RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10327
(289 letters)
>gnl|CDD|238907 cd01926, cyclophilin_ABH_like, cyclophilin_ABH_like: Cyclophilin
A, B and H-like cyclophilin-type peptidylprolyl cis-
trans isomerase (PPIase) domain. This family represents
the archetypal cystolic cyclophilin similar to human
cyclophilins A, B and H. PPIase is an enzyme which
accelerates protein folding by catalyzing the cis-trans
isomerization of the peptide bonds preceding proline
residues. These enzymes have been implicated in protein
folding processes which depend on catalytic
/chaperone-like activities. As cyclophilins, Human
hCyP-A, human cyclophilin-B (hCyP-19), S. cerevisiae
Cpr1 and C. elegans Cyp-3, are inhibited by the
immunosuppressive drug cyclopsporin A (CsA). CsA binds
to the PPIase active site. Cyp-3. S. cerevisiae Cpr1
interacts with the Rpd3 - Sin3 complex and in addition
is a component of the Set3 complex. S. cerevisiae Cpr1
has also been shown to have a role in Zpr1p nuclear
transport. Human cyclophilin H associates with the
[U4/U6.U5] tri-snRNP particles of the splicesome.
Length = 164
Score = 242 bits (620), Expect = 2e-81
Identities = 86/123 (69%), Positives = 99/123 (80%), Gaps = 5/123 (4%)
Query: 170 PQVYMDIKIGKQEVGRITIQLRYDLVPRTAENFRCLCTHEKG-----FGYQGSSFHRIIP 224
P+V+ DI IG + GRI ++L D+VP+TAENFR LCT EKG FGY+GS+FHR+IP
Sbjct: 1 PKVFFDITIGGEPAGRIVMELFADVVPKTAENFRALCTGEKGKGGKPFGYKGSTFHRVIP 60
Query: 225 DFMCQGGDFTNHNGTGGKSIYGNKFEDENFILKHTGPGVLSMANSGPNTNGSQFFLCTTK 284
DFM QGGDFT NGTGGKSIYG KF DENF LKHTGPG+LSMAN+GPNTNGSQFF+ T K
Sbjct: 61 DFMIQGGDFTRGNGTGGKSIYGEKFPDENFKLKHTGPGLLSMANAGPNTNGSQFFITTVK 120
Query: 285 TEW 287
T W
Sbjct: 121 TPW 123
Score = 92.7 bits (231), Expect = 4e-23
Identities = 35/58 (60%), Positives = 43/58 (74%), Gaps = 5/58 (8%)
Query: 1 MDIKIGKQEVGRITIQLRYDLVPRTAENFRCLCTHEKG-----FGYQGSSFHRIIPDF 53
DI IG + GRI ++L D+VP+TAENFR LCT EKG FGY+GS+FHR+IPDF
Sbjct: 5 FDITIGGEPAGRIVMELFADVVPKTAENFRALCTGEKGKGGKPFGYKGSTFHRVIPDF 62
>gnl|CDD|240249 PTZ00060, PTZ00060, cyclophilin; Provisional.
Length = 183
Score = 196 bits (501), Expect = 3e-63
Identities = 78/130 (60%), Positives = 90/130 (69%), Gaps = 6/130 (4%)
Query: 164 PKTKKNPQVYMDIKIGKQEVGRITIQLRYDLVPRTAENFRCLCTHE------KGFGYQGS 217
P+ K P+V+ DI I GRI +L D+ P+TAENFR LC + K Y+GS
Sbjct: 10 PEMSKRPKVFFDISIDNAPAGRIVFELFSDVTPKTAENFRALCIGDKVGSSGKNLHYKGS 69
Query: 218 SFHRIIPDFMCQGGDFTNHNGTGGKSIYGNKFEDENFILKHTGPGVLSMANSGPNTNGSQ 277
FHRIIP FMCQGGD TNHNGTGG+SIYG KF DENF LKH PG+LSMAN+GPNTNGSQ
Sbjct: 70 IFHRIIPQFMCQGGDITNHNGTGGESIYGRKFTDENFKLKHDQPGLLSMANAGPNTNGSQ 129
Query: 278 FFLCTTKTEW 287
FF+ T W
Sbjct: 130 FFITTVPCPW 139
Score = 65.3 bits (159), Expect = 8e-13
Identities = 28/59 (47%), Positives = 34/59 (57%), Gaps = 6/59 (10%)
Query: 2 DIKIGKQEVGRITIQLRYDLVPRTAENFRCLCTHE------KGFGYQGSSFHRIIPDFV 54
DI I GRI +L D+ P+TAENFR LC + K Y+GS FHRIIP F+
Sbjct: 21 DISIDNAPAGRIVFELFSDVTPKTAENFRALCIGDKVGSSGKNLHYKGSIFHRIIPQFM 79
>gnl|CDD|178694 PLN03149, PLN03149, peptidyl-prolyl isomerase H (cyclophilin H);
Provisional.
Length = 186
Score = 183 bits (465), Expect = 8e-58
Identities = 77/129 (59%), Positives = 90/129 (69%), Gaps = 5/129 (3%)
Query: 164 PKTKKNPQVYMDIKIGKQEVGRITIQLRYDLVPRTAENFRCLCTHE---KGF--GYQGSS 218
P KNP V+ D+ IG GRI ++L D+ P+TAENFR CT E G GY+G
Sbjct: 13 PPNPKNPVVFFDVTIGGIPAGRIKMELFADIAPKTAENFRQFCTGEFRKAGLPQGYKGCQ 72
Query: 219 FHRIIPDFMCQGGDFTNHNGTGGKSIYGNKFEDENFILKHTGPGVLSMANSGPNTNGSQF 278
FHR+I DFM QGGDF +GTG SIYG+KFEDENFI KHTGPG+LSMANSGPNTNG QF
Sbjct: 73 FHRVIKDFMIQGGDFLKGDGTGCVSIYGSKFEDENFIAKHTGPGLLSMANSGPNTNGCQF 132
Query: 279 FLCTTKTEW 287
F+ K +W
Sbjct: 133 FITCAKCDW 141
Score = 64.5 bits (157), Expect = 2e-12
Identities = 28/58 (48%), Positives = 36/58 (62%), Gaps = 5/58 (8%)
Query: 2 DIKIGKQEVGRITIQLRYDLVPRTAENFRCLCTHE---KGF--GYQGSSFHRIIPDFV 54
D+ IG GRI ++L D+ P+TAENFR CT E G GY+G FHR+I DF+
Sbjct: 24 DVTIGGIPAGRIKMELFADIAPKTAENFRQFCTGEFRKAGLPQGYKGCQFHRVIKDFM 81
>gnl|CDD|238194 cd00317, cyclophilin, cyclophilin: cyclophilin-type peptidylprolyl
cis- trans isomerases. This family contains eukaryotic,
bacterial and archeal proteins which exhibit a
peptidylprolyl cis- trans isomerases activity (PPIase,
Rotamase) and in addition bind the immunosuppressive
drug cyclosporin (CsA). Immunosuppression in
vertebrates is believed to be the result of the
cyclophilin A-cyclosporin protein drug complex binding
to and inhibiting the protein-phosphatase calcineurin.
