RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4141
(353 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 = 120 bits (302), Expect = 2e-34
Identities = 53/80 (66%), Positives = 63/80 (78%)
Query: 73 PPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPD 132
G TI+VRVPY+VVGLVVGPKGATIKRIQ +T+TYIVTP RDKEPVF VTG P+
Sbjct: 2 SSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGMPE 61
Query: 133 SVEIARQEIESHIIRRTGSC 152
+V+ AR+EIE+HI R+G
Sbjct: 62 NVDRAREEIEAHITLRSGPS 81
Score = 60.7 bits (147), Expect = 3e-12
Identities = 27/63 (42%), Positives = 37/63 (58%), Gaps = 4/63 (6%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
+ G IK ++ +T+TYI TP R +EPVF VTG E+V RA+ EI + LR+
Sbjct: 25 VGPKGATIKRIQQRTHTYIVTPGRDKEPVFAVTGMPENVDRAREEI----EAHITLRSGP 80
Query: 64 KSG 66
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 = 110 bits (276), Expect = 3e-29
Identities = 31/153 (20%), Positives = 53/153 (34%), Gaps = 11/153 (7%)
Query: 4 ISRSGCKIKALRAKTNTYIK------TPVRGEEPVFVVTGRKEDVARAKREILSAADHFS 57
I + G I L+ +T IK E V ++ G E + I
Sbjct: 21 IGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNAVHGFIAEKIREMP 80
Query: 58 ALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTP 117
A + ++ +++ VP GL++G GAT+K I Q+ ++
Sbjct: 81 QNVAKTEPVSILQPQTTVNPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLS 140
Query: 118 SRDKEP-----VFEVTGAPDSVEIARQEIESHI 145
+ V V+G P+ A + I I
Sbjct: 141 QKPDGINLQNRVVTVSGEPEQNRKAVELIIQKI 173
Score = 64.1 bits (156), Expect = 2e-12
Identities = 17/98 (17%), Positives = 37/98 (37%), Gaps = 6/98 (6%)
Query: 77 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP-----VFEVTGA 130
+ ++V +P G ++G G TI ++Q +T I ++ S+D P V + G
Sbjct: 2 LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61
Query: 131 PDSVEIARQEIESHIIRRTGSCVTPAEAVLNGDDNSAD 168
+++ I I + + + +
Sbjct: 62 IEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVN 99
>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 = 104 bits (261), Expect = 3e-27
Identities = 32/150 (21%), Positives = 50/150 (33%), Gaps = 16/150 (10%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGEEP-----VFVVTGRKEDVARAKREILSAADHFSA 58
I + G IK L+ + + G + + G V +A ++
Sbjct: 17 IGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQ 76
Query: 59 LRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPS 118
G I+V VP VG+V+G G IK+IQ+ I
Sbjct: 77 --------GGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQ 128
Query: 119 RD---KEPVFEVTGAPDSVEIARQEIESHI 145
D E + + G PD E A + I +
Sbjct: 129 DDGTGPEKIAHIMGPPDRCEHAARIINDLL 158
Score = 60.2 bits (146), Expect = 3e-11
Identities = 20/119 (16%), Positives = 41/119 (34%), Gaps = 7/119 (5%)
Query: 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP-----VFEVTGAPDSVEI 136
E+ +P GLV+G G TIK++Q + ++ + + G P V+
Sbjct: 3 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQ 62
Query: 137 ARQEIESHIIRRTGSCVTPAEAVLNGDDNSADLL--ASLCNSGLGSLGTILNYVNGTSG 193
A + + + R + D+ +G G ++ + +G
Sbjct: 63 ACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAG 121
>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 = 100 bits (251), Expect = 1e-25
Identities = 36/157 (22%), Positives = 51/157 (32%), Gaps = 15/157 (9%)
Query: 4 ISRSGCKIKALRAKTNTYIK---TPVRGEEPVFVVTGRKEDVARAKREILS------AAD 54
I R+G IK ++ I+ E + +TG + A I A +
Sbjct: 18 IGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQHAAEIITDLLRSVQAGN 77
Query: 55 HFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 114
R G G VP GL++G G TIK I Q+ I
Sbjct: 78 PGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARI 137
Query: 115 VTPSR------DKEPVFEVTGAPDSVEIARQEIESHI 145
+F + G P ++ ARQ IE I
Sbjct: 138 ELQRNPPPNADPNMKLFTIRGTPQQIDYARQLIEEKI 174
Score = 63.0 bits (153), Expect = 4e-12
Identities = 23/93 (24%), Positives = 35/93 (37%), Gaps = 3/93 (3%)
Query: 79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVTGAPDSVE 135
G I+V +P VG+V+G G IK+IQ+ I P P + ++TG PD +
Sbjct: 1 GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQ 60
Query: 136 IARQEIESHIIRRTGSCVTPAEAVLNGDDNSAD 168
A + I + G
Sbjct: 61 HAAEIITDLLRSVQAGNPGGPGPGGRGRGRGQG 93
>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 = 98.3 bits (245), Expect = 5e-25
Identities = 26/148 (17%), Positives = 52/148 (35%), Gaps = 14/148 (9%)
Query: 4 ISRSGCKIKALRAKTNTYIK-TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRAS 62
I + G +K +R ++ I + E + + G + +A I+
Sbjct: 20 IGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIIDKL--------- 70
Query: 63 RKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDK- 121
+ + S + VT+ + VP G ++G G IK I+ T +
Sbjct: 71 EEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLP 130
Query: 122 ---EPVFEVTGAPDSVEIARQEIESHII 146
E + G P S+ ++I ++
Sbjct: 131 NSTERAITIAGIPQSIIECVKQICVVML 158
Score = 64.4 bits (157), Expect = 9e-13
Identities = 23/116 (19%), Positives = 51/116 (43%), Gaps = 4/116 (3%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGAPDSVEIARQ 139
+TI + + K VG ++G KG ++K+++ ++ I ++ E + + G +++ A
Sbjct: 5 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFA 64
Query: 140 EIESHIIRRTGSCVTPAEAVLNGDDNSADLL--ASLCNSGLGSLGTILNYVNGTSG 193
I + S + + L+ AS C S +G G + + ++G
Sbjct: 65 MIID-KLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTG 119
>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 = 80.2 bits (198), Expect = 3e-18
Identities = 30/151 (19%), Positives = 58/151 (38%), Gaps = 23/151 (15%)
Query: 4 ISRSGCKIKALRAKTNTYIK----TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSAL 59
I + G IK L + IK + + ++TG E +A+ I L
Sbjct: 18 IGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGK------L 71
Query: 60 RASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV---- 115
+ G + +RVP G V+G G T+ +Q+ T +V
Sbjct: 72 KEENFFGP--------KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRD 123
Query: 116 -TPSRDKEPVFEVTGAPDSVEIARQEIESHI 145
TP + + + ++ G + ++A+++I +
Sbjct: 124 QTPDENDQVIVKIIGHFYASQMAQRKIRDIL 154
Score = 58.6 bits (142), Expect = 1e-10
Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 4/73 (5%)
Query: 80 HVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRD---KEPVFEVTGAPDSVE 135
++V +P + VG ++G KG IK++ + I + P K + +TG P++
Sbjct: 2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQF 61
Query: 136 IARQEIESHIIRR 148
A+ I +
Sbjct: 62 KAQGRIYGKLKEE 74
>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 = 75.6 bits (186), Expect = 3e-17
Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP-VFEVTGAPDSVEIARQ 139
VTIEV VP+ + V+G KG+ I+++ + I P+ + + + +TG +++ A+
Sbjct: 17 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKA 76
Query: 140 EIESHI 145
+ +
Sbjct: 77 GLLERV 82
Score = 47.9 bits (114), Expect = 2e-07
Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 1/62 (1%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGEEP-VFVVTGRKEDVARAKREILSAADHFSALRAS 62
I + G I+ + + I P + + +TG ++ RAK +L A +
Sbjct: 32 IGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKAGLLERVKELQAEQED 91
Query: 63 RK 64
R
Sbjct: 92 RA 93
>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 = 74.4 bits (183), Expect = 5e-17
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 1/66 (1%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGAPDSVEIARQ 139
+ V +P + V+G G ++ ++ +T T I P D ++TG + +E AR
Sbjct: 17 ASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARH 76
Query: 140 EIESHI 145
E+
Sbjct: 77 EVLLIS 82
Score = 50.1 bits (120), Expect = 2e-08
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGEEPVFV-VTGRKEDVARAKREILSAADHFSALRAS 62
I ++G K++ L KT T I+ P + + +TG KE + +A+ E+L + R+
Sbjct: 32 IGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISAEQDK-RSG 90
Query: 63 RKSG 66
SG
Sbjct: 91 PSSG 94
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo
sapiens}
Length = 85
Score = 73.2 bits (180), Expect = 1e-16
Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 5/79 (6%)
Query: 72 SPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV-----TPSRDKEPVFE 126
G E+ +P GLV+G G TIK++Q + ++ + + + +
Sbjct: 5 DNANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLR 64
