RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1630
(149 letters)
>gnl|CDD|240876 cd12430, RRM_LARP4_5_like, RNA recognition motif in La-related
protein 4 (LARP4), La-related protein 5 (LARP5 or
LARP4B) and similar proteins. This subfamily
corresponds to the RRM of LARP4 and LARP5. LARP4 is a
cytoplasmic factor that can bind poly(A) RNA and
interact with poly(A) binding protein (PABP). It may
play a role in promoting translation by stabilizing
mRNA. LARP5 is a cytosolic protein that co-sediments
with polysomes and accumulates upon stress induction in
cellular stress granules. It can interact with the
cytosolic poly(A) binding protein 1 (PABPC1) and the
receptor for activated C Kinase (RACK1), a component of
the 40S ribosomal subunit. LARP5 may function as a
stimulatory factor of translation through bridging mRNA
factors of the 3' end with initiating ribosomes. Both,
LARP4 and LARP5, are structurally related to the La
autoantigen. Like other La-related proteins (LARPs)
family members, LARP4 and LARP5 contain a La motif (LAM)
and an RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 76
Score = 122 bits (308), Expect = 2e-37
Identities = 46/67 (68%), Positives = 58/67 (86%)
Query: 80 CIVILREIPDSTPLEEIRGLFSGKSCPRFISCEFAHNNSWYITFENDEDAQKAYRYLRED 139
CIVILREIP+STP EE++ LFSG++CP+F SC F NNSW++TFE +EDAQ+AYRYLRE+
Sbjct: 1 CIVILREIPESTPEEEVKALFSGQNCPKFTSCRFDINNSWFVTFETEEDAQEAYRYLREE 60
Query: 140 VREFQNK 146
V+ FQ K
Sbjct: 61 VKTFQGK 67
>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 = 117 bits (295), Expect = 1e-35
Identities = 52/62 (83%), Positives = 57/62 (91%)
Query: 14 RENLANDAYLLSQMDNDQYVPIWTVANFNQVKKLTKDIKLITEVLRESPNVQVDEEGIKV 73
RENLANDAYLLSQMD+DQYVPIWT+ANFN++KKLT DI LI E LRESPNVQVDE+G KV
Sbjct: 14 RENLANDAYLLSQMDSDQYVPIWTIANFNKIKKLTTDIDLIVEALRESPNVQVDEKGEKV 73
Query: 74 RP 75
RP
Sbjct: 74 RP 75
>gnl|CDD|241151 cd12707, RRM_LARP4, RNA recognition motif in vertebrate La-related
protein 4 (LARP4). This subgroup corresponds to the RRM
of LARP4, a cytoplasmic factor that can bind poly(A) RNA
and interact with poly(A) binding protein (PABP). It may
play a role in promoting translation by stabilizing
mRNA. LARP4 is structurally related to the La
autoantigen. Like other La-related proteins (LARPs)
family members, LARP4 contains a La motif (LAM) and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 108 bits (271), Expect = 7e-32
Identities = 44/67 (65%), Positives = 60/67 (89%)
Query: 80 CIVILREIPDSTPLEEIRGLFSGKSCPRFISCEFAHNNSWYITFENDEDAQKAYRYLRED 139
CI+ILREIP++TP+EE++ LF ++CP+ ISCEFAHNN+WYITF++D DAQ+A+RYLRE+
Sbjct: 1 CIIILREIPETTPVEEVKALFKSENCPKVISCEFAHNNNWYITFQSDTDAQQAFRYLREE 60
Query: 140 VREFQNK 146
V+ FQ K
Sbjct: 61 VKTFQGK 67
>gnl|CDD|241150 cd12706, RRM_LARP5, RNA recognition motif in vertebrate La-related
protein 5 (LARP5 or LARP4B). This subgroup corresponds
to the RRM of LARP5, a cytosolic protein that
co-sediments with polysomes and accumulates upon stress
induction in cellular stress granules. It can interact
with the cytosolic poly(A) binding protein 1 (PABPC1)
and the receptor for activated C Kinase (RACK1), a
component of the 40S ribosomal subunit. LARP5 may
function as a stimulatory factor of translation through
bridging mRNA factors of the 3' end with initiating
ribosomes. Like other La-related proteins (LARPs) family
members, LARP5 contains a La motif (LAM) and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 102 bits (254), Expect = 2e-29
Identities = 44/70 (62%), Positives = 60/70 (85%)
Query: 80 CIVILREIPDSTPLEEIRGLFSGKSCPRFISCEFAHNNSWYITFENDEDAQKAYRYLRED 139
CIVILREIP+STP+EE+ LF G + P+FI+CEFA+N++W+ITFE++ DAQ+AY+YLRE+
Sbjct: 1 CIVILREIPESTPVEEVEALFKGDNLPKFINCEFAYNDNWFITFESEADAQQAYKYLREE 60
Query: 140 VREFQNKESK 149
V+ FQ K K
Sbjct: 61 VKTFQGKPIK 70
>gnl|CDD|128955 smart00715, LA, Domain in the RNA-binding Lupus La protein;
unknown function.