PPIase is an enzyme which accelerates protein folding by
catalyzing the cis-trans isomerization of the peptide
bonds preceding proline residues. Cyclophilins are a
diverse family in terms of function and have been
implicated in protein folding processes which depend on
catalytic /chaperone-like activities. This group
contains human cyclophilin 40, a co-chaperone of the
hsp90 chaperone system; human cyclophilin A, a
chaperone in the HIV-1 infectious process and; human
cyclophilin H, a component of the U4/U6 snRNP, whose
isomerization or chaperoning activities may play a role
in RNA splicing. .
Length = 146
Score = 140 bits (356), Expect = 8e-42
Identities = 59/106 (55%), Positives = 66/106 (62%), Gaps = 6/106 (5%)
Query: 183 VGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFMCQGGDFTNHNGTGGK 242
GRI I+L D P+T ENF L GF Y G++FHR+IP FM QGGD T G G
Sbjct: 6 KGRIVIELYGDEAPKTVENFLSLA--RGGF-YDGTTFHRVIPGFMIQGGDPTGTGG--GG 60
Query: 243 SIYGNKFEDENFILK-HTGPGVLSMANSGPNTNGSQFFLCTTKTEW 287
S G KF DENF LK H G LSMAN+GPNTNGSQFF+ T T
Sbjct: 61 SGPGYKFPDENFPLKYHHRRGTLSMANAGPNTNGSQFFITTAPTPH 106
Score = 61.5 bits (150), Expect = 7e-12
Identities = 22/45 (48%), Positives = 28/45 (62%), Gaps = 3/45 (6%)
Query: 10 VGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFV 54
GRI I+L D P+T ENF L GF Y G++FHR+IP F+
Sbjct: 6 KGRIVIELYGDEAPKTVENFLSLA--RGGF-YDGTTFHRVIPGFM 47
>gnl|CDD|223725 COG0652, PpiB, Peptidyl-prolyl cis-trans isomerase (rotamase) -
cyclophilin family [Posttranslational modification,
protein turnover, chaperones].
Length = 158
Score = 139 bits (353), Expect = 3e-41
Identities = 52/113 (46%), Positives = 63/113 (55%), Gaps = 9/113 (7%)
Query: 178 IGKQEVGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFMCQGGDFTNHN 237
I + G ITI+L D P+T NF L GF Y G+ FHR+IP FM QGGD T +
Sbjct: 3 ILETNKGDITIELYPDKAPKTVANFLQLVKE--GF-YDGTIFHRVIPGFMIQGGDPTGGD 59
Query: 238 GTGGKSIYGNKFEDENFILKH--TGPGVLSMANSG-PNTNGSQFFLCTTKTEW 287
GTGG F+DENF L G LSMA +G PN+NGSQFF+ +
Sbjct: 60 GTGGPGP---PFKDENFALNGDRHKRGTLSMARAGDPNSNGSQFFITVVDNPF 109
Score = 60.3 bits (147), Expect = 3e-11
Identities = 22/50 (44%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 5 IGKQEVGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFV 54
I + G ITI+L D P+T NF L GF Y G+ FHR+IP F+
Sbjct: 3 ILETNKGDITIELYPDKAPKTVANFLQLVKE--GF-YDGTIFHRVIPGFM 49
>gnl|CDD|215759 pfam00160, Pro_isomerase, Cyclophilin type peptidyl-prolyl
cis-trans isomerase/CLD. The peptidyl-prolyl cis-trans
isomerases, also known as cyclophilins, share this
domain of about 109 amino acids. Cyclophilins have been
found in all organisms studied so far and catalyze
peptidyl-prolyl isomerisation during which the peptide
bond preceding proline (the peptidyl-prolyl bond) is
stabilised in the cis conformation. Mammalian
cyclophilin A (CypA) is a major cellular target for the
immunosuppressive drug cyclosporin A (CsA). Other roles
for cyclophilins may include chaperone and cell
signalling function.
Length = 144
Score = 131 bits (332), Expect = 3e-38
Identities = 51/115 (44%), Positives = 61/115 (53%), Gaps = 11/115 (9%)
Query: 173 YMDIKIGKQEVGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFMCQGGD 232
++DI GRI I+L D P+T ENF LC +KGF Y G+ FHR+IP FM QGGD
Sbjct: 1 FLDITTNL---GRIVIELFGDEAPKTVENFLSLC--KKGF-YDGTIFHRVIPGFMIQGGD 54
Query: 233 FTNHNGTGGKSIYGNKFEDENFILKHTGPGVLSMANSGPNTNGSQFFLCTTKTEW 287
T G +SI DE G LSMA SGPN+ GSQFF+
Sbjct: 55 PTGPGTGGKRSI-----PDEFVSKLKHKRGTLSMARSGPNSAGSQFFITLGDAPH 104
Score = 63.8 bits (156), Expect = 1e-12
Identities = 26/54 (48%), Positives = 33/54 (61%), Gaps = 6/54 (11%)
Query: 1 MDIKIGKQEVGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFV 54
+DI GRI I+L D P+T ENF LC +KGF Y G+ FHR+IP F+
Sbjct: 2 LDITTNL---GRIVIELFGDEAPKTVENFLSLC--KKGF-YDGTIFHRVIPGFM 49
>gnl|CDD|238903 cd01922, cyclophilin_SpCYP2_like, cyclophilin_SpCYP2_like:
cyclophilin 2-like peptidylprolyl cis- trans isomerase
(PPIase) domain similar to Schizosaccharomyces pombe
cyp-2. These proteins bind their respective SNW
chromatin binding protein in autologous systems, in a
CsA independent manner indicating interaction with a
surface outside the PPIase active site. SNW proteins
play a basic and broad range role in signaling.
Length = 146
Score = 128 bits (323), Expect = 6e-37
Identities = 59/106 (55%), Positives = 74/106 (69%), Gaps = 5/106 (4%)
Query: 183 VGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFMCQGGDFTNHNGTGGK 242
+G IT++L ++ P+T +NF L +G+ Y G+ FHR+I DFM QGGD T G GG
Sbjct: 6 MGEITLELYWNHAPKTCKNFYELAK--RGY-YNGTIFHRLIKDFMIQGGDPTG-TGRGGA 61
Query: 243 SIYGNKFEDE-NFILKHTGPGVLSMANSGPNTNGSQFFLCTTKTEW 287
SIYG KFEDE + LKHTG G+LSMAN+GPNTNGSQFF+ T W
Sbjct: 62 SIYGKKFEDEIHPELKHTGAGILSMANAGPNTNGSQFFITLAPTPW 107
Score = 44.4 bits (105), Expect = 8e-06
Identities = 35/144 (24%), Positives = 61/144 (42%), Gaps = 32/144 (22%)
Query: 10 VGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFV--------------S 55
+G IT++L ++ P+T +NF L +G+ Y G+ FHR+I DF+ S
Sbjct: 6 MGEITLELYWNHAPKTCKNFYELAK--RGY-YNGTIFHRLIKDFMIQGGDPTGTGRGGAS 62
Query: 56 FMTK------HQSLKSRFSNLGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLF 109
K H LK + + +A + + FI P + KH +F
Sbjct: 63 IYGKKFEDEIHPELKHTGAGILSMANAGPNTNGSQFFITLA-------PTPWLDGKHTIF 115
Query: 110 GRIIR--VNLAKPQKVQQTSSKPV 131
GR+ + + +VQ + +P+
Sbjct: 116 GRVSKGMKVIENMVEVQTQTDRPI 139
>gnl|CDD|238908 cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclophilin-type
peptidylprolyl cis- trans isomerases (cyclophilins)
having a WD40 domain. This group consists of several
hypothetical and putative eukaryotic and bacterial
proteins which have a cyclophilin domain and a WD40
domain. Function of the protein is not known.