Query: 127 VTGAPDSVEIARQEIESHI 145
+ G P V+ A + + +
Sbjct: 65 IIGDPYKVQQACEMVMDIL 83
Score = 38.5 bits (90), Expect = 3e-04
Identities = 8/53 (15%), Positives = 18/53 (33%), Gaps = 5/53 (9%)
Query: 4 ISRSGCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREILS 51
I + G IK L+ + + + + + G V +A ++
Sbjct: 29 IGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMD 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 = 72.4 bits (178), Expect = 3e-16
Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 72 SPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIV-----TPSRDKEPVFE 126
S PG+ E+ +P GLV+G G TIK++Q + +V + +
Sbjct: 6 SGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLR 65
Query: 127 VTGAPDSVEIARQEIESHI 145
+TG P V+ A++ + I
Sbjct: 66 ITGDPYKVQQAKEMVLELI 84
Score = 38.2 bits (89), Expect = 4e-04
Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 5/52 (9%)
Query: 4 ISRSGCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREIL 50
I + G IK L+ + + G + +TG V +AK +L
Sbjct: 30 IGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVL 81
>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 = 71.3 bits (175), Expect = 7e-16
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 2/65 (3%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP--VFEVTGAPDSVEIAR 138
V+ +V + ++V ++G +G I++I + I P VTG P++VE A
Sbjct: 17 VSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAI 76
Query: 139 QEIES 143
I +
Sbjct: 77 DHILN 81
Score = 51.3 bits (123), Expect = 1e-08
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 2/55 (3%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGEEP--VFVVTGRKEDVARAKREILSAADHF 56
I G I+ + + I+ P G VTG E+V A IL+ + +
Sbjct: 32 IGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEEY 86
>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens}
SCOP: d.51.1.1 PDB: 1vih_A
Length = 71
Score = 68.5 bits (168), Expect = 4e-15
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR-DKEPVFEVTGAPDSVEIARQ 139
+E+ + +K ++G GA I RI+ Q + P +K + + G P V+ A++
Sbjct: 5 DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKR 64
Query: 140 EIES 143
E+
Sbjct: 65 ELLE 68
Score = 43.5 bits (103), Expect = 3e-06
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILS 51
I +SG I ++ + ++ P E + + G + V +AKRE+L
Sbjct: 20 IGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLE 68
>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 106
Score = 67.5 bits (165), Expect = 2e-14
Identities = 23/77 (29%), Positives = 33/77 (42%), Gaps = 3/77 (3%)
Query: 72 SPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVT 128
+ TG I+V VP VG+V+G G IK+IQ+ I P + +
Sbjct: 2 AMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIM 61
Query: 129 GAPDSVEIARQEIESHI 145
G PD E A + I +
Sbjct: 62 GPPDRCEHAARIINDLL 78
Score = 38.6 bits (90), Expect = 3e-04
Identities = 16/79 (20%), Positives = 23/79 (29%), Gaps = 3/79 (3%)
Query: 4 ISRSGCKIKALRAKTNTYIK---TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALR 60
I RSG IK ++ I+ G E + + G + A R I +
Sbjct: 26 IGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLRSGP 85
Query: 61 ASRKSGALSPLSPPTGVPG 79
G P G
Sbjct: 86 PGPPGGPGMPPGGRGRGRG 104
>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 = 66.0 bits (161), Expect = 6e-14
Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 4/69 (5%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFE----VTGAPDSVEI 136
+ V V K ++G KGA I +I+ + + I P +D + +TG + E
Sbjct: 17 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEA 76
Query: 137 ARQEIESHI 145
AR I +
Sbjct: 77 ARDAILRIV 85
Score = 48.7 bits (116), Expect = 9e-08
Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 4/52 (7%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGEEP----VFVVTGRKEDVARAKREILS 51
I R G I +R + + I+ P + + +TG +++ A+ IL
Sbjct: 32 IGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNTEAARDAILR 83
>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 = 4e-13
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 300 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 351
+ C +C + E+ PCGH C CA + ++CP+CR V +
Sbjct: 18 AMLCMVCCEEEINSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEHVQHV 65
>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 = 63.2 bits (154), Expect = 5e-13
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 3/80 (3%)
Query: 69 SPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VF 125
S S +T E +VP +VG ++G G I RIQ ++ I + P P
Sbjct: 3 SGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSC 62
Query: 126 EVTGAPDSVEIARQEIESHI 145
+TG P+SV+ A++ ++ +
Sbjct: 63 MLTGTPESVQSAKRLLDQIV 82
Score = 31.6 bits (72), Expect = 0.065
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 4 ISRSGCKIKALRAKTNTYIK-TPVRGEEP--VFVVTGRKEDVARAKREI 49
I R G +I ++ ++ I+ P G P ++TG E V AKR +
Sbjct: 30 IGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLL 78
>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 = 60.4 bits (147), Expect = 4e-12
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP-----VFEVTGAPDSV 134
+E+ VP +VG ++G G T+ Q T I ++ + P +TG+P +
Sbjct: 3 ELVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT 62
Query: 135 EIARQEIESHI 145
+ A+ I +
Sbjct: 63 QAAQYLISQRV 73
Score = 31.5 bits (72), Expect = 0.059
Identities = 9/52 (17%), Positives = 17/52 (32%), Gaps = 6/52 (11%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGEEP------VFVVTGRKEDVARAKREI 49
+ + G + + T I+ +GE +TG A+ I
Sbjct: 18 LGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLI 69
>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 = 59.0 bits (143), Expect = 8e-12
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 4/63 (6%)
Query: 289 SSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQA 348
S+ S S+ C +C + V L+PC H C C + + CPMCR V ++
Sbjct: 4 GSSGVEPSEENSKDCVVCQNGTVNWVLLPCRHTCLCDGCVKYF----QQCPMCRQFVQES 59
Query: 349 MRI 351
+
Sbjct: 60 FAL 62
>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian,
zinc-binding domain, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 75
Score = 59.0 bits (143), Expect = 1e-11
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 300 SRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 351
+ C +C DR + +PCGH C +CAE CPMC + +I
Sbjct: 25 EKLCKICMDRNIAIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFKQKI 72
>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 = 59.3 bits (144), Expect = 1e-11
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP-----VFEVTGAPDSV 134
+E+ VP +VG ++G G T+ Q T I ++ + P +TG+P +
Sbjct: 3 ELVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAAT 62
Query: 135 EIARQEIESHI 145
+ A+ I +
Sbjct: 63 QAAQYLISQRV 73
Score = 33.1 bits (76), Expect = 0.019
Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 6/65 (9%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGEEP------VFVVTGRKEDVARAKREILSAADHFS 57
+ + G + + T I+ +GE +TG A+ I +
Sbjct: 18 LGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQRVTYEQ 77
Query: 58 ALRAS 62
+RAS
Sbjct: 78 GVRAS 82
>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 = 58.4 bits (142), Expect = 1e-11
Identities = 14/68 (20%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGAPDSVEIA 137
+TI + + K VG ++G KG ++K+++ ++ I ++ E + + G +++ A
Sbjct: 3 VTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKA 62
Query: 138 RQEIESHI 145
I +
Sbjct: 63 FAMIIDKL 70
Score = 35.7 bits (83), Expect = 0.002
Identities = 9/49 (18%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVARAKREILS 51
I + G +K +R ++ I E + + G + +A I+
Sbjct: 20 IGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAFAMIID 68
>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 = 63.5 bits (152), Expect = 2e-11
Identities = 20/50 (40%), Positives = 26/50 (52%), Gaps = 4/50 (8%)
Query: 302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 351
C +C D+EV+ IPCGH C ECA R CP+CR + +R
Sbjct: 297 TCKVCMDKEVSVVFIPCGHLVVCQECAPSL----RKCPICRGIIKGTVRT 342
>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 = 58.1 bits (141), Expect = 3e-11
Identities = 16/78 (20%), Positives = 42/78 (53%), Gaps = 3/78 (3%)
