RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1031
(456 letters)
>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 = 180 bits (457), Expect = 3e-55
Identities = 74/98 (75%), Positives = 84/98 (85%), Gaps = 1/98 (1%)
Query: 352 GGDPTGTGRGGSSIYGKTFADEIHEELKHTGAGILSMANSGPDTNGSQFFITLAPTQWLD 411
GGDPTGTGRGG+SIYGK F DEIH ELKHTGAGILSMAN+GP+TNGSQFFITLAPT WLD
Sbjct: 50 GGDPTGTGRGGASIYGKKFEDEIHPELKHTGAGILSMANAGPNTNGSQFFITLAPTPWLD 109
Query: 412 GKHAIFGRIYSGMSVVKRIGLVETDKNDRPVDDVKILK 449
GKH IFGR+ GM V++ + V+T DRP+D+VKILK
Sbjct: 110 GKHTIFGRVSKGMKVIENMVEVQTQ-TDRPIDEVKILK 146
Score = 96.8 bits (241), Expect = 7e-24
Identities = 36/62 (58%), Positives = 42/62 (67%), Gaps = 5/62 (8%)
Query: 55 LVFHNMGEIIVELYWKHAPNTCRNFAELCRRNYYNGIKFHRIIRDFMIQ-----AMGVGG 109
+ MGEI +ELYW HAP TC+NF EL +R YYNG FHR+I+DFMIQ G GG
Sbjct: 1 TLETTMGEITLELYWNHAPKTCKNFYELAKRGYYNGTIFHRLIKDFMIQGGDPTGTGRGG 60
Query: 110 AS 111
AS
Sbjct: 61 AS 62
>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 = 162 bits (411), Expect = 3e-48
Identities = 60/97 (61%), Positives = 70/97 (72%)
Query: 352 GGDPTGTGRGGSSIYGKTFADEIHEELKHTGAGILSMANSGPDTNGSQFFITLAPTQWLD 411
GDPTG G GG SI+GK F DE LKH LSMAN+GP+TNGSQFFIT T WLD
Sbjct: 50 TGDPTGDGTGGESIWGKEFEDEFSPSLKHDRPYTLSMANAGPNTNGSQFFITTVATPWLD 109
Query: 412 GKHAIFGRIYSGMSVVKRIGLVETDKNDRPVDDVKIL 448
KH +FGR+ GM VV+RI V+TDKNDRP +D+KI+
Sbjct: 110 NKHTVFGRVVKGMDVVQRIENVKTDKNDRPYEDIKII 146
Score = 63.2 bits (154), Expect = 4e-12
Identities = 24/57 (42%), Positives = 30/57 (52%), Gaps = 5/57 (8%)
Query: 60 MGEIIVELYWKHAPNTCRNFAELCRRNYYNGIKFHRIIRDFMIQ-----AMGVGGAS 111
G+I + L+ + AP T NF R YYN FHR+I+ FMIQ G GG S
Sbjct: 6 KGDIHIRLFPEEAPKTVENFTTHARNGYYNNTIFHRVIKGFMIQTGDPTGDGTGGES 62
>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 = 145 bits (368), Expect = 8e-42
Identities = 56/101 (55%), Positives = 69/101 (68%)
Query: 352 GGDPTGTGRGGSSIYGKTFADEIHEELKHTGAGILSMANSGPDTNGSQFFITLAPTQWLD 411
GGDPTGTGRGG SI+GK F DE L H G G+LSMANSGP+TNGSQFFIT + LD
Sbjct: 52 GGDPTGTGRGGESIWGKPFKDEFKPNLSHDGRGVLSMANSGPNTNGSQFFITYRSCKHLD 111
Query: 412 GKHAIFGRIYSGMSVVKRIGLVETDKNDRPVDDVKILKTHV 452
GKH +FGR+ G+ ++ + V DRP +++KI T V
Sbjct: 112 GKHTVFGRVVGGLETLEAMENVPDPGTDRPKEEIKIEDTSV 152
Score = 68.2 bits (167), Expect = 1e-13
Identities = 27/58 (46%), Positives = 36/58 (62%), Gaps = 5/58 (8%)
Query: 59 NMGEIIVELYWKHAPNTCRNFAELCRRNYYNGIKFHRIIRDFMIQ-----AMGVGGAS 111
N G++ +EL+ AP C NF +LC++ YY+G FHR IR+FMIQ G GG S
Sbjct: 7 NKGDLNLELHCDKAPKACENFIKLCKKGYYDGTIFHRSIRNFMIQGGDPTGTGRGGES 64
>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 = 143 bits (363), Expect = 5e-41
Identities = 57/97 (58%), Positives = 69/97 (71%), Gaps = 3/97 (3%)
Query: 352 GGDPT-GTGRGGSSIYGKTFADEIHEELKHTGAGILSMANSGPDTNGSQFFITLAPTQWL 410
GGD T G G GG SIYG+ F DE + +LKHTG G+LSMAN+GP+TNGSQFFIT T WL
Sbjct: 66 GGDFTRGNGTGGKSIYGEKFPDE-NFKLKHTGPGLLSMANAGPNTNGSQFFITTVKTPWL 124
Query: 411 DGKHAIFGRIYSGMSVVKRIGLVETDKNDRPVDDVKI 447