Length = 148
Score = 121 bits (304), Expect = 4e-34
Identities = 55/105 (52%), Positives = 68/105 (64%), Gaps = 5/105 (4%)
Query: 184 GRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFMCQGGDFTNHNGTGGKS 243
G I I+L + P+T ENF TH + Y + FHR+I FM Q GD T +GTGG+S
Sbjct: 7 GDIHIRLFPEEAPKTVENF---TTHARNGYYNNTIFHRVIKGFMIQTGDPTG-DGTGGES 62
Query: 244 IYGNKFEDE-NFILKHTGPGVLSMANSGPNTNGSQFFLCTTKTEW 287
I+G +FEDE + LKH P LSMAN+GPNTNGSQFF+ T T W
Sbjct: 63 IWGKEFEDEFSPSLKHDRPYTLSMANAGPNTNGSQFFITTVATPW 107
Score = 42.1 bits (99), Expect = 5e-05
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 11 GRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDF 53
G I I+L + P+T ENF TH + Y + FHR+I F
Sbjct: 7 GDIHIRLFPEEAPKTVENF---TTHARNGYYNNTIFHRVIKGF 46
>gnl|CDD|238904 cd01923, cyclophilin_RING, cyclophilin_RING: cyclophilin-type
peptidylprolyl cis- trans isomerases (cyclophilins)
having a modified RING finger domain. This group
includes the nuclear proteins, Human hCyP-60 and
Caenorhabditis elegans MOG-6 which, compared to the
archetypal cyclophilin Human cyclophilin A exhibit
reduced peptidylprolyl cis- trans isomerase activity and
lack a residue important for cyclophilin binding. Human
hCyP-60 has been shown to physically interact with the
proteinase inhibitor peptide eglin c and; C. elegans
MOG-6 to physically interact with MEP-1, a nuclear zinc
finger protein. MOG-6 has been shown to function in
germline sex determination.
Length = 159
Score = 117 bits (295), Expect = 1e-32
Identities = 54/98 (55%), Positives = 66/98 (67%), Gaps = 5/98 (5%)
Query: 184 GRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFMCQGGDFTNHNGTGGKS 243
G + ++L D P+ ENF LC +KG+ Y G+ FHR I +FM QGGD T G GG+S
Sbjct: 9 GDLNLELHCDKAPKACENFIKLC--KKGY-YDGTIFHRSIRNFMIQGGDPTG-TGRGGES 64
Query: 244 IYGNKFEDE-NFILKHTGPGVLSMANSGPNTNGSQFFL 280
I+G F+DE L H G GVLSMANSGPNTNGSQFF+
Sbjct: 65 IWGKPFKDEFKPNLSHDGRGVLSMANSGPNTNGSQFFI 102
Score = 42.0 bits (99), Expect = 7e-05
Identities = 18/44 (40%), Positives = 27/44 (61%), Gaps = 3/44 (6%)
Query: 11 GRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFV 54
G + ++L D P+ ENF LC +KG+ Y G+ FHR I +F+
Sbjct: 9 GDLNLELHCDKAPKACENFIKLC--KKGY-YDGTIFHRSIRNFM 49
>gnl|CDD|238909 cd01928, Cyclophilin_PPIL3_like, Cyclophilin_PPIL3_like. Proteins
similar to Human cyclophilin-like peptidylprolyl cis-
trans isomerase (PPIL3). Members of this family lack a
key residue important for cyclosporin binding: the
tryptophan residue corresponding to W121 in human
hCyP-18a; most members have a histidine at this
position. The exact function of the protein is not
known.
Length = 153
Score = 115 bits (291), Expect = 4e-32
Identities = 54/99 (54%), Positives = 63/99 (63%), Gaps = 5/99 (5%)
Query: 183 VGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFMCQGGDFTNHNGTGGK 242
+G I I+L D P+ ENF LC G+ Y G FHR I FM Q GD T G GG+
Sbjct: 9 LGDIKIELFCDDCPKACENFLALCA--SGY-YNGCIFHRNIKGFMVQTGDPTG-TGKGGE 64
Query: 243 SIYGNKFEDENF-ILKHTGPGVLSMANSGPNTNGSQFFL 280
SI+G KFEDE LKH GV+SMAN+GPNTNGSQFF+
Sbjct: 65 SIWGKKFEDEFRETLKHDSRGVVSMANNGPNTNGSQFFI 103
Score = 44.3 bits (105), Expect = 1e-05
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 10 VGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFV 54
+G I I+L D P+ ENF LC G+ Y G FHR I F+
Sbjct: 9 LGDIKIELFCDDCPKACENFLALCA--SGY-YNGCIFHRNIKGFM 50
>gnl|CDD|238906 cd01925, cyclophilin_CeCYP16-like, cyclophilin_CeCYP16-like:
cyclophilin-type peptidylprolyl cis- trans isomerase)
(PPIase) domain similar to Caenorhabditis elegans
cyclophilin 16. C. elegans CeCYP-16, compared to the
archetypal cyclophilin Human cyclophilin A has, a
reduced peptidylprolyl cis- trans isomerase activity, is
cyclosporin insensitive and shows an altered substrate
preference favoring, hydrophobic, acidic or amide amino
acids. Most members of this subfamily have a glutamate
residue in the active site at the position equivalent to
a tryptophan (W121 in Human cyclophilin A), which has
been shown to be important for cyclophilin binding.
Length = 171
Score = 93.2 bits (232), Expect = 3e-23
Identities = 45/106 (42%), Positives = 63/106 (59%), Gaps = 5/106 (4%)
Query: 183 VGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFMCQGGDFTNHNGTGGK 242
G I I+L P+ NF LC +G+ Y + FHR++P F+ QGGD T GTGG+
Sbjct: 14 AGDIDIELWSKEAPKACRNFIQLCL--EGY-YDNTIFHRVVPGFIIQGGDPTG-TGTGGE 69
Query: 243 SIYGNKFEDE-NFILKHTGPGVLSMANSGPNTNGSQFFLCTTKTEW 287
SIYG F+DE + L+ G++ MAN+G ++NGSQFF K +
Sbjct: 70 SIYGEPFKDEFHSRLRFNRRGLVGMANAGDDSNGSQFFFTLDKADE 115
Score = 36.6 bits (85), Expect = 0.006
Identities = 31/123 (25%), Positives = 45/123 (36%), Gaps = 30/123 (24%)
Query: 10 VGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFV--------------S 55
G I I+L P+ NF LC +G+ Y + FHR++P F+ S
Sbjct: 14 AGDIDIELWSKEAPKACRNFIQLCL--EGY-YDNTIFHRVVPGFIIQGGDPTGTGTGGES 70
Query: 56 FMTK------HQSLKSRFSNLGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLF 109
+ H L+ L G+A DD + F D KH LF
Sbjct: 71 IYGEPFKDEFHSRLRFNRRGLVGMANAGDDSNGSQFFFTLD-------KADELNNKHTLF 123
Query: 110 GRI 112
G++
Sbjct: 124 GKV 126
>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33)
and similar proteins. This subfamily corresponds to the
RRM of Cyp33, also termed peptidyl-prolyl cis-trans
isomerase E (PPIase E), or cyclophilin E, or rotamase E.