Length = 80
Score = 92.7 bits (231), Expect = 9e-26
Identities = 34/64 (53%), Positives = 44/64 (68%), Gaps = 1/64 (1%)
Query: 14 RENLANDAYLLSQMD-NDQYVPIWTVANFNQVKKLTKDIKLITEVLRESPNVQVDEEGIK 72
ENL D +L +MD ND YVPI T+A+F +VK LT D+ LI E LR SP ++V E+G+K
Sbjct: 17 DENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSPKLEVSEDGLK 76
Query: 73 VRPN 76
VR
Sbjct: 77 VRRR 80
>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 = 92.0 bits (228), Expect = 2e-25
Identities = 43/62 (69%), Positives = 50/62 (80%)
Query: 14 RENLANDAYLLSQMDNDQYVPIWTVANFNQVKKLTKDIKLITEVLRESPNVQVDEEGIKV 73
RENL+ D YL+SQMD+DQ+VPIWTVAN +KKLT D+ LI +VLR SP VQVDE G KV
Sbjct: 14 RENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSPMVQVDETGEKV 73
Query: 74 RP 75
RP
Sbjct: 74 RP 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 = 90.9 bits (225), Expect = 5e-25
Identities = 42/62 (67%), Positives = 51/62 (82%)
Query: 14 RENLANDAYLLSQMDNDQYVPIWTVANFNQVKKLTKDIKLITEVLRESPNVQVDEEGIKV 73
RENLA+D YL+SQMD+DQYVPI TVAN + +KKL+ D+ LI +VLR P VQVDE+G KV
Sbjct: 14 RENLASDMYLISQMDSDQYVPIMTVANLDHIKKLSTDVDLIVDVLRSLPLVQVDEKGEKV 73
Query: 74 RP 75
RP
Sbjct: 74 RP 75
>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 = 84.9 bits (211), Expect = 1e-22
Identities = 33/63 (52%), Positives = 45/63 (71%)
Query: 13 CRENLANDAYLLSQMDNDQYVPIWTVANFNQVKKLTKDIKLITEVLRESPNVQVDEEGIK 72
ENL D +L S MD+D +VP+ +A+FN+VKKLT D++LI E LR+S V+V E+G K
Sbjct: 13 SDENLCKDRFLRSLMDDDGWVPLSLLASFNRVKKLTTDVELILEALRDSSVVEVSEDGTK 72
Query: 73 VRP 75
VR
Sbjct: 73 VRR 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 = 73.0 bits (180), Expect = 3e-18
Identities = 26/49 (53%), Positives = 33/49 (67%), Gaps = 1/49 (2%)
Query: 14 RENLANDAYLLSQMD-NDQYVPIWTVANFNQVKKLTKDIKLITEVLRES 61
ENL D +L QMD + YVPI T+A+F ++KKLT D+ LI E LR S
Sbjct: 11 DENLPRDKFLRKQMDKDPGYVPISTIASFKRIKKLTTDVNLIVEALRSS 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 = 66.9 bits (164), Expect = 1e-15
Identities = 27/62 (43%), Positives = 40/62 (64%), Gaps = 2/62 (3%)
Query: 15 ENLANDAYLLSQM--DNDQYVPIWTVANFNQVKKLTKDIKLITEVLRESPNVQVDEEGIK 72
ENL DA+LL + + + YVPI +A+F +VK LT+D +++ LR S + V E+G K
Sbjct: 15 ENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSSKLVVSEDGKK 74
Query: 73 VR 74
VR
Sbjct: 75 VR 76
>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 = 55.1 bits (133), Expect = 3e-11
Identities = 25/60 (41%), Positives = 41/60 (68%), Gaps = 2/60 (3%)
Query: 15 ENLANDAYLLSQMDNDQYVPIWTVANFNQVKKLTKDIKLITEVLRESPNVQVDEEGIKVR 74
+NL D +L +MD + Y+PI +A+F++V+ LT D+ LI E L++S V++ +E KVR
Sbjct: 15 DNLEKDFFLRRKMDPEGYLPIALIASFHRVQALTTDVNLILEALKDSTVVELVDE--KVR 72
>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 = 50.7 bits (121), Expect = 3e-09
Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 2/61 (3%)
Query: 16 NLANDAYLLSQMDN--DQYVPIWTVANFNQVKKLTKDIKLITEVLRESPNVQVDEEGIKV 73
NL D +L Q++ D Y+ I + +FN++KKLT D KLI L+ S V+++ EG ++
Sbjct: 21 NLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVELNLEGTRI 80
Query: 74 R 74
R
Sbjct: 81 R 81
>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 = 48.0 bits (114), Expect = 2e-08
Identities = 21/58 (36%), Positives = 39/58 (67%)
Query: 15 ENLANDAYLLSQMDNDQYVPIWTVANFNQVKKLTKDIKLITEVLRESPNVQVDEEGIK 72
+NL D +L +MD D ++P+ +A+F++V+ LT DI LI + L++S V++ + I+
Sbjct: 15 DNLERDFFLRRKMDEDGFLPVTLIASFHRVQALTTDISLIIKALKDSKVVEIIDMKIR 72
>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 = 46.1 bits (110), Expect = 1e-07
Identities = 22/63 (34%), Positives = 39/63 (61%), Gaps = 3/63 (4%)
