKDVKV 347
+ A+ KE+ ++++V
Sbjct: 57 MDAMDGKELDGRELRV 72
>gnl|CDD|181076 PRK07671, PRK07671, cystathionine beta-lyase; Provisional.
Length = 377
Score = 29.3 bits (66), Expect = 4.1
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 265 SKQVVLELPTGALLKISDIKE 285
+K + +E PT LLKI+DIK+
Sbjct: 135 TKAIYVETPTNPLLKITDIKK 155
>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 = 26.9 bits (60), Expect = 4.3
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 318 AFVRYKKENNAEAVLKALGSKEIVIKDVKVS 348
FV Y EN+A+ + L EI K +KVS
Sbjct: 45 GFVDYVDENDAQKAINTLNGFEIRNKRLKVS 75
>gnl|CDD|176500 cd08557, PI-PLCc_bacteria_like, Catalytic domain of bacterial
phosphatidylinositol-specific phospholipase C and
similar proteins. This subfamily corresponds to the
catalytic domain present in bacterial
phosphatidylinositol-specific phospholipase C (PI-PLC,
EC 4.6.1.13) and their sequence homologs found in
eukaryota. Bacterial PI-PLCs participate in
Ca2+-independent PI metabolism, hydrolyzing the membrane
lipid phosphatidylinositol (PI) to produce
phosphorylated myo-inositol and diacylglycerol (DAG).
Although their precise physiological function remains
unclear, bacterial PI-PLCs may function as virulence
factors in some pathogenic bacteria. Bacterial PI-PLCs
contain a single TIM-barrel type catalytic domain. Its
catalytic mechanism is based on general base and acid
catalysis utilizing two well conserved histidines, and
consists of two steps, a phosphotransfer and a
phosphodiesterase reaction. Eukaryotic homologs in this
family are named as phosphatidylinositol-specific
phospholipase C X domain containing proteins (PI-PLCXD).
They are distinct from the typical eukaryotic
phosphoinositide-specific phospholipases C (PI-PLC, EC
3.1.4.11), which have a multidomain organization that
consists of a PLC catalytic core domain, and various
regulatory domains. The catalytic core domain is
assembled from two highly conserved X- and Y-regions
split by a divergent linker sequence. In contrast,
eukaryotic PI-PLCXDs contain a single TIM-barrel type
catalytic domain, X domain, which is closely related to
that of bacterial PI-PLCs. Although the biological
function of eukaryotic PI-PLCXDs still remains unclear,
it may be distinct from that of typical eukaryotic
PI-PLCs. This family also includes a distinctly
different type of eukaryotic PLC,
glycosylphosphatidylinositol-specific phospholipase C
(GPI-PLC), an integral membrane protein characterized in
the protozoan parasite Trypanosoma brucei. T. brucei
GPI-PLC hydrolyzes the GPI-anchor on the variant
specific glycoprotein (VSG), releasing dimyristyl
glycerol (DMG), which may facilitate the evasion of the
protozoan to the host's immune system. It does not
require Ca2+ for its activity and is more closely
related to bacterial PI-PLCs, but not mammalian PI-PLCs.
Length = 271
Score = 29.0 bits (65), Expect = 4.5
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 7/45 (15%)
Query: 109 FDIDFVKDLIAQSLYV-------KYIPVDATLDDIKDFFKKNTSE 146
D+ D LYV ++ L+++KDF + SE
Sbjct: 54 LDLRVAYDPDDGDLYVCHGLFLLNGQTLEDVLNEVKDFLDAHPSE 98
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 77
Score = 26.9 bits (60), Expect = 4.6
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 11/70 (15%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
+L+V + A DD+++FFK+ DV+ I ++ + KG V F +
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVR----IAQDDDG------RSKGFGHVEFATE 50
Query: 180 ENAEKFLNEN 189
E A+K L ++
Sbjct: 51 EGAQKALEKS 60
>gnl|CDD|187797 cd09666, Cas8a2_I-A, CRISPR/Cas system-associated protein Csa8a2.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Zn-finger domain containing protein, distant homologs of
Cas8 proteins; signature gene for I-A subtype; also
known as Csa4 family.