DGKH +FG++ GM VVK+I V + N +P V I
Sbjct: 125 DGKHVVFGKVVEGMDVVKKIENVGSG-NGKPKKKVVI 160
Score = 51.1 bits (123), Expect = 1e-07
Identities = 25/65 (38%), Positives = 29/65 (44%), Gaps = 14/65 (21%)
Query: 61 GEIIVELYWKHAPNTCRNFAELCRRNY--------YNGIKFHRIIRDFMIQA------MG 106
G I++EL+ P T NF LC Y G FHR+I DFMIQ G
Sbjct: 15 GRIVMELFADVVPKTAENFRALCTGEKGKGGKPFGYKGSTFHRVIPDFMIQGGDFTRGNG 74
Query: 107 VGGAS 111
GG S
Sbjct: 75 TGGKS 79
>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 = 3e-40
Identities = 55/98 (56%), Positives = 64/98 (65%), Gaps = 1/98 (1%)
Query: 352 GGDPTGTGRGGSSIYGKTFADEIHEELKHTGAGILSMANSGPDTNGSQFFITLAPTQWLD 411
GGDPTGTG GGS G F DE H G LSMAN+GP+TNGSQFFIT APT LD
Sbjct: 50 GGDPTGTGGGGS-GPGYKFPDENFPLKYHHRRGTLSMANAGPNTNGSQFFITTAPTPHLD 108
Query: 412 GKHAIFGRIYSGMSVVKRIGLVETDKNDRPVDDVKILK 449
GKH +FG++ GM VV +I +TD+N RP+ V I
Sbjct: 109 GKHTVFGKVVEGMDVVDKIERGDTDENGRPIKPVTISD 146
Score = 79.2 bits (196), Expect = 1e-17
Identities = 23/51 (45%), Positives = 28/51 (54%)
Query: 59 NMGEIIVELYWKHAPNTCRNFAELCRRNYYNGIKFHRIIRDFMIQAMGVGG 109
G I++ELY AP T NF L R +Y+G FHR+I FMIQ G
Sbjct: 5 TKGRIVIELYGDEAPKTVENFLSLARGGFYDGTTFHRVIPGFMIQGGDPTG 55
>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 = 136 bits (344), Expect = 4e-38
Identities = 50/103 (48%), Positives = 68/103 (66%), Gaps = 3/103 (2%)
Query: 352 GGDPTGTGRGGSSIYGKTFADEIHEELKHTGAGILSMANSGPDTNGSQFFITLAPTQWLD 411
GGDPTGTG GG SIYG+ F DE H L+ G++ MAN+G D+NGSQFF TL L+
Sbjct: 58 GGDPTGTGTGGESIYGEPFKDEFHSRLRFNRRGLVGMANAGDDSNGSQFFFTLDKADELN 117
Query: 412 GKHAIFGRIYSGMSV--VKRIGLVETDKNDRPVDDVKILKTHV 452
KH +FG++ +G ++ + ++ VETDK++RPV KI V
Sbjct: 118 NKHTLFGKV-TGDTIYNLLKLAEVETDKDERPVYPPKITSVEV 159
Score = 65.8 bits (161), Expect = 1e-12
Identities = 25/56 (44%), Positives = 33/56 (58%), Gaps = 5/56 (8%)
Query: 61 GEIIVELYWKHAPNTCRNFAELCRRNYYNGIKFHRIIRDFMIQ-----AMGVGGAS 111
G+I +EL+ K AP CRNF +LC YY+ FHR++ F+IQ G GG S
Sbjct: 15 GDIDIELWSKEAPKACRNFIQLCLEGYYDNTIFHRVVPGFIIQGGDPTGTGTGGES 70
>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 = 134 bits (338), Expect = 2e-37
Identities = 49/96 (51%), Positives = 67/96 (69%)
Query: 352 GGDPTGTGRGGSSIYGKTFADEIHEELKHTGAGILSMANSGPDTNGSQFFITLAPTQWLD 411
GDPTGTG+GG SI+GK F DE E LKH G++SMAN+GP+TNGSQFFIT A LD
Sbjct: 53 TGDPTGTGKGGESIWGKKFEDEFRETLKHDSRGVVSMANNGPNTNGSQFFITYAKQPHLD 112
Query: 412 GKHAIFGRIYSGMSVVKRIGLVETDKNDRPVDDVKI 447
GK+ +FG++ G + + + DK RP+++++I
Sbjct: 113 GKYTVFGKVIDGFETLDTLEKLPVDKKYRPLEEIRI 148
Score = 62.5 bits (152), Expect = 9e-12
Identities = 24/51 (47%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 54 SLVFH-NMGEIIVELYWKHAPNTCRNFAELCRRNYYNGIKFHRIIRDFMIQ 103
S+ H N+G+I +EL+ P C NF LC YYNG FHR I+ FM+Q
Sbjct: 2 SVTLHTNLGDIKIELFCDDCPKACENFLALCASGYYNGCIFHRNIKGFMVQ 52
>gnl|CDD|223725 COG0652, PpiB, Peptidyl-prolyl cis-trans isomerase (rotamase) -
cyclophilin family [Posttranslational modification,
protein turnover, chaperones].
Length = 158
Score = 124 bits (313), Expect = 8e-34
Identities = 47/105 (44%), Positives = 58/105 (55%), Gaps = 10/105 (9%)
Query: 352 GGDPTGT-GRGGSSIYGKTFADEIHEELKHT-GAGILSMANSG-PDTNGSQFFITLAPTQ 408
GGDPTG G GG F DE G LSMA +G P++NGSQFFIT+
Sbjct: 52 GGDPTGGDGTGGPGP---PFKDENFALNGDRHKRGTLSMARAGDPNSNGSQFFITVVDNP 108
Query: 409 WLDGKHAIFGRIYSGMSVVKRIGLVETDK----NDRPVDDVKILK 449
+LDGK+ +FG++ GM VV +I +TD D P D VKIL
Sbjct: 109 FLDGKYTVFGQVVEGMDVVDKIKNGDTDDSGYVQDVPADPVKILS 153
Score = 82.3 bits (204), Expect = 1e-18
Identities = 25/59 (42%), Positives = 32/59 (54%), Gaps = 6/59 (10%)
Query: 59 NMGEIIVELYWKHAPNTCRNFAELCRRNYYNGIKFHRIIRDFMIQA------MGVGGAS 111
N G+I +ELY AP T NF +L + +Y+G FHR+I FMIQ G GG
Sbjct: 7 NKGDITIELYPDKAPKTVANFLQLVKEGFYDGTIFHRVIPGFMIQGGDPTGGDGTGGPG 65
>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 = 123 bits (310), Expect = 1e-33
Identities = 52/99 (52%), Positives = 63/99 (63%), Gaps = 6/99 (6%)
Query: 352 GGDPTGTGRGGSSIYGKTFADEIHEELKHTGAGILSMANSGPDTNGSQFFITLAPTQWLD 411
GGDPTG G GG ++ DE +LKH G LSMA SGP++ GSQFFITL LD
Sbjct: 52 GGDPTGPGTGG----KRSIPDEFVSKLKHK-RGTLSMARSGPNSAGSQFFITLGDAPHLD 106
Query: 412 GKHAIFGRIYSGMSVVKRIGLVETDKNDRPVDDVKILKT 450
G + +FGR+ GM VV++I VETD DRP+ DVKI
Sbjct: 107 GGYTVFGRVVEGMDVVEKIEKVETD-GDRPLKDVKITSC 144
Score = 80.4 bits (199), Expect = 4e-18
Identities = 22/45 (48%), Positives = 31/45 (68%)
Query: 59 NMGEIIVELYWKHAPNTCRNFAELCRRNYYNGIKFHRIIRDFMIQ 103
N+G I++EL+ AP T NF LC++ +Y+G FHR+I FMIQ
Sbjct: 7 NLGRIVIELFGDEAPKTVENFLSLCKKGFYDGTIFHRVIPGFMIQ 51
>gnl|CDD|240249 PTZ00060, PTZ00060, cyclophilin; Provisional.
Length = 183
Score = 117 bits (294), Expect = 6e-31
Identities = 50/97 (51%), Positives = 64/97 (65%), Gaps = 3/97 (3%)
Query: 352 GGDPT-GTGRGGSSIYGKTFADEIHEELKHTGAGILSMANSGPDTNGSQFFITLAPTQWL 410
GGD T G GG SIYG+ F DE + +LKH G+LSMAN+GP+TNGSQFFIT P WL
Sbjct: 82 GGDITNHNGTGGESIYGRKFTDE-NFKLKHDQPGLLSMANAGPNTNGSQFFITTVPCPWL 140
Query: 411 DGKHAIFGRIYSGMSVVKRIGLVETDKNDRPVDDVKI 447
DGKH +FG++ GM VV+ + T ++ P V +
Sbjct: 141 DGKHVVFGKVIEGMEVVRAMEKEGT-QSGYPKKPVVV 176
Score = 44.8 bits (106), Expect = 2e-05
Identities = 28/89 (31%), Positives = 36/89 (40%), Gaps = 22/89 (24%)
Query: 45 FTVVEIILRSLVFHNM-------GEIIVELYWKHAPNTCRNFAELC---------RRNYY 88
+ E+ R VF ++ G I+ EL+ P T NF LC + +Y
Sbjct: 7 QSFPEMSKRPKVFFDISIDNAPAGRIVFELFSDVTPKTAENFRALCIGDKVGSSGKNLHY 66
Query: 89 NGIKFHRIIRDFMIQA------MGVGGAS 111
G FHRII FM Q G GG S
Sbjct: 67 KGSIFHRIIPQFMCQGGDITNHNGTGGES 95
>gnl|CDD|178694 PLN03149, PLN03149, peptidyl-prolyl isomerase H (cyclophilin H);
Provisional.
Length = 186
Score = 111 bits (279), Expect = 1e-28
Identities = 52/92 (56%), Positives = 61/92 (66%), Gaps = 3/92 (3%)
Query: 352 GGD-PTGTGRGGSSIYGKTFADEIHEELKHTGAGILSMANSGPDTNGSQFFITLAPTQWL 410
GGD G G G SIYG F DE + KHTG G+LSMANSGP+TNG QFFIT A WL
Sbjct: 84 GGDFLKGDGTGCVSIYGSKFEDE-NFIAKHTGPGLLSMANSGPNTNGCQFFITCAKCDWL 142
Query: 411 DGKHAIFGRIY-SGMSVVKRIGLVETDKNDRP 441
D KH +FGR+ G+ VV++I V T N+RP
Sbjct: 143 DNKHVVFGRVLGDGLLVVRKIENVATGPNNRP 174
Score = 51.4 bits (123), Expect = 1e-07
Identities = 21/52 (40%), Positives = 28/52 (53%), Gaps = 8/52 (15%)
Query: 61 GEIIVELYWKHAPNTCRNFAELCRRNY--------YNGIKFHRIIRDFMIQA 104
G I +EL+ AP T NF + C + Y G +FHR+I+DFMIQ
Sbjct: 33 GRIKMELFADIAPKTAENFRQFCTGEFRKAGLPQGYKGCQFHRVIKDFMIQG 84
>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 = 105 bits (264), Expect = 8e-27
Identities = 48/108 (44%), Positives = 66/108 (61%), Gaps = 8/108 (7%)
Query: 353 GDPTGTGRGGSSIYGKT-------FADEIHEELKHTGAGILSMANSGPDTNGSQFFITLA 405
GDPTGTG GG SIY + F EI LKH+ G +SM N+G + NGSQF+ITL
Sbjct: 51 GDPTGTGAGGESIYSQLYGRQARFFEPEILPLLKHSKKGTVSMVNAGDNLNGSQFYITLG 110
Query: 406 P-TQWLDGKHAIFGRIYSGMSVVKRIGLVETDKNDRPVDDVKILKTHV 452
+LDGKH +FG++ G V+++I D + RP+ D++I TH+
Sbjct: 111 ENLDYLDGKHTVFGQVVEGFDVLEKINDAIVDDDGRPLKDIRIKHTHI 158
Score = 53.9 bits (130), Expect = 1e-08
Identities = 15/44 (34%), Positives = 28/44 (63%)
Query: 60 MGEIIVELYWKHAPNTCRNFAELCRRNYYNGIKFHRIIRDFMIQ 103
+G+++++L+ P C NF +LC+ YYN F+ + +DF+ Q
Sbjct: 6 LGDLVIDLFTDECPLACLNFLKLCKLKYYNFCLFYNVQKDFIAQ 49
>gnl|CDD|140248 PTZ00221, PTZ00221, cyclophilin; Provisional.