Query: 14 RENLANDAYL--LSQMDNDQYVPIWTVANFNQVKKLTKDIKLITEVLRESPNVQVDEEGI 71
NL D +L L+ N+ +VPI T+A+F ++++ + ++ + E LRES ++V E+G
Sbjct: 14 DSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRF-QPLEAVVEALRESELLEVSEDGE 72
Query: 72 KVR 74
VR
Sbjct: 73 NVR 75
>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 = 45.4 bits (108), Expect = 2e-07
Identities = 20/62 (32%), Positives = 39/62 (62%), Gaps = 3/62 (4%)
Query: 16 NLANDAYLLSQM-DNDQYVPIWTVANFNQVKKLTKDIKLITEVLRES--PNVQVDEEGIK 72
NL D +L Q+ ++D +VP+ + FN++K L+ D ++I + L++S ++V E+ K
Sbjct: 20 NLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKSGLIEVSEDKTK 79
Query: 73 VR 74
+R
Sbjct: 80 IR 81
>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 = 3e-07
Identities = 21/58 (36%), Positives = 37/58 (63%)
Query: 15 ENLANDAYLLSQMDNDQYVPIWTVANFNQVKKLTKDIKLITEVLRESPNVQVDEEGIK 72
ENL D +L +MD ++PI +A F +V+ LT ++ LI E L++S V++ ++ I+
Sbjct: 15 ENLERDFFLRRKMDLQGFLPISLIAGFYRVQALTTNVDLILEALKDSTEVEIVDQKIR 72
>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 = 35.0 bits (81), Expect = 0.002
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 8/61 (13%)
Query: 82 VILREIPDSTPLEEIRGLFSGKSCPRFISCEFAHNNSW------YITFENDEDAQKAYRY 135
+ + +P T E++R LFS S + ++ FE+ EDA+KA
Sbjct: 1 LFVGNLPPDTTEEDLRELFS--KFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEA 58
Query: 136 L 136
L
Sbjct: 59 L 59
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 34.1 bits (79), Expect = 0.003
Identities = 14/68 (20%), Positives = 28/68 (41%), Gaps = 5/68 (7%)
Query: 82 VILREIPDSTPLEEIRGLFSGKSCP---RFISCEFAHNNSWYITFENDEDAQKAYRYLRE 138
+ +R +P S E++R FS R + + ++ F + EDA+ A + L
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKL-- 58
Query: 139 DVREFQNK 146
+ +
Sbjct: 59 NGLVLDGR 66
>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 = 34.6 bits (79), Expect = 0.014
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 30 DQYVPIWTVANFNQVKKLTKDIKLITEVLRESPN---VQVDEEGIKVRPNHKR 79
D++VPI T+A FN++K + ++ LR+S + ++V G K
Sbjct: 110 DKWVPIKTIATFNRMKNSGSPVSAVSGALRKSLDARVLEVSSSGSNKNRTEKL 162
Score = 31.2 bits (70), Expect = 0.16
Identities = 16/81 (19%), Positives = 29/81 (35%), Gaps = 2/81 (2%)
Query: 15 ENLANDAYLLSQMDNDQYVPIWTVANFNQVKKLTKDIKLITEVLRESPNVQVDEEGIKVR 74
ENL +D +L + ++P+ + F + D LI ++E VQ
Sbjct: 285 ENLKSDEFLRKKFKKAGFIPLSFIGKFYRNLSFGGDKNLILAAMKEV--VQNKATNHLEI 342
Query: 75 PNHKRCIVILREIPDSTPLEE 95
E D +P ++
Sbjct: 343 ALGSIEDAQKNEAKDFSPGKK 363
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 32.2 bits (74), Expect = 0.015
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 11/73 (15%)
Query: 82 VILREIPDSTPLEEIRGLFSGKSCPRFISCEFAHNNSW-------YITFENDEDAQKAYR 134
+ + +P T EE+R LFS + S + ++ FE++EDA+KA
Sbjct: 2 LFVGNLPPDTTEEELRELFS--KFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALE 59
Query: 135 YLREDVREFQNKE 147
L +E +
Sbjct: 60 ALNG--KELDGRP 70
>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 = 32.0 bits (73), Expect = 0.024
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 14/76 (18%)
Query: 13 CRENLANDAYLLSQM--DNDQYVPIWTVANFNQVKKL------------TKDIKLITEVL 58
NL D +LL ++ D D V + + +F++++ L +K + E L
Sbjct: 14 SDSNLPRDDFLLEEVEEDPDGMVSLALICSFSRMRSLLGLGGGKPEDVPEDTLKAVAEAL 73
Query: 59 RESPNVQVDEEGIKVR 74
R S ++V E+G +V
Sbjct: 74 RTSTLLKVSEDGKRVG 89
>gnl|CDD|240707 cd12261, RRM1_3_MRN1, RNA recognition motif 1 and 3 in RNA-binding
protein MRN1 and similar proteins. This subfamily
corresponds to the RRM1 and RRM3 of MRN1, also termed
multicopy suppressor of RSC-NHP6 synthetic lethality
protein 1, or post-transcriptional regulator of 69 kDa,
which is an RNA-binding protein found in yeast. Although
its specific biological role remains unclear, MRN1 might
be involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 73
Score = 29.5 bits (67), Expect = 0.18
Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 14/63 (22%)
Query: 82 VILREIPDSTPLEE----IRG--LFSGKSCPRFISCEFAHNNSWYITFENDEDAQKAYRY 135
V L +P+ T + + IRG L S K P S ++F ++ A+ Y Y
Sbjct: 3 VYLGNLPEDTTIRDILSAIRGGPLESIKLLPTKNSAT--------VSFLDEAAAEAFYAY 54
Query: 136 LRE 138
R
Sbjct: 55 ARN 57
>gnl|CDD|240954 cd12510, RRM1_RBM12_like, RNA recognition motif 1 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM1 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 show high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 74
Score = 29.2 bits (66), Expect = 0.22
Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 8/68 (11%)
Query: 80 CIVI-LREIPDSTPLEEIRGLFSGKSCPR----FISCEFAHNNSWYITFENDEDAQKAYR 134
+VI L+ +P +IR FSG + P I E +I F DEDA+ A
Sbjct: 1 SVVIRLQNLPWEAGSLDIRRFFSGLTIPDGGVHIIGGEMGEA---FIAFATDEDARLAMS 57
Query: 135 YLREDVRE 142
+ ++
Sbjct: 58 RDGQTIKG 65
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in mRNA
surveillance. Furthermore, RNPS1 is a splicing regulator
whose activator function is controlled in part by CK2
(casein kinase II) protein kinase phosphorylation. It
can also function as a squamous-cell carcinoma antigen
recognized by T cells-3 (SART3)-binding protein, and is
involved in the regulation of mRNA splicing. RNPS1
contains an N-terminal serine-rich (S) domain, a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
the C-terminal arginine/serine/proline-rich (RS/P)
domain. .
Length = 73
Score = 29.1 bits (66), Expect = 0.22
Identities = 8/17 (47%), Positives = 14/17 (82%)
Query: 120 YITFENDEDAQKAYRYL 136
Y+ FE+ EDA+KA +++
Sbjct: 44 YVEFESPEDAEKAIKHM 60
>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 = 29.2 bits (66), Expect = 0.22
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 80 CIVILREIPDSTPLEEIRGLFSGKSCPRFISCEFAHNNSW-YITFENDEDAQKA 132
I+ + I E+I+ +F+ +++ +F YI F+ E AQKA
Sbjct: 2 VILKITSIGPGVTREDIKAVFAQFGEVKYV--DFTEGADTGYIRFKTPEAAQKA 53
>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 = 29.3 bits (66), Expect = 0.27
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 15/73 (20%)
Query: 87 IPDSTPLEEIRGLFS--GK----SCPRFIS----CEFAHNNSWYITFENDEDAQKAYRYL 136
+P + E ++ +FS G S PR+ FA +I FE E+AQKA ++L
Sbjct: 7 LPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFA-----FIEFETPEEAQKACKHL 61
Query: 137 REDVREFQNKESK 149
+K K
Sbjct: 62 NNPPETATDKPGK 74
>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 = 28.7 bits (65), Expect = 0.32
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 82 VILREIPDSTPLEEIRGLFS--GKSCPRFISCEFAHNNSWYITFENDEDAQKAYRYL 136
+++R +P ++ L G S R +S N+ + TF+N++ A +A L
Sbjct: 2 LLVRHLPPELSEDDKEDLLKHFGASSVRVMSRRGKLKNTAFATFDNEQAASQALSRL 58
>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 = 28.7 bits (65), Expect = 0.32
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 10/72 (13%)
Query: 82 VILREIPDSTPLEEIRGLFSGKSCPRFISCEFAHNNSW------YITFENDEDAQKAYRY 135
+ + +P T E+++ LFS S + + ++ FE++EDA+KA
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSK--FGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEA 58
Query: 136 LREDVREFQNKE 147
L +E +E
Sbjct: 59 LNG--KELGGRE 68
>gnl|CDD|222350 pfam13732, DUF4162, Domain of unknown function (DUF4162). This
domain is found at the C-terminus of bacterial ABC
transporter proteins. The function is not known.