Length = 352
Score = 29.0 bits (65), Expect = 5.0
Identities = 14/55 (25%), Positives = 19/55 (34%), Gaps = 4/55 (7%)
Query: 273 PTGALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENN 327
P G I + E I L +Q +E++ E T R KE N
Sbjct: 37 PVGERYVIKVDADNCHLESIELALRGLQEALEEVLSGH----EATGRARSSKEGN 87
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 107
Score = 27.6 bits (61), Expect = 5.1
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+L+V+ +P DAT + + F K S V+ ++ DK + KG+ FV F ++
Sbjct: 3 TLFVRNLPYDATEESLAPHFSKFGS--VRYALPVI----DKSTGRA--KGTGFVCFKDQY 54
Query: 181 NAEKFL 186
L
Sbjct: 55 TYNACL 60
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 29.3 bits (66), Expect = 5.2
Identities = 11/91 (12%), Positives = 32/91 (35%), Gaps = 17/91 (18%)
Query: 132 TLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTF------DNKENAEKF 185
+D + F + + Y+++ ++ F +++T E++
Sbjct: 88 VIDYPESDFPN------PFSASLDEEYRERFEGERHFVNELYLTILYRPLPSLIGKLERY 141
Query: 186 LNENKDKNLKFNENCEHKNAEKFLNENKDKN 216
N+ L+ + + ++ L +DK
Sbjct: 142 KNK-----LRAAQANTENDLKEILRNLEDKT 167
>gnl|CDD|149587 pfam08586, Rsc14, RSC complex, Rsc14/Ldb7 subunit. RSC is an
ATP-dependent chromatin remodelling complex found in
yeast. The RSC components Rsc7/Npl6 and Rsc14/Ldb7
interact physically and/or functionally with Rsc3,
Rsc30, and Htl1 to form a module important for a broad
range of RSC functions.
Length = 101
Score = 27.5 bits (61), Expect = 5.6
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 2/52 (3%)
Query: 156 RNYQDKLANQKKFKGSIFVTFDNKENAEKFLNENKDKNLKFNENCEHKNAEK 207
Y D +A + S V+F +E E L + +D K + E K +
Sbjct: 1 MGYYDVIAGLSALEKSEQVSFTKEELRE--LTQQEDDQRKDRDLPELKRNDT 50
>gnl|CDD|233634 TIGR01914, cas_Csa4, CRISPR-associated protein Cas8a2/Csa4, subtype
I-A/APERN. CRISPR loci appear to be mobile elements
with a wide host range. This model represents a protein
that tends to be found near CRISPR repeats. The species
range for this species, so far, is exclusively archaeal.
It is found so far in only four different species, and
includes two tandem genes in Pyrococcus furiosus DSM
3638. This subfamily is found in a CRISPR/Cas locus we
designate APERN, so the family is designated Csa4, for
CRISPR/Cas Subtype Protein 4 [Mobile and
extrachromosomal element functions, Other].
Length = 354
Score = 28.6 bits (64), Expect = 5.7
Identities = 12/55 (21%), Positives = 17/55 (30%), Gaps = 4/55 (7%)
Query: 273 PTGALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENN 327
P G I + L +Q +E++ E T R KE N
Sbjct: 37 PVGERYVIKVDADNCHLVSQELALRGLQEALEEVLSGH----EATGRARSSKEGN 87
>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM2 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B shows high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 73
Score = 26.7 bits (59), Expect = 5.8
Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 10/69 (14%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+++ +P A D+K+FF EDV I + N G+ V F ++
Sbjct: 2 VFLHGLPYTADEHDVKEFFHGLDVEDV-----IFLKRHNGRNN-----GNAIVKFATFQD 51
Query: 182 AEKFLNENK 190
A++ L ++
Sbjct: 52 AKEALKRHR 60
>gnl|CDD|217011 pfam02388, FemAB, FemAB family. The femAB operon codes for two
nearly identical approximately 50-kDa proteins involved
in the formation of the Staphylococcal pentaglycine
interpeptide bridge in peptidoglycan. These proteins are
also considered as a factor influencing the level of
methicillin resistance.