Cyp33 is a nuclear RNA-binding cyclophilin with an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal PPIase domain. Cyp33 possesses
RNA-binding activity and preferentially binds to
polyribonucleotide polyA and polyU, but hardly to polyG
and polyC. It binds specifically to mRNA, which can
stimulate its PPIase activity. Moreover, Cyp33 interacts
with the third plant homeodomain (PHD3) zinc finger
cassette of the mixed lineage leukemia (MLL)
proto-oncoprotein and a poly-A RNA sequence through its
RRM domain. It further mediates downregulation of the
expression of MLL target genes HOXC8, HOXA9, CDKN1B, and
C-MYC, in a proline isomerase-dependent manner. Cyp33
also possesses a PPIase activity that catalyzes
cis-trans isomerization of the peptide bond preceding a
proline, which has been implicated in the stimulation of
folding and conformational changes in folded and
unfolded proteins. The PPIase activity can be inhibited
by the immunosuppressive drug cyclosporin A. .
Length = 73
Score = 79.6 bits (197), Expect = 2e-19
Identities = 38/71 (53%), Positives = 45/71 (63%), Gaps = 24/71 (33%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKH----------------------- 106
+GGLAEEVD+KVL+AAFIPFGD+ DIQ+PLDYET+KH
Sbjct: 3 VGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNMNE 62
Query: 107 -QLFGRIIRVN 116
+LFGR IRVN
Sbjct: 63 SELFGRTIRVN 73
>gnl|CDD|238902 cd01921, cyclophilin_RRM, cyclophilin_RRM: cyclophilin-type
peptidylprolyl cis- trans isomerase domain occuring with
a C-terminal RNA recognition motif domain (RRM). This
subfamily of the cyclophilin domain family contains a
number of eukaryotic cyclophilins having the RRM domain
including the nuclear proteins: human hCyP-57,
Arabidopsis thaliana AtCYP59, Caenorhabditis elegans
CeCyP-44 and Paramecium tetrurelia Kin241. The Kin241
protein has been shown to have a role in cell
morphogenesis.
Length = 166
Score = 75.1 bits (185), Expect = 2e-16
Identities = 41/109 (37%), Positives = 53/109 (48%), Gaps = 12/109 (11%)
Query: 183 VGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFMCQGGDFTNHNGTGGK 242
+G + I L D P NF LC K Y F+ + DF+ Q GD T G GG+
Sbjct: 6 LGDLVIDLFTDECPLACLNFLKLC---KLKYYNFCLFYNVQKDFIAQTGDPTG-TGAGGE 61
Query: 243 SIYGNK-------FEDE-NFILKHTGPGVLSMANSGPNTNGSQFFLCTT 283
SIY FE E +LKH+ G +SM N+G N NGSQF++
Sbjct: 62 SIYSQLYGRQARFFEPEILPLLKHSKKGTVSMVNAGDNLNGSQFYITLG 110
Score = 34.2 bits (79), Expect = 0.036
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 3/45 (6%)
Query: 10 VGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFV 54
+G + I L D P NF LC K Y F+ + DF+
Sbjct: 6 LGDLVIDLFTDECPLACLNFLKLC---KLKYYNFCLFYNVQKDFI 47
>gnl|CDD|140248 PTZ00221, PTZ00221, cyclophilin; Provisional.
Length = 249
Score = 63.0 bits (153), Expect = 1e-11
Identities = 37/117 (31%), Positives = 56/117 (47%), Gaps = 13/117 (11%)
Query: 171 QVYMDIKIGKQEVGRITIQLRYDLVPRTAENFRCLCTHEKG--------FGYQGSSFHRI 222
+ ++DI IG GR+ +L D+VP T ENFR L T G Y + H +
Sbjct: 54 RAFLDISIGDVLAGRLVFELFEDVVPETVENFRALITGSCGIDTNTGVKLDYLYTPVHHV 113
Query: 223 IPDF-MCQGGDFTNHNGTGGKSIYGNKFEDENFILKHTGPGVLSMANSGPNTNGSQF 278
+ + G+ + N S G DE + +HT G+L+M + GP+T+GS F
Sbjct: 114 DRNNNIIVLGELDSFN----VSSTGTPIADEGYRHRHTERGLLTMISEGPHTSGSVF 166
Score = 42.5 bits (100), Expect = 1e-04
Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 8/57 (14%)
Query: 1 MDIKIGKQEVGRITIQLRYDLVPRTAENFRCLCTHEKG--------FGYQGSSFHRI 49
+DI IG GR+ +L D+VP T ENFR L T G Y + H +
Sbjct: 57 LDISIGDVLAGRLVFELFEDVVPETVENFRALITGSCGIDTNTGVKLDYLYTPVHHV 113
>gnl|CDD|238901 cd01920, cyclophilin_EcCYP_like, cyclophilin_EcCYP_like:
cyclophilin-type A-like peptidylprolyl cis- trans
isomerase (PPIase) domain similar to the cytosolic E.
coli cyclophilin A and Streptomyces antibioticus
SanCyp18. Compared to the archetypal cyclophilin Human
cyclophilin A, these have reduced affinity for
cyclosporin A. E. coli cyclophilin A has a similar
peptidylprolyl cis- trans isomerase activity to the
human cyclophilin A. Most members of this subfamily
contain a phenylalanine residue at the position
equivalent to Human cyclophilin W121, where a tyrptophan
has been shown to be important for cyclophilin binding.
Length = 155
Score = 55.9 bits (135), Expect = 1e-09
Identities = 34/100 (34%), Positives = 47/100 (47%), Gaps = 11/100 (11%)
Query: 184 GRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFMCQGGDFTNHNGTGGKS 243
G I ++L D P T ENF KGF Y + FHR+I F+ QGG FT
Sbjct: 7 GDIVVELYDDKAPITVENFLAYV--RKGF-YDNTIFHRVISGFVIQGGGFT----PDLAQ 59
Query: 244 IYGNK--FEDENFILKHTGPGVLSMANSG-PNTNGSQFFL 280
K + L +T G ++MA + P++ SQFF+
Sbjct: 60 KETLKPIKNEAGNGLSNTR-GTIAMARTNAPDSATSQFFI 98
Score = 43.2 bits (102), Expect = 2e-05
Identities = 19/44 (43%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 11 GRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFV 54
G I ++L D P T ENF KGF Y + FHR+I FV
Sbjct: 7 GDIVVELYDDKAPITVENFLAYV--RKGF-YDNTIFHRVISGFV 47
>gnl|CDD|182734 PRK10791, PRK10791, peptidyl-prolyl cis-trans isomerase B (rotamase
B); Provisional.
Length = 164
Score = 47.5 bits (113), Expect = 9e-07
Identities = 36/98 (36%), Positives = 50/98 (51%), Gaps = 7/98 (7%)
Query: 184 GRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFMCQGGDFTNHNGTGGKS 243
G I I+ D P T +NF C +GF Y + FHR+I FM QGG F G K+
Sbjct: 9 GDIVIKTFDDKAPETVKNFLDYCR--EGF-YNNTIFHRVINGFMIQGGGF--EPGMKQKA 63
Query: 244 IYGNKFEDENFILKHTGPGVLSMANSG-PNTNGSQFFL 280
+ N LK+T G L+MA + P++ +QFF+
Sbjct: 64 TKEPIKNEANNGLKNT-RGTLAMARTQAPHSATAQFFI 100
Score = 30.2 bits (68), Expect = 0.80
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 11 GRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFV 54
G I I+ D P T +NF C +GF Y + FHR+I F+
Sbjct: 9 GDIVIKTFDDKAPETVKNFLDYCR--EGF-YNNTIFHRVINGFM 49
>gnl|CDD|238905 cd01924, cyclophilin_TLP40_like, cyclophilin_TLP40_like:
cyclophilin-type peptidylprolyl cis- trans isomerases
(cyclophilins) similar ot the Spinach thylakoid lumen
protein TLP40. Compared to the archetypal cyclophilin
Human cyclophilin A, these proteins have similar
peptidylprolyl cis- trans isomerase activity and reduced
affinity for cyclosporin A. Spinach TLP40 has been shown
to have a dual function as a folding catalyst and
regulator of dephosphorylation.
Length = 176
Score = 44.7 bits (106), Expect = 1e-05
Identities = 39/123 (31%), Positives = 49/123 (39%), Gaps = 30/123 (24%)
Query: 184 GRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFMCQGGDFTNHNGTG--- 240
G ITI L P TA NF L E+GF Y G FHR+ F+ Q GD N
Sbjct: 7 GTITIVLDGYNAPVTAGNFVDLV--ERGF-YDGMEFHRVEGGFVVQTGDPQGKNPGFPDP 63
Query: 241 -----------------GKSIYGNKFE-----DENFILKHTGPGVLSMANS--GPNTNGS 276
+ +YG E DE +L G ++MA + PN+ S
Sbjct: 64 ETGKSRTIPLEIKPEGQKQPVYGKTLEEAGRYDEQPVLPFNAFGAIAMARTEFDPNSASS 123
Query: 277 QFF 279
QFF
Sbjct: 124 QFF 126
>gnl|CDD|182824 PRK10903, PRK10903, peptidyl-prolyl cis-trans isomerase A (rotamase
A); Provisional.
Length = 190
Score = 43.7 bits (103), Expect = 3e-05
Identities = 21/52 (40%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 183 VGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFMCQGGDFT 234
G I ++L P + +NF + GF Y ++FHR+IP FM QGG FT
Sbjct: 37 AGNIELELNSQKAPVSVKNF--VDYVNSGF-YNNTTFHRVIPGFMIQGGGFT 85
Score = 29.8 bits (67), Expect = 1.1
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 10 VGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFV 54
G I ++L P + +NF + GF Y ++FHR+IP F+
Sbjct: 37 AGNIELELNSQKAPVSVKNF--VDYVNSGF-YNNTTFHRVIPGFM 78
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor 3b
(SF3B), 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 is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 74
Score = 37.2 bits (87), Expect = 8e-04
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 24/71 (33%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQ---------------------- 107
+G L E+V +++L FI G +V++ +P D T+ HQ
Sbjct: 3 VGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNM 62
Query: 108 --LFGRIIRVN 116
L+G+ IRVN
Sbjct: 63 IKLYGKPIRVN 73
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 35.6 bits (83), Expect = 0.003
Identities = 11/43 (25%), Positives = 21/43 (48%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRI 112
+G L + ++ L F FG + +++ D ET K + F +
Sbjct: 4 VGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFV 46
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 35.0 bits (80), Expect = 0.013
Identities = 18/41 (43%), Positives = 26/41 (63%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFG 110
+GGL+ DD L AF FGD+VD ++ +D ET + + FG
Sbjct: 39 IGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFG 79
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis. TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 33.5 bits (77), Expect = 0.016
Identities = 16/40 (40%), Positives = 26/40 (65%)
Query: 71 GGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFG 110
G L+ E+D + L AAF PFG++ D ++ D +T K + +G
Sbjct: 5 GDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYG 44
>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8
(NOL8) and similar proteins. This model corresponds to
the RRM of NOL8 (also termed Nop132) encoded by a novel
NOL8 gene that is up-regulated in the majority of
diffuse-type, but not intestinal-type, gastric cancers.
Thus, NOL8 may be a good molecular target for treatment
of diffuse-type gastric cancer. Also, NOL8 is a
phosphorylated protein that contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), suggesting
NOL8 is likely to function as a novel RNA-binding
protein. It may be involved in regulation of gene
expression at the post-transcriptional level or in
ribosome biogenesis in cancer cells.
Length = 78
Score = 32.9 bits (76), Expect = 0.027
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRI-IRVNLAKPQKVQQTSS 128
+GGL+ V + L F FG + D+++ + + F I +R + A+ +K + T +
Sbjct: 4 VGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKSTLN 63
Query: 129 KPVW 132
W
Sbjct: 64 GTKW 67
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 34.5 bits (79), Expect = 0.058
Identities = 16/43 (37%), Positives = 25/43 (58%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRI 112
+G L + ++ L F PFGD+ D+Q+ D ET + + FG I
Sbjct: 191 VGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFI 233
>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 = 31.8 bits (73), Expect = 0.060
Identities = 11/43 (25%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRI 112
+G L + ++ L F FG + I++ D ET + + F +
Sbjct: 3 VGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFV 44
>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 = 31.2 bits (71), Expect = 0.091
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFG 110
+G L+ VDD+ L A F FG +V ++ D ET + + FG
Sbjct: 4 VGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFG 44
>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM3 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC 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 AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. 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 = 85
Score = 31.2 bits (70), Expect = 0.12
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 73 LAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRIIRVN 116
L+ E D+ VL F PFG + ++++ D+ T K + FG + N
Sbjct: 9 LSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTN 52
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM3 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB 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 AU-rich RNA element (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 = 86
Score = 30.8 bits (69), Expect = 0.17
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 73 LAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRIIRVN 116
LA + D+ +L F PFG + ++++ D+ T K + FG + N
Sbjct: 11 LAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTN 54
>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM3 in
hnRNP R, hnRNP Q, and APOBEC-1 complementation factor
(ACF). hnRNP R is a ubiquitously expressed nuclear
RNA-binding protein that specifically bind mRNAs with a
preference for poly(U) stretches and has been implicated
in mRNA processing and mRNA transport, and also acts as
a regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as a
component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA transport.
ACF is an RNA-binding subunit of a core complex that
interacts with apoB mRNA to facilitate C to U RNA
editing. It may also act as an apoB mRNA recognition
factor and chaperone and play a key role in cell growth
and differentiation. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members contain three conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains).
Length = 72
Score = 29.5 bits (67), Expect = 0.31
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 16/64 (25%)
Query: 73 LAEEVDDKVLNAAFIPFGDLVDIQMPLDY----------------ETEKHQLFGRIIRVN 116
L ++ L F +G++ ++ DY E +L G I V+
Sbjct: 9 LPLSTTEEQLRELFSEYGEVERVKKIKDYAFVHFEERDDAVKAMEEMNGKELEGSPIEVS 68
Query: 117 LAKP 120
LAKP
Sbjct: 69 LAKP 72
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0 is a UUAG-specific nuclear RNA
binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 29.8 bits (67), Expect = 0.32
Identities = 17/56 (30%), Positives = 30/56 (53%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRIIRVNLAKPQKVQQ 125
+GGL+ + K L F FG++VD + +D T + + FG ++ + A +KV
Sbjct: 3 VGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLD 58
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate
and cooperate with hnRNP particles to regulate
adenylate-uridylate-rich elements (AU-rich element or
ARE)-containing mRNAs. DAZAP1 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal proline-rich domain. .