Length = 84
Score = 29.1 bits (66), Expect = 0.32
Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 11/74 (14%)
Query: 73 VRPNHKRCIVILREIPDSTPLEEIRGLFSGKSCPRFISCEFAHNNSWYITFENDEDAQKA 132
++ ++ + +++ LEE+ L P S E + + E++EDAQ+
Sbjct: 6 IKRSYGKNKLLVE---TDGDLEELEEL------PGVESVEKTGDGKVELKLEDEEDAQEI 56
Query: 133 YRYLRED--VREFQ 144
L E +R F+
Sbjct: 57 LEELTEKGYIRRFE 70
>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 = 28.3 bits (64), Expect = 0.41
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 7/63 (11%)
Query: 81 IVILREIPDSTPLEEIRGLFSGKSCPRFISCEFAHNNSW------YITFENDEDAQKAYR 134
+V LR +P S E+IR FSG +++ Y+ F + EDA++A R
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSG-LDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALR 59
Query: 135 YLR 137
Sbjct: 60 KHN 62
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
3 in multiple RNA-binding domain-containing protein 1
(MRD1). This subfamily corresponds to the RRM4 of RBM19
and the RRM3 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 homologues exist in all eukaryotes. MRD1
is present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 72
Score = 28.3 bits (64), Expect = 0.42
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 80 CIVILREIPDSTPLEEIRGLFSGK-SCPRFISCEFAHNNSWYIT-FENDEDAQKAYRYL 136
+++++ +P T EE+R LF S R + + + + F DA+KA++ L
Sbjct: 1 TVILVKNLPFGTTEEELRELFEKFGSLGRLL---LPPSRTIALVEFLEPSDARKAFKSL 56
>gnl|CDD|241111 cd12667, RRM3_RAVER1, RNA recognition motif 3 in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM3 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 = 92
Score = 28.3 bits (63), Expect = 0.65
Identities = 11/62 (17%), Positives = 24/62 (38%), Gaps = 4/62 (6%)
Query: 77 HKRCIVILREIPDSTPLEEIRGLFSGKSCPRFISCEFAHNNSW----YITFENDEDAQKA 132
H +C+ + + P + ++R FS P F + + +E+ E A+
Sbjct: 1 HSKCLCVDQLPPSLCDVGDLREAFSKIHAPTFCQLACGQDGQLKGFAVLEYESAEMAEMV 60
Query: 133 YR 134
+
Sbjct: 61 QQ 62
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and four
hnRNP K homology (KH) domains. .
Length = 76
Score = 27.7 bits (62), Expect = 0.72
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 8/61 (13%)
Query: 82 VILREIPDSTPLEEIRGLFSGKSCPRFISCEFAHNNSW-----YITFENDEDAQKAYRYL 136
+ + IP E++ L S + +CE +T+E+ E AQ+A L
Sbjct: 3 IQISNIPPHVRWEDLDSLLS--TYGTVKNCE-QVPTKSETATVNVTYESPEQAQQAVNKL 59
Query: 137 R 137
Sbjct: 60 N 60
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and the
RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 27.5 bits (62), Expect = 0.76
Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 13/63 (20%)
Query: 78 KRCIVILREIP-DSTPLEEIRGLFSGKSCPRF-----ISCEFAHNNSWYITFENDEDAQK 131
+ + R IP + + ++ FS +F I + + S + F E+A+K
Sbjct: 1 NTTLEV-RNIPPELNNITKLNEHFS-----KFGTIVNIQVNY-NPESALVQFSTSEEAKK 53
Query: 132 AYR 134
AYR
Sbjct: 54 AYR 56
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the RRM
of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19), is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates distal
alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 27.7 bits (62), Expect = 0.78
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 7/59 (11%)
Query: 84 LREIPDSTPLEEIRGLFSGKSCP---RFISCEFAHNNSW---YITFENDEDAQKAYRYL 136
+R + D+T +++R LF GK P +I +F Y+ FE+ DA+ A YL
Sbjct: 5 VRNVADATRPDDLRRLF-GKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM2
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the 35
S pre-rRNA. MRD1 contains 5 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which may play an
important structural role in organizing specific rRNA
processing events. .
Length = 79
Score = 27.7 bits (62), Expect = 0.83
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 7/68 (10%)
Query: 84 LREIPDSTPLEEIRGLFS--GKSCPRFISCEFAHNNS---WYITFENDEDAQKAYRYLRE 138
+R +P S +++ LFS G+ ++ + S Y+ F + EDA KAY+ L
Sbjct: 7 VRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL-- 64
Query: 139 DVREFQNK 146
D + FQ +
Sbjct: 65 DGKVFQGR 72
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to the
RRM1 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 = 76
Score = 27.4 bits (61), Expect = 0.91
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 120 YITFENDEDAQKAY 133
Y+ FE+ EDA+KA
Sbjct: 45 YVDFESPEDAKKAI 58
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end)
protein family. This subfamily corresponds to the RRM3
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B) and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and is a novel component of the
NXF1 pathway. It binds to NXF1 and serves as receptor
for the RNA export element RTE. It also possess mRNA
export activity and can facilitate the access of
DEAD-box protein DBP5 to mRNA at the nuclear pore
complex (NPC). RNA-binding protein 15B (RBM15B), also
termed one twenty-two 3 (OTT3), is a paralog of RBM15
and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15 the
association with the splicing factor compartment and the
nuclear envelope as well as the binding to mRNA export
factors NXF1 and Aly/REF. Members in this family belong
to the Spen (split end) protein family, which shares a
domain architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 72
Score = 27.2 bits (61), Expect = 0.95
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 9/51 (17%)
Query: 91 TPLEEIRGLFSGKSCPRF--I-SCEFAHNNSW-YITFENDEDAQKAYRYLR 137
T L E+ F RF I ++ ++ YI +E+ E AQ A LR
Sbjct: 10 TSLAELEREFD-----RFGAIRRIDYDPGRNYAYIEYESIEAAQAAKEALR 55
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 92
Score = 27.6 bits (62), Expect = 0.96
Identities = 16/64 (25%), Positives = 27/64 (42%), Gaps = 8/64 (12%)
Query: 77 HKRCIVILREIPDSTPLEEIRGLFSGKSCPRFISCEFAHNNSWY------ITFENDEDAQ 130
H RC+ + R + +R LFS P F C+ A + + + EDA+
Sbjct: 1 HSRCLFVDRLPKTFRDVSILRKLFSQVGKPTF--CQLAIAPNGQPRGFAFVEYATAEDAE 58
Query: 131 KAYR 134
+A +
Sbjct: 59 EAQQ 62
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 26.7 bits (60), Expect = 1.3
Identities = 8/32 (25%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 115 HNNSWYITFENDEDAQKAYRYLREDVREFQNK 146
++ F +E A+KA +YL F +
Sbjct: 20 KPGFAFVEFSTEEAAEKAVQYLNG--VLFGGR 49
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the RRM
of TRMT2A, also known as HpaII tiny fragments locus 9c
protein (HTF9C), a novel cell cycle regulated protein.
It is an independent biologic factor expressed in tumors
associated with clinical outcome in HER2 expressing
breast cancer. The function of TRMT2A remains unclear
although by sequence homology it has a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), related to RNA
methyltransferases. .
Length = 79
Score = 26.4 bits (59), Expect = 2.5
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 120 YITFENDEDAQKAYRYL 136
++TF ++E+ QKA L
Sbjct: 46 FVTFRSEEERQKALEIL 62
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which 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 the 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. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. 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. .
Length = 78
Score = 25.8 bits (57), Expect = 4.1
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 9/61 (14%)
Query: 83 ILREIPDSTPLEEIRGLFSGKSCPRFISCEFAHNNS-------WYITFENDEDAQKAYRY 135
I+ +P + +EIR LFS S SC+ + ++ + + EDA+KA
Sbjct: 5 IVNYLPQNMTQDEIRSLFS--SIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINT 62
Query: 136 L 136
L
Sbjct: 63 L 63
>gnl|CDD|153181 cd04909, ACT_PDH-BS, C-terminal ACT domain of the monofunctional,
NAD dependent, prephenate dehydrogenase (PDH). The
C-terminal ACT domain of the monofunctional, NAD
dependent, prephenate dehydrogenase (PDH) enzyme that
catalyzes the formation of 4-hydroxyphenylpyruvate from
prephenate, found in Bacillus subtilis (BS) and other
Firmicutes, Deinococci, and Bacteroidetes. PDH is the
first enzyme in the aromatic amino acid pathway specific
for the biosynthesis of tyrosine. This enzyme is
feedback-inhibited by tyrosine in B. subtilis and other
microorganisms. Both phenylalanine and tryptophan have
been shown to be inhibitors of this activity in B.
subtilis. Bifunctional chorismate mutase-PDH (TyrA)
enzymes such as those seen in Escherichia coli do not
contain an ACT domain. Members of this CD belong to the
superfamily of ACT regulatory domains.
Length = 69
Score = 25.7 bits (57), Expect = 4.2
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 121 ITFENDEDAQKAYRYLRE 138
I+F+ ED ++A L+E
Sbjct: 47 ISFKTQEDRERAKEILKE 64
>gnl|CDD|240948 cd12504, RRM2_hnRNPH_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein (hnRNP) H protein family.
This subfamily corresponds to the RRM2 of hnRNP H
protein family which 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). They
represent a group of nuclear RNA binding proteins that
are involved in pre-mRNA processing, having similar RNA
binding affinities and specifically recognizing the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA only
in the presence of cap-binding proteins. Furthermore,
hnRNP H and hnRNP H2 are almost identical; both have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation. hnRNP
H3 may be involved in the splicing arrest induced by
heat shock. Most family members contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), except for
hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction with
the exonic GGG motifs. The lack of RRM1 could account
for the reduced silencing activity within hnRNP H3. In
addition, the family members have an extensive
glycine-rich region near the C-terminus, which may allow
them to homo- or heterodimerize. .
Length = 77
Score = 25.4 bits (56), Expect = 5.2
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 80 CIVILREIPDSTPLEEIRGLFSG-KSCPRFISCEFAHN----NSWYITFENDEDAQKA 132
+V LR +P EEI FSG + P I+ + Y+ F + E A++A
Sbjct: 1 GVVRLRGLPFGCSKEEIAQFFSGLEIVPNGITLPMDYRGRSTGEAYVQFASQESAERA 58
>gnl|CDD|240982 cd12538, RRM_U2AF35, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35). This subgroup corresponds to the RRM of
U2AF35, also termed U2AF1, which is one of the small
subunits of U2 small nuclear ribonucleoprotein (snRNP)
auxiliary factor (U2AF). It has been implicated in the
recruitment of U2 snRNP to pre-mRNAs and is a highly
conserved heterodimer composed of large and small
subunits. U2AF35 directly binds to the 3' splice site of
the conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF, U2AF65 (also
termed U2AF2). U2AF35 contains two N-terminal zinc
fingers, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich segment interrupted by
glycines. U2AF35 binds both U2AF65 and the pre-mRNA
through its RRM domain. .
Length = 104
Score = 25.8 bits (57), Expect = 5.6
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 120 YITFENDEDAQKA 132
Y+ F +EDA+KA
Sbjct: 72 YVKFRREEDAEKA 84
>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 = 25.8 bits (57), Expect = 5.9
Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 7/71 (9%)
Query: 80 CIVILREIPDSTPLEEIRGLFSGKSCPRFISCEFAHNN---SWYITFENDEDAQKAYRYL 136
I+ + T E+I+ FS +++ Y+ F+ E A+KA
Sbjct: 2 VILKFSGLNKPTSREDIKEAFSQHGEVKYV----DFLEGDKEGYVRFKTPEAAKKALEKA 57
Query: 137 REDVREFQNKE 147
E + + E
Sbjct: 58 TEAKLKIKEAE 68
>gnl|CDD|227113 COG4772, FecA, Outer membrane receptor for Fe3+-dicitrate
[Inorganic ion transport and metabolism].
Length = 753
Score = 26.6 bits (59), Expect = 6.2
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 54 ITEVLRESPNVQV-DEEGIKVRP 75
I E LR P VQ+ D G +RP
Sbjct: 75 IEEALRNVPGVQIRDATGTGLRP 97
>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 = 25.2 bits (56), Expect = 6.4
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 120 YITFENDEDAQKAYRYL 136
++TF EDA++A L
Sbjct: 45 FVTFHTREDAERAIEKL 61
>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 = 25.0 bits (55), Expect = 6.6
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 17/73 (23%)
Query: 84 LREIPDSTPLEEIRGLFS--GKSCPRFISCE--------FAHNNSWYITFENDEDAQKAY 133
+R +P +T EE+R LF G+ + + FA +++F E A KAY
Sbjct: 4 VRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFA-----FVSFMFPEHAVKAY 58
Query: 134 RYLREDVREFQNK 146
L D FQ +
Sbjct: 59 SEL--DGSIFQGR 69
>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF
family. This subfamily corresponds to the RRM of
Aly/REF family which includes THO complex subunit 4
(THOC4, also termed Aly/REF), S6K1 Aly/REF-like target
(SKAR, also termed PDIP3 or PDIP46) and similar
proteins. THOC4 is an mRNA transporter protein with a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It is involved in RNA transportation from the
nucleus, and was initially identified as a transcription
coactivator of LEF-1 and AML-1 for the TCRalpha enhancer
function. In addition, THOC4 specifically binds to
rhesus (RH) promoter in erythroid, and might be a novel
transcription cofactor for erythroid-specific genes.
SKAR shows high sequence homology with THOC4 and
possesses one RRM as well. SKAR is widely expressed and
localizes to the nucleus. It may be a critical player in
the function of S6K1 in cell and organism growth control
by binding the activated, hyperphosphorylated form of
S6K1 but not S6K2. Furthermore, SKAR functions as a
protein partner of the p50 subunit of DNA polymerase
delta. In addition, SKAR may have particular importance
in pancreatic beta cell size determination and insulin
secretion. .
Length = 75
Score = 24.9 bits (55), Expect = 7.0
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 120 YITFENDEDAQKAYR 134
+ FE EDA++A +
Sbjct: 45 DVVFEKREDAERAIK 59
>gnl|CDD|193452 pfam12979, DUF3863, Domain of Unknown Function with PDB structure
(DUF3863). Domain based on 1-364 domain of PDB:3LM3
which is encoded by the BDI_3119 gene from
Parabacteroides distasonis atcc 8503.
Length = 352
Score = 26.1 bits (57), Expect = 8.5
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 5/39 (12%)
Query: 113 FAHNN-----SWYITFENDEDAQKAYRYLREDVREFQNK 146
FA NN +W T ED +K YR +R+ V E Q K
Sbjct: 51 FAKNNPNGRLTWGFTLNALEDGRKNYRQIRDYVVECQKK 89
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM1
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 24.9 bits (55), Expect = 9.3
Identities = 7/17 (41%), Positives = 14/17 (82%)
Query: 120 YITFENDEDAQKAYRYL 136
++ F+++EDAQ+A +Y
Sbjct: 45 FVGFKSEEDAQQAVKYF 61
>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35) and similar proteins. This subfamily
corresponds to the RRM in U2 small nuclear
ribonucleoprotein (snRNP) auxiliary factor (U2AF) which
has been implicated in the recruitment of U2 snRNP to
pre-mRNAs. It is a highly conserved heterodimer composed
of large and small subunits; this family includes the
small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa
subunit B (U2AF35B or C3H60). U2AF35 directly binds to
the 3' splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF (U2AF65 or
U2AF2). Although the biological role of U2AF35B remains
unclear, it shows high sequence homolgy to U2AF35, which
contains two N-terminal zinc fingers, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal arginine/serine (SR) -rich segment
interrupted by glycines. In contrast to U2AF35, U2AF35B
has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 102
Score = 24.9 bits (55), Expect = 9.4
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 120 YITFENDEDAQKAYRYLR 137
Y+ FE +EDA+ A + L
Sbjct: 70 YVKFETEEDAEAALQALN 87
>gnl|CDD|241513 cd13359, PH_ELMO1_CED-12, Engulfment and cell motility protein 1
pleckstrin homology (PH) domain. DOCK2 (Dedicator of
cytokinesis 2), a hematopoietic cell-specific, atypical
GEF, controls lymphocyte migration through Rac
activation. A DOCK2-ELMO1 complex s necessary for
DOCK2-mediated Rac signaling. DOCK2 contains a SH3
domain at its N-terminus, followed by a lipid binding
DHR1 domain, and a Rac-binding DHR2 domain at its
C-terminus. ELMO1, a mammalian homolog of C. elegans
CED-12, contains the N-terminal RhoG-binding region, the
ELMO domain, the PH domain, and the C-terminal sequence
with three PxxP motifs. The C-terminal region of ELMO1,
including the Pro-rich sequence, binds the
SH3-containing region of DOCK2 forming a intermolecular
five-helix bundle along with the PH domain of ELMO1.
Autoinhibition of ELMO1 and DOCK2 is accomplished by the
interactions of the EID and EAD domains and SH3 and DHR2
domains, respectively. The interaction of DOCK2 and
ELMO1 mutually relieve their autoinhibition and results
in the activation of Rac1. The PH domain of ELMO1 does
not bind phosphoinositides due to the absence of key
binding residues. It more closely resembles the FERM
domain rather than other PH domains. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 126
Score = 25.3 bits (56), Expect = 9.8
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 16/45 (35%)
Query: 75 PNHKRCIVI-------------LREIPDSTPLEEIRGLFSGKSCP 106
PNHK V+ L +P+ P+ +I+ L +GK CP
Sbjct: 36 PNHK---VLHYGDCEESAQPAPLESLPEKLPVADIKALVTGKDCP 77
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.135 0.411
Gapped
Lambda K H
0.267 0.0769 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,555,999
Number of extensions: 675250
Number of successful extensions: 883
Number of sequences better than 10.0: 1
Number of HSP's gapped: 871
Number of HSP's successfully gapped: 82
Length of query: 149
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 61
Effective length of database: 7,034,450
Effective search space: 429101450
Effective search space used: 429101450
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (24.5 bits)