RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13279
(287 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 = 162 bits (413), Expect = 4e-50
Identities = 77/177 (43%), Positives = 91/177 (51%), Gaps = 67/177 (37%)
Query: 1 MDIKIGKQEVGRITIQLRYDLVPRTAENFRCLCTHEKG-----FGYQGSSFHRIIPDFVS 55
DI IG + GRI ++L D+VP+TAENFR LCT EKG FGY+GS+FHR+IPDF+
Sbjct: 5 FDITIGGEPAGRIVMELFADVVPKTAENFRALCTGEKGKGGKPFGYKGSTFHRVIPDFM- 63
Query: 56 FMTKRQSLKSRFSKFRFDFAAGGNRTRHSFPIPLPMKYIRPCLDCGSKGTFQSHSSRINK 115
GG+ TR + GT
Sbjct: 64 -------------------IQGGDFTRGN-------------------GT---------- 75
Query: 116 MCQGGDFTNHNGTGGKSIYGNKFEDENFVLKHTGPGVLSMANSGPNTNGSQFFLCTT 172
GGKSIYG KF DENF LKHTGPG+LSMAN+GPNTNGSQFF+ T
Sbjct: 76 -------------GGKSIYGEKFPDENFKLKHTGPGLLSMANAGPNTNGSQFFITTV 119
Score = 135 bits (342), Expect = 2e-39
Identities = 47/58 (81%), Positives = 50/58 (86%)
Query: 193 MCQGGDFTNHNGTGGKSIYGNKFEDENFILKHTGPGVLSMANSGPNTNGSQFFLCTTK 250
M QGGDFT NGTGGKSIYG KF DENF LKHTGPG+LSMAN+GPNTNGSQFF+ T K
Sbjct: 63 MIQGGDFTRGNGTGGKSIYGEKFPDENFKLKHTGPGLLSMANAGPNTNGSQFFITTVK 120
>gnl|CDD|240249 PTZ00060, PTZ00060, cyclophilin; Provisional.
Length = 183
Score = 114 bits (287), Expect = 3e-31
Identities = 49/74 (66%), Positives = 57/74 (77%), Gaps = 2/74 (2%)
Query: 175 NKHYYYYYYYIFLTRFTQMCQGGDFTNHNGTGGKSIYGNKFEDENFILKHTGPGVLSMAN 234
N HY ++ + +F MCQGGD TNHNGTGG+SIYG KF DENF LKH PG+LSMAN
Sbjct: 63 NLHYKGSIFHRIIPQF--MCQGGDITNHNGTGGESIYGRKFTDENFKLKHDQPGLLSMAN 120
Query: 235 SGPNTNGSQFFLCT 248
+GPNTNGSQFF+ T
Sbjct: 121 AGPNTNGSQFFITT 134
Score = 114 bits (286), Expect = 4e-31
Identities = 45/56 (80%), Positives = 49/56 (87%)
Query: 116 MCQGGDFTNHNGTGGKSIYGNKFEDENFVLKHTGPGVLSMANSGPNTNGSQFFLCT 171
MCQGGD TNHNGTGG+SIYG KF DENF LKH PG+LSMAN+GPNTNGSQFF+ T
Sbjct: 79 MCQGGDITNHNGTGGESIYGRKFTDENFKLKHDQPGLLSMANAGPNTNGSQFFITT 134
>gnl|CDD|178694 PLN03149, PLN03149, peptidyl-prolyl isomerase H (cyclophilin H);
Provisional.