Length = 80
Score = 29.6 bits (67), Expect = 0.34
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRI 112
+GGL V + L F FG + ++ + D+E ++ + FG I
Sbjct: 7 VGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFI 49
>gnl|CDD|237108 PRK12467, PRK12467, peptide synthase; Provisional.
Length = 3956
Score = 32.4 bits (74), Expect = 0.35
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 14/79 (17%)
Query: 53 FVSFMTKHQSLKSRFSNL-GGLAEEVDDKVLNAAFIPFGDLV-------DIQMPLDYETE 104
F + + +H+SL++RF G + +D + + IP DL + Q+ E
Sbjct: 93 FDALVARHESLRTRFVQDEEGFRQVIDASL--SLTIPLDDLANEQGRARESQIEAYINEE 150
Query: 105 KHQLF----GRIIRVNLAK 119
+ F G ++RV L +
Sbjct: 151 VARPFDLANGPLLRVRLLR 169
Score = 31.7 bits (72), Expect = 0.52
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 8/73 (10%)
Query: 53 FVSFMTKHQSLKSRFSNLGGLAEEVDDKVLNAAF----IPFGDLVDIQMPLDYETEKHQL 108
F + + +H+SL++ F G +V V + + D + Q+ + E E Q
Sbjct: 1160 FDALVARHESLRTTFVQEDGRTRQVIHPVGSLTLEEPLLLAADKDEAQLKVYVEAEARQP 1219
Query: 109 F----GRIIRVNL 117
F G ++RV L
Sbjct: 1220 FDLEQGPLLRVGL 1232
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0, a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP A/B is an RNA unwinding
protein with a high affinity for G- followed by U-rich
regions. It has also been identified as an
APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 29.6 bits (67), Expect = 0.36
Identities = 14/39 (35%), Positives = 26/39 (66%)
Query: 71 GGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLF 109
GGL+ E ++ + F FG++V+I++P+D +T K + F
Sbjct: 5 GGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGF 43
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM3 of HuR,
also termed ELAV-like protein 1 (ELAV-1), 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. Like other
Hu proteins, HuR 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 AU-rich RNA element (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 = 84
Score = 29.7 bits (66), Expect = 0.39
Identities = 13/44 (29%), Positives = 25/44 (56%)
Query: 73 LAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRIIRVN 116
L ++ D+ +L F PFG + ++++ D+ T K + FG + N
Sbjct: 9 LGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTN 52
>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins
family. This subfamily corresponds to the RRM3 of the
Hu proteins family which represent 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. 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 = 29.6 bits (67), Expect = 0.40
Identities = 12/47 (25%), Positives = 23/47 (48%)
Query: 72 GLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRIIRVNLA 118
L + D+ +L F PFG + ++++ D T K + +G + N
Sbjct: 8 NLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYE 54
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 32.0 bits (72), Expect = 0.41
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLF 109
+G ++ E+ + + AF PFG + I M D T KH+ F
Sbjct: 112 VGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGF 151
>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway; it binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 75
Score = 29.3 bits (66), Expect = 0.53
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 71 GGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFG 110
GGL +V ++ F FG +VD Q+ D++T + + FG
Sbjct: 5 GGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFG 44
>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 = 29.3 bits (66), Expect = 0.59
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 82 LNAAFIPFGDLVDIQMPLDYETEKHQLFGRI 112
L F FG+L ++ + +D ++ K + F +
Sbjct: 19 LEKLFSKFGELSEVHVAIDKKSGKSKGFAYV 49
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM2
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA). However, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 75
Score = 29.0 bits (65), Expect = 0.63
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFG 110
+G L+ EV D L AAF F D ++ D ++ + + +G
Sbjct: 4 VGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYG 44
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 28.9 bits (64), Expect = 0.71
Identities = 14/41 (34%), Positives = 23/41 (56%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFG 110
+G L+ E+ + AAF PFG + D ++ D T K + +G
Sbjct: 6 VGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYG 46
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM2
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal, highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 28.9 bits (64), Expect = 0.83
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFG 110
+G L+ E+ + + +AF PFG + D ++ D T K + +G
Sbjct: 6 VGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 46
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of Oskar
(Osk) expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 79
Score = 28.4 bits (63), Expect = 0.93
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 73 LAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFG 110
L +E D L F+PFG+++ ++ +D +T + FG
Sbjct: 12 LPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFG 49
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional and
post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 28.4 bits (63), Expect = 0.99
Identities = 11/40 (27%), Positives = 26/40 (65%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLF 109
+GGL+ + ++ + F FG++ +I++P+D +T + + F
Sbjct: 4 VGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGF 43
>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains 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 effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contains
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-4, can activate cardiac troponin T (cTNT)
exon 5 inclusion. CELF-5, expressed in brain, is also
known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein 6
(BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent manner
and can activate inclusion via multiple copies of a
single element, MSE2. CELF-6 also promotes skipping of
exon 11 of insulin receptor, a known target of CELF
activity that is expressed in kidney. In addition to
three highly conserved RRMs, CELF-6 also possesses
numerous potential phosphorylation sites, a potential
nuclear localization signal (NLS) at the C terminus, and
an alanine-rich region within the divergent linker
region. .
Length = 79
Score = 28.3 bits (63), Expect = 1.2
Identities = 16/54 (29%), Positives = 27/54 (50%)
Query: 73 LAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRIIRVNLAKPQKVQQT 126
L +E D L F+PFG+++ ++ +D T + + FG + N A Q Q
Sbjct: 12 LPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA 65
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long C-terminal glycine-rich domain that
contains a potential ATP/GTP binding loop. .
Length = 75
Score = 28.0 bits (62), Expect = 1.2
Identities = 16/54 (29%), Positives = 29/54 (53%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRIIRVNLAKPQKV 123
+GGL+ + K L F FG++ D + +D T + + FG I+ + + +KV
Sbjct: 4 VGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKV 57
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 76
Score = 28.2 bits (63), Expect = 1.2
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLF 109
+G ++ E+ + + AF PFG + I M D T KH+ F
Sbjct: 5 VGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGF 44
>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8 and similar proteins. This subfamily
corresponds to the RRM3 of NGR1 and NAM8. NGR1, also
termed RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA) in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 72
Score = 28.0 bits (63), Expect = 1.2
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 71 GGLAEEVDDKVLNAAFIPFGDLVDIQMP 98
GGL V + L + F PFG++V +++P
Sbjct: 7 GGLDPAVTEDELRSLFGPFGEIVYVKIP 34
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), in the
middle and an RGG box rich in glycine and arginine
residues in the C-terminal part. Each of RRMs can bind
solely to the UUAG sequence specifically. .
Length = 74
Score = 28.0 bits (62), Expect = 1.3
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRII 113
+GGL+ + K L F FG++VD + LD T + + FG ++
Sbjct: 3 IGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVL 46
>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core protein
A1, and is an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced transcripts
of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can
shuttle between the nucleus and the cytoplasm. Thus, it
may be involved in transport of cellular RNAs, including
the packaging of pre-mRNA into hnRNP particles and
transport of poly A+ mRNA from the nucleus to the
cytoplasm. The cytoplasmic hnRNP A1 has high affinity
with AU-rich elements, whereas the nuclear hnRNP A1 has
high affinity with a polypyrimidine stretch bordered by
AG at the 3' ends of introns. hnRNP A1 is also involved
in the replication of an RNA virus, such as mouse
hepatitis virus (MHV), through an interaction with the
transcription-regulatory region of viral RNA. hnRNP A1,
together with the scaffold protein septin 6, serves as
host protein to form a complex with NS5b and viral RNA,
and further plays important roles in the replication of
Hepatitis C virus (HCV). hnRNP A1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. The
RRMs of hnRNP A1 play an important role in silencing the
exon and the glycine-rich domain is responsible for
protein-protein interactions. .
Length = 81
Score = 28.1 bits (62), Expect = 1.4
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRIIRVNL--------AKPQ 121
+GGL+ E D+ L + F +G L D + D T++ + FG + ++ A+P
Sbjct: 7 IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNARPH 66
Query: 122 KVQQTSSKP 130
KV +P
Sbjct: 67 KVDGRVVEP 75
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM3 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA translation
and deadenylation. CELF-1 is strongly expressed in all
adult and fetal tissues tested. Human CELF-1 is a
nuclear and cytoplasmic RNA-binding protein that
regulates multiple aspects of nuclear and cytoplasmic
mRNA processing, with implications for onset of type 1
myotonic dystrophy (DM1), a neuromuscular disease
associated with an unstable CUG triplet expansion in the
3'-UTR (3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element involved
in translational control of oskar mRNA in Drosophila,
and share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 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 two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it binds preferentially
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contain three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are important
for localization in the cytoplasm. The splicing
activation or repression activity of CELF-2 on some
specific substrates is mediated by RRM1/RRM2. Both, RRM1
and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 92
Score = 28.5 bits (63), Expect = 1.4
Identities = 16/54 (29%), Positives = 27/54 (50%)
Query: 73 LAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRIIRVNLAKPQKVQQT 126
L +E D+ L F+PFG++V ++ +D +T + FG + N Q Q
Sbjct: 15 LPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQA 68
>gnl|CDD|237154 PRK12644, PRK12644, putative monovalent cation/H+ antiporter
subunit A; Reviewed.
Length = 965
Score = 30.3 bits (69), Expect = 1.5
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 106 HQLFGRIIRVNLAKPQKVQQTSSKPVWASDTWLQKHAGETLDPEN 150
++ FGR RV+ A + + TWL+ AG TL PE
Sbjct: 763 NRRFGRAPRVSDAAGRAAGAAAKSAAATRRTWLR--AGRTLAPER 805
>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM3 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells. And it also
regulates the neurite elongation and morphological
differentiation. HuD specifically bound poly(A) RNA.
Like other Hu proteins, HuD 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 = 86
Score = 28.1 bits (62), Expect = 1.5
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 73 LAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRIIRVN 116
L+ + D+ VL F PFG + ++++ D+ T K + FG + N
Sbjct: 11 LSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTN 54
>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate
RNA-binding protein RBM23, RBM39 and similar proteins.
This subfamily corresponds to the RRM2 of RBM39 (also
termed HCC1), a nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Although the
cellular function of RBM23 remains unclear, it shows
high sequence homology to RBM39 and contains two RRMs.
It may possibly function as a pre-mRNA splicing factor.
.
Length = 73
Score = 27.6 bits (62), Expect = 1.6
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 71 GGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRI 112
G L + + L F PFG++ +Q+ D ET + + +G I
Sbjct: 4 GNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFI 45
>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 = 27.9 bits (63), Expect = 1.8
Identities = 20/75 (26%), Positives = 29/75 (38%), Gaps = 10/75 (13%)
Query: 54 VSFMTKHQSLKSRFSNLGGL--AEEVDDKV----LNAAFIPFGDLVD----IQMPLDYET 103
+ F + LK FS G + A V DK+ AF+ F ++ + E
Sbjct: 8 LPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAED 67
Query: 104 EKHQLFGRIIRVNLA 118
L GR + V LA
Sbjct: 68 SGLSLDGRRLIVTLA 82
>gnl|CDD|240176 cd05155, APH_ChoK_like_1, Uncharacterized bacterial proteins with
similarity to Aminoglycoside 3'-phosphotransferase (APH)
and Choline kinase (ChoK) family members. The APH/ChoK
subfamily is part of a larger superfamily that includes
the catalytic domains of other kinases, such as the
typical serine/threonine/tyrosine protein kinases (PKs),
RIO kinases, actin-fragmin kinase (AFK), and
phosphoinositide 3-kinase (PI3K). This family is
composed of APH, ChoK, ethanolamine kinase (ETNK),
macrolide 2'-phosphotransferase (MPH2'), an unusual
homoserine kinase, and uncharacterized proteins with
similarity to the N-terminal domain of acyl-CoA
dehydrogenase 10 (ACAD10). The members of this family
catalyze the transfer of the gamma-phosphoryl group from
ATP (or CTP) to small molecule substrates, such as
aminoglycosides, macrolides, choline, ethanolamine, and
homoserine. Phosphorylation of the antibiotics,
aminoglycosides, and macrolides leads to their
inactivation and to bacterial antibiotic resistance.
Phosphorylation of choline, ethanolamine, and homoserine
serves as precursors to the synthesis of important
biological compounds, such as the major phospholipids,
phosphatidylcholine and phosphatidylethanolamine and the
amino acids, threonine, methionine, and isoleucine.
Length = 235
Score = 29.2 bits (66), Expect = 2.0
Identities = 15/42 (35%), Positives = 16/42 (38%), Gaps = 12/42 (28%)
Query: 132 WASDTWLQKHAGETLDPENQIDP---AEKLAA------SIDP 164
W+ WL GET DP AE LA IDP
Sbjct: 70 WSVYRWL---EGETATAAALSDPSEFAEDLADFLAALRQIDP 108
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to the
RRM domain of hnRNP G, also termed glycoprotein p43 or
RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several pre-mRNAs.
Moreover, hnRNP G may function as a regulator of
transcription for SREBP-1c and GnRH1. Research has shown
that hnRNP G may also act as a tumor-suppressor since it
upregulates the Txnip gene and promotes the fidelity of
DNA end-joining activity. In addition, hnRNP G appears
to play a critical role in proper neural development of
zebrafish and frog embryos. The family also includes
several paralogs of hnRNP G, such as hRBMY and hnRNP G-T
(also termed RNA-binding motif protein,
X-linked-like-2). Both, hRBMY and hnRNP G-T, are
exclusively expressed in testis and critical for male
fertility. Like hnRNP G, hRBMY and hnRNP G-T interact
with factors implicated in the regulation of pre-mRNA
splicing, such as hTra2-beta1 and T-STAR. Although
members in this family share a high conserved N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), they
appear to recognize different RNA targets. For instance,
hRBMY interacts specifically with a stem-loop structure
in which the loop is formed by the sequence CA/UCAA. In
contrast, hnRNP G associates with single stranded RNA
sequences containing a CCA/C motif. In addition to the
RRM, hnRNP G contains a nascent transcripts targeting
domain (NTD) in the middle region and a novel auxiliary
RNA-binding domain (RBD) in its C-terminal region. The
C-terminal RBD exhibits distinct RNA binding
specificity, and would play a critical role in the
regulation of alternative splicing by hnRNP G. .
Length = 80
Score = 27.6 bits (62), Expect = 2.1
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFG 110
+ GL+ +K L A F FG + ++ + D ET + + FG
Sbjct: 6 VSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFG 46
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein 3
(RBM3) and similar proteins. This subfamily corresponds
to the RRM domain of two structurally related
heterogenous nuclear ribonucleoproteins, CIRBP (also
termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL),
both of which belong to a highly conserved cold shock
proteins family. The cold shock proteins can be induced
after exposure to a moderate cold-shock and other
cellular stresses such as UV radiation and hypoxia.
CIRBP and RBM3 may function in posttranscriptional
regulation of gene expression by binding to different
transcripts, thus allowing the cell to response rapidly
to environmental signals. However, the kinetics and
degree of cold induction are different between CIRBP and
RBM3. Tissue distribution of their expression is
different. CIRBP and RBM3 may be differentially
regulated under physiological and stress conditions and
may play distinct roles in cold responses of cells.
CIRBP, also termed glycine-rich RNA-binding protein
CIRP, is localized in the nucleus and mediates the
cold-induced suppression of cell cycle progression.
CIRBP also binds DNA and possibly serves as a chaperone
that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore, RBM3
may be essential for cell proliferation and mitosis.
Both, CIRBP and RBM3, contain an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), that is
involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 27.5 bits (61), Expect = 2.4
Identities = 11/41 (26%), Positives = 25/41 (60%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFG 110
+GGL+ + +++ L F +G + ++ + D ET++ + FG
Sbjct: 5 IGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFG 45
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), in the middle and an RGG
box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 27.3 bits (60), Expect = 2.8
Identities = 12/40 (30%), Positives = 25/40 (62%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLF 109
+GGL+ + ++ + F FG++ I++P+D +T K + F
Sbjct: 4 VGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGF 43
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 73
Score = 26.8 bits (60), Expect = 2.9
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFG 110
+GGL E+V ++ L F +G++ +++ D ET K + F
Sbjct: 4 VGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFA 44
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 28.8 bits (63), Expect = 3.1
Identities = 18/85 (21%), Positives = 31/85 (36%), Gaps = 24/85 (28%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKH----------------------- 106
+G L +V ++ L F FG + +++ D ET K
Sbjct: 120 VGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNG 179
Query: 107 -QLFGRIIRVNLAKPQKVQQTSSKP 130
+L GR +RV A+P ++
Sbjct: 180 KELEGRPLRVQKAQPASQPRSELSN 204
>gnl|CDD|178462 PLN02874, PLN02874, 3-hydroxyisobutyryl-CoA hydrolase-like protein.
Length = 379
Score = 29.0 bits (65), Expect = 3.5
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 75 EEVDDKVLNAAFIPFGDLVDIQMPLDYE 102
+EV D+ ++ F PF ++Q+P + E
Sbjct: 342 DEVTDEKVDLVFQPFKAREELQLPEEEE 369
>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 = 26.5 bits (59), Expect = 3.9
Identities = 7/31 (22%), Positives = 16/31 (51%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLD 100
+G L + ++ L F FG++ +++ D
Sbjct: 3 VGNLPPDTTEEDLRELFSKFGEIESVRIVRD 33
>gnl|CDD|152111 pfam11675, DUF3271, Protein of unknown function (DUF3271). This
family of proteins with unknown function appears to be
restricted to Plasmodium.
Length = 249
Score = 28.5 bits (64), Expect = 4.1
Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 39 FGYQGSSFHRIIPDF-VSFMTKHQSLKSRFSN 69
+ Y+G ++H +I DF +S +SLK +FS
Sbjct: 70 YAYEGGNYHWVITDFDISIDNSSRSLKKKFSK 101
>gnl|CDD|241140 cd12696, RRM3_PTBP2, RNA recognition motif 3 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM3 of PTBP2, also known as
neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein (PTB)
and perhaps specific to the vertebrates. Unlike PTB,
PTBP2 is enriched in the brain and in some neural cell
lines. It binds more stably to the downstream control
sequence (DCS) RNA than PTB does but is a weaker
repressor of splicing in vitro. PTBP2 also greatly
enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 107
Score = 27.3 bits (60), Expect = 4.4
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 83 NAAFIPFGDLVDIQMPLDYETEKHQLFGRIIRVNLAKPQKVQ 124
++A I D Q+ + + +++G+IIRV L+K Q VQ
Sbjct: 52 DSALIQMADGNQSQLAMSH-LNGQKMYGKIIRVTLSKHQTVQ 92
>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 78
Score = 26.6 bits (59), Expect = 4.5
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFG 110
+GGL+ E D L F +G++ D + D T++ + FG
Sbjct: 4 IGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFG 44
>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 = 26.3 bits (59), Expect = 5.1
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 66 RFSNLGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYET 103
R +NL +E+ D+ L F PFG + + + D ET
Sbjct: 3 RVTNL---SEDADEDDLRELFRPFGPISRVYLAKDKET 37
>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), an RNA unwinding protein with a high affinity
for G- followed by U-rich regions. hnRNP A/B has also
been identified as an APOBEC1-binding protein that
interacts with apolipoprotein B (apoB) mRNA transcripts
around the editing site and thus plays an important role
in apoB mRNA editing. hnRNP A/B contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long C-terminal glycine-rich domain that contains a
potential ATP/GTP binding loop. .
Length = 80
Score = 26.5 bits (58), Expect = 5.8
Identities = 13/40 (32%), Positives = 24/40 (60%)
Query: 70 LGGLAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLF 109
+GGL E ++ + F FG++ I++P+D +T K + F
Sbjct: 9 VGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGF 48
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element (TAR)
RNA which is synthesized by cellular RNA polymerase II
at the viral long terminal repeat. NELF is a
heterotetrameric protein consisting of NELF A, B, C or
the splice variant D, and E. NELF-E contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It plays a
role in the control of HIV transcription by binding to
TAR RNA. In addition, NELF-E is associated with the
NELF-B subunit, probably via a leucine zipper motif. .
Length = 75
Score = 26.1 bits (58), Expect = 6.2
Identities = 12/34 (35%), Positives = 21/34 (61%), Gaps = 4/34 (11%)
Query: 76 EVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLF 109
+ +++L AF PFG++++I M E EK+ F
Sbjct: 13 GLTEEILKKAFSPFGNIINISM----EKEKNCGF 42
>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor. This
model describes the ELAV/HuD subfamily of splicing
factors found in metazoa. HuD stands for the human
paraneoplastic encephalomyelitis antigen D of which
there are 4 variants in human. ELAV stnds for the
Drosophila Embryonic lethal abnormal visual protein.
ELAV-like splicing factors are also known in human as
HuB (ELAV-like protein 2), HuC (ELAV-like protein 3,
Paraneoplastic cerebellar degeneration-associated
antigen) and HuR (ELAV-like protein 1). These genes are
most closely related to the sex-lethal subfamily of
splicing factors found in Dipteran insects (TIGR01659).
These proteins contain 3 RNA-recognition motifs (rrm:
pfam00076).
Length = 352
Score = 27.2 bits (60), Expect = 9.9
Identities = 12/44 (27%), Positives = 24/44 (54%)
Query: 73 LAEEVDDKVLNAAFIPFGDLVDIQMPLDYETEKHQLFGRIIRVN 116
L+ + D+ VL F PFG + ++++ D T + + +G + N
Sbjct: 277 LSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTN 320
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 0.137 0.420
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,631,735
Number of extensions: 1372629
Number of successful extensions: 1221
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1179
Number of HSP's successfully gapped: 94
Length of query: 289
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 193
Effective length of database: 6,679,618
Effective search space: 1289166274
Effective search space used: 1289166274
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: 58 (26.0 bits)