Length = 249
Score = 60.3 bits (146), Expect = 3e-10
Identities = 30/86 (34%), Positives = 48/86 (55%), Gaps = 1/86 (1%)
Query: 362 GSSIYGKTFADEIHEELKHTGAGILSMANSGPDTNGSQFFITLAPTQWLDGKHAIFGRIY 421
S G ADE + +HT G+L+M + GP T+GS F ITL P+ LD K +FG+
Sbjct: 129 NVSSTGTPIADEGYRH-RHTERGLLTMISEGPHTSGSVFGITLGPSPSLDFKQVVFGKAV 187
Query: 422 SGMSVVKRIGLVETDKNDRPVDDVKI 447
+S+++++ + D RP+ V +
Sbjct: 188 DDLSLLEKLESLPLDDVGRPLLPVTV 213
>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 = 57.1 bits (138), Expect = 8e-10
Identities = 21/48 (43%), Positives = 30/48 (62%)
Query: 59 NMGEIIVELYWKHAPNTCRNFAELCRRNYYNGIKFHRIIRDFMIQAMG 106
++G+I+VELY AP T NF R+ +Y+ FHR+I F+IQ G
Sbjct: 5 SLGDIVVELYDDKAPITVENFLAYVRKGFYDNTIFHRVISGFVIQGGG 52
Score = 46.3 bits (110), Expect = 4e-06
Identities = 29/75 (38%), Positives = 37/75 (49%), Gaps = 10/75 (13%)
Query: 383 AGILSMANSG-PDTNGSQFFITLAPTQWLD-----GKHAIFGRIYSGMSVVKRIGLVETD 436
G ++MA + PD+ SQFFI L LD + +FG + GM VV +I VET
Sbjct: 78 RGTIAMARTNAPDSATSQFFINLKDNASLDYQNEQWGYTVFGEVTEGMDVVDKIAGVETY 137
Query: 437 KN----DRPVDDVKI 447
D PV DV I
Sbjct: 138 SFGSYQDVPVQDVII 152
>gnl|CDD|182734 PRK10791, PRK10791, peptidyl-prolyl cis-trans isomerase B (rotamase
B); Provisional.
Length = 164
Score = 54.5 bits (131), Expect = 8e-09
Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 55 LVFH-NMGEIIVELYWKHAPNTCRNFAELCRRNYYNGIKFHRIIRDFMIQAMGVGGASNV 113
+ FH N G+I+++ + AP T +NF + CR +YN FHR+I FMIQ G
Sbjct: 2 VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGGFEPGMKQ 61
Query: 114 NQLQDVIQN 122
++ I+N
Sbjct: 62 KATKEPIKN 70
Score = 37.9 bits (88), Expect = 0.003
Identities = 28/97 (28%), Positives = 45/97 (46%), Gaps = 14/97 (14%)
Query: 369 TFADEIHEELKHTGAGILSMANSG-PDTNGSQFFITLAPTQWLDGK--------HAIFGR 419
+E + LK+T G L+MA + P + +QFFI + +L+ + +F
Sbjct: 67 PIKNEANNGLKNT-RGTLAMARTQAPHSATAQFFINVVDNDFLNFSGESLQGWGYCVFAE 125
Query: 420 IYSGMSVVKRIGLVETDKN----DRPVDDVKILKTHV 452
+ GM VV +I V T ++ D P +DV I V
Sbjct: 126 VVEGMDVVDKIKGVATGRSGMHQDVPKEDVIIESVTV 162
>gnl|CDD|182824 PRK10903, PRK10903, peptidyl-prolyl cis-trans isomerase A (rotamase
A); Provisional.
Length = 190
Score = 49.8 bits (119), Expect = 4e-07
Identities = 21/62 (33%), Positives = 30/62 (48%)
Query: 61 GEIIVELYWKHAPNTCRNFAELCRRNYYNGIKFHRIIRDFMIQAMGVGGASNVNQLQDVI 120
G I +EL + AP + +NF + +YN FHR+I FMIQ G + I
Sbjct: 38 GNIELELNSQKAPVSVKNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQKKPNPPI 97
Query: 121 QN 122
+N
Sbjct: 98 KN 99
Score = 43.3 bits (102), Expect = 6e-05
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 10/79 (12%)
Query: 384 GILSMA-NSGPDTNGSQFFITLAPTQWLD-GK----HAIFGRIYSGMSVVKRIGLVETDK 437
G ++MA + D+ SQFFI +A +LD G+ +A+FG++ GM V +I V T
Sbjct: 110 GTIAMARTADKDSATSQFFINVADNAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHD 169
Query: 438 ----NDRPVDDVKILKTHV 452
+ P V IL V
Sbjct: 170 VGPYQNVPSKPVVILSAKV 188
>gnl|CDD|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat)
retrotransposon and non-LTR retrovirus reverse
transcriptase (RT). This subfamily contains both non-LTR
retrotransposons and non-LTR retrovirus RTs. RTs
catalyze the conversion of single-stranded RNA into
double-stranded DNA for integration into host
chromosomes. RT is a multifunctional enzyme with
RNA-directed DNA polymerase, DNA directed DNA polymerase
and ribonuclease hybrid (RNase H) activities.
Length = 220
Score = 50.4 bits (121), Expect = 4e-07
Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 109 GASNVNQLQDVIQNLHCWCNENLMVLNLEKCKVMSFYTNKHPILINYNINNVQLERVNNI 168
+LQ+++Q L W E+ + +N K KVM NK L + +N +E V
Sbjct: 155 SEGKSRKLQELLQRLQEWSKESGLKINPSKSKVMLI-GNKKKRLKDITLNGTPIEAVETF 213
Query: 169 KDLGVTF 175
K LGVT
Sbjct: 214 KYLGVTI 220
>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 = 43.6 bits (103), Expect = 4e-05
Identities = 14/32 (43%), Positives = 22/32 (68%)
Query: 72 APNTCRNFAELCRRNYYNGIKFHRIIRDFMIQ 103
AP T NF +L R +Y+G++FHR+ F++Q
Sbjct: 18 APVTAGNFVDLVERGFYDGMEFHRVEGGFVVQ 49
Score = 38.6 bits (90), Expect = 0.002
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 15/80 (18%)
Query: 365 IYGKTFA-----DEIHEELKHTGAGILSMANSGPDTNG--SQFFITL-------APTQWL 410
+YGKT DE + G ++MA + D N SQFF L + L
Sbjct: 84 VYGKTLEEAGRYDEQPVLPFNA-FGAIAMARTEFDPNSASSQFFFLLKDNELTPSRNNVL 142
Query: 411 DGKHAIFGRIYSGMSVVKRI 430
DG++A+FG + G+ +++ +
Sbjct: 143 DGRYAVFGYVTDGLDILREL 162
>gnl|CDD|215698 pfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA
polymerase). A reverse transcriptase gene is usually
indicative of a mobile element such as a retrotransposon
or retrovirus. Reverse transcriptases occur in a variety
of mobile elements, including retrotransposons,
retroviruses, group II introns, bacterial msDNAs,
hepadnaviruses, and caulimoviruses.
Length = 194
Score = 31.9 bits (73), Expect = 0.44
Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 85 RNYYNGIKFHRIIRDFMIQAMGVGGASNVNQLQDVIQNLHCWCNENLMVLNLEKCKVMS 143
R + G+ + R D +I + + +LQ++++ + + E + LN EK K+
Sbjct: 131 RKRFPGLTYLRYADDILI------FSKSPEELQEILEEVLEFLKELGLKLNPEKTKITH 183
>gnl|CDD|224318 COG1400, SEC65, Signal recognition particle 19 kDa protein
[Intracellular trafficking and secretion].
Length = 93
Score = 28.9 bits (65), Expect = 1.4
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 182 NLHYSEIKSKALRMLGFLYRHTQDFKHPK 210
N EI +ALR LG + +D K+P+
Sbjct: 31 NPSLEEIA-EALRELGLKPKVERDKKYPR 58
>gnl|CDD|211960 TIGR04237, seadorna_VP9, seadornavirus/coltivirus VP9 protein.
This model, broader than related pfam08978, describes
proteins VP9 in Coltivirus, and proteins with various
designations in the seadornavirus group: VP9 in Banna
virus, VP10 in Liao ning virus, and VP11 in Kadipiro
virus.
Length = 280
Score = 30.7 bits (69), Expect = 1.5
Identities = 20/89 (22%), Positives = 31/89 (34%), Gaps = 12/89 (13%)
Query: 3 RPKRQSTGRSPSDPDLYRILQDEDLVEKLAFSQAEICRRTVQFTVVEIILRSLVFHNMGE 62
R + T PS+ L + VEKLA ++ E+ + Q + I L + G+
Sbjct: 19 RVAGEQTLALPSNVKL-----SKGEVEKLAVTKKEMKDKLAQCNLPSIELNTREHTFNGD 73
Query: 63 IIVELYWK-----HAPNTCRNFAELCRRN 86
+ W R A R N
Sbjct: 74 FARFMAWAFIMHGQLLMHARPVA--VRMN 100
>gnl|CDD|133211 cd05080, PTKc_Tyk2_rpt2, Catalytic (repeat 2) domain of the Protein
Tyrosine Kinase, Tyrosine kinase 2. Protein Tyrosine
Kinase (PTK) family; Tyrosine kinase 2 (Tyk2); catalytic
(c) domain (repeat 2). The PTKc family is part of a
larger superfamily that includes the catalytic domains
of other kinases such as protein serine/threonine
kinases, RIO kinases, and phosphoinositide 3-kinase
(PI3K). PTKs catalyze the transfer of the
gamma-phosphoryl group from ATP to tyrosine (tyr)
residues in protein substrates. Tyk2 is a member of the
Janus kinase (Jak) subfamily of proteins, which are
cytoplasmic (or nonreceptor) tyr kinases containing an
N-terminal FERM domain, followed by a Src homology 2
(SH2) domain, a pseudokinase domain, and a C-terminal
tyr kinase catalytic domain. Jaks are crucial for
cytokine receptor signaling. They are activated by
autophosphorylation upon cytokine-induced receptor
aggregation, and subsequently trigger downstream
signaling events such as the phosphorylation of signal
transducers and activators of transcription (STATs).
Tyk2 is widely expressed in many tissues. It is involved
in signaling via the cytokine receptors IFN-alphabeta,
IL-6, IL-10, IL-12, IL-13, and IL-23. It mediates cell
surface urokinase receptor (uPAR) signaling and plays a
role in modulating vascular smooth muscle cell (VSMC)
functional behavior in response to injury. Tyk2 is also
important in dendritic cell function and T helper (Th)1
cell differentiation. A homozygous mutation of Tyk2 was
found in a patient with hyper-IgE syndrome (HIES), a
primary immunodeficiency characterized by recurrent skin
abscesses, pneumonia, and elevated serum IgE. This
suggests that Tyk2 may play important roles in multiple
cytokine signaling involved in innate and adaptive
immunity.
Length = 283
Score = 30.6 bits (69), Expect = 1.7
Identities = 35/139 (25%), Positives = 53/139 (38%), Gaps = 34/139 (24%)
Query: 131 LMVLNLEKCKVMSFYTNKHPILINYNINNVQLERVNNIK--DLGVTFQYNLKFNLHYSEI 188
L++ + C+ M++ ++H I + NV L+ +K D G+
Sbjct: 109 LLLFAQQICEGMAYLHSQHYIHRDLAARNVLLDNDRLVKIGDFGLA-------------- 154
Query: 189 KSKALRMLGFLYRHTQDFKHPKTLTNLYYTYVRSCLE-----YCSTVWS---PQYE--TH 238
KA+ YR +D P + Y CL+ Y S VWS YE TH
Sbjct: 155 --KAVPEGHEYYRVREDGDSP------VFWYAVECLKENKFSYASDVWSFGVTLYELLTH 206
Query: 239 IKSLESVQHKFLIMLAFKS 257
S +S KF M+ K
Sbjct: 207 CDSKQSPPKKFEEMIGPKQ 225
>gnl|CDD|233902 TIGR02506, NrdE_NrdA, ribonucleoside-diphosphate reductase, alpha
subunit. This model represents the alpha (large) chain
of the class I ribonucleotide reductase (RNR). RNR's are
responsible for the conversion of the ribose sugar of
RNA into the deoxyribose sugar of DNA. This is the
rate-limiting step of DNA biosynthesis. Class I RNR's
generate the required radical (on tyrosine) via a
"non-heme" iron cofactor which resides in the beta
(small) subunit. The alpha subunit contains the
catalytic and allosteric regulatory sites. The mechanism
of this enzyme requires molecular oxygen. E. Coli
contains two versions of this enzyme which are regulated
independently (NrdAB and NrdEF, where NrdA and NrdE are
the large chains ). Most organisms contain only one, but
the application of the gene symbols NrdA and NrdE are
somewhat arbitrary. This model identifies RNR's in
diverse clades of bacteria, eukaryotes as well as
numerous DNA viruses and phage [Purines, pyrimidines,
nucleosides, and nucleotides, 2'-Deoxyribonucleotide
metabolism].
Length = 617
Score = 29.7 bits (67), Expect = 3.9
Identities = 22/93 (23%), Positives = 34/93 (36%), Gaps = 8/93 (8%)
Query: 282 RDMQDLVFIYKVLHNLIYSPEILSNFNLKVPLRKTRSCDMFVLEKNKTNIGEFSPIQRME 341
+ D + Y +L L SP + FN P + SC F+L+ + I +
Sbjct: 44 TRLADAIRFYDLLSRLKISPATPTLFNAGTPRGQLSSC--FLLDVTDDTL---ESIYKAI 98
Query: 342 KIGNHITSGAGG---DPTGTGRGGSSIYGKTFA 371
++ GG + T GS I G A
Sbjct: 99 DDVAQLSKHGGGIGLNLTKLRAIGSPIRGTNNA 131
>gnl|CDD|107029 PHA01351, PHA01351, putative minor structural protein.
Length = 1070
Score = 29.5 bits (66), Expect = 4.5
Identities = 32/120 (26%), Positives = 51/120 (42%), Gaps = 26/120 (21%)
Query: 122 NLHCWCNENLMVLNLEKCKVMSFYTNKHPILINYNINNVQLERVNNIKDLGVT------- 174
NL+ ++L+V +V SF + LI YN N+QLE + +K G+
Sbjct: 900 NLYVNYYQHLLVGQ----EVQSFKSEYITALI-YNYQNLQLE--SLLKQYGINEALLSVL 952
Query: 175 --FQYNLKFNLHYSEI---KSKALRMLGFLYRHTQ-------DFKHPKTLTNLYYTYVRS 222
F K E+ SKAL + ++ Q +F+ P+ L N Y+ Y R+
Sbjct: 953 KLFAQVRKIVTGLQELYLTPSKALSISEYVSNPQQLLQKVFAEFQIPQELQNTYFEYARN 1012
>gnl|CDD|222894 PHA02588, cd, deoxycytidylate deaminase; Provisional.
Length = 168
Score = 28.6 bits (64), Expect = 4.6
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 373 EIHEELKHTGAGILSMANSGPDTNGSQFFITLAP 406
EIH EL IL A +G G+ ++T +P
Sbjct: 81 EIHAELN----AILFAARNGISIEGATMYVTASP 110
>gnl|CDD|180660 PRK06696, PRK06696, uridine kinase; Validated.
Length = 223
Score = 28.8 bits (65), Expect = 5.6
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 338 QRMEKIGNHITSGAGGDPTGTGRGGSSIYGKT-FADEIHEELKHTGAGIL 386
Q ++++ HI + P G + GKT FADE+ EE+K G ++
Sbjct: 5 QLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAEEIKKRGRPVI 54
>gnl|CDD|235079 PRK02866, PRK02866, cyanate hydratase; Validated.
Length = 147
Score = 27.9 bits (63), Expect = 6.2
Identities = 18/56 (32%), Positives = 23/56 (41%), Gaps = 15/56 (26%)
Query: 364 SIYGKTFADEIHEELKHTGAGILSMAN------SGPDTNGSQFFITLAPTQWLDGK 413
+YG T IHE+ G GI+S + D G + IT LDGK
Sbjct: 94 QVYGTTLKALIHEKF---GDGIMSAIDFKLDVDKVEDPKGDRVVIT------LDGK 140
>gnl|CDD|132978 cd06647, STKc_PAK_I, Catalytic domain of the Protein
Serine/Threonine Kinase, Group I p21-activated kinase.
Serine/threonine kinases (STKs), p21-activated kinase
(PAK) subfamily, Group I, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The PAK subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. PAKs are Rho family GTPase-regulated kinases
that serve as important mediators in the function of
Cdc42 (cell division cycle 42) and Rac. PAKs are
implicated in the regulation of many cellular processes
including growth factor receptor-mediated proliferation,
cell polarity, cell motility, cell death and survival,
and actin cytoskeleton organization. PAKs from higher
eukaryotes are classified into two groups (I and II),
according to their biochemical and structural features.
Group I PAKs, also called conventional PAKs, include
PAK1, PAK2, and PAK3. Group I PAKs contain a PBD
(p21-binding domain) overlapping with an AID
(autoinhibitory domain), a C-terminal catalytic domain,
SH3 binding sites and a non-classical SH3 binding site
for PIX (PAK-interacting exchange factor). They interact
with the SH3 domain containing proteins Nck, Grb2 and
PIX. Binding of group I PAKs to activated GTPases leads
to conformational changes that destabilize the AID,
allowing autophosphorylation and full activation of the
kinase domain. Known group I PAK substrates include
MLCK, Bad, Raf, MEK1, LIMK, Merlin, Vimentin, Myc,
Stat5a, and Aurora A, among others.
Length = 293
Score = 28.7 bits (64), Expect = 6.6
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 15/76 (19%)
Query: 203 TQDFKHPKTLTNLYYTYVRSCLEYCSTVWSPQYETHIKSLESVQHKFL-IMLAFKSFTRI 261
T + ++P+ L+ ++ ++ CLE E + E +QH FL I S T +
Sbjct: 232 TPELQNPEKLSAIFRDFLNRCLEM-------DVEKRGSAKELLQHPFLKIAKPLSSLTPL 284
Query: 262 DDHNYDNIMAANKITS 277
I AA + T
Sbjct: 285 -------IAAAKEATK 293
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 0.138 0.414
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,318,803
Number of extensions: 2277440
Number of successful extensions: 1882
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1860
Number of HSP's successfully gapped: 51
Length of query: 456
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 356
Effective length of database: 6,502,202
Effective search space: 2314783912
Effective search space used: 2314783912
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: 61 (27.2 bits)