Length = 186
Score = 109 bits (274), Expect = 3e-29
Identities = 70/180 (38%), Positives = 82/180 (45%), Gaps = 61/180 (33%)
Query: 2 DIKIGKQEVGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFVSFMTKRQ 61
D+ IG GRI ++L D+ P+TAENF RQ
Sbjct: 24 DVTIGGIPAGRIKMELFADIAPKTAENF------------------------------RQ 53
Query: 62 SLKSRFSKFRFDFAAGGNRTRHSFPIPLPMKYIRPCLDCGSKGTFQSHSSRINKMCQGGD 121
F G R + P G KG Q H + M QGGD
Sbjct: 54 ------------FCTGEFR-KAGLPQ-------------GYKGC-QFHRVIKDFMIQGGD 86
Query: 122 FTNHNGTGGKSIYGNKFEDENFVLKHTGPGVLSMANSGPNTNGSQFFL----CTTSINKH 177
F +GTG SIYG+KFEDENF+ KHTGPG+LSMANSGPNTNG QFF+ C NKH
Sbjct: 87 FLKGDGTGCVSIYGSKFEDENFIAKHTGPGLLSMANSGPNTNGCQFFITCAKCDWLDNKH 146
Score = 102 bits (255), Expect = 1e-26
Identities = 43/60 (71%), Positives = 48/60 (80%)
Query: 193 MCQGGDFTNHNGTGGKSIYGNKFEDENFILKHTGPGVLSMANSGPNTNGSQFFLCTTKQE 252
M QGGDF +GTG SIYG+KFEDENFI KHTGPG+LSMANSGPNTNG QFF+ K +
Sbjct: 81 MIQGGDFLKGDGTGCVSIYGSKFEDENFIAKHTGPGLLSMANSGPNTNGCQFFITCAKCD 140
>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 = 83.7 bits (207), Expect = 6e-20
Identities = 39/55 (70%), Positives = 43/55 (78%), Gaps = 2/55 (3%)
Query: 116 MCQGGDFTNHNGTGGKSIYGNKFEDE-NFVLKHTGPGVLSMANSGPNTNGSQFFL 169
M QGGD T G GG SIYG KFEDE + LKHTG G+LSMAN+GPNTNGSQFF+
Sbjct: 47 MIQGGDPTG-TGRGGASIYGKKFEDEIHPELKHTGAGILSMANAGPNTNGSQFFI 100
Score = 83.4 bits (206), Expect = 7e-20
Identities = 39/55 (70%), Positives = 43/55 (78%), Gaps = 2/55 (3%)
Query: 193 MCQGGDFTNHNGTGGKSIYGNKFEDE-NFILKHTGPGVLSMANSGPNTNGSQFFL 246
M QGGD T G GG SIYG KFEDE + LKHTG G+LSMAN+GPNTNGSQFF+
Sbjct: 47 MIQGGDPTG-TGRGGASIYGKKFEDEIHPELKHTGAGILSMANAGPNTNGSQFFI 100
Score = 42.5 bits (100), Expect = 4e-05
Identities = 18/45 (40%), Positives = 30/45 (66%), Gaps = 3/45 (6%)
Query: 10 VGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFV 54
+G IT++L ++ P+T +NF L +G+ Y G+ FHR+I DF+
Sbjct: 6 MGEITLELYWNHAPKTCKNFYELAK--RGY-YNGTIFHRLIKDFM 47
>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 = 81.9 bits (203), Expect = 2e-19
Identities = 36/59 (61%), Positives = 38/59 (64%), Gaps = 3/59 (5%)
Query: 114 NKMCQGGDFTNHNGTGGKSIYGNKFEDENFVLK-HTGPGVLSMANSGPNTNGSQFFLCT 171
M QGGD T G G S G KF DENF LK H G LSMAN+GPNTNGSQFF+ T
Sbjct: 45 GFMIQGGDPTGTGG--GGSGPGYKFPDENFPLKYHHRRGTLSMANAGPNTNGSQFFITT 101
Score = 81.2 bits (201), Expect = 5e-19
Identities = 36/61 (59%), Positives = 38/61 (62%), Gaps = 3/61 (4%)
Query: 193 MCQGGDFTNHNGTGGKSIYGNKFEDENFILK-HTGPGVLSMANSGPNTNGSQFFLCTTKQ 251
M QGGD T G G S G KF DENF LK H G LSMAN+GPNTNGSQFF+ T
Sbjct: 47 MIQGGDPTGTGG--GGSGPGYKFPDENFPLKYHHRRGTLSMANAGPNTNGSQFFITTAPT 104
Query: 252 E 252
Sbjct: 105 P 105
Score = 60.4 bits (147), Expect = 2e-11
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 = 81.9 bits (203), Expect = 3e-19
Identities = 30/62 (48%), Positives = 35/62 (56%), Gaps = 6/62 (9%)
Query: 114 NKMCQGGDFTNHNGTGGKSIYGNKFEDENFVLKH--TGPGVLSMANSG-PNTNGSQFFLC 170
M QGGD T +GTGG F+DENF L G LSMA +G PN+NGSQFF+
Sbjct: 47 GFMIQGGDPTGGDGTGGPGP---PFKDENFALNGDRHKRGTLSMARAGDPNSNGSQFFIT 103
Query: 171 TT 172
Sbjct: 104 VV 105
Score = 80.0 bits (198), Expect = 2e-18
Identities = 30/63 (47%), Positives = 35/63 (55%), Gaps = 6/63 (9%)
Query: 193 MCQGGDFTNHNGTGGKSIYGNKFEDENFILKH--TGPGVLSMANSG-PNTNGSQFFLCTT 249
M QGGD T +GTGG F+DENF L G LSMA +G PN+NGSQFF+
Sbjct: 49 MIQGGDPTGGDGTGGPGP---PFKDENFALNGDRHKRGTLSMARAGDPNSNGSQFFITVV 105
Query: 250 KQE 252
Sbjct: 106 DNP 108
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|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 = 80.5 bits (199), Expect = 1e-18
Identities = 42/74 (56%), Positives = 46/74 (62%), Gaps = 6/74 (8%)
Query: 109 HSSRINKMCQGGDFTNHNGTGGKSIYGNKFEDE-NFVLKHTGPGVLSMANSGPNTNGSQF 167
H S N M QGGD T G GG+SI+G F+DE L H G GVLSMANSGPNTNGSQF
Sbjct: 42 HRSIRNFMIQGGDPTG-TGRGGESIWGKPFKDEFKPNLSHDGRGVLSMANSGPNTNGSQF 100
Query: 168 FL----CTTSINKH 177
F+ C KH
Sbjct: 101 FITYRSCKHLDGKH 114
Score = 77.8 bits (192), Expect = 1e-17
Identities = 36/55 (65%), Positives = 40/55 (72%), Gaps = 2/55 (3%)
Query: 193 MCQGGDFTNHNGTGGKSIYGNKFEDE-NFILKHTGPGVLSMANSGPNTNGSQFFL 246
M QGGD T G GG+SI+G F+DE L H G GVLSMANSGPNTNGSQFF+
Sbjct: 49 MIQGGDPTG-TGRGGESIWGKPFKDEFKPNLSHDGRGVLSMANSGPNTNGSQFFI 102
Score = 40.5 bits (95), Expect = 2e-04
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|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 = 77.9 bits (192), Expect = 8e-18
Identities = 39/67 (58%), Positives = 47/67 (70%), Gaps = 6/67 (8%)
Query: 116 MCQGGDFTNHNGTGGKSIYGNKFEDE-NFVLKHTGPGVLSMANSGPNTNGSQFFLCTTSI 174
M Q GD T +GTGG+SI+G +FEDE + LKH P LSMAN+GPNTNGSQFF+ T +
Sbjct: 47 MIQTGDPTG-DGTGGESIWGKEFEDEFSPSLKHDRPYTLSMANAGPNTNGSQFFITTVAT 105
Query: 175 ----NKH 177
NKH
Sbjct: 106 PWLDNKH 112
Score = 76.7 bits (189), Expect = 3e-17
Identities = 41/73 (56%), Positives = 49/73 (67%), Gaps = 7/73 (9%)
Query: 180 YYYYYIF---LTRFTQMCQGGDFTNHNGTGGKSIYGNKFEDE-NFILKHTGPGVLSMANS 235
YY IF + F M Q GD T +GTGG+SI+G +FEDE + LKH P LSMAN+
Sbjct: 33 YYNNTIFHRVIKGF--MIQTGDPTG-DGTGGESIWGKEFEDEFSPSLKHDRPYTLSMANA 89
Query: 236 GPNTNGSQFFLCT 248
GPNTNGSQFF+ T
Sbjct: 90 GPNTNGSQFFITT 102
Score = 42.1 bits (99), Expect = 6e-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|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 = 75.6 bits (186), Expect = 8e-17
Identities = 37/60 (61%), Positives = 42/60 (70%), Gaps = 2/60 (3%)
Query: 193 MCQGGDFTNHNGTGGKSIYGNKFEDENF-ILKHTGPGVLSMANSGPNTNGSQFFLCTTKQ 251
M Q GD T G GG+SI+G KFEDE LKH GV+SMAN+GPNTNGSQFF+ KQ
Sbjct: 50 MVQTGDPTG-TGKGGESIWGKKFEDEFRETLKHDSRGVVSMANNGPNTNGSQFFITYAKQ 108
Score = 74.4 bits (183), Expect = 2e-16
Identities = 35/55 (63%), Positives = 40/55 (72%), Gaps = 2/55 (3%)
Query: 116 MCQGGDFTNHNGTGGKSIYGNKFEDENF-VLKHTGPGVLSMANSGPNTNGSQFFL 169
M Q GD T G GG+SI+G KFEDE LKH GV+SMAN+GPNTNGSQFF+
Sbjct: 50 MVQTGDPTG-TGKGGESIWGKKFEDEFRETLKHDSRGVVSMANNGPNTNGSQFFI 103
Score = 43.2 bits (102), Expect = 3e-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|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 = 68.1 bits (167), Expect = 3e-14
Identities = 25/62 (40%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 114 NKMCQGGDFTNHNGTGGKSIYGNKFEDENFVLKHTGPGVLSMANSGPNTNGSQFFLCTTS 173
M QGGD T G +SI DE G LSMA SGPN+ GSQFF+
Sbjct: 47 GFMIQGGDPTGPGTGGKRSI-----PDEFVSKLKHKRGTLSMARSGPNSAGSQFFITLGD 101
Query: 174 IN 175
Sbjct: 102 AP 103
Score = 67.7 bits (166), Expect = 5e-14
Identities = 25/60 (41%), Positives = 28/60 (46%), Gaps = 5/60 (8%)
Query: 193 MCQGGDFTNHNGTGGKSIYGNKFEDENFILKHTGPGVLSMANSGPNTNGSQFFLCTTKQE 252
M QGGD T G +SI DE G LSMA SGPN+ GSQFF+
Sbjct: 49 MIQGGDPTGPGTGGKRSI-----PDEFVSKLKHKRGTLSMARSGPNSAGSQFFITLGDAP 103
Score = 62.7 bits (153), Expect = 3e-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|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 = 61.6 bits (150), Expect = 1e-11
Identities = 28/53 (52%), Positives = 37/53 (69%), Gaps = 2/53 (3%)
Query: 118 QGGDFTNHNGTGGKSIYGNKFEDE-NFVLKHTGPGVLSMANSGPNTNGSQFFL 169
QGGD T GTGG+SIYG F+DE + L+ G++ MAN+G ++NGSQFF
Sbjct: 57 QGGDPTG-TGTGGESIYGEPFKDEFHSRLRFNRRGLVGMANAGDDSNGSQFFF 108
Score = 61.6 bits (150), Expect = 1e-11
Identities = 28/53 (52%), Positives = 37/53 (69%), Gaps = 2/53 (3%)
Query: 195 QGGDFTNHNGTGGKSIYGNKFEDE-NFILKHTGPGVLSMANSGPNTNGSQFFL 246
QGGD T GTGG+SIYG F+DE + L+ G++ MAN+G ++NGSQFF
Sbjct: 57 QGGDPTG-TGTGGESIYGEPFKDEFHSRLRFNRRGLVGMANAGDDSNGSQFFF 108
Score = 31.9 bits (73), Expect = 0.17
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 10 VGRITIQLRYDLVPRTAENFRCLCTHEKGFGYQGSSFHRIIPDFV 54
G I I+L P+ NF LC +G+ Y + FHR++P F+
Sbjct: 14 AGDIDIELWSKEAPKACRNFIQLCL--EGY-YDNTIFHRVVPGFI 55
>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 = 45.8 bits (109), Expect = 4e-06
Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 179 YYYYYYIFLTRFTQMCQGGDFTNHNGTGGKSIYGNK-------FEDE-NFILKHTGPGVL 230
YY + + + + Q GD T G GG+SIY FE E +LKH+ G +
Sbjct: 33 YYNFCLFYNVQKDFIAQTGDPTG-TGAGGESIYSQLYGRQARFFEPEILPLLKHSKKGTV 91
Query: 231 SMANSGPNTNGSQFFLCTT 249
SM N+G N NGSQF++
Sbjct: 92 SMVNAGDNLNGSQFYITLG 110
Score = 45.8 bits (109), Expect = 4e-06
Identities = 27/64 (42%), Positives = 34/64 (53%), Gaps = 9/64 (14%)
Query: 117 CQGGDFTNHNGTGGKSIYGNK-------FEDE-NFVLKHTGPGVLSMANSGPNTNGSQFF 168
Q GD T G GG+SIY FE E +LKH+ G +SM N+G N NGSQF+
Sbjct: 48 AQTGDPTG-TGAGGESIYSQLYGRQARFFEPEILPLLKHSKKGTVSMVNAGDNLNGSQFY 106
Query: 169 LCTT 172
+
Sbjct: 107 ITLG 110
Score = 34.2 bits (79), Expect = 0.030
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|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 = 43.2 bits (102), Expect = 3e-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|140248 PTZ00221, PTZ00221, cyclophilin; Provisional.
Length = 249
Score = 43.3 bits (102), Expect = 5e-05
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
Score = 37.2 bits (86), Expect = 0.005
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 104 GTFQSHSSRINKMCQGGDFTNHNGTGGKSIYGNKFEDENFVLKHTGPGVLSMANSGPNTN 163
T H R N + G+ + N S G DE + +HT G+L+M + GP+T+
Sbjct: 107 YTPVHHVDRNNNIIVLGELDSFN----VSSTGTPIADEGYRHRHTERGLLTMISEGPHTS 162
Query: 164 GSQF 167
GS F
Sbjct: 163 GSVF 166
Score = 36.4 bits (84), Expect = 0.011
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 207 GKSIYGNKFEDENFILKHTGPGVLSMANSGPNTNGSQF 244
S G DE + +HT G+L+M + GP+T+GS F
Sbjct: 129 NVSSTGTPIADEGYRHRHTERGLLTMISEGPHTSGSVF 166
>gnl|CDD|182824 PRK10903, PRK10903, peptidyl-prolyl cis-trans isomerase A
(rotamase A); Provisional.
Length = 190
Score = 30.2 bits (68), Expect = 0.81
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|182734 PRK10791, PRK10791, peptidyl-prolyl cis-trans isomerase B
(rotamase B); Provisional.
Length = 164
Score = 29.8 bits (67), Expect = 1.1
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|152111 pfam11675, DUF3271, Protein of unknown function (DUF3271). This
family of proteins with unknown function appears to be
restricted to Plasmodium.
Length = 249
Score = 29.3 bits (66), Expect = 1.9
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 39 FGYQGSSFHRIIPDF-VSFMTKRQSLKSRFSK 69
+ Y+G ++H +I DF +S +SLK +FSK
Sbjct: 70 YAYEGGNYHWVITDFDISIDNSSRSLKKKFSK 101
>gnl|CDD|225497 COG2946, COG2946, Putative phage replication protein RstA [DNA
replication, recombination, and repair].
Length = 377
Score = 28.2 bits (63), Expect = 5.4
Identities = 12/43 (27%), Positives = 20/43 (46%)
Query: 102 SKGTFQSHSSRINKMCQGGDFTNHNGTGGKSIYGNKFEDENFV 144
G F H+ C+G + N +G+GGK+ Y + +V
Sbjct: 186 DNGAFDCHNVAPKGECRGTAWLNDDGSGGKTFYVGSKKSSKYV 228
>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 = 26.4 bits (59), Expect = 6.0
Identities = 19/75 (25%), Positives = 26/75 (34%), Gaps = 26/75 (34%)
Query: 54 VSFMTKRQSLKSRFSKFRFDFAAGGNRTRHSFPIPLPMKYIRPCLDCG---SKGT----F 106
+ F + LK FS+F G +KY R D SKGT F
Sbjct: 8 LPFDATEEELKELFSQF------G------------EVKYARIVKDKLTGHSKGTAFVKF 49
Query: 107 QSHSSRINKMCQGGD 121
++ S K + D
Sbjct: 50 KTKES-AQKCLEAAD 63
>gnl|CDD|233304 TIGR01180, aman2_put, alpha-1,2-mannosidase, putative. The
identification of members of this family as putative
alpha-1,2-mannosidases is based on an unpublished
characterization of the aman2 gene in Bacillus sp. M-90
by Maruyama,Y., Nakajima,M. and Nakajima,T. (Genbank
accession BAA76709, pid g4587313). Most members of this
family appear to have signal sequences. Members from the
dental pathogen Porphyromonas gingivalis have been
described as immunoreactive with periodontitis patient
serum [Cell envelope, Biosynthesis and degradation of
surface polysaccharides and lipopolysaccharides].
Length = 750
Score = 27.6 bits (61), Expect = 9.5
Identities = 18/108 (16%), Positives = 31/108 (28%), Gaps = 21/108 (19%)
Query: 86 PIPLPMKYIRPCLDCGSKGTFQSHSSRINKMCQGGDFTNHNGTGGKSIYGNKFEDENFVL 145
LP S+ I QG T +G G + +
Sbjct: 55 GAGLPNGMPMTGPPNDGWQYTYSYHK-IRGFKQGFSHTPLSGDGAQFLS----------- 102
Query: 146 KHTGPGVLSMANSGPNTN----GSQFFLCTTSINKHYYYYYYYIFLTR 189
+L+M S + F ++ N++ YY ++L R
Sbjct: 103 -----LILTMPQSPSSALTKWPTDWFSHKASTANEYARSGYYAVYLDR 145
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
0.322 0.139 0.448
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,235,985
Number of extensions: 1286623
Number of successful extensions: 920
Number of sequences better than 10.0: 1
Number of HSP's gapped: 886
Number of HSP's successfully gapped: 54
Length of query: 287
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 191
Effective length of database: 6,679,618
Effective search space: 1275807038
Effective search space used: 1275807038
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 (21.9 bits)
S2: 58 (26.2 bits)