Query: 76 GVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRD--KEPVFEVTGAPD 132
+ +T +V +P + G ++G G IK+I+H++ I + + ++ + +TG D
Sbjct: 2 AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQD 61
Query: 133 SVEIARQEIESHIIRRTG 150
++ A+ +++ + + +G
Sbjct: 62 QIQNAQYLLQNSVKQYSG 79
Score = 31.5 bits (72), Expect = 0.061
Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 4 ISRSGCKIKALRAKTNTYIK---TPVRGEEPVFVVTGRKEDVARAKREI 49
I + G +IK +R ++ IK E+ + +TG ++ + A+ +
Sbjct: 22 IGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLL 70
>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 = 57.3 bits (139), Expect = 6e-11
Identities = 16/73 (21%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRD--KEPVFEVTGAPDSVEIA 137
+T +V +P + G ++G G IK+I+H++ I + + ++ + +TG D ++ A
Sbjct: 14 ITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNA 73
Query: 138 RQEIESHIIRRTG 150
+ +++ + + +G
Sbjct: 74 QYLLQNSVKQYSG 86
Score = 31.1 bits (71), Expect = 0.090
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 4 ISRSGCKIKALRAKTNTYIK--TPVRG-EEPVFVVTGRKEDVARAKREI 49
I + G +IK +R ++ IK P+ G E+ + +TG ++ + A+ +
Sbjct: 29 IGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLL 77
>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 = 14/53 (26%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 301 RQCYLCNDREVTHALI--PCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 351
+ C LC R +I GH C CA R +CP+C+ + +++
Sbjct: 8 KPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQLVIKV 60
>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA
binding protein/DNA complex; 1.60A {Homo sapiens}
Length = 76
Score = 56.5 bits (137), Expect = 8e-11
Identities = 15/72 (20%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVTGAPDSVEIA 137
+ E+ +P ++G ++G +GA I I+ + I + + +TG+ S+ +A
Sbjct: 5 TSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLA 64
Query: 138 RQEIESHIIRRT 149
+ I + T
Sbjct: 65 QYLINVRLSSET 76
Score = 30.0 bits (68), Expect = 0.20
Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 5/50 (10%)
Query: 4 ISRSGCKIKALRAKTNTYIK----TPVRGEEPVFVVTGRKEDVARAKREI 49
I R G KI +R + IK + V +TG ++ A+ I
Sbjct: 20 IGRQGAKINEIRQMSGAQIKIANPVEGSTDRQV-TITGSAASISLAQYLI 68
>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 = 56.5 bits (137), Expect = 1e-10
Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 77 VPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEP--VFEVTGAPDS 133
+ T E+ +P ++G ++G +GA I I+ + I + + +TG+ S
Sbjct: 2 LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAAS 61
Query: 134 VEIARQEIESHI 145
+ +A+ I + +
Sbjct: 62 ISLAQYLINARL 73
Score = 28.0 bits (63), Expect = 1.1
Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 3/49 (6%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGEEP---VFVVTGRKEDVARAKREI 49
I R G I +R + IK E +TG ++ A+ I
Sbjct: 21 IGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLI 69
>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 = 57.7 bits (139), Expect = 2e-10
Identities = 27/151 (17%), Positives = 46/151 (30%), Gaps = 38/151 (25%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASR 63
I G I+ R + + F + G +D + R L A+
Sbjct: 19 IGTHGANIQQARKVPGV-TAIDLDEDTCTFHIYGEDQDAVKKARSFLEFAEDV------- 70
Query: 64 KSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP 123
++VP +VG V+G G I+ I ++ V + E
Sbjct: 71 ---------------------IQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEK 109
Query: 124 ---------VFEVTGAPDSVEIARQEIESHI 145
F G DS+ A ++ H+
Sbjct: 110 NVPQEEGMVPFVFVGTKDSIANATVLLDYHL 140
Score = 53.1 bits (127), Expect = 8e-09
Identities = 13/61 (21%), Positives = 24/61 (39%)
Query: 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEI 141
+ V ++GL +G GA I++ + + D D+V+ AR +
Sbjct: 5 HEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFL 64
Query: 142 E 142
E
Sbjct: 65 E 65
Score = 30.4 bits (68), Expect = 0.47
Identities = 12/61 (19%), Positives = 25/61 (40%), Gaps = 9/61 (14%)
Query: 4 ISRSGCKIKALRAKTN-TYIKTPVRGEEPV--------FVVTGRKEDVARAKREILSAAD 54
I ++G I+ + K+ ++ E+ V FV G K+ +A A + +
Sbjct: 82 IGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDSIANATVLLDYHLN 141
Query: 55 H 55
+
Sbjct: 142 Y 142
>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 107
Score = 56.4 bits (136), Expect = 2e-10
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEP-------VFEVTGAP 131
+ +P GLV+G G +K I QT ++ SR P +F + G+P
Sbjct: 5 PGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFV-EISRQLPPNGDPNFKLFIIRGSP 63
Query: 132 DSVEIARQEIESHI 145
++ A+Q IE I
Sbjct: 64 QQIDHAKQLIEEKI 77
Score = 33.7 bits (77), Expect = 0.017
Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 8/83 (9%)
Query: 4 ISRSGCKIKALRAKTNTYIKTPVRGE------EPVFVVTGRKEDVARAKREILS--AADH 55
I R G +KA+ +T +++ + +F++ G + + AK+ I
Sbjct: 22 IGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDHAKQLIEEKIEGPL 81
Query: 56 FSALRASRKSGALSPLSPPTGVP 78
G P+ P P
Sbjct: 82 CPVGPGPGGPGPAGPMGPFNPGP 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 = 54.8 bits (132), Expect = 3e-10
Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 2/60 (3%)
Query: 294 SGSISGSRQCYLCNDREVTHALIP--CGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRI 351
S ++ C +C R ++ GH C CA++ ++ CP+CR P+ +
Sbjct: 2 SLPLNAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLT 61
>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 = 57.8 bits (139), Expect = 6e-10
Identities = 33/145 (22%), Positives = 53/145 (36%), Gaps = 7/145 (4%)
Query: 4 ISRSGCKIKALRAKTNTYIK-TPVRGEEPVFVV--TGRKEDVARAKREILSAADHFSALR 60
I + G K + +T T I GE + T V +A+ +L+ FS R
Sbjct: 49 IGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPER 108
Query: 61 ASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRD 120
A R L + E +V G ++G KG T + I+ + + +
Sbjct: 109 AFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYGK- 167
Query: 121 KEPVFEVTGAPDSVEIARQEIESHI 145
+ G P +EIA+ IE
Sbjct: 168 ---TVAIIGNPIQIEIAKTAIEKLA 189
Score = 37.4 bits (86), Expect = 0.003
Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 2/83 (2%)
Query: 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-VTPSRDKEPVFEVTGAPDSVEIARQE 140
V++P + +++G KG T K I+ +T T I + + + D + + +
Sbjct: 35 EEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKAR 94
Query: 141 IESHIIRRTGSCVTPAEAVLNGD 163
I R G A +LN
Sbjct: 95 DIVLAIGR-GFSPERAFRLLNEG 116
>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 = 52.5 bits (126), Expect = 4e-09
Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 2/67 (2%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVT--GAPDSVEIAR 138
+EV +P K+ ++G KG I+ I + + + V G VE A+
Sbjct: 17 AEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAK 76
Query: 139 QEIESHI 145
+++
Sbjct: 77 KQLLHLA 83
Score = 32.1 bits (73), Expect = 0.049
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 4 ISRSGCKIKALRAK-TNTYIKTPVRGEEP-VFVVTGRKEDVARAKREILS 51
I G I+++ + +I PV G V+ G DV +AK+++L
Sbjct: 32 IGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLH 81
>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 = 50.6 bits (121), Expect = 2e-08
Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 12/90 (13%)
Query: 61 ASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI-----V 115
+S SG L+ +P V ++ VP + VG ++G G TI+ I + I
Sbjct: 2 SSGSSGILTENTP-------VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKES 54
Query: 116 TPSRDKEPVFEVTGAPDSVEIARQEIESHI 145
+ + +++G V A+ I +
Sbjct: 55 EGTLLLSRLIKISGTQKEVAAAKHLILEKV 84
Score = 32.9 bits (75), Expect = 0.039
Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 8/78 (10%)
Query: 4 ISRSGCKIKALRAKTNTYIK-----TPVRGEEPVFVVTGRKEDVARAKREILSAADHFSA 58
I R G I+++ + I + ++G +++VA AK IL
Sbjct: 30 IGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEE 89
Query: 59 LRASRKSGALSPLSPPTG 76
L RK A S P +G
Sbjct: 90 L---RKRIAHSASGPSSG 104
>4epo_C E3 ubiquitin-protein ligase RNF8; coiled-coil, E3 ubiquitin ligase,
protein binding complex; 4.80A {Homo sapiens}
Length = 149
Score = 51.2 bits (122), Expect = 3e-08
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
QC +C++ + + C H+F CS C CP+CR +
Sbjct: 66 QCIICSEYFIEAVTLNCAHSF-CSYCINEWMKRKIECPICRKDIKS 110
>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 = 49.9 bits (119), Expect = 3e-08
Identities = 12/65 (18%), Positives = 29/65 (44%), Gaps = 1/65 (1%)
Query: 81 VTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQE 140
V P + ++G KG + +I Q + + ++ + + G + V +A+++
Sbjct: 27 TVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDKIT-LEGPTEDVSVAQEQ 85
Query: 141 IESHI 145
IE +
Sbjct: 86 IEGMV 90
Score = 28.3 bits (63), Expect = 1.5
Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 4 ISRSGCKIKALRAK-TNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAAD 54
I + G + + + +I+ GE+ + + G EDV+ A+ +I
Sbjct: 42 IGKKGQNLAKITQQMPKVHIEFT-EGEDKITL-EGPTEDVSVAQEQIEGMVK 91
>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 71
Score = 49.1 bits (117), Expect = 4e-08
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 1/58 (1%)
Query: 289 SSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 346
S+ + +C +C V +PC H F C C + + C +CR +
Sbjct: 4 GSSGNTAPSLTVPECAICLQTCVHPVSLPCKHVF-CYLCVKGASWLGKRCALCRQEIP 60
>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 = 52.5 bits (125), Expect = 8e-08
Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFD-RTCPMCRVPVNQAMRII 352
S + C +C + + + PCGH C+ C + + + CP CR + I+
Sbjct: 330 STFQLCKICAENDKDVKIEPCGHLM-CTSCLTSWQESEGQGCPFCRCEIKGTEPIV 384
>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 81
Score = 47.9 bits (114), Expect = 1e-07
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 1/45 (2%)
Query: 302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVN 346
+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 = 46.7 bits (111), Expect = 2e-07
Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 2/47 (4%)
Query: 302 QCYLCNDR-EVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
C +C + C H F C C R + CP C + V+Q
Sbjct: 17 LCSICKGYLIDATTITECLHTF-CKSCIVRHFYYSNRCPKCNIVVHQ 62
>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 = 47.5 bits (113), Expect = 3e-07
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 302 QCYLCND---REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
C LC T +I C H+F C C R + + CP+C V V++
Sbjct: 17 MCVLCGGYFIDATT--IIECLHSF-CKTCIVRYLETSKYCPICDVQVHK 62
>2ea6_A Ring finger protein 4; RNF4, RES4-26, ring domain, zinc- binding
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 69
Score = 46.4 bits (110), Expect = 3e-07
Identities = 19/66 (28%), Positives = 25/66 (37%), Gaps = 8/66 (12%)
Query: 289 SSTSPSGSISGSRQCYLCND-------REVTHALIPCGHNFFCSECAERTCDFDRTCPMC 341
S+ SG+ C +C D CGH F CS+C + TCP C
Sbjct: 4 GSSGTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVF-CSQCLRDSLKNANTCPTC 62
Query: 342 RVPVNQ 347
R +N
Sbjct: 63 RKKINH 68
>1chc_A Equine herpes virus-1 ring domain; viral protein; NMR {Equid
herpesvirus 1} SCOP: g.44.1.1
Length = 68
Score = 45.9 bits (109), Expect = 4e-07
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 298 SGSRQCYLC-NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAMRIIS 353
+ + +C +C D +PC H F C C R + TCP+C+VPV + I
Sbjct: 3 TVAERCPICLEDPSNYSMALPCLHAF-CYVCITRWIRQNPTCPLCKVPVESVVHTIE 58
>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 = 45.6 bits (108), Expect = 6e-07
Identities = 18/63 (28%), Positives = 24/63 (38%), Gaps = 8/63 (12%)
Query: 292 SPSGSISGSRQCYLCND-------REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVP 344
+ SG+ C +C D CGH F CS+C + TCP CR
Sbjct: 2 TTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVF-CSQCLRDSLKNANTCPTCRKK 60
Query: 345 VNQ 347
+N
Sbjct: 61 INH 63
>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 = 3e-06
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 302 QCYLCNDR-EVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
+C +C + + + C HN+ CS C + + CP C V V +
Sbjct: 24 RCGICFEYFNIAMIIPQCSHNY-CSLCIRKFLSYKTQCPTCCVTVTE 69
>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 = 46.2 bits (109), Expect = 4e-06
Identities = 26/146 (17%), Positives = 49/146 (33%), Gaps = 14/146 (9%)
Query: 1 MKKIS-RSGCKIKALRAKTNTYIKTPVRGEEPVFVVTGRKEDVARAKREILSAADHFSAL 59
+I R+G I + ++ G PV ++ + +V +A F L
Sbjct: 26 KAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLM--KAAEVVKAISLGFPPEKAFRLL 83
Query: 60 RASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSR 119
+ + H+ ++ G ++G G + I+ T+TYI
Sbjct: 84 EEDQILVVVDLKQVVGDSQNHLK-------RIKGRIIGEGGRARRTIEEMTDTYINV--- 133
Query: 120 DKEPVFEVTGAPDSVEIARQEIESHI 145
E + G + A+Q IE
Sbjct: 134 -GEYEVAIIGDYERAMAAKQAIEMLA 158
Score = 39.6 bits (92), Expect = 5e-04
Identities = 17/88 (19%), Positives = 33/88 (37%), Gaps = 3/88 (3%)
Query: 82 TIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEI 141
I V+V + +G V+GP+G I +T T I + + V + +
Sbjct: 5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSM--VIVEPEAEGIPPVNLMK 62
Query: 142 ESHIIRRTGSCVTPAEAV-LNGDDNSAD 168
+ +++ P +A L +D
Sbjct: 63 AAEVVKAISLGFPPEKAFRLLEEDQILV 90
>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA
binding, cell cycle; 2.79A {Caenorhabditis elegans}
Length = 376
Score = 47.2 bits (111), Expect = 4e-06
Identities = 16/73 (21%), Positives = 25/73 (34%), Gaps = 10/73 (13%)
Query: 80 HVTIEVRVPYKVVGLVVGPKG--ATIKRIQHQTNTYIVTPSRDKEPVFE--------VTG 129
VT+ + + L+ G + I +TNT I P R +TG
Sbjct: 29 RVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITG 88
Query: 130 APDSVEIARQEIE 142
V+ AR +
Sbjct: 89 YFGDVDRARMLMR 101
Score = 43.8 bits (102), Expect = 4e-05
Identities = 19/122 (15%), Positives = 37/122 (30%), Gaps = 23/122 (18%)
Query: 31 PVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYK 90
+T R+++ + + ++ T+ +
Sbjct: 150 TYLRITAREKNQHELIEAAKRLNEILFRESPAPENN--------------FTLHFTLSTY 195
Query: 91 VVGLVVGPKGA--TIKRIQHQTNTYIVTP-------SRDKEPVFEVTGAPDSVEIARQEI 141
V V+G + I+ +T T I P +R +V G D+V AR+ I
Sbjct: 196 YVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYI 255
Query: 142 ES 143
Sbjct: 256 MD 257
Score = 33.8 bits (76), Expect = 0.072
Identities = 24/167 (14%), Positives = 50/167 (29%), Gaps = 41/167 (24%)
Query: 4 ISRSGCK--IKALRAKTNTYIKTPVRGEEPVF--------VVTGRKEDVARAKREILSAA 53
S +G + ++ A+TNT I+ P R +TG DV RA+ +
Sbjct: 45 TSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLMRRNC 104
Query: 54 DHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTY 113
H T+ + + + L IQ+ ++
Sbjct: 105 --------------------------HFTVFMALSKMKMPLHELQAHVRQNPIQNVEMSF 138
Query: 114 IVTPSRDKE--PVFEVTGAP---DSVEIARQEIESHIIRRTGSCVTP 155
+ P ++ +T + A + + + R + +
Sbjct: 139 VDAPEKNGIVTTYLRITAREKNQHELIEAAKRLNEILFRESPAPENN 185
>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 = 47.7 bits (113), Expect = 5e-06
Identities = 45/243 (18%), Positives = 75/243 (30%), Gaps = 81/243 (33%)
Query: 1 MKKISRSGCKIKALR---AKTNTYIKTPVRGEEPV----------FVVTGRKEDVARAKR 47
M +S S + ++ KTN+++ P + V VV+G + +
Sbjct: 338 M--LSISNLTQEQVQDYVNKTNSHL--P--AGKQVEISLVNGAKNLVVSGPPQSLYGLNL 391
Query: 48 EILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPY---KVVG----LVVG-P- 98
+ RK+ A P+G+ R+P+ K+ L V P
Sbjct: 392 TL-------------RKAKA------PSGLDQS-----RIPFSERKLKFSNRFLPVASPF 427
Query: 99 -----KGATIKRIQHQTNTYIVTPSRD-KEPVFEVTGAPDSVEIARQEIESHIIRRTGSC 152
A+ + + ++D + PV++ D + + I R C
Sbjct: 428 HSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSD-----LRVLSGSISERIVDC 482
Query: 153 VT--PA--EAVLNGDDNSADLLASLCNSGLGSLGTILNYVNGT-----------SGPASD 197
+ P E SGLG L T N +GT P D
Sbjct: 483 IIRLPVKWETTTQFKATHILDFGPGGASGLGVL-THRN-KDGTGVRVIVAGTLDINPDDD 540
Query: 198 SYG 200
YG
Sbjct: 541 -YG 542
Score = 38.1 bits (88), Expect = 0.005
Identities = 29/155 (18%), Positives = 55/155 (35%), Gaps = 59/155 (38%)
Query: 53 ADH----FSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVV---GLVVGPKGATIKR 105
A H ++AL + + +S IE V +VV G+ + + R
Sbjct: 1760 AGHSLGEYAALASL--ADVMS-------------IESLV--EVVFYRGMTMQ---VAVPR 1799
Query: 106 IQHQTNTYI---VTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVTPAEAVLNG 162
+ + Y + P R + + ++++ + + +RTG V E V N
Sbjct: 1800 DELGRSNYGMIAINPGR-----VAASFSQEALQ----YVVERVGKRTGWLV---EIV-N- 1845
Query: 163 DDNSA--------DLLASLCNSGLGSLGTILNYVN 189
N DL A L ++ +LN++
Sbjct: 1846 -YNVENQQYVAAGDLRA------LDTVTNVLNFIK 1873
>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS),
leukemia, transcription regulation; NMR {Homo sapiens}
SCOP: g.44.1.1
Length = 56
Score = 41.2 bits (97), Expect = 1e-05
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345
+C C L+PC H CS C E + CP+C+ P
Sbjct: 8 RCQQCQAEAKCPKLLPCLHT-LCSGCLEAS---GMQCPICQAPW 47
>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 = 42.6 bits (100), Expect = 2e-05
Identities = 12/37 (32%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 316 IPCGHNFFCSECAERTCDF-DRTCPMCRVPVNQAMRI 351
+PC H C C + T + CP CR V+ R
Sbjct: 31 LPCNHTL-CKPCFQSTVEKASLCCPFCRRRVSSWTRY 66
>2xeu_A Ring finger protein 4; transcription, zinc-finger, metal-binding;
HET: SUC; 1.50A {Homo sapiens}
Length = 64
Score = 40.1 bits (94), Expect = 4e-05
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 317 PCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
CGH F CS+C + TCP CR +N
Sbjct: 27 ECGHVF-CSQCLRDSLKNANTCPTCRKKINH 56
>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 = 40.6 bits (95), Expect = 6e-05
Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 3/50 (6%)
Query: 302 QCYLCNDREVTHALIP-CGHNFFCSECAER-TCDFDRTCPMCRVPVNQAM 349
+C++C ++ L P C C C R + CP CR P+
Sbjct: 24 RCFICMEKLRDARLCPHCSKLC-CFSCIRRWLTEQRAQCPHCRAPLQLRE 72
>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 = 41.1 bits (96), Expect = 1e-04
Identities = 25/128 (19%), Positives = 38/128 (29%), Gaps = 8/128 (6%)
Query: 224 GSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIW 283
GSS SS +P +S + + D
Sbjct: 2 GSSHHHHHHSSGLVPRGSPSASKVYKASDSAEAIEAFQLTPQQQHLIREDCQNQKLWDEV 61
Query: 284 SYPPVSSTSPSGSISGSRQCYLCND---REVTHALIPCGHNFFCSECAERTCDFD-RTCP 339
V + + S C C + + VT C HN C +C +R+ +CP
Sbjct: 62 LSHLVEGPNFLKKLEQSFMCVCCQELVYQPVT---TECFHN-VCKDCLQRSFKAQVFSCP 117
Query: 340 MCRVPVNQ 347
CR + Q
Sbjct: 118 ACRHDLGQ 125
>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 = 39.7 bits (93), Expect = 2e-04
Identities = 8/35 (22%), Positives = 15/35 (42%), Gaps = 4/35 (11%)
Query: 316 IPCGHNFFCSECAERTCDFDR---TCPMCRVPVNQ 347
C H FC C + + + CP+C+ + +
Sbjct: 37 TKCDHI-FCKFCMLKLLNQKKGPSQCPLCKNDITK 70
>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 = 40.0 bits (93), Expect = 2e-04
Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 9/67 (13%)
Query: 287 PVSSTSPSGSISGSR---QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDR---TCPM 340
P S + +S QC C + C HN C +C +R+ F +CP
Sbjct: 36 PASGSPFQLFLSKVEETFQCICCQELVFRPITTVCQHN-VCKDCLDRS--FRAQVFSCPA 92
Query: 341 CRVPVNQ 347
CR + +
Sbjct: 93 CRYDLGR 99
>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: 316 IPCGHNFFCSECAERTCDFDRT---CPMCRVPVNQ 347
I CGHN FC +C + + CP+C+ V +
Sbjct: 36 IDCGHN-FCLKCITQIGETSCGFFKCPLCKTSVRK 69
>2ecn_A Ring finger protein 141; RNF141, ring domain, zinc-binding domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 70
Score = 38.1 bits (89), Expect = 2e-04
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 302 QCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345
+C +C D L PC H FC +C ++ D R CP+CR+ +
Sbjct: 17 ECCICMDGRADLIL-PCAH-SFCQKCIDKWSDRHRNCPICRLQM 58
>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 = 39.5 bits (92), Expect = 3e-04
Identities = 21/93 (22%), Positives = 39/93 (41%), Gaps = 26/93 (27%)
Query: 76 GVPGHVTIEVRVP------YKVVGLVVGPKGATIKRIQHQTNTYIV-------------- 115
+ V+ +V +P VGL++GP+G T+K I+ + N I+
Sbjct: 2 AMATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGR 61
Query: 116 ----TPSRDKEPVF-EVTG-APDSVEIARQEIE 142
+ EP+ VT ++V+ A ++I
Sbjct: 62 KDGQMLPGEDEPLHALVTANTMENVKKAVEQIR 94
>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: 316 IPCGHNFFCSECAERTCDFDRT-------CPMCRVPVNQ 347
+ 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: 316 IPCGHNFFCSECAERTCDFDRT------CPMCRVPVNQ 347
C H+ FC C + +R CP+CRVP
Sbjct: 35 ADCNHS-FCRACITLNYESNRNTDGKGNCPVCRVPYPF 71
>2ecv_A Tripartite motif-containing protein 5; metal binding protein,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 85
Score = 37.2 bits (87), Expect = 6e-04
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 7/38 (18%)
Query: 316 IPCGHNFFCSECAERTCD------FDRTCPMCRVPVNQ 347
+ CGH+ FC C + +CP+CR+
Sbjct: 35 LDCGHS-FCQACLTANHKKSMLDKGESSCPVCRISYQP 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 = 38.0 bits (88), Expect = 7e-04
Identities = 14/47 (29%), Positives = 17/47 (36%), Gaps = 8/47 (17%)
Query: 302 QCYLCND---REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345
+C C + V L C H F CS C CP+C P
Sbjct: 24 RCSRCTNILREPVC--LGGCEHIF-CSNCVSDC--IGTGCPVCYTPA 65
>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 = 9e-04
Identities = 10/35 (28%), Positives = 13/35 (37%), Gaps = 4/35 (11%)
Query: 315 LIPCGHNFFCSECAERTCDFDR---TCPMCRVPVN 346
L+ CGH C +C E+ CP C
Sbjct: 34 LLHCGHT-ICRQCLEKLLASSINGVRCPFCSKITR 67
>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 = 38.4 bits (89), Expect = 0.001
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 302 QCYLCND--REVTHALIPCGHNFFCSECAERTC-DFDRTCPMCRVPVNQ 347
C +C D + T C H F C++C ++ CP CR +
Sbjct: 56 MCPICLDMLKN-TMTTKECLHRF-CADCIITALRSGNKECPTCRKKLVS 102
>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 66
Score = 35.9 bits (83), Expect = 0.001
Identities = 10/47 (21%), Positives = 16/47 (34%), Gaps = 2/47 (4%)
Query: 302 QCYLCNDREVTHALIPCGHNFFCSECAERTC-DFDRTCPMCRVPVNQ 347
+C C+ + CGH F C C C C+ + +
Sbjct: 17 KCEKCHLVLCSPKQTECGHRF-CESCMAALLSSSSPKCTACQESIVK 62
>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex,
chimera; 2.21A {Rattus norvegicus}
Length = 133
Score = 37.5 bits (86), Expect = 0.002
Identities = 18/57 (31%), Positives = 23/57 (40%), Gaps = 8/57 (14%)
Query: 298 SGSRQCYLCNDREVTHAL-------IPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
SG+ C +C D CGH F CS+C + TCP CR +N
Sbjct: 5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVF-CSQCLRDSLKNANTCPTCRKKINH 60
Score = 33.6 bits (76), Expect = 0.032
Identities = 15/41 (36%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 307 NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQ 347
N R + CGH FCS+C + TCP CR +N
Sbjct: 88 NGRLIVST--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 = 35.3 bits (82), Expect = 0.002
Identities = 19/53 (35%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 298 SGSRQCYLCND-----REVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345
SGS C +C + R V H L PCGH C E CP+C P
Sbjct: 3 SGSSGCPICLEDIHTSRVVAHVL-PCGH-LLHRTCYEEMLKEGYRCPLCSGPS 53
>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 = 38.9 bits (90), Expect = 0.002
Identities = 28/149 (18%), Positives = 45/149 (30%), Gaps = 9/149 (6%)
Query: 161 NGDDNSADLLASLCNSGLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHH 220
+ D+ + ++ NS L S + + P+ PG+ + + SS +N
Sbjct: 7 HHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGM 66
Query: 221 VFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGLGDSPSFDASPVNPS 280
S S S S P + S M+ S S D P
Sbjct: 67 GPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNP--------VSSSEDIKPPLGL 118
Query: 281 SIWSYPPVSSTSPSGSISGSRQCYLCNDR 309
+ P + S C +C DR
Sbjct: 119 NGVLKVPAHPSGNMAS-FTKHICAICGDR 146
Score = 30.1 bits (67), Expect = 1.2
Identities = 22/141 (15%), Positives = 39/141 (27%), Gaps = 17/141 (12%)
Query: 218 NHHVFSGSSGCSSASSSSSSSACAPHS-------STQLDLGSIWSGMSSLDKD------- 263
+HH S+ +SS +P S LG L
Sbjct: 3 HHHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSP 62
Query: 264 -EGLGDSPSFDASPVNPSSIW--SYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGH 320
G+G S +SP+ P S+ + P + ++ S +S ++ +
Sbjct: 63 INGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVL 122
Query: 321 NFFCSECAERTCDFDRTCPMC 341
C +C
Sbjct: 123 KVPAHPSGNMASFTKHICAIC 143
>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural
genomics, PSI-2, protein struc initiative; NMR {Homo
sapiens}
Length = 91
Score = 36.2 bits (84), Expect = 0.002
Identities = 20/74 (27%), Positives = 29/74 (39%), Gaps = 6/74 (8%)
Query: 276 PVNPSSIWSYPPVSSTSPSGSISGSRQCYLC----NDREVTHALIPCGHNFFCSECAERT 331
P + SI + P + T G++ C +C +V L PC H +F C
Sbjct: 16 PASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATEL-PCHH-YFHKPCVSIW 73
Query: 332 CDFDRTCPMCRVPV 345
TCP+CR
Sbjct: 74 LQKSGTCPVCRCMF 87
>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: 89 YKVVGLVVGPKGATIKRIQHQTNTYI 114
+ VG ++GP+G T K+++ +T I
Sbjct: 16 FNFVGRILGPRGLTAKQLEAETGCKI 41
>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding
domain; 1.90A {Mus musculus}
Length = 101
Score = 36.0 bits (82), Expect = 0.003
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 303 CYLCNDR-EVTHALIPCGHNFFCSECAER-TCDFDRTCPMCRVPVN 346
C C +V +IPC H FC +CA D+ CP C PV
Sbjct: 4 CDKCGLPIKVYGRMIPCKH-VFCYDCAILHEKKGDKMCPGCSDPVQ 48
>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 = 35.4 bits (81), Expect = 0.003
Identities = 15/76 (19%), Positives = 28/76 (36%)
Query: 67 ALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVFE 126
S S + E V ++GL +G G+ I++ + + D
Sbjct: 1 GSSGSSGTKQLAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRI 60
Query: 127 VTGAPDSVEIARQEIE 142
+ D+V+ AR +E
Sbjct: 61 YGESADAVKKARGFLE 76
>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 = 35.3 bits (81), Expect = 0.006
Identities = 13/47 (27%), Positives = 14/47 (29%), Gaps = 2/47 (4%)
Query: 303 CYLCNDREVTHALIPCGHNFFCSECAERTCD-FDRTCPMCRVPVNQA 348
C +C C H F C C R CP CR P
Sbjct: 26 CQICEHILADPVETSCKHLF-CRICILRCLKVMGSYCPSCRYPCFPT 71
>2ysj_A Tripartite motif-containing protein 31; ring-type zinc finger
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 63
Score = 33.1 bits (76), Expect = 0.011
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 4/29 (13%)
Query: 316 IPCGHNFFCSECAERTCDFDRT---CPMC 341
I CGHN FC +C + + CP+C
Sbjct: 36 IDCGHN-FCLKCITQIGETSCGFFKCPLC 63
>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 = 35.4 bits (81), Expect = 0.012
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 2/47 (4%)
Query: 302 QCYLCNDREVTHALIPCGHNFFCSECAER-TCDFDRTCPMCRVPVNQ 347
+C +C PCGH F C C + D CP+ + +
Sbjct: 20 ECPICLMALREAVQTPCGHRF-CKACIIKSIRDAGHKCPVDNEILLE 65
>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: 316 IPCGHNFFCSECAERTCDFDRT---CPMC 341
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 = 17/77 (22%), Positives = 30/77 (38%), Gaps = 15/77 (19%)
Query: 81 VTIEVRVP-YKVVGLVVGPKGATIKRIQHQTNTYIV---TPSRDKEPVFE---------- 126
V +E VP + V V GP + ++ IQ +T + S EP
Sbjct: 18 VGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIY 77
Query: 127 VTG-APDSVEIARQEIE 142
++ P+ + A++ E
Sbjct: 78 ISHPKPEGLAAAKKLCE 94
>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 = 35.8 bits (82), Expect = 0.020
Identities = 29/110 (26%), Positives = 43/110 (39%), Gaps = 6/110 (5%)
Query: 193 GPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASS---SSSSSACAPHSSTQLD 249
P S SY ++ P S +S +S S +S S +S + +P S +
Sbjct: 1571 SPTSPSYSPTSPSYSPTSPSYS--PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1628
Query: 250 LGSIWSGMSSLDKDEGLGDSP-SFDASPVNPSSIWSYPPVSSTSPSGSIS 298
+S S SP S SP +P+ + P S TSPS S +
Sbjct: 1629 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPT 1678
Score = 29.7 bits (66), Expect = 1.8
Identities = 23/153 (15%), Positives = 46/153 (30%), Gaps = 20/153 (13%)
Query: 157 EAVLNGDDN-----SADL-LASLCNSGLGSLGTILNYVNGTSG----PASDSYGAGPGEF 206
EA + + + S ++ L + G G+ +++ + ++ G
Sbjct: 1411 EAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGV 1470
Query: 207 NFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEGL 266
S S S S+ A + ++ D E
Sbjct: 1471 TPYSNESGLVNADLDVKDELMFSPLVDSGSNDA----------MAGGFTAYGGADYGEAT 1520
Query: 267 GDSPSFDASPVNPSSIWSYPPVSSTSPSGSISG 299
++ +P +P S P S TSP+ S +
Sbjct: 1521 SPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTS 1553
Score = 29.7 bits (66), Expect = 2.0
Identities = 25/105 (23%), Positives = 33/105 (31%), Gaps = 7/105 (6%)
Query: 193 GPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGS 252
P S SY ++ P S +S +S S +S S S +S T
Sbjct: 1613 SPTSPSYSPTSPSYSPTSPSYSP--TSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSP 1670
Query: 253 IWSGMSSLDKDEGLGDSPSFDASPV-NPSSIWSYPPVSSTSPSGS 296
S SP +P+S P S TSP S
Sbjct: 1671 TSPSYSPTSPSYSPTSPSYSPTSPNYSPTS----PSYSPTSPGYS 1711
Score = 29.3 bits (65), Expect = 2.5
Identities = 31/119 (26%), Positives = 42/119 (35%), Gaps = 17/119 (14%)
Query: 191 TSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDL 250
T P S +Y ++ P S +S +S S +S S S +S T
Sbjct: 1548 TYSPTSPAYSPTSPSYSPTSPSYSP--TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1605
Query: 251 GSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVSSTSP-----SGSISGSRQCY 304
S SPS+ SP +PS + P S TSP S S S + Y
Sbjct: 1606 SPTSPSYSPT--------SPSY--SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1654
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH
domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}
Length = 630
Score = 36.0 bits (84), Expect = 0.020
Identities = 26/106 (24%), Positives = 38/106 (35%), Gaps = 15/106 (14%)
Query: 43 ARAKR-EILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGA 101
A + EIL + + R S P V V+VP VGP G
Sbjct: 539 ASVAKKEILQIMN--KTISKPRAS--RKENGP-------VVETVQVPLSKRAKFVGPGGY 587
Query: 102 TIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIR 147
+K++Q +T I D+E P ++ AR I I +
Sbjct: 588 NLKKLQAETGVTISQ--VDEETFSVFAPTPSAMHEARDFITE-ICK 630
>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 = 33.6 bits (77), Expect = 0.024
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 316 IPCGHNFFCSECAERTC-DFDRTCPMCRVPVN 346
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 = 0.042
Identities = 14/50 (28%), Positives = 19/50 (38%), Gaps = 6/50 (12%)
Query: 303 CYLC----NDREVTHALIPCGHNFFCSECAERT-CDFDRTCPMCRVPVNQ 347
C LC ++ CG+ C C R D + CP CR P +
Sbjct: 14 CPLCMEPLEIDDINFFPCTCGYQI-CRFCWHRIRTDENGLCPACRKPYPE 62
>2ep4_A Ring finger protein 24; zinc binding, ubiquitin, E3 enzyme,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 74
Score = 31.7 bits (72), Expect = 0.045
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 6/66 (9%)
Query: 289 SSTSPSGSISGSRQCYLC----NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVP 344
S+ ++ C +C R+ PC H F +C + + + CP+C +P
Sbjct: 4 GSSGKVKELNLHELCAVCLEDFKPRDELGIC-PCKH-AFHRKCLIKWLEVRKVCPLCNMP 61
Query: 345 VNQAMR 350
V Q +
Sbjct: 62 VLQLAQ 67
>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 = 32.9 bits (76), Expect = 0.15
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 83 IEVRVPYKVVGLVVGPKGATIKRIQHQTNTYI 114
I V++P +G V+GPK I +IQ T I
Sbjct: 600 ITVKIPVDKIGEVIGPKRQMINQIQEDTGAEI 631
>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 = 0.17
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 287 PVSSTSPSGSISGSRQCYLC----NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCR 342
P +P+ S C +C R++ L PC H F +C ++ +RTCP+CR
Sbjct: 10 PSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVL-PCNHEFHA-KCVDKWLKANRTCPICR 67
Query: 343 VPV 345
Sbjct: 68 ADS 70
>2ecl_A Ring-box protein 2; RNF7, ring domian, zinc-binding domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 81
Score = 30.3 bits (68), Expect = 0.18
Identities = 9/44 (20%), Positives = 15/44 (34%), Gaps = 5/44 (11%)
Query: 303 CYLC----NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCR 342
C C + C H+F + C + CP+C+
Sbjct: 29 CLRCQAENKQEDCVVVWGECNHSF-HNCCMSLWVKQNNRCPLCQ 71
>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 = 30.1 bits (68), Expect = 0.19
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 315 LIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345
+PC H F C + +CP+CR +
Sbjct: 33 QLPCNH-LFHDSCIVPWLEQHDSCPVCRKSL 62
>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 = 30.5 bits (68), Expect = 0.22
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 2/68 (2%)
Query: 284 SYPPVSSTSPSGSISGSRQCYLCNDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRV 343
P +S P + G + C C L+ C +++ C C CP+C++
Sbjct: 12 KDSPRASLIPDATHLGPQFCKSC--WFENKGLVECNNHYLCLNCLTLLLSVSNRCPICKM 69
Query: 344 PVNQAMRI 351
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 = 0.26
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 92 VGLVVGPKGATIKRIQHQTNTYI 114
+ V+G G+ I+ + +T T I
Sbjct: 571 IKDVIGKGGSVIRALTEETGTTI 593
>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 = 0.28
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 302 QCYLCNDREVTHALIP-CGHNFFCSECAERTCDF--DRTCPMCR 342
C +C D +IP CG+++ C EC + TCP C
Sbjct: 17 LCLICKDIMTDAVVIPCCGNSY-CDECIRTALLESDEHTCPTCH 59
>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 = 30.6 bits (68), Expect = 0.30
Identities = 10/41 (24%), Positives = 11/41 (26%), Gaps = 6/41 (14%)
Query: 310 EVTHALIPCGHNFFCSEC-----AERTCDFDRTCPMCRVPV 345
V L C H F C D CP C+
Sbjct: 53 MVVGRLTKCSHA-FHLLCLLAMYCNGNKDGSLQCPSCKTIY 92
>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 = 31.3 bits (71), Expect = 0.45
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 4/60 (6%)
Query: 10 KIKALRAKTNTYIKTPVRGEEPVF---VVTGR-KEDVARAKREILSAADHFSALRASRKS 65
KIK R+ + + P+ V TG ED+ +A AD + +R + +S
Sbjct: 130 KIKNNRSIRESRFEEYGDKSGPLLYVIVATGNIYEDITQAVAAAKQGADVIAVIRTTGQS 189
>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 = 0.46
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 315 LIPCGHNFFCSECAERTCDFDRTCPMCRVPVNQAM 349
+PC H F C ++ ++ CP+CRV + +
Sbjct: 32 RLPCMHLFHQ-VCVDQWLITNKKCPICRVDIEAQL 65
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 31.3 bits (72), Expect = 0.51
Identities = 6/23 (26%), Positives = 10/23 (43%)
Query: 92 VGLVVGPKGATIKRIQHQTNTYI 114
+ V+G G I+ I T +
Sbjct: 581 IREVIGSGGKVIREIVATTGAKV 603
>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 = 28.7 bits (64), Expect = 0.64
Identities = 8/54 (14%), Positives = 16/54 (29%), Gaps = 8/54 (14%)
Query: 299 GSRQCYLCNDREVTH--ALIPCGHNFFCSECAE---RTCDFDRTCPMCRVPVNQ 347
+ C +C+ + + CG C ++ + CP C
Sbjct: 14 AVKICNICHS-LLIQGQSCETCGI-RMHLPCVAKYFQSNA-EPRCPHCNDYWPH 64
>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 = 30.6 bits (70), Expect = 0.87
Identities = 12/72 (16%), Positives = 19/72 (26%), Gaps = 14/72 (19%)
Query: 38 RKEDVAR------------AKREILSAADHF--SALRASRKSGALSPLSPPTGVPGHVTI 83
+ A A E+ +A D + L + G P +
Sbjct: 93 NLDVFAEVLVMNAGKPKSAAVGEVKAAVDRLRLAELDLKKIGGDYIPGDWTYDTLETEGL 152
Query: 84 EVRVPYKVVGLV 95
R P VV +
Sbjct: 153 VRREPLGVVAAI 164
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 30.4 bits (68), Expect = 1.0
Identities = 14/97 (14%), Positives = 28/97 (28%), Gaps = 4/97 (4%)
Query: 202 GPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLD 261
G G F+ M + G++ + A S +S + T + + +
Sbjct: 1443 GTGAFDI---YLDQDMLMNYSLGTAVPTLAGSGMGTSQLPEGAGTPYERSPMVDS-GFVG 1498
Query: 262 KDEGLGDSPSFDASPVNPSSIWSYPPVSSTSPSGSIS 298
+ SP Y + + SP +
Sbjct: 1499 SPDAAAFSPLVQGGSEGREGFGDYGLLGAASPYKGVQ 1535
Score = 29.7 bits (66), Expect = 2.0
Identities = 27/117 (23%), Positives = 36/117 (30%), Gaps = 3/117 (2%)
Query: 189 NGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSS--SSSSACAPHSST 246
G+ G G + + S S S +S S SS S
Sbjct: 1511 GGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPA 1570
Query: 247 QLDLGSIWSGMSSLDKDEGLGDSP-SFDASPVNPSSIWSYPPVSSTSPSGSISGSRQ 302
+ +S S SP S SP +PS + P S TSPS S +
Sbjct: 1571 YMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSY 1627
Score = 29.7 bits (66), Expect = 2.0
Identities = 31/103 (30%), Positives = 40/103 (38%), Gaps = 5/103 (4%)
Query: 194 PASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSI 253
P S SY ++ P S +S +S S +S S S +S T S
Sbjct: 1615 PTSPSYSPTSPSYSPTSPSYSPTSP--SYSPTSPSYSPTSPSYSPTSPSYSPTSPSY-SP 1671
Query: 254 WSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVSSTSPSGS 296
S S SPS+ SP +PS + P S TSPS S
Sbjct: 1672 TSPSYSPTSPSYSPTSPSY--SPTSPSYSPTSPSYSPTSPSYS 1712
Score = 28.9 bits (64), Expect = 3.8
Identities = 25/116 (21%), Positives = 35/116 (30%), Gaps = 9/116 (7%)
Query: 191 TSGPASDSYGAGPGEFNF---NMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAPHSSTQ 247
S + P F S + + S S +P SS
Sbjct: 1488 RSPMVDSGFVGSPDAAAFSPLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSSAM 1547
Query: 248 LDLGSIWSGMSSLDKDEGLGDSPSFDA-----SPVNPSSIWSYPPVSSTSPSGSIS 298
+ S S G SP++ SP +PS + P S TSPS S +
Sbjct: 1548 SPGYGLTSPSYS-PSSPGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1602
Score = 28.5 bits (63), Expect = 4.3
Identities = 30/111 (27%), Positives = 43/111 (38%), Gaps = 10/111 (9%)
Query: 191 TSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDL 250
+S S S P +++ S +S +S S +S S S+ +S T
Sbjct: 1561 SSPGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTS-PS 1619
Query: 251 GSIWSGMSSLDKDEGLGDSPSFDASPVNPSSIWSYPPVSSTSPSGSISGSR 301
S S S SPS+ SP +PS + P S TSPS S +
Sbjct: 1620 YSPTSPSYS-------PTSPSY--SPTSPSYSPTSPSYSPTSPSYSPTSPS 1661
>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 = 29.1 bits (64), Expect = 1.1
Identities = 8/43 (18%), Positives = 14/43 (32%), Gaps = 18/43 (41%)
Query: 102 TIKRIQHQTNTYIVTPSRDKEPVFEVTGAPDSV-EIA-RQEIE 142
+K++Q Y A DS +A + +E
Sbjct: 21 ALKKLQASLKLY----------------ADDSAPALAIKATME 47
>3d7r_A Esterase; alpha/beta fold, hydrolase; 2.01A {Staphylococcus aureus
subsp}
Length = 326
Score = 29.6 bits (67), Expect = 1.3
Identities = 5/65 (7%), Positives = 15/65 (23%)
Query: 42 VARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEVRVPYKVVGLVVGPKGA 101
+ + + R+ P+ + +E + +
Sbjct: 35 LLHNRSIMFKNDQDVERFFYKREIENRKKHKQPSTLNVKANLEKLSLDDMQVFRFNFRHQ 94
Query: 102 TIKRI 106
K+I
Sbjct: 95 IDKKI 99
>3fip_A Outer membrane usher protein PAPC; beta barrel, protein
translocase, cell membrane, cell outer fimbrium,
transmembrane, transport; 3.15A {Escherichia coli} PDB:
2vqi_A*
Length = 493
Score = 29.9 bits (67), Expect = 1.4
Identities = 15/101 (14%), Positives = 31/101 (30%), Gaps = 15/101 (14%)
Query: 206 FNFNMPLSSSQMNHHVFSGSSGCSSASSSSSSSACAPHSSTQLDLGSIWSGMSSLDKDEG 265
++PL + ++ + + + + + D +S + L+ G
Sbjct: 398 LRISVPLGTGTASYSGSMSNDRYVNMAGYTDTFN---------DGLDSYSLNAGLNSGGG 448
Query: 266 LGDSPSFDASP------VNPSSIWSYPPVSSTSPSGSISGS 300
L +A N S+ + TS S SG
Sbjct: 449 LTSQRQINAYYSHRSPLANLSANIASLQKGYTSFGVSASGG 489
>1qkl_A RPB6, DNA-directed RNA polymerase II 14.4 KD polypeptide;
transcription; NMR {Homo sapiens} SCOP: a.143.1.2
Length = 127
Score = 28.4 bits (63), Expect = 1.8
Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 118 SRDKEPVFEVTGAPDSVEIARQEIESH----IIRRT 149
+ + E+ G D + IA +E+++ IIRR
Sbjct: 74 AMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRY 109
>3h0g_F DNA-directed RNA polymerases I, II, and III subunit rpabc2;
transcription, multi-protein complex, DNA- binding,
magnesium; 3.65A {Schizosaccharomyces pombe}
Length = 142
Score = 28.5 bits (63), Expect = 1.8
Identities = 8/36 (22%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 118 SRDKEPVFEVTGAPDSVEIARQEIESH----IIRRT 149
S + + ++ G D ++IA +E+ ++RR
Sbjct: 92 SMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRY 127
>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 = 29.4 bits (65), Expect = 1.9
Identities = 16/141 (11%), Positives = 41/141 (29%), Gaps = 16/141 (11%)
Query: 176 SGLGSLGTILNYVNGTSGPASDSYGAGPGEFNFNMPLSSSQMNHHVFSGSSGCSSASSSS 235
+ ++ P ++ P + + V S A ++
Sbjct: 54 RARPGIASVQRATESAELPMKNNDEGTPDK-------KGNTRGDLVNEHSEAKDEADEAT 106
Query: 236 S------SSACAPHSSTQLDLGSI--WSGMSSLDKDEGLGDSPSFD-ASPVNPSSIWSYP 286
+ A + + + + S ++D + G P + + + +P
Sbjct: 107 QKQAKDTDKSKAQVTYSDTGINNANELSRSGNVDNEGGSNQKPMSTRIAEATSAIVSKHP 166
Query: 287 PVSSTSPSGSISGSRQCYLCN 307
P+ S QC++C+
Sbjct: 167 ARVGLPPTASSGHGYQCHVCS 187
>3nw0_A Non-structural maintenance of chromosomes element homolog; E3
ligase, Zn, metal binding protein; 2.92A {Homo sapiens}
Length = 238
Score = 28.9 bits (64), Expect = 2.1
Identities = 6/50 (12%), Positives = 13/50 (26%), Gaps = 4/50 (8%)
Query: 298 SGSRQCYLCNDREVTHALIPCGHNFFCSECAE---RTCDFDRTCPMCRVP 344
+ C +C+ + C ++ + CP C
Sbjct: 178 DAVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNA-EPRCPHCNDY 226
>1twf_F ABC23, DNA-directed RNA polymerases I, II, and III 23 KD
polypeptide; transcription, mRNA, multiprotein complex;
HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP:
a.143.1.2 PDB: 1i3q_F 1i6h_F 1k83_F* 1nik_F 1nt9_F
1pqv_F 1r5u_F 1r9s_F* 1r9t_F* 1sfo_F* 1twa_F* 1twc_F*
1i50_F* 1twg_F* 1twh_F* 1wcm_F 1y1v_F 1y1w_F 1y1y_F
1y77_F* ...
Length = 155
Score = 28.5 bits (63), Expect = 2.2
Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 118 SRDKEPVFEVTGAPDSVEIARQEIESH----IIRRT 149
S + ++ G D + IA +E+ +IRR
Sbjct: 102 SMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRY 137
>4a7k_A Aldos-2-ulose dehydratase; lyase, dehydratase/isomerase, lignin
degradation, cortalcerone/microthecin forming,
metalloenzyme; 2.00A {Phanerochaete chrysosporium} PDB:
4a7y_A* 4a7z_A*
Length = 900
Score = 29.2 bits (64), Expect = 2.2
Identities = 16/70 (22%), Positives = 25/70 (35%), Gaps = 3/70 (4%)
Query: 189 NGTSGPASDSYGAGPGEFNFNM---PLSSSQMNHHVFSGSSGCSSASSSSSSSACAPHSS 245
+GT A GP +N+ P + H +GS C+ + HS
Sbjct: 773 DGTPVLALLDLDGGPSPQAWNISHVPGTDMYEIAHAKTGSLVCARWPPVKNQRVAGTHSP 832
Query: 246 TQLDLGSIWS 255
+ L S W+
Sbjct: 833 AAMGLTSRWA 842
>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 = 26.4 bits (58), Expect = 2.8
Identities = 11/37 (29%), Positives = 14/37 (37%), Gaps = 2/37 (5%)
Query: 293 PSGSISGSRQCYLCNDREVTHALIPCG--HNFFCSEC 327
P +G R CY C + C N FC +C
Sbjct: 8 PLEEYNGERFCYGCQGELKDQHVYVCAVCQNVFCVDC 44
>2wco_A Putative secreted lyase; family 8, glycosaminoglycans (GAGS)
hydrolysis; HET: GC4 NAG; 1.94A {Streptomyces coelicolor
A3} PDB: 2wda_A* 2x03_A
Length = 765
Score = 28.6 bits (63), Expect = 3.9
Identities = 4/42 (9%), Positives = 11/42 (26%)
Query: 113 YIVTPSRDKEPVFEVTGAPDSVEIARQEIESHIIRRTGSCVT 154
Y V P + + + + + + +T
Sbjct: 633 YTVMPGASRAALARRAADRHWLTVLANDDRRQAVSVPSLGLT 674
>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 = 4.0
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 4/32 (12%)
Query: 79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT 110
V IE R P GLV+G G+T + I T
Sbjct: 100 CEVIIEARKP----GLVIGKYGSTSREIVKNT 127
>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 = 27.9 bits (61), Expect = 4.0
Identities = 18/100 (18%), Positives = 36/100 (36%)
Query: 26 VRGEEPVFVVTGRKEDVARAKREILSAADHFSALRASRKSGALSPLSPPTGVPGHVTIEV 85
V F+ G K + RAKR+ L + ++ + V
Sbjct: 37 VEKGSAGFLGIGSKPAIIRAKRKETLQDKAIEFLEQVFDAMNMAVDISVEYNETEKEMNV 96
Query: 86 RVPYKVVGLVVGPKGATIKRIQHQTNTYIVTPSRDKEPVF 125
+ +G+++G +G T+ +Q+ + + S D V
Sbjct: 97 NLKGDDMGILIGKRGQTLDSLQYLVSLVVNKSSSDYIRVK 136
>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 = 4.2
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT 110
G V IE P GLV+G GAT++ I Q
Sbjct: 104 GEVIIEAEKP----GLVIGKHGATLREITKQI 131
>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 = 4.3
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 79 GHVTIEVRVPYKVVGLVVGPKGATIKRIQHQT 110
G V IE + P GLV+G G T++ I +
Sbjct: 109 GEVLIEAKKP----GLVIGKNGETLRLITQKV 136
>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 = 4.5
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 302 QCYLC----NDREVTHALIPCGHNFFCSECAERTCDFDRTCPMCRVPV 345
+C +C D E L CGH F EC + TCP+CR+ V
Sbjct: 7 ECAVCLAELEDGEEARFLPRCGHGFHA-ECVDMWLGSHSTCPLCRLTV 53
>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 = 26.7 bits (59), Expect = 4.6
Identities = 13/55 (23%), Positives = 19/55 (34%), Gaps = 12/55 (21%)
Query: 298 SGSRQCYLCND---REVTHALIPCGHNFFCSECAERTCD--------FDRTCPMC 341
SGS C LC E + C FC+ C ++ + +CP
Sbjct: 3 SGSSGCKLCLGEYPVEQMTTIAQCQC-IFCTLCLKQYVELLIKEGLETAISCPDA 56
>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 = 4.9
Identities = 8/42 (19%), Positives = 13/42 (30%), Gaps = 7/42 (16%)
Query: 221 VFSGSSGCSSASSSSSSSACAPH-------SSTQLDLGSIWS 255
V + C S ++ C SS DL + +
Sbjct: 40 VPDVNVDCQVTYSDQTADFCKQKGTYDPSGSSASQDLNTPFK 81
>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 = 5.6
Identities = 17/46 (36%), Positives = 18/46 (39%), Gaps = 15/46 (32%)
Query: 10 KIKALRAKTNTYIKTPVRGE--------EPVF-------VVTGRKE 40
KI L + YI TPVR E VF V TGR E
Sbjct: 198 KIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIE 243
>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 = 27.3 bits (61), Expect = 6.0
Identities = 8/43 (18%), Positives = 15/43 (34%), Gaps = 5/43 (11%)
Query: 27 RGEEPVFVVTGRKEDVARAKREILSAADHFSALR-----ASRK 64
R + + ++TG E R K ++ +F R
Sbjct: 108 RSDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRN 150
>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 = 28.0 bits (62), Expect = 6.2
Identities = 16/46 (34%), Positives = 18/46 (39%), Gaps = 15/46 (32%)
Query: 10 KIKALRAKTNTYIKTPVRGE--------EPVF-------VVTGRKE 40
KI L ++YI P R E VF VVTGR E
Sbjct: 472 KILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVE 517
>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 = 27.3 bits (60), Expect = 7.0
Identities = 6/36 (16%), Positives = 13/36 (36%), Gaps = 9/36 (25%)
Query: 324 CSECAERTCDF-------DRTCPMCRVPVNQAMRII 352
C EC D C +C + ++ +++
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSD--KLV 57
>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 = 7.9
Identities = 13/46 (28%), Positives = 17/46 (36%), Gaps = 15/46 (32%)
Query: 10 KIKALRAKTNTYIKTPVRGE--------EPVF-------VVTGRKE 40
++ L +TYI P R E V+ VVTG E
Sbjct: 181 SVQKLLDAVDTYIPVPTRDLEKPFLLPVESVYSIPGRGTVVTGTLE 226
>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 = 9.7
Identities = 12/77 (15%), Positives = 21/77 (27%), Gaps = 6/77 (7%)
Query: 268 DSPSFDASPVNPSSIWSYPPVSSTSPSGSISGSRQCYLCN----DREVTHALIPCGHN-- 321
+ S S ++C C DR + +A+ H+
Sbjct: 29 KMDVTVIDTKDGSQSKLGGGGSGGHMGSGGLSWKRCAGCGGKIADRFