RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3263
(329 letters)
>2dgr_A Ring finger and KH domain-containing protein 1; structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 83
Score = 95.4 bits (237), Expect = 6e-25
Identities = 42/57 (73%), Positives = 46/57 (80%)
Query: 78 PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG 134
G TI+VRVPY+VVGLVVGPKGATIKRIQ +T+TYIVTP RDKEPVF VTG
Sbjct: 2 SSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTG 58
Score = 61.5 bits (149), Expect = 1e-12
Identities = 28/63 (44%), Positives = 38/63 (60%), Gaps = 4/63 (6%)
Query: 9 INPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 68
+ P G IK ++ +T+TYI TP R +EPVF VTG E+V RA+ EI + LR+
Sbjct: 25 VGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGMPENVDRAREEI----EAHITLRSGP 80
Query: 69 KSG 71
SG
Sbjct: 81 SSG 83
>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH
domain, hairpin, RNA-binding protein complex; HET: 5BU;
1.94A {Homo sapiens} PDB: 2ann_A*
Length = 178
Score = 93.0 bits (231), Expect = 5e-23
Identities = 26/134 (19%), Positives = 45/134 (33%), Gaps = 11/134 (8%)
Query: 13 GCKIKALRAKTNTYIK------TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRA 66
G I L+ +T IK E V ++ G E + I A
Sbjct: 25 GQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMPQNVA 84
Query: 67 SRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK 126
+ ++ +++ VP GL++G GAT+K I Q+ ++ +
Sbjct: 85 KTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPD 144
Query: 127 EP-----VFEVTGN 135
V V+G
Sbjct: 145 GINLQNRVVTVSGE 158
Score = 53.7 bits (129), Expect = 6e-09
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 82 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP-----VFEVTGN 135
+ ++V +P G ++G G TI ++Q +T I ++ S+D P V + G
Sbjct: 2 LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61
Score = 37.5 bits (87), Expect = 0.002
Identities = 10/53 (18%), Positives = 22/53 (41%), Gaps = 5/53 (9%)
Query: 9 INPFGCKIKALRAKTNTYIKTPVRGEEP-----VFVVTGRKEDVARAKREILS 56
I G +KA+ ++ +++ + + V V+G E +A I+
Sbjct: 119 IGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGEPEQNRKAVELIIQ 171
>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA
binding protein, KH domain, KSRP, posttranscriptional
regulation, mRNA decay; NMR {Homo sapiens}
Length = 164
Score = 88.7 bits (220), Expect = 1e-21
Identities = 26/131 (19%), Positives = 41/131 (31%), Gaps = 16/131 (12%)
Query: 13 GCKIKALRAKTNTYIKTPVRGEEP-----VFVVTGRKEDVARAKREILSAADHFSALRAS 67
G IK L+ + + G + + G V +A ++
Sbjct: 21 GETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQ---- 76
Query: 68 RKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD-- 125
G I+V VP VG+V+G G IK+IQ+ I D
Sbjct: 77 ----GGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGT 132
Query: 126 -KEPVFEVTGN 135
E + + G
Sbjct: 133 GPEKIAHIMGP 143
Score = 49.4 bits (118), Expect = 2e-07
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 5/54 (9%)
Query: 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP-----VFEVTGN 135
E+ +P GLV+G G TIK++Q + ++ + + G+
Sbjct: 3 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGD 56
Score = 40.5 bits (95), Expect = 2e-04
Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 3/46 (6%)
Query: 13 GCKIKALRAKTNTYIK---TPVRGEEPVFVVTGRKEDVARAKREIL 55
G IK ++ I+ G E + + G + A R I
Sbjct: 110 GEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIIN 155
>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding,
DNA-binding, nucleus, phosph ribonucleoprotein,
RNA-binding, RNA binding protein; NMR {Homo sapiens}
Length = 160
Score = 82.9 bits (205), Expect = 2e-19
Identities = 22/128 (17%), Positives = 42/128 (32%), Gaps = 14/128 (10%)
Query: 13 GCKIKALRAKTNTYIK-TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSG 71
G +K +R ++ I + E + + G + +A I+ +
Sbjct: 24 GESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKL---------EEDI 74
Query: 72 ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK----E 127
+ S + VT+ + VP G ++G G IK I+ T + E
Sbjct: 75 SSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTE 134
Query: 128 PVFEVTGN 135
+ G
Sbjct: 135 RAITIAGI 142
Score = 52.9 bits (127), Expect = 8e-09
Identities = 12/51 (23%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGN 135
+TI + + K VG ++G KG ++K+++ ++ I ++ E + + G
Sbjct: 5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGP 55
Score = 36.7 bits (85), Expect = 0.004
Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 4/48 (8%)
Query: 13 GCKIKALRAKTNTYIK----TPVRGEEPVFVVTGRKEDVARAKREILS 56
GCKIK +R T ++ E + G + + ++I
Sbjct: 108 GCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICV 155
>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET:
DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1
Length = 174
Score = 83.0 bits (205), Expect = 2e-19
Identities = 29/138 (21%), Positives = 41/138 (29%), Gaps = 15/138 (10%)
Query: 13 GCKIKALRAKTNTYIK-TPVRGEEP--VFVVTGRKEDVARAKREILS------AADHFSA 63
G IK ++ I+ P G P + +TG + A I A +
Sbjct: 22 GEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQAGNPGGP 81
Query: 64 LRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 123
R G G VP GL++G G TIK I Q+ I
Sbjct: 82 GPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQR 141
Query: 124 R------DKEPVFEVTGN 135
+F + G
Sbjct: 142 NPPPNADPNMKLFTIRGT 159
Score = 52.6 bits (126), Expect = 2e-08
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVTGN 135
G I+V +P VG+V+G G IK+IQ+ I P P + ++TG
Sbjct: 1 GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGP 55
Score = 35.6 bits (82), Expect = 0.009
Identities = 8/50 (16%), Positives = 19/50 (38%), Gaps = 6/50 (12%)
Query: 13 GCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVARAKREILS 56
G IK++ ++ I+ +F + G + + A++ I
Sbjct: 123 GETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEE 172
>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain,
cell projection, cytoplasm, nucleus, phosphoprotein,
translation regulation; 2.75A {Homo sapiens}
Length = 163
Score = 66.3 bits (162), Expect = 2e-13
Identities = 31/134 (23%), Positives = 50/134 (37%), Gaps = 25/134 (18%)
Query: 13 GCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRAS 67
G IK L + IK TP V ++TG E +A+ I L+
Sbjct: 22 GQHIKQLSRFASASIKIAPPETPDSKVRMV-IITGPPEAQFKAQGRIYGK------LKEE 74
Query: 68 RKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV-----TP 122
G + +RVP G V+G G T+ +Q+ T +V TP
Sbjct: 75 NFFGP--------KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTP 126
Query: 123 SRDKEPVFEVTGNF 136
+ + + ++ G+F
Sbjct: 127 DENDQVIVKIIGHF 140
Score = 47.8 bits (114), Expect = 5e-07
Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 85 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRD---KEPVFEVTGN 135
++V +P + VG ++G KG IK++ + I + P K + +TG
Sbjct: 2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGP 56
Score = 37.4 bits (87), Expect = 0.002
Identities = 9/49 (18%), Positives = 18/49 (36%), Gaps = 5/49 (10%)
Query: 13 GCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREILS 56
G + L+ T + TP ++ + + G A+R+I
Sbjct: 104 GKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRD 152
>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase
complex, ring zinc-finger, UBL conjugation pathway;
2.10A {Homo sapiens} PDB: 2yhn_A
Length = 79
Score = 62.9 bits (153), Expect = 5e-13
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 304
+ C +C + E+ PCGH C CA + ++CP+CR V +
Sbjct: 18 AMLCMVCCEEEINSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEHVQHV 65
>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1,
ring domain, zinc-binding domain, structural genomics,
NPPSFA; NMR {Homo sapiens}
Length = 68
Score = 60.2 bits (146), Expect = 3e-12
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 4/63 (6%)
Query: 242 SSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA 301
S+ S S+ C +C + V L+PC H C C + + CPMCR V ++
Sbjct: 4 GSSGVEPSEENSKDCVVCQNGTVNWVLLPCRHTCLCDGCVKYF----QQCPMCRQFVQES 59
Query: 302 MRI 304
+
Sbjct: 60 FAL 62
>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 94
Score = 60.5 bits (147), Expect = 4e-12
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGNFPEG 139
+ V +P + V+G G ++ ++ +T T I P D ++TG EG
Sbjct: 17 ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGT-KEG 70
Score = 49.7 bits (119), Expect = 4e-08
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 2/64 (3%)
Query: 9 INPFGCKIKALRAKTNTYIKTPVRGEEPVFV-VTGRKEDVARAKREILSAADHFSALRAS 67
I G K++ L KT T I+ P + + +TG KE + +A+ E+L + R+
Sbjct: 32 IGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISAEQDK-RSG 90
Query: 68 RKSG 71
SG
Sbjct: 91 PSSG 94
>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian,
zinc-binding domain, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 75
Score = 59.8 bits (145), Expect = 5e-12
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 253 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 304
+ C +C DR + +PCGH C +CAE CPMC + +I
Sbjct: 25 EKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFKQKI 72
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo
sapiens}
Length = 85
Score = 60.1 bits (146), Expect = 6e-12
Identities = 13/65 (20%), Positives = 27/65 (41%), Gaps = 5/65 (7%)
Query: 77 SPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV-----TPSRDKEPVFE 131
G E+ +P GLV+G G TIK++Q + ++ + + + +
Sbjct: 5 DNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLR 64
Query: 132 VTGNF 136
+ G+
Sbjct: 65 IIGDP 69
Score = 36.9 bits (86), Expect = 8e-04
Identities = 7/49 (14%), Positives = 16/49 (32%), Gaps = 5/49 (10%)
Query: 13 GCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREILS 56
G IK L+ + + + + + G V +A ++
Sbjct: 33 GETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMD 81
>1x4m_A FAR upstream element binding protein 1; KH domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.51.1.1
Length = 94
Score = 59.7 bits (145), Expect = 7e-12
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 5/64 (7%)
Query: 77 SPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV-----TPSRDKEPVFE 131
S PG+ E+ +P GLV+G G TIK++Q + +V + +
Sbjct: 6 SGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLR 65
Query: 132 VTGN 135
+TG+
Sbjct: 66 ITGD 69
Score = 37.4 bits (87), Expect = 7e-04
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 5/48 (10%)
Query: 13 GCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREIL 55
G IK L+ + + G + +TG V +AK +L
Sbjct: 34 GETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVL 81
>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 104
Score = 58.7 bits (142), Expect = 2e-11
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP-VFEVTG 134
VTIEV VP+ + V+G KG+ I+++ + I P+ + + + +TG
Sbjct: 17 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITG 66
Score = 46.3 bits (110), Expect = 5e-07
Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 1/62 (1%)
Query: 9 INPFGCKIKALRAKTNTYIKTPVRGEEP-VFVVTGRKEDVARAKREILSAADHFSALRAS 67
I G I+ + + I P + + +TG ++ RAK +L A +
Sbjct: 32 IGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLERVKELQAEQED 91
Query: 68 RK 69
R
Sbjct: 92 RA 93
>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 95
Score = 57.5 bits (139), Expect = 5e-11
Identities = 11/48 (22%), Positives = 22/48 (45%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVT 133
V+ +V + ++V ++G +G I++I + I P VT
Sbjct: 17 VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVT 64
Score = 50.5 bits (121), Expect = 2e-08
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 2/55 (3%)
Query: 9 INPFGCKIKALRAKTNTYIKTPVRGEEP--VFVVTGRKEDVARAKREILSAADHF 61
I G I+ + + I+ P G VTG E+V A IL+ + +
Sbjct: 32 IGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY 86
>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative
splicing, HOST-virus interaction, UBL conjugation
pathway, zinc-finger, polymorphism; HET: FLC; 2.20A
{Homo sapiens} PDB: 2vjf_B*
Length = 63
Score = 56.0 bits (135), Expect = 8e-11
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 254 RQCYLCNDREVTHALI--PCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF 306
+ C LC R +I GH C CA R +CP+C+ + +++
Sbjct: 8 KPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQLVIKVFI 62
>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA,
apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase,
IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB:
1qbh_A 2l9m_A 3eb5_A 3eb6_A
Length = 345
Score = 61.1 bits (146), Expect = 1e-10
Identities = 20/52 (38%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 255 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF 306
C +C D+EV+ IPCGH C ECA R CP+CR + +R
Sbjct: 297 TCKVCMDKEVSVVFIPCGHLVVCQECAPSL----RKCPICRGIIKGTVRTFL 344
>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 106
Score = 56.3 bits (136), Expect = 2e-10
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 3/63 (4%)
Query: 77 SPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVT 133
+ TG I+V VP VG+V+G G IK+IQ+ I P + +
Sbjct: 2 AMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIM 61
Query: 134 GNF 136
G
Sbjct: 62 GPP 64
Score = 37.5 bits (87), Expect = 8e-04
Identities = 13/75 (17%), Positives = 20/75 (26%), Gaps = 3/75 (4%)
Query: 13 GCKIKALRAKTNTYIK---TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRK 69
G IK ++ I+ G E + + G + A R I +
Sbjct: 30 GEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRSGPPGPP 89
Query: 70 SGALSPLSPPTGVPG 84
G P G
Sbjct: 90 GGPGMPPGGRGRGRG 104
>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation,
alternative splicing, HOST-virus interaction, UBL
conjugation pathway, zinc-finger, polymorphism; HET:
FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A
Length = 64
Score = 54.4 bits (131), Expect = 3e-10
Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 2/62 (3%)
Query: 247 SGSISGSRQCYLCNDREVTHALIP--CGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 304
S ++ C +C R ++ GH C CA++ ++ CP+CR P+ +
Sbjct: 2 SLPLNAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLT 61
Query: 305 IF 306
F
Sbjct: 62 YF 63
>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens}
SCOP: d.51.1.1 PDB: 1vih_A
Length = 71
Score = 53.1 bits (128), Expect = 1e-09
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGNFPEG 139
+E+ + +K ++G GA I RI+ Q + P +K + + G+ P+G
Sbjct: 5 DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGD-PQG 58
Score = 41.2 bits (97), Expect = 2e-05
Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 9 INPFGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILS 56
I G I ++ + ++ P E + + G + V +AKRE+L
Sbjct: 20 IGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLE 68
>1x4n_A FAR upstream element binding protein 1; KH domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.51.1.1 PDB: 2opu_A
Length = 92
Score = 51.7 bits (124), Expect = 6e-09
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 3/65 (4%)
Query: 74 SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VF 130
S S +T E +VP +VG ++G G I RIQ ++ I + P P
Sbjct: 3 SGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSC 62
Query: 131 EVTGN 135
+TG
Sbjct: 63 MLTGT 67
Score = 30.5 bits (69), Expect = 0.17
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 13 GCKIKALRAKTNTYIK-TPVRGEEP--VFVVTGRKEDVARAKREI 54
G +I ++ ++ I+ P G P ++TG E V AKR +
Sbjct: 34 GEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLL 78
>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 97
Score = 51.7 bits (124), Expect = 6e-09
Identities = 12/46 (26%), Positives = 21/46 (45%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFE 131
+ V V K ++G KGA I +I+ + + I P +D +
Sbjct: 17 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQ 62
Score = 47.1 bits (112), Expect = 3e-07
Identities = 10/48 (20%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 13 GCKIKALRAKTNTYIKTPVRGEEP----VFVVTGRKEDVARAKREILS 56
G I +R + + I+ P + + +TG +++ A+ IL
Sbjct: 36 GAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILR 83
>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin
ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB:
2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A
2ldr_A*
Length = 389
Score = 54.4 bits (130), Expect = 2e-08
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFD-RTCPMCRVPVNQAMRIIFNQF 309
S + C +C + + + PCGH C+ C + + + CP CR + I+ + F
Sbjct: 330 STFQLCKICAENDKDVKIEPCGHLM-CTSCLTSWQESEGQGCPFCRCEIKGTEPIVVDPF 388
>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 71
Score = 49.4 bits (118), Expect = 2e-08
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 1/58 (1%)
Query: 242 SSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 299
S+ + +C +C V +PC H F C C + + C +CR +
Sbjct: 4 GSSGNTAPSLTVPECAICLQTCVHPVSLPCKHVF-CYLCVKGASWLGKRCALCRQEIP 60
>4epo_C E3 ubiquitin-protein ligase RNF8; coiled-coil, E3 ubiquitin ligase,
protein binding complex; 4.80A {Homo sapiens}
Length = 149
Score = 51.6 bits (123), Expect = 3e-08
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 1/62 (1%)
Query: 255 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFLFGKL 314
QC +C++ + + C H+F CS C CP+CR + + K+
Sbjct: 66 QCIICSEYFIEAVTLNCAHSF-CSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCINKM 124
Query: 315 WE 316
Sbjct: 125 VN 126
>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding
protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1
PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*
Length = 73
Score = 47.7 bits (114), Expect = 1e-07
Identities = 12/52 (23%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTG 134
+TI + + K VG ++G KG ++K+++ ++ I ++ E + + G
Sbjct: 3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAG 54
>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 81
Score = 47.5 bits (113), Expect = 1e-07
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 1/45 (2%)
Query: 255 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 299
+C++C + C H F C CA C +C P
Sbjct: 17 RCFICRQAFQNPVVTKCRHYF-CESCALEHFRATPRCYICDQPTG 60
>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 72
Score = 47.1 bits (112), Expect = 1e-07
Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 2/47 (4%)
Query: 255 QCYLCNDR-EVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300
C +C + C H F C C R + CP C + V+Q
Sbjct: 17 LCSICKGYLIDATTITECLHTF-CKSCIVRHFYYSNRCPKCNIVVHQ 62
>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain,
alpha-beta fold RNA-binding motif, immune system; 2.00A
{Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A
Length = 76
Score = 46.9 bits (112), Expect = 2e-07
Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP-----VFEVTGN 135
+E+ VP +VG ++G G T+ Q T I ++ + P +TG+
Sbjct: 3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58
Score = 29.9 bits (68), Expect = 0.20
Identities = 9/48 (18%), Positives = 15/48 (31%), Gaps = 6/48 (12%)
Query: 13 GCKIKALRAKTNTYIKTPVRGEEP------VFVVTGRKEDVARAKREI 54
G + + T I+ +GE +TG A+ I
Sbjct: 22 GKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLI 69
>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 69
Score = 46.8 bits (111), Expect = 2e-07
Identities = 19/66 (28%), Positives = 25/66 (37%), Gaps = 8/66 (12%)
Query: 242 SSTSPSGSISGSRQCYLCND-------REVTHALIPCGHNFFCSECAERTCDFDRTCPMC 294
S+ SG+ C +C D CGH F CS+C + TCP C
Sbjct: 4 GSSGTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVF-CSQCLRDSLKNANTCPTC 62
Query: 295 RVPVNQ 300
R +N
Sbjct: 63 RKKINH 68
>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding
motif, protein/RNA structure, RNA binding protein/RNA
complex; 2.40A {Homo sapiens} SCOP: d.51.1.1
Length = 87
Score = 46.6 bits (111), Expect = 3e-07
Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP-----VFEVTGN 135
+E+ VP +VG ++G G T+ Q T I ++ + P +TG+
Sbjct: 3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGS 58
Score = 31.5 bits (72), Expect = 0.073
Identities = 12/61 (19%), Positives = 20/61 (32%), Gaps = 6/61 (9%)
Query: 13 GCKIKALRAKTNTYIKTPVRGEEP------VFVVTGRKEDVARAKREILSAADHFSALRA 66
G + + T I+ +GE +TG A+ I + +RA
Sbjct: 22 GKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQGVRA 81
Query: 67 S 67
S
Sbjct: 82 S 82
>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb,
E3-ligase, nuclear protein, chromosomal protein,
transcription regulation; 2.0A {Mus musculus} PDB:
3rpg_B 2h0d_A
Length = 108
Score = 47.1 bits (112), Expect = 4e-07
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 255 QCYLCND---REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300
C LC T +I C H+F C C R + + CP+C V V++
Sbjct: 17 MCVLCGGYFIDATT--IIECLHSF-CKTCIVRYLETSKYCPICDVQVHK 62
>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains,
type I domains, fragIle X mental retardation protein,
RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A
Length = 144
Score = 47.7 bits (113), Expect = 4e-07
Identities = 8/43 (18%), Positives = 16/43 (37%)
Query: 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPV 129
+ V ++GL +G GA I++ + + D
Sbjct: 5 HEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTF 47
Score = 41.9 bits (98), Expect = 5e-05
Identities = 23/131 (17%), Positives = 39/131 (29%), Gaps = 35/131 (26%)
Query: 4 FVVPS------INPFGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSA 57
F+V I G I+ R + + F + G +D + R L
Sbjct: 8 FIVREDLMGLAIGTHGANIQQARKVPGV-TAIDLDEDTCTFHIYGEDQDAVKKARSFLEF 66
Query: 58 ADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNT 117
A+ ++VP +VG V+G G I+ I ++
Sbjct: 67 AEDV----------------------------IQVPRNLVGKVIGKNGKLIQEIVDKSGV 98
Query: 118 YIVTPSRDKEP 128
V + E
Sbjct: 99 VRVRIEAENEK 109
Score = 29.2 bits (65), Expect = 1.1
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 9/61 (14%)
Query: 9 INPFGCKIKALRAKTN-TYIKTPVRGEEPV--------FVVTGRKEDVARAKREILSAAD 59
I G I+ + K+ ++ E+ V FV G K+ +A A + +
Sbjct: 82 IGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLN 141
Query: 60 H 60
+
Sbjct: 142 Y 142
>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid
herpesvirus 1} SCOP: g.44.1.1
Length = 68
Score = 45.1 bits (107), Expect = 7e-07
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 2/64 (3%)
Query: 251 SGSRQCYLC-NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQF 309
+ + +C +C D +PC H F C C R + TCP+C+VPV + I +
Sbjct: 3 TVAERCPICLEDPSNYSMALPCLHAF-CYVCITRWIRQNPTCPLCKVPVESVVHTIESDS 61
Query: 310 LFGK 313
FG
Sbjct: 62 EFGD 65
>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta
fold, DNA binding protein; 0.95A {Homo sapiens} SCOP:
d.51.1.1 PDB: 1zzj_A 1zzi_A
Length = 82
Score = 45.4 bits (108), Expect = 7e-07
Identities = 13/59 (22%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 81 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRD--KEPVFEVTGNF 136
+ +T +V +P + G ++G G IK+I+H++ I + + ++ + +TG
Sbjct: 2 AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 60
Score = 29.2 bits (66), Expect = 0.46
Identities = 10/45 (22%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 13 GCKIKALRAKTNTYIK---TPVRGEEPVFVVTGRKEDVARAKREI 54
G +IK +R ++ IK E+ + +TG ++ + A+ +
Sbjct: 26 GQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLL 70
>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase,
ubiquitylation, sumoylation, zinc-FI metal binding
protein; 1.80A {Rattus norvegicus}
Length = 71
Score = 45.2 bits (107), Expect = 8e-07
Identities = 18/63 (28%), Positives = 24/63 (38%), Gaps = 8/63 (12%)
Query: 245 SPSGSISGSRQCYLCND-------REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVP 297
+ SG+ C +C D CGH F CS+C + TCP CR
Sbjct: 2 TTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVF-CSQCLRDSLKNANTCPTCRKK 60
Query: 298 VNQ 300
+N
Sbjct: 61 INH 63
>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA
binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1
Length = 82
Score = 44.6 bits (106), Expect = 1e-06
Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 82 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVTGN 135
+ T E+ +P ++G ++G +GA I I+ + I + + +TG+
Sbjct: 2 LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGS 58
>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA
binding protein, transcription factor, hnRNP K, CT
element, C-MYC oncogene; NMR {Homo sapiens} SCOP:
d.51.1.1 PDB: 1khm_A
Length = 89
Score = 44.6 bits (106), Expect = 2e-06
Identities = 13/54 (24%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRD--KEPVFEVTGNF 136
+T +V +P + G ++G G IK+I+H++ I + + ++ + +TG
Sbjct: 14 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQ 67
Score = 28.8 bits (65), Expect = 0.55
Identities = 12/45 (26%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 13 GCKIKALRAKTNTYIK--TPVRG-EEPVFVVTGRKEDVARAKREI 54
G +IK +R ++ IK P+ G E+ + +TG ++ + A+ +
Sbjct: 33 GQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLL 77
>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA
binding protein/DNA complex; 1.60A {Homo sapiens}
Length = 76
Score = 43.8 bits (104), Expect = 2e-06
Identities = 11/53 (20%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVTGN 135
+ E+ +P ++G ++G +GA I I+ + I + + +TG+
Sbjct: 5 TSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGS 57
>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding,
translesion synthesis, UB conjugation pathway; 1.80A
{Homo sapiens}
Length = 99
Score = 44.4 bits (105), Expect = 2e-06
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 255 QCYLCNDR-EVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIFNQFL 310
+C +C + + + C HN+ CS C + + CP C V V + + N+ L
Sbjct: 24 RCGICFEYFNIAMIIPQCSHNY-CSLCIRKFLSYKTQCPTCCVTVTEP-DLKNNRIL 78
>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 107
Score = 44.5 bits (105), Expect = 3e-06
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 8/60 (13%)
Query: 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP-------VFEVTGNF 136
+ +P GLV+G G +K I QT ++ SR P +F + G+
Sbjct: 5 PGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFV-EISRQLPPNGDPNFKLFIIRGSP 63
Score = 32.5 bits (74), Expect = 0.050
Identities = 13/79 (16%), Positives = 27/79 (34%), Gaps = 8/79 (10%)
Query: 13 GCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVARAKREILS--AADHFSAL 64
G +KA+ +T +++ + +F++ G + + AK+ I
Sbjct: 26 GENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPLCPVG 85
Query: 65 RASRKSGALSPLSPPTGVP 83
G P+ P P
Sbjct: 86 PGPGGPGPAGPMGPFNPGP 104
>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA
damage, chromatin regulator, chromosomal protein, DNA
repair, metal-binding; 2.12A {Homo sapiens}
Length = 115
Score = 42.2 bits (99), Expect = 2e-05
Identities = 12/37 (32%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 269 IPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMRI 304
+PC H C C + T + CP CR V+ R
Sbjct: 31 LPCNHTL-CKPCFQSTVEKASLCCPFCRRRVSSWTRY 66
>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS),
leukemia, transcription regulation; NMR {Homo sapiens}
SCOP: g.44.1.1
Length = 56
Score = 40.4 bits (95), Expect = 2e-05
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 255 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298
+C C L+PC H CS C E + CP+C+ P
Sbjct: 8 RCQQCQAEAKCPKLLPCLHT-LCSGCLEAS---GMQCPICQAPW 47
>1we8_A Tudor and KH domain containing protein; structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Mus musculus} SCOP: d.51.1.1
Length = 104
Score = 41.7 bits (98), Expect = 2e-05
Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 12/75 (16%)
Query: 66 ASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-----V 120
+S SG L+ +P V ++ VP + VG ++G G TI+ I + I
Sbjct: 2 SSGSSGILTENTP-------VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKES 54
Query: 121 TPSRDKEPVFEVTGN 135
+ + +++G
Sbjct: 55 EGTLLLSRLIKISGT 69
Score = 32.1 bits (73), Expect = 0.057
Identities = 17/74 (22%), Positives = 28/74 (37%), Gaps = 8/74 (10%)
Query: 13 GCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRAS 67
G I+++ + I + ++G +++VA AK IL L
Sbjct: 34 GETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEEL--- 90
Query: 68 RKSGALSPLSPPTG 81
RK A S P +G
Sbjct: 91 RKRIAHSASGPSSG 104
>1z6u_A NP95-like ring finger protein isoform B; structural genomics
consortium, ligase, ubiquitin-protein ligase, cell cycle
regulation, SGC; 2.10A {Homo sapiens}
Length = 150
Score = 42.7 bits (100), Expect = 2e-05
Identities = 28/138 (20%), Positives = 43/138 (31%), Gaps = 8/138 (5%)
Query: 177 GSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIW 236
GSS SS +P +S + + D
Sbjct: 2 GSSHHHHHHSSGLVPRGSPSASKVYKASDSAEAIEAFQLTPQQQHLIREDCQNQKLWDEV 61
Query: 237 SYPPVSSTSPSGSISGSRQCYLCND---REVTHALIPCGHNFFCSECAERTCDFD-RTCP 292
V + + S C C + + VT C HN C +C +R+ +CP
Sbjct: 62 LSHLVEGPNFLKKLEQSFMCVCCQELVYQPVT---TECFHN-VCKDCLQRSFKAQVFSCP 117
Query: 293 MCRVPVNQAMRIIFNQFL 310
CR + Q +I N+ L
Sbjct: 118 ACRHDLGQNYIMIPNEIL 135
>2ctj_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 95
Score = 40.9 bits (96), Expect = 4e-05
Identities = 10/48 (20%), Positives = 19/48 (39%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVT 133
+EV +P K+ ++G KG I+ I + + + V
Sbjct: 17 AEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVV 64
Score = 32.1 bits (73), Expect = 0.053
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 9 INPFGCKIKALRAK-TNTYIKTPVRGEEP-VFVVTGRKEDVARAKREILS 56
I G I+++ + +I PV G V+ G DV +AK+++L
Sbjct: 32 IGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLH 81
>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA
repair, ring finger domain, metal binding, DNA
replication; 1.75A {Homo sapiens}
Length = 124
Score = 41.5 bits (97), Expect = 5e-05
Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 9/77 (11%)
Query: 240 PVSSTSPSGSISGSR---QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDR---TCPM 293
P S + +S QC C + C HN C +C +R+ F +CP
Sbjct: 36 PASGSPFQLFLSKVEETFQCICCQELVFRPITTVCQHNV-CKDCLDRS--FRAQVFSCPA 92
Query: 294 CRVPVNQAMRIIFNQFL 310
CR + ++ + NQ L
Sbjct: 93 CRYDLGRSYAMQVNQPL 109
>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding;
HET: SUC; 1.50A {Homo sapiens}
Length = 64
Score = 39.4 bits (92), Expect = 6e-05
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 270 PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300
CGH F CS+C + TCP CR +N
Sbjct: 27 ECGHVF-CSQCLRDSLKNANTCPTCRKKINH 56
>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA
recognition, complex E, KH domain, QUA2 homology; NMR
{Homo sapiens} SCOP: d.51.1.1
Length = 131
Score = 41.0 bits (96), Expect = 7e-05
Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 8/79 (10%)
Query: 81 GVPGHVTIEVRVP------YKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTG 134
+ V+ +V +P VGL++GP+G T+K I+ + N I+ R K V E
Sbjct: 2 AMATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMI--RGKGSVKEGKV 59
Query: 135 NFPEGPGFESHHGQKIVFI 153
+G +
Sbjct: 60 GRKDGQMLPGEDEPLHALV 78
>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2,
protein structure initiative, northeast structural
genomics consortium, NESG; HET: MSE; 2.29A {Homo
sapiens}
Length = 100
Score = 40.3 bits (94), Expect = 8e-05
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 255 QCYLCNDREVTHALIP-CGHNFFCSECAER-TCDFDRTCPMCRVPVNQAMRIIFNQFL 310
+C++C ++ L P C C C R + CP CR P+ ++ ++
Sbjct: 24 RCFICMEKLRDARLCPHCSKLC-CFSCIRRWLTEQRAQCPHCRAPLQLRE-LVNCRWA 79
>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 70
Score = 38.9 bits (91), Expect = 1e-04
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 255 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298
+C +C D L PC H FC +C ++ D R CP+CR+ +
Sbjct: 17 ECCICMDGRADLIL-PCAH-SFCQKCIDKWSDRHRNCPICRLQM 58
>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing
factor, RNA binding protein; 2.30A {Pyrococcus
horikoshii} PDB: 3aev_B
Length = 219
Score = 41.6 bits (97), Expect = 1e-04
Identities = 26/119 (21%), Positives = 42/119 (35%), Gaps = 3/119 (2%)
Query: 9 INPFGCKIKALRAKTNTYIK-TPVRGEEPVFVV--TGRKEDVARAKREILSAADHFSALR 65
I G K + +T T I GE + T V +A+ +L+ FS R
Sbjct: 49 IGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPER 108
Query: 66 ASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 124
A R L + E +V G ++G KG T + I+ + + +
Sbjct: 109 AFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYGK 167
Score = 33.1 bits (75), Expect = 0.089
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 119
V++P + +++G KG T K I+ +T T I
Sbjct: 35 EEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKI 67
>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 73
Score = 38.5 bits (90), Expect = 2e-04
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 269 IPCGHNFFCSECAERTCDFDRT---CPMCRVPVNQ 300
I CGHN FC +C + + CP+C+ V +
Sbjct: 36 IDCGHN-FCLKCITQIGETSCGFFKCPLCKTSVRK 69
>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger,
zinc-binding protein, heterodimer, ubiquitin ligase,
antitumor; NMR {Homo sapiens} SCOP: g.44.1.1
Length = 112
Score = 39.3 bits (92), Expect = 2e-04
Identities = 8/35 (22%), Positives = 15/35 (42%), Gaps = 4/35 (11%)
Query: 269 IPCGHNFFCSECAERTCDFDR---TCPMCRVPVNQ 300
C H FC C + + + CP+C+ + +
Sbjct: 37 TKCDHI-FCKFCMLKLLNQKKGPSQCPLCKNDITK 70
>2egp_A Tripartite motif-containing protein 34; ZF-C3HC4 domain, tripartite
motif protein 34, interferon- responsive finger protein
1; NMR {Homo sapiens}
Length = 79
Score = 38.0 bits (89), Expect = 3e-04
Identities = 9/39 (23%), Positives = 15/39 (38%), Gaps = 8/39 (20%)
Query: 269 IPCGHNFFCSECAERTCDFDRT-------CPMCRVPVNQ 300
+ CGH+ C C + T CP+C + +
Sbjct: 28 LDCGHS-LCRACITVSNKEAVTSMGGKSSCPVCGISYSF 65
>2ecw_A Tripartite motif-containing protein 30; metal binding protein,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 85
Score = 37.7 bits (88), Expect = 4e-04
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 7/38 (18%)
Query: 269 IPCGHNFFCSECAERTCDFDRT------CPMCRVPVNQ 300
C H+ FC C + +R CP+CRVP
Sbjct: 35 ADCNHS-FCRACITLNYESNRNTDGKGNCPVCRVPYPF 71
>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger,
zinc-binding protein, heterodimer, ubiquitin ligase,
antitumor; NMR {Homo sapiens} SCOP: g.44.1.1
Length = 117
Score = 38.3 bits (89), Expect = 5e-04
Identities = 14/47 (29%), Positives = 17/47 (36%), Gaps = 8/47 (17%)
Query: 255 QCYLCND---REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298
+C C + V L C H F CS C CP+C P
Sbjct: 24 RCSRCTNILREPVC--LGGCEHIF-CSNCVSDC--IGTGCPVCYTPA 65
>2ecv_A Tripartite motif-containing protein 5; metal binding protein,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 85
Score = 37.2 bits (87), Expect = 5e-04
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 7/38 (18%)
Query: 269 IPCGHNFFCSECAERTCD------FDRTCPMCRVPVNQ 300
+ CGH+ FC C + +CP+CR+
Sbjct: 35 LDCGHS-FCQACLTANHKKSMLDKGESSCPVCRISYQP 71
>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase,
nuclear protein, chromosomal protein, transcription
regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B
Length = 165
Score = 38.8 bits (90), Expect = 6e-04
Identities = 13/59 (22%), Positives = 21/59 (35%), Gaps = 5/59 (8%)
Query: 255 QCYLCND--REVTHALIPCGHNFFCSECAERTCDFD-RTCPMCRVPVNQAMRIIFNQFL 310
C +C D + T C H F C++C + CP CR + + +
Sbjct: 56 MCPICLDMLKN-TMTTKECLHRF-CADCIITALRSGNKECPTCRKKLVSKRSLRPDPNF 112
>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT-
interacting protein, ring domain, structural genomics,
NPPSFA; NMR {Homo sapiens}
Length = 88
Score = 37.0 bits (86), Expect = 8e-04
Identities = 10/35 (28%), Positives = 13/35 (37%), Gaps = 4/35 (11%)
Query: 268 LIPCGHNFFCSECAERTCDFDR---TCPMCRVPVN 299
L+ CGH C +C E+ CP C
Sbjct: 34 LLHCGHT-ICRQCLEKLLASSINGVRCPFCSKITR 67
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 40.0 bits (93), Expect = 0.001
Identities = 44/313 (14%), Positives = 86/313 (27%), Gaps = 123/313 (39%)
Query: 54 ILSAADHFSAL-RASRKSGALSP--------LSPPTGVPGH---VTIEVRVPYKVVGLVV 101
I +A+ S L R + + + L P+ P ++I + P ++G++
Sbjct: 188 IKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCP--LIGVI- 244
Query: 102 GPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNFPEGPGFESHHGQKIVFILTSNLYSF 161
Q Y+VT ++ G G+
Sbjct: 245 ------------QLAHYVVT--------AKLLG---------FTPGE------------L 263
Query: 162 FDCRIFQRMNHHVFSGSSGCSSA-------SSSSSSSACAPHSSTQLDLGSIWSGMSSLD 214
G++G S + + S + + + + G+ +
Sbjct: 264 RSY----------LKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITV-LFFIGVRCYE 312
Query: 215 KDEGLGDSPSFDASPVNPSSIWSYPPVSSTSPSG--SISGSRQCYL------CN-----D 261
++ + + PS + + PS SIS Q + N
Sbjct: 313 ---------AYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAG 363
Query: 262 REVTHALI--P-----CGH--------NFFCSECAERTCDFDRTCPMCRVPVNQAMRIIF 306
++V +L+ G A D R+P ++
Sbjct: 364 KQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLD------QSRIPFSERKLKFS 417
Query: 307 NQFLFGKLWEPVA 319
N+FL PVA
Sbjct: 418 NRFL------PVA 424
Score = 35.0 bits (80), Expect = 0.037
Identities = 40/265 (15%), Positives = 80/265 (30%), Gaps = 101/265 (38%)
Query: 1 MFIFVVPSINPFGCKIKALR---AKTNTYIKTPVRGEEPV----------FVVTGRKEDV 47
M SI+ + ++ KTN+++ P + V VV+G + +
Sbjct: 338 ML-----SIS--NLTQEQVQDYVNKTNSHL--P--AGKQVEISLVNGAKNLVVSGPPQSL 386
Query: 48 ARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPY---KVVG----LV 100
+ RK+ A P+G+ R+P+ K+ L
Sbjct: 387 YGLNLTL-------------RKAKA------PSGLDQS-----RIPFSERKLKFSNRFLP 422
Query: 101 VG-P------KGATIKRIQHQTNTYIVTPSRD-KEPVFEV-TGNFPEGPGFESHHGQKIV 151
V P A+ + + ++D + PV++ G + +
Sbjct: 423 VASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDG----------SDLRVLS 472
Query: 152 FILTSNLYSFFDCRIFQRMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLG-SIWSGM 210
++ + DC I + + ++ LD G SG+
Sbjct: 473 GSISERI---VDCIIRLPVKW-----------------ETTTQFKATHILDFGPGGASGL 512
Query: 211 SSLDKD--EGLG----DSPSFDASP 229
L +G G + + D +P
Sbjct: 513 GVLTHRNKDGTGVRVIVAGTLDINP 537
>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA
binding; NMR {Xenopus laevis} SCOP: d.51.1.1
Length = 140
Score = 37.2 bits (86), Expect = 0.002
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 94 YKVVGLVVGPKGATIKRIQHQTNTYI 119
+ VG ++GP+G T K+++ +T I
Sbjct: 16 FNFVGRILGPRGLTAKQLEAETGCKI 41
>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex,
chimera; 2.21A {Rattus norvegicus}
Length = 133
Score = 37.1 bits (85), Expect = 0.002
Identities = 18/66 (27%), Positives = 23/66 (34%), Gaps = 8/66 (12%)
Query: 251 SGSRQCYLCNDREVTHAL-------IPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMR 303
SG+ C +C D CGH F CS+C + TCP CR +N
Sbjct: 5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVF-CSQCLRDSLKNANTCPTCRKKINHKRY 63
Query: 304 IIFNQF 309
Sbjct: 64 HPIYIG 69
Score = 33.2 bits (75), Expect = 0.042
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 270 PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 300
CGH FCS+C + TCP CR +N
Sbjct: 96 ECGH-VFCSQCLRDSLKNANTCPTCRKKINH 125
>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1;
RCHY1, ring domain, zinc-binding domain, structural
genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A
Length = 55
Score = 34.9 bits (81), Expect = 0.002
Identities = 19/53 (35%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 251 SGSRQCYLCND-----REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298
SGS C +C + R V H L PCGH C E CP+C P
Sbjct: 3 SGSSGCPICLEDIHTSRVVAHVL-PCGH-LLHRTCYEEMLKEGYRCPLCSGPS 53
>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural
genomics, PSI-2, protein struc initiative; NMR {Homo
sapiens}
Length = 91
Score = 35.8 bits (83), Expect = 0.002
Identities = 20/74 (27%), Positives = 29/74 (39%), Gaps = 6/74 (8%)
Query: 229 PVNPSSIWSYPPVSSTSPSGSISGSRQCYLC----NDREVTHALIPCGHNFFCSECAERT 284
P + SI + P + T G++ C +C +V L PC H +F C
Sbjct: 16 PASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATEL-PCHH-YFHKPCVSIW 73
Query: 285 CDFDRTCPMCRVPV 298
TCP+CR
Sbjct: 74 LQKSGTCPVCRCMF 87
>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 66
Score = 35.1 bits (81), Expect = 0.002
Identities = 10/47 (21%), Positives = 16/47 (34%), Gaps = 2/47 (4%)
Query: 255 QCYLCNDREVTHALIPCGHNFFCSECAERTC-DFDRTCPMCRVPVNQ 300
+C C+ + CGH F C C C C+ + +
Sbjct: 17 KCEKCHLVLCSPKQTECGHRF-CESCMAALLSSSSPKCTACQESIVK 62
>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 102
Score = 36.0 bits (83), Expect = 0.003
Identities = 8/41 (19%), Positives = 15/41 (36%), Gaps = 1/41 (2%)
Query: 86 VTIEVRVPYKVVGLVVGPKGATIKRIQHQ-TNTYIVTPSRD 125
V P + ++G KG + +I Q +I +
Sbjct: 27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGE 67
Score = 27.6 bits (61), Expect = 2.0
Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 3/52 (5%)
Query: 9 INPFGCKIKALRAK-TNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD 59
I G + + + +I+ GE+ + + G EDV+ A+ +I
Sbjct: 42 IGKKGQNLAKITQQMPKVHIEFT-EGEDKITL-EGPTEDVSVAQEQIEGMVK 91
>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA
binding, cell cycle; 2.79A {Caenorhabditis elegans}
Length = 376
Score = 37.6 bits (86), Expect = 0.004
Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 2/45 (4%)
Query: 85 HVTIEVRVPYKVVGLVVGPKG--ATIKRIQHQTNTYIVTPSRDKE 127
VT+ + + L+ G + I +TNT I P R
Sbjct: 29 RVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVG 73
Score = 31.1 bits (69), Expect = 0.51
Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 10/56 (17%)
Query: 9 INPFGCK--IKALRAKTNTYIKTPVRGEEPVF--------VVTGRKEDVARAKREI 54
+ G + ++ A+TNT I+ P R +TG DV RA+ +
Sbjct: 45 TSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLM 100
Score = 29.9 bits (66), Expect = 1.0
Identities = 20/136 (14%), Positives = 39/136 (28%), Gaps = 33/136 (24%)
Query: 10 NPFGCKIKALRAKTNTYIKTP-------VRGEEPVFVVTGRKEDVARAKREILSAADHFS 62
+ + + +T T I P RG V G ++V +A+R I+
Sbjct: 204 SSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMD------ 257
Query: 63 ALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTP 122
L P +++ + + I I ++ +
Sbjct: 258 ----------LLP----------ISMCFNIKNTDMAEPSRVSDRNIHMIIDESGIILKMT 297
Query: 123 SRDKEPVFEVTGNFPE 138
EP ++G P
Sbjct: 298 PSVYEPADLLSGEVPL 313
>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding
domain; 1.90A {Mus musculus}
Length = 101
Score = 34.8 bits (79), Expect = 0.006
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 256 CYLCNDR-EVTHALIPCGHNFFCSECAER-TCDFDRTCPMCRVPVN 299
C C +V +IPC H FC +CA D+ CP C PV
Sbjct: 4 CDKCGLPIKVYGRMIPCKH-VFCYDCAILHEKKGDKMCPGCSDPVQ 48
>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 63
Score = 33.5 bits (77), Expect = 0.009
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 4/29 (13%)
Query: 269 IPCGHNFFCSECAERTCDFDRT---CPMC 294
I CGHN FC +C + + CP+C
Sbjct: 36 IDCGHN-FCLKCITQIGETSCGFFKCPLC 63
>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc
binuclear cluster, zinc finger, DNA-binding protein;
2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1
Length = 116
Score = 34.9 bits (80), Expect = 0.009
Identities = 13/47 (27%), Positives = 14/47 (29%), Gaps = 2/47 (4%)
Query: 256 CYLCNDREVTHALIPCGHNFFCSECAERTCD-FDRTCPMCRVPVNQA 301
C +C C H F C C R CP CR P
Sbjct: 26 CQICEHILADPVETSCKHLF-CRICILRCLKVMGSYCPSCRYPCFPT 71
>3ztg_A E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mRNA processing,
mRNA splicing; NMR {Homo sapiens}
Length = 92
Score = 34.0 bits (78), Expect = 0.010
Identities = 18/67 (26%), Positives = 26/67 (38%), Gaps = 12/67 (17%)
Query: 255 QCYLCNDREVTHALIP-CGHNFFCSECAERTCDF--DRTCPMCRVP--------VNQAMR 303
C +C D +IP CG+++ C EC + TCP C N+ +R
Sbjct: 15 LCLICKDIMTDAVVIPCCGNSY-CDECIRTALLESDEHTCPTCHQNDVSPDALIANKFLR 73
Query: 304 IIFNQFL 310
N F
Sbjct: 74 QAVNNFK 80
>2ecj_A Tripartite motif-containing protein 39; TRIM39, ring domain,
zinc-binding domain, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 58
Score = 32.7 bits (75), Expect = 0.013
Identities = 12/29 (41%), Positives = 14/29 (48%), Gaps = 4/29 (13%)
Query: 269 IPCGHNFFCSECAERTCDFDRT---CPMC 294
I CGHN FC C R + CP+C
Sbjct: 31 IECGHN-FCKACITRWWEDLERDFPCPVC 58
>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 119
Score = 34.1 bits (78), Expect = 0.016
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 86 VTIEVRVP-YKVVGLVVGPKGATIKRIQHQTNTYIV 120
V +E VP + V V GP + ++ IQ +T +
Sbjct: 18 VGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVF 53
>1tua_A Hypothetical protein APE0754; structural genomics, protein
structure initiative, MCSG, four layers alpha-beta
sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1
d.51.1.1
Length = 191
Score = 35.0 bits (80), Expect = 0.019
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 87 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 119
I V+V + +G V+GP+G I +T T I
Sbjct: 5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVI 37
Score = 33.4 bits (76), Expect = 0.058
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 95 KVVGLVVGPKGATIKRIQHQTNTYIV 120
++ G ++G G + I+ T+TYI
Sbjct: 107 RIKGRIIGEGGRARRTIEEMTDTYIN 132
>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha,
coiled coil, cytoplasm, metal- binding, UBL conjugation,
UBL conjugation pathway; 2.20A {Homo sapiens}
Length = 170
Score = 34.3 bits (78), Expect = 0.021
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 2/47 (4%)
Query: 255 QCYLCNDREVTHALIPCGHNFFCSECAER-TCDFDRTCPMCRVPVNQ 300
+C +C PCGH F C C + D CP+ + +
Sbjct: 20 ECPICLMALREAVQTPCGHRF-CKACIIKSIRDAGHKCPVDNEILLE 65
>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 74
Score = 32.4 bits (74), Expect = 0.027
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 6/66 (9%)
Query: 242 SSTSPSGSISGSRQCYLC----NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVP 297
S+ ++ C +C R+ PC H F +C + + + CP+C +P
Sbjct: 4 GSSGKVKELNLHELCAVCLEDFKPRDELGIC-PCKH-AFHRKCLIKWLEVRKVCPLCNMP 61
Query: 298 VNQAMR 303
V Q +
Sbjct: 62 VLQLAQ 67
>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha,
coiled coil, cytoplasm, metal- binding, UBL conjugation,
UBL conjugation pathway; 2.10A {Homo sapiens} PDB:
3hcu_A 2eci_A 2jmd_A
Length = 118
Score = 32.9 bits (75), Expect = 0.037
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 269 IPCGHNFFCSECAERTC-DFDRTCPMCRVPVN 299
PCGH F C C ++ D CP+ +
Sbjct: 34 TPCGHRF-CKACIIKSIRDAGHKCPVDNEILL 64
>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional
control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B
Length = 78
Score = 32.0 bits (72), Expect = 0.043
Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 6/50 (12%)
Query: 256 CYLC----NDREVTHALIPCGHNFFCSECAERT-CDFDRTCPMCRVPVNQ 300
C LC ++ CG+ C C R D + CP CR P +
Sbjct: 14 CPLCMEPLEIDDINFFPCTCGYQI-CRFCWHRIRTDENGLCPACRKPYPE 62
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH
domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}
Length = 630
Score = 34.0 bits (79), Expect = 0.061
Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 12/73 (16%)
Query: 48 ARAKR-EILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGA 106
A + EIL + + R S P V V+VP VGP G
Sbjct: 539 ASVAKKEILQIMN--KTISKPRAS--RKENGP-------VVETVQVPLSKRAKFVGPGGY 587
Query: 107 TIKRIQHQTNTYI 119
+K++Q +T I
Sbjct: 588 NLKKLQAETGVTI 600
>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform
B'; KH domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.51.1.1
Length = 91
Score = 31.6 bits (71), Expect = 0.080
Identities = 12/67 (17%), Positives = 23/67 (34%), Gaps = 1/67 (1%)
Query: 72 ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFE 131
S S + E V ++GL +G G+ I++ + + D F
Sbjct: 1 GSSGSSGTKQLAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTG-TFR 59
Query: 132 VTGNFPE 138
+ G +
Sbjct: 60 IYGESAD 66
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide
transferase, ATP-GTP diphosphotransferase RNA
processing, RNA degradation; 2.5A {Streptomyces
antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4
d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A
Length = 757
Score = 33.3 bits (77), Expect = 0.11
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 88 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 119
I V++P +G V+GPK I +IQ T I
Sbjct: 600 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEI 631
>2ect_A Ring finger protein 126; metal binding protein, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus}
Length = 78
Score = 30.5 bits (69), Expect = 0.12
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 268 LIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298
+PC H F C + +CP+CR +
Sbjct: 33 QLPCNH-LFHDSCIVPWLEQHDSCPVCRKSL 62
>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 75
Score = 30.4 bits (69), Expect = 0.14
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 240 PVSSTSPSGSISGSRQCYLC----NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCR 295
P +P+ S C +C R++ L PC H F +C ++ +RTCP+CR
Sbjct: 10 PSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVL-PCNHEFHA-KCVDKWLKANRTCPICR 67
Query: 296 VPV 298
Sbjct: 68 ADS 70
>3knv_A TNF receptor-associated factor 2; cross-brace, alternative
splicing, apoptosis, cytoplasm, metal-binding, UBL
conjugation, zinc, zinc-finger; 1.90A {Homo sapiens}
Length = 141
Score = 31.6 bits (71), Expect = 0.15
Identities = 8/31 (25%), Positives = 10/31 (32%), Gaps = 2/31 (6%)
Query: 270 PCGHNFFCSECAER-TCDFDRTCPMCRVPVN 299
CGH +CS C + C C
Sbjct: 48 QCGHR-YCSFCLASILSSGPQNCAACVHEGI 77
>2ko5_A Ring finger protein Z; lassa fever virus-Z, negative regulator of
EIF4E, cytoplasm, HOST-virus interaction, lipoprotein,
membrane; NMR {Lassa virus josiah}
Length = 99
Score = 30.9 bits (69), Expect = 0.17
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 2/68 (2%)
Query: 237 SYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRV 296
P +S P + G + C C L+ C +++ C C CP+C++
Sbjct: 12 KDSPRASLIPDATHLGPQFCKSC--WFENKGLVECNNHYLCLNCLTLLLSVSNRCPICKM 69
Query: 297 PVNQAMRI 304
P+ +R
Sbjct: 70 PLPTKLRP 77
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 32.5 bits (75), Expect = 0.19
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 97 VGLVVGPKGATIKRIQHQTNTYI 119
+ V+G G+ I+ + +T T I
Sbjct: 571 IKDVIGKGGSVIRALTEETGTTI 593
>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch
signaling, structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus musculus}
SCOP: g.44.1.1
Length = 114
Score = 31.0 bits (69), Expect = 0.21
Identities = 10/41 (24%), Positives = 11/41 (26%), Gaps = 6/41 (14%)
Query: 263 EVTHALIPCGHNFFCSEC-----AERTCDFDRTCPMCRVPV 298
V L C H F C D CP C+
Sbjct: 53 MVVGRLTKCSHA-FHLLCLLAMYCNGNKDGSLQCPSCKTIY 92
>2yur_A Retinoblastoma-binding protein 6; P53-associated cellular protein
of testis, proliferation potential-related protein,
protein P2P-R; NMR {Homo sapiens}
Length = 74
Score = 29.7 bits (67), Expect = 0.21
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 255 QCYLCNDREVTHALIP-CGHNFFCSECAERTCDF--DRTCPMCR 295
C +C D +IP CG+++ C EC + TCP C
Sbjct: 17 LCLICKDIMTDAVVIPCCGNSY-CDECIRTALLESDEHTCPTCH 59
>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 81
Score = 29.9 bits (67), Expect = 0.25
Identities = 9/44 (20%), Positives = 15/44 (34%), Gaps = 5/44 (11%)
Query: 256 CYLC----NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCR 295
C C + C H+F + C + CP+C+
Sbjct: 29 CLRCQAENKQEDCVVVWGECNHSF-HNCCMSLWVKQNNRCPLCQ 71
>1xrs_A D-lysine 5,6-aminomutase alpha subunit; TIM barrel, rossmann
domain, PLP, cobalamin, 5'-deoxyad radical,
adenosylcobalamin; HET: B12 PLP 5AD; 2.80A {Clostridium
sticklandii} SCOP: c.1.19.4
Length = 516
Score = 31.7 bits (72), Expect = 0.33
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 4/60 (6%)
Query: 15 KIKALRAKTNTYIKTPVRGEEPVF---VVTGR-KEDVARAKREILSAADHFSALRASRKS 70
KIK R+ + + P+ V TG ED+ +A AD + +R + +S
Sbjct: 130 KIKNNRSIRESRFEEYGDKSGPLLYVIVATGNIYEDITQAVAAAKQGADVIAVIRTTGQS 189
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 31.7 bits (73), Expect = 0.36
Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 12/73 (16%)
Query: 48 ARAKR-EILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGA 106
A+ R IL + A+ A R + +P + +P + V+G G
Sbjct: 542 AKEGRAHILGEMN--KAMDAPRAD--VGDFAP-------KIETINIPTDKIREVIGSGGK 590
Query: 107 TIKRIQHQTNTYI 119
I+ I T +
Sbjct: 591 VIREIVATTGAKV 603
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 31.6 bits (71), Expect = 0.38
Identities = 14/90 (15%), Positives = 28/90 (31%), Gaps = 1/90 (1%)
Query: 162 FDCRIFQRMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGD 221
FD + Q M + G++ + A S +S + T + + + +
Sbjct: 1447 FDIYLDQDMLMNYSLGTAVPTLAGSGMGTSQLPEGAGTPYERSPMVDS-GFVGSPDAAAF 1505
Query: 222 SPSFDASPVNPSSIWSYPPVSSTSPSGSIS 251
SP Y + + SP +
Sbjct: 1506 SPLVQGGSEGREGFGDYGLLGAASPYKGVQ 1535
>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn
binding domain, metal zinc, zinc-finger, metal binding
protein; NMR {Homo sapiens}
Length = 69
Score = 28.9 bits (65), Expect = 0.40
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 268 LIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM 302
+PC H F C ++ ++ CP+CRV + +
Sbjct: 32 RLPCMHLFHQ-VCVDQWLITNKKCPICRVDIEAQL 65
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, receptor,
transcription, transcription regulation, zinc-FIN
activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_A* 3e00_A*
Length = 467
Score = 31.2 bits (70), Expect = 0.51
Identities = 15/95 (15%), Positives = 29/95 (30%), Gaps = 2/95 (2%)
Query: 170 MNHHVFSGSSGCSSASSSSS--SSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDA 227
++ + + SS + S SS PHS + ++ S + S +
Sbjct: 52 LHSPISTLSSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSED 111
Query: 228 SPVNPSSIWSYPPVSSTSPSGSISGSRQCYLCNDR 262
+ S + + C +C DR
Sbjct: 112 IKPPLGLNGVLKVPAHPSGNMASFTKHICAICGDR 146
Score = 30.1 bits (67), Expect = 1.00
Identities = 22/141 (15%), Positives = 39/141 (27%), Gaps = 17/141 (12%)
Query: 171 NHHVFSGSSGCSSASSSSSSSACAPHS-------STQLDLGSIWSGMSSLDKD------- 216
+HH S+ +SS +P S LG L
Sbjct: 3 HHHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSP 62
Query: 217 -EGLGDSPSFDASPVNPSSIW--SYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGH 273
G+G S +SP+ P S+ + P + ++ S +S ++ +
Sbjct: 63 INGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVL 122
Query: 274 NFFCSECAERTCDFDRTCPMC 294
C +C
Sbjct: 123 KVPAHPSGNMASFTKHICAIC 143
>1uxt_A Glyceraldehyde-3-phosphate dehydrogenase (NADP+); GAPN, ALDH,
glucose 1-phosphate, glycolysis, regulation, catatysis,
oxidoreductase; HET: G1P NAD; 2.2A {Thermoproteus tenax}
SCOP: c.82.1.1 PDB: 1uxp_A* 1uxq_A* 1uxr_A* 1uxn_A*
1uxu_A* 1uxv_A* 1ky8_A*
Length = 501
Score = 31.0 bits (71), Expect = 0.60
Identities = 12/72 (16%), Positives = 19/72 (26%), Gaps = 14/72 (19%)
Query: 43 RKEDVAR------------AKREILSAADHF--SALRASRKSGALSPLSPPTGVPGHVTI 88
+ A A E+ +A D + L + G P +
Sbjct: 93 NLDVFAEVLVMNAGKPKSAAVGEVKAAVDRLRLAELDLKKIGGDYIPGDWTYDTLETEGL 152
Query: 89 EVRVPYKVVGLV 100
R P VV +
Sbjct: 153 VRREPLGVVAAI 164
>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 74
Score = 28.4 bits (63), Expect = 0.64
Identities = 8/54 (14%), Positives = 16/54 (29%), Gaps = 8/54 (14%)
Query: 252 GSRQCYLCNDREVTH--ALIPCGHNFFCSECAE---RTCDFDRTCPMCRVPVNQ 300
+ C +C+ + + CG C ++ + CP C
Sbjct: 14 AVKICNICHS-LLIQGQSCETCGI-RMHLPCVAKYFQSNA-EPRCPHCNDYWPH 64
>3d7r_A Esterase; alpha/beta fold, hydrolase; 2.01A {Staphylococcus aureus
subsp}
Length = 326
Score = 30.0 bits (68), Expect = 0.92
Identities = 5/65 (7%), Positives = 15/65 (23%)
Query: 47 VARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGA 106
+ + + R+ P+ + +E + +
Sbjct: 35 LLHNRSIMFKNDQDVERFFYKREIENRKKHKQPSTLNVKANLEKLSLDDMQVFRFNFRHQ 94
Query: 107 TIKRI 111
K+I
Sbjct: 95 IDKKI 99
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 29.4 bits (65), Expect = 1.9
Identities = 21/138 (15%), Positives = 37/138 (26%), Gaps = 36/138 (26%)
Query: 142 FES----HHGQKIVFILTSNLYSFFDCRIFQRMNHHVFSGSSGCSSASSSSSSSAC---- 193
FE+ + + I+ + FDC+ Q M + S
Sbjct: 9 FETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSIL-------------SKEEIDHII 55
Query: 194 -APHSSTQLDLGSIW----SGMSSLDK--DEGLGDSPSFDASPVNPSSIWSYPPVSSTSP 246
+ + + W + K +E L + F SP +
Sbjct: 56 MSKDAVSGTLR-LFWTLLSKQEEMVQKFVEEVLRINYKFLMSP------IKTEQRQPSMM 108
Query: 247 SGSISGSRQCYLCNDREV 264
+ R L ND +V
Sbjct: 109 TRMYIEQRD-RLYNDNQV 125
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 29.7 bits (66), Expect = 2.0
Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 2/79 (2%)
Query: 176 SGSSGCSSASSSSSSSACAP--HSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPS 233
+ S ++ +P S + + ++ D E ++ +P +P
Sbjct: 1475 NESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPG 1534
Query: 234 SIWSYPPVSSTSPSGSISG 252
S P S TSP+ S +
Sbjct: 1535 FGVSSPGFSPTSPTYSPTS 1553
Score = 28.1 bits (62), Expect = 5.7
Identities = 22/84 (26%), Positives = 32/84 (38%), Gaps = 9/84 (10%)
Query: 169 RMNHHVFSGSSGCSSASS---SSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSF 225
+S +S S +S S +S + +P S + +S S S
Sbjct: 1592 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS------PTSP 1645
Query: 226 DASPVNPSSIWSYPPVSSTSPSGS 249
SP +PS + P S TSPS S
Sbjct: 1646 SYSPTSPSYSPTSPAYSPTSPSYS 1669
>3elg_A Uncharacterized periplasmic protein; BLIP-like fold, structural
genomics, joint center for struct genomics, JCSG; HET:
CIT; 1.64A {Bacteroides vulgatus atcc 8482} SCOP:
d.98.2.1
Length = 128
Score = 28.0 bits (62), Expect = 2.4
Identities = 8/33 (24%), Positives = 12/33 (36%)
Query: 104 KGATIKRIQHQTNTYIVTPSRDKEPVFEVTGNF 136
G +I+ Y +T E F+ G F
Sbjct: 91 NGHKTVKIERNRKGYELTLENGLEVDFDQFGGF 123
>1ej6_B Lambda1; icosahedral, non-equivalence, dsRNA virus, methylase,
methyltransferase, guanylyltransferase, zinc finger,
icosahedral virus; 3.60A {Reovirus SP} SCOP: i.7.1.1
PDB: 2cse_V
Length = 1275
Score = 29.1 bits (64), Expect = 2.5
Identities = 11/88 (12%), Positives = 31/88 (35%), Gaps = 3/88 (3%)
Query: 176 SGSSGCSSASSSSSSSACAPHSSTQLDLGSI--WSGMSSLDKDEGLGDSPSFD-ASPVNP 232
+ + + + + A + + + + S ++D + G P +
Sbjct: 100 DEADEATQKQAKDTDKSKAQVTYSDTGINNANELSRSGNVDNEGGSNQKPMSTRIAEATS 159
Query: 233 SSIWSYPPVSSTSPSGSISGSRQCYLCN 260
+ + +P P+ S QC++C+
Sbjct: 160 AIVSKHPARVGLPPTASSGHGYQCHVCS 187
>3db7_A Putative calcium-regulated periplasmic protein; structural
genomics, joint center for structural genomics; HET:
MSE; 1.40A {Bacteroides thetaiotaomicron} PDB: 3due_A*
Length = 127
Score = 27.6 bits (61), Expect = 2.6
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 105 GATIKRIQHQTNTYIVTPSRDKEPVFEVTGNF 136
A + +I+ Y V S E F++ N
Sbjct: 91 DAKVLKIERDKKDYEVKLSNRTELKFDLKFNL 122
>3gku_A Probable RNA-binding protein; APC21302, clostridium symbiosum ATCC
14 structural genomics, PSI-2, protein structure
initiative; 2.95A {Clostridium symbiosum atcc 14940}
Length = 225
Score = 28.3 bits (62), Expect = 3.0
Identities = 18/100 (18%), Positives = 36/100 (36%)
Query: 31 VRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEV 90
V F+ G K + RAKR+ L + ++ + V
Sbjct: 37 VEKGSAGFLGIGSKPAIIRAKRKETLQDKAIEFLEQVFDAMNMAVDISVEYNETEKEMNV 96
Query: 91 RVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 130
+ +G+++G +G T+ +Q+ + + S D V
Sbjct: 97 NLKGDDMGILIGKRGQTLDSLQYLVSLVVNKSSSDYIRVK 136
>3nw0_A Non-structural maintenance of chromosomes element homolog; E3
ligase, Zn, metal binding protein; 2.92A {Homo sapiens}
Length = 238
Score = 28.2 bits (62), Expect = 3.0
Identities = 6/50 (12%), Positives = 13/50 (26%), Gaps = 4/50 (8%)
Query: 251 SGSRQCYLCNDREVTHALIPCGHNFFCSECAE---RTCDFDRTCPMCRVP 297
+ C +C+ + C ++ + CP C
Sbjct: 178 DAVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNA-EPRCPHCNDY 226
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 27.6 bits (60), Expect = 3.5
Identities = 5/26 (19%), Positives = 9/26 (34%), Gaps = 4/26 (15%)
Query: 107 TIKRIQHQTNTYIVTPSRDKEPVFEV 132
+K++Q Y D P +
Sbjct: 21 ALKKLQASLKLY--AD--DSAPALAI 42
>2hcf_A Hydrolase, haloacid dehalogenase-like family; NP_662590.1, ST
genomics, PSI-2, protein structure initiative; 1.80A
{Chlorobaculum tepidum} SCOP: c.108.1.6
Length = 234
Score = 28.1 bits (63), Expect = 3.6
Identities = 8/43 (18%), Positives = 15/43 (34%), Gaps = 5/43 (11%)
Query: 32 RGEEPVFVVTGRKEDVARAKREILSAADHFSALR-----ASRK 69
R + + ++TG E R K ++ +F R
Sbjct: 108 RSDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRN 150
>2ycb_A Beta-CAsp RNAse, cleavage and polyadenylation specificity factor;
hydrolase, KH, metallo-beta-lactamase; 3.10A
{Methanothermobacter thermautotrophicusorganism_taxid}
Length = 636
Score = 28.4 bits (64), Expect = 3.7
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 4/32 (12%)
Query: 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT 115
V IE R P GLV+G G+T + I T
Sbjct: 100 CEVIIEARKP----GLVIGKYGSTSREIVKNT 127
>3pvk_A Candidapepsin-2; hydrolase; 1.27A {Candida albicans} PDB: 1eag_A
3q70_A* 1zap_A* 2qzw_A 2h6t_A* 2h6s_A*
Length = 342
Score = 28.1 bits (63), Expect = 3.9
Identities = 8/42 (19%), Positives = 13/42 (30%), Gaps = 7/42 (16%)
Query: 174 VFSGSSGCSSASSSSSSSACAPH-------SSTQLDLGSIWS 208
V + C S ++ C SS DL + +
Sbjct: 40 VPDVNVDCQVTYSDQTADFCKQKGTYDPSGSSASQDLNTPFK 81
>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit;
hydrolase, metallo-beta-lactamase, beta-CAsp, RNA
processing; 2.59A {Methanosarcina mazei}
Length = 640
Score = 28.4 bits (64), Expect = 3.9
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT 115
G V IE P GLV+G GAT++ I Q
Sbjct: 104 GEVIIEAEKP----GLVIGKHGATLREITKQI 131
>4dsd_A Putative periplasmic protein; BLIP-like fold, structural genomics,
joint center for struct genomics, JCSG, protein
structure initiative; 1.75A {Bacteroides ovatus}
Length = 129
Score = 27.3 bits (60), Expect = 4.0
Identities = 8/47 (17%), Positives = 15/47 (31%), Gaps = 2/47 (4%)
Query: 92 VPYKVVGLVVGPK--GATIKRIQHQTNTYIVTPSRDKEPVFEVTGNF 136
VP V + + +++ Y + S F+ G F
Sbjct: 78 VPGFAVNYLKAHNFVNEGVTKVERDRKGYEIELSTGLSFKFDKKGKF 124
>3af5_A Putative uncharacterized protein PH1404; archaeal CPSF, beta-CAsp
family, KH domain, ribonuclease, ME beta-lactamase
superfamily, archaea; 2.60A {Pyrococcus horikoshii} PDB:
3af6_A*
Length = 651
Score = 28.5 bits (64), Expect = 4.0
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT 115
G V IE + P GLV+G G T++ I +
Sbjct: 109 GEVLIEAKKP----GLVIGKNGETLRLITQKV 136
>1z60_A TFIIH basal transcription factor complex P44 subunit; basic
transcription factor, zinc binding protein, ring finger;
NMR {Homo sapiens} SCOP: g.49.1.2
Length = 59
Score = 26.0 bits (57), Expect = 4.2
Identities = 11/37 (29%), Positives = 14/37 (37%), Gaps = 2/37 (5%)
Query: 246 PSGSISGSRQCYLCNDREVTHALIPCG--HNFFCSEC 280
P +G R CY C + C N FC +C
Sbjct: 8 PLEEYNGERFCYGCQGELKDQHVYVCAVCQNVFCVDC 44
>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR
{Oryza sativa} SCOP: g.44.1.1
Length = 55
Score = 25.6 bits (57), Expect = 4.4
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 255 QCYLC----NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 298
+C +C D E L CGH F EC + TCP+CR+ V
Sbjct: 7 ECAVCLAELEDGEEARFLPRCGHGFHA-ECVDMWLGSHSTCPLCRLTV 53
>3avx_A Elongation factor TS, elongation factor TU, linke replicase; RNA
polymerase, translation, transferase-RNA complex; HET:
GH3; 2.41A {Escherichia coli O157} PDB: 3agq_A 3agp_A*
3avu_A 3avv_A 3avt_A* 3avw_A* 3avy_A* 3mmp_A* 3mmp_G*
1efu_B
Length = 1289
Score = 28.4 bits (63), Expect = 4.5
Identities = 16/46 (34%), Positives = 18/46 (39%), Gaps = 15/46 (32%)
Query: 15 KIKALRAKTNTYIKTPVRGE--------EPVF-------VVTGRKE 45
KI L ++YI P R E VF VVTGR E
Sbjct: 472 KILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVE 517
>2c78_A Elongation factor TU-A; hydrolase, GTPase, translation elongation
factor, protein synthesis, antibiotic, GTP-binding,
nucleotide-binding; HET: GNP PUL; 1.4A {Thermus
thermophilus} SCOP: b.43.3.1 b.44.1.1 c.37.1.8 PDB:
2y0u_Z* 2y0w_Z* 2y0y_Z* 2y10_Z* 2y12_Z* 2y14_Z* 2y16_Z*
2y18_Z* 2wrn_Z* 2wrq_Z* 2c77_A* 1aip_A 1exm_A* 1ha3_A*
2xqd_Z* 3fic_Z* 4abr_Z* 1b23_P* 1ob5_A* 1ttt_A* ...
Length = 405
Score = 27.9 bits (63), Expect = 4.8
Identities = 17/46 (36%), Positives = 18/46 (39%), Gaps = 15/46 (32%)
Query: 15 KIKALRAKTNTYIKTPVRGE--------EPVF-------VVTGRKE 45
KI L + YI TPVR E VF V TGR E
Sbjct: 198 KIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIE 243
>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4,
UIP4, structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: g.44.1.1
Length = 94
Score = 26.4 bits (58), Expect = 5.1
Identities = 13/55 (23%), Positives = 19/55 (34%), Gaps = 12/55 (21%)
Query: 251 SGSRQCYLCND---REVTHALIPCGHNFFCSECAERTCD--------FDRTCPMC 294
SGS C LC E + C FC+ C ++ + +CP
Sbjct: 3 SGSSGCKLCLGEYPVEQMTTIAQCQC-IFCTLCLKQYVELLIKEGLETAISCPDA 56
>1d2e_A Elongation factor TU (EF-TU); G-protein, beta-barrel, RNA binding
protein; HET: GDP; 1.94A {Bos taurus} SCOP: b.43.3.1
b.44.1.1 c.37.1.8 PDB: 1xb2_A* 2hcj_A* 2hdn_A*
Length = 397
Score = 27.5 bits (62), Expect = 6.6
Identities = 13/46 (28%), Positives = 17/46 (36%), Gaps = 15/46 (32%)
Query: 15 KIKALRAKTNTYIKTPVRGE--------EPVF-------VVTGRKE 45
++ L +TYI P R E V+ VVTG E
Sbjct: 181 SVQKLLDAVDTYIPVPTRDLEKPFLLPVESVYSIPGRGTVVTGTLE 226
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 26.9 bits (59), Expect = 7.0
Identities = 6/36 (16%), Positives = 13/36 (36%), Gaps = 9/36 (25%)
Query: 277 CSECAERTCDF-------DRTCPMCRVPVNQAMRII 305
C EC D C +C + ++ +++
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSD--KLV 57
>3pie_A 5'->3' exoribonuclease (XRN1); beta berrel, tudor domain, chromo
domain, mRNA turnover, RRN processing, RNA binding, DNA
binding; 2.90A {Kluyveromyces lactis} PDB: 3pif_A
Length = 1155
Score = 27.6 bits (60), Expect = 7.1
Identities = 17/86 (19%), Positives = 27/86 (31%), Gaps = 20/86 (23%)
Query: 84 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTY----IVTPSRDKEPVF------EVT 133
++ +V V GLV G+ K Y IV ++K+ + +
Sbjct: 840 DDISALAKV-VPVNGLVRNSDGSYSKSFNETIEYYPLQLIVEDVKNKDERYIEKEPLPIN 898
Query: 134 GNFPEGPGFESHHGQKIVFILTSNLY 159
FP+G V L Y
Sbjct: 899 KEFPKG---------SKVVFLGDYAY 915
>2l4z_A DNA endonuclease RBBP8, LIM domain transcription LMO4;
protein-protein interaction, LIM-interaction DOM LMO4,
RBBP8/CTIP, LIM-only protein; HET: DNA; NMR {Homo
sapiens}
Length = 123
Score = 26.2 bits (57), Expect = 8.0
Identities = 12/77 (15%), Positives = 21/77 (27%), Gaps = 6/77 (7%)
Query: 221 DSPSFDASPVNPSSIWSYPPVSSTSPSGSISGSRQCYLCN----DREVTHALIPCGHN-- 274
+ S S ++C C DR + +A+ H+
Sbjct: 29 KMDVTVIDTKDGSQSKLGGGGSGGHMGSGGLSWKRCAGCGGKIADRFLLYAMDSYWHSRC 88
Query: 275 FFCSECAERTCDFDRTC 291
CS C + D +
Sbjct: 89 LKCSSCQAQLGDIGTSS 105
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.133 0.413
Gapped
Lambda K H
0.267 0.0548 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,012,382
Number of extensions: 296912
Number of successful extensions: 854
Number of sequences better than 10.0: 1
Number of HSP's gapped: 790
Number of HSP's successfully gapped: 174
Length of query: 329
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 235
Effective length of database: 4,077,219
Effective search space: 958146465
Effective search space used: 958146465
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: 57 (26.1 bits)