Length = 408
Score = 28.8 bits (65), Expect = 6.4
Identities = 21/134 (15%), Positives = 49/134 (36%), Gaps = 23/134 (17%)
Query: 81 LKKSTSKLIE-VNEDGTKIRRNPEKELPTF----------------DIDFVKDLI---AQ 120
K T + I+ + G K+RR EL F +D+ + L+
Sbjct: 170 FSKKTRRNIKKAQKKGVKVRRLGRDELDIFYELMKKTEERKGFHDRSLDYYEKLLDTYGD 229
Query: 121 SLYVK--YIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
Y+ LD++++ +K + K+ + +N K N+ + +
Sbjct: 230 KAEFMLAYLNFKEYLDELQEKLEKLEKDLAKLEEKLEKNPNSKKKNKLAELEQQLASLEK 289
Query: 179 K-ENAEKFLNENKD 191
+ + A++ + + +
Sbjct: 290 RIDEAKELIAKYGN 303
>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM1 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), 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 = 72
Score = 26.5 bits (59), Expect = 6.5
Identities = 14/67 (20%), Positives = 30/67 (44%), Gaps = 11/67 (16%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
+++V + D+++ F K DV++ + K KG +V F+N+
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVK----------NYKGKSKGYAYVEFENE 50
Query: 180 ENAEKFL 186
E+ ++ L
Sbjct: 51 ESVQEAL 57
>gnl|CDD|240986 cd12542, RRM2_LARP7, RNA recognition motif 2 in La-related protein
7 (LARP7) and similar proteins. This subgroup
corresponds to the RRM2 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S), an
oligopyrimidine-binding protein that binds to the highly
conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK
RNA. LARP7 is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP). It intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. LARP7 plays an essential role in the inhibition
of positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
LARP7 contains a La motif (LAM) and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the N-terminal region,
which mediates binding to the U-rich 3' terminus of 7SK
RNA. LARP7 also carries another putative RRM domain at
its C-terminus. .
Length = 78
Score = 26.5 bits (59), Expect = 6.8
Identities = 20/84 (23%), Positives = 45/84 (53%), Gaps = 11/84 (13%)
Query: 275 GALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKA 334
G ++KI + R++ ++ L+ D ++ +++ G+ A+VR+K A+ V+K
Sbjct: 1 GVIVKIKLDEPLPDRKEFKDELK----DHADVAYVDVKEGDTEAYVRFKTPEAAQKVVKQ 56
Query: 335 LGSKEIVIKDVKVSIEVVTGEEEQ 358
+ K S+E+++G+EE+
Sbjct: 57 ESKE-------KGSLEILSGDEEK 73
>gnl|CDD|200101 TIGR01435, glu_cys_lig_rel, glutamate--cysteine
ligase/gamma-glutamylcysteine synthetase, Streptococcus
agalactiae type. This model represents a bifunctional
protein family for the biosynthesis of glutathione, and
perhaps a range of related gamma-glutamyltripeptides of
the form gamma-Glu-Cys-X(aa). The N-terminal region is
similar to proteobacterial glutamate-cysteine ligase.
The C-terminal region is homologous to cyanophycin
synthetase of cyanobacteria and, more distantly, to
D-alanine-D-alanine ligases. Members of This model
family are found in Listeria and Enterococcus,
Gram-positive lineages in which glutathione is produced
(see PUBMED:8606174), and in Pasteurella multocida, a
Proteobacterium. In Clostridium acetobutylicum, adjacent
genes include separate proteins rather than a fusion
protein [Biosynthesis of cofactors, prosthetic groups,
and carriers, Glutathione and analogs].
Length = 737
Score = 28.7 bits (64), Expect = 7.4
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 278 LKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLK 333
L I+ K+ V ED E LE +D+E++ EF G T + + + AVL
Sbjct: 525 LGITIFKQGVQLEDFAEALEIAFREDKEVIIEEFLPG--TEYRFFVLGDEVLAVLL 578
>gnl|CDD|240739 cd12293, RRM_Rrp7p, RNA recognition motif in yeast ribosomal
RNA-processing protein 7 (Rrp7p) and similar proteins.
This subfamily corresponds to the RRM of Rrp7p which is
encoded by YCL031C gene from Saccharomyces cerevisiae.
It is an essential yeast protein involved in pre-rRNA
processing and ribosome assembly, and is speculated to
be required for correct assembly of rpS27 into the
pre-ribosomal particle. Rrp7p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal RRP7 domain. .
Length = 96
Score = 26.6 bits (59), Expect = 7.9
Identities = 6/22 (27%), Positives = 12/22 (54%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK 142
+L++ +PVD T ++ F
Sbjct: 2 TLFLVNLPVDTTERHLRKLFGS 23
>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM1 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
highly acidic carboxyl-terminal half. The family also
includes CUS2, a yeast homolog of human Tat-SF1. CUS2
interacts with U2 RNA in splicing extracts and functions
as a splicing factor that aids assembly of the
splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the conserved
splicing factor SF3a. Like Tat-SF1, CUS2 contains two
RRMs as well. .
Length = 92
Score = 26.7 bits (60), Expect = 8.0
Identities = 7/22 (31%), Positives = 15/22 (68%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK 142
++YV +P+D T+++ + F K
Sbjct: 3 NVYVSGLPLDITVEEFVEVFSK 24
>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 = 26.4 bits (59), Expect = 8.2
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 11/75 (14%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNKE 180
+YVK + D + +K+ F + KIT+ +M++ ++ K KG FV F+N E
Sbjct: 4 VYVKNLGEDMDDEKLKELF----GKYGKITSAKVMKD------DEGKSKGFGFVNFENHE 53
Query: 181 NAEKFLNENKDKNLK 195
A+K + E K +
Sbjct: 54 AAQKAVEELNGKEVN 68
>gnl|CDD|215453 PLN02844, PLN02844, oxidoreductase/ferric-chelate reductase.
Length = 722
Score = 28.3 bits (63), Expect = 8.8
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 144 TSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKENA--EKFLNE 188
S+D+ + N I ++ +NQ K +FVT + K NA + LN+
Sbjct: 467 KSQDICLLNPISSLLLNQSSNQLNLKLKVFVTQEEKPNATLRELLNQ 513
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin.
This subfamily corresponds to the RRM2 of ubiquitously
expressed protein nucleolin, also termed protein C23, a
multifunctional major nucleolar phosphoprotein that has
been implicated in various metabolic processes, such as
ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines.RRM2, together with RRM1, binds
specifically to RNA stem-loops containing the sequence
(U/G)CCCG(A/G) in the loop. .
Length = 77
Score = 26.3 bits (58), Expect = 9.2
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 12/70 (17%)
Query: 119 AQSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
A++L+VK +P + T+D++K+ F ED + KG ++ F
Sbjct: 3 ARTLFVKNLPYNITVDELKEVF-----EDAVDIRLPSG-------KDGSSKGIAYIEFKT 50
Query: 179 KENAEKFLNE 188
+ AEK L E
Sbjct: 51 EAEAEKALEE 60
>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 = 26.1 bits (58), Expect = 9.2
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 12/69 (17%)
Query: 122 LYVKYIPVDATLDDIKDFFKK--NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
L+V+ +P T +++++ F+ SE ++ + DK K+ KG FV+F
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISE----VHLPL----DKET--KRSKGFAFVSFMFP 51
Query: 180 ENAEKFLNE 188
E+A K +E
Sbjct: 52 EHAVKAYSE 60
>gnl|CDD|216763 pfam01885, PTS_2-RNA, RNA 2'-phosphotransferase, Tpt1 / KptA
family. Tpt1 catalyzes the last step of tRNA splicing
in yeast. It transfers the splice junction 2'-phosphate
from ligated tRNA to NAD, to produce ADP-ribose
1"-2"-cyclic phosphate. This is presumed to be followed
by a transesterification step to release the RNA. The
first step of this reaction is similar to that
catalyzed by some bacterial toxins. E. coli KptA and
mouse Tpt1 are likely to use the same reaction
mechanism.
Length = 169
Score = 27.5 bits (62), Expect = 9.7
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 53 DGWVELTTMLKFARLAKMTTEAKVIVDALKKSTSKLIEVNEDGTKIR 99
DGWV++ +LK R + + + + K E++EDG +IR
Sbjct: 26 DGWVDVDELLKALRKKGRWVTREDLERVVATNDKKRFELSEDGDRIR 72
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
0.310 0.130 0.349
Gapped
Lambda K H
0.267 0.0715 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,274,263
Number of extensions: 2024853
Number of successful extensions: 2730
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2636
Number of HSP's successfully gapped: 277
Length of query: 410
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 311
Effective length of database: 6,546,556
Effective search space: 2035978916
Effective search space used: 2035978916
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 60 (26.9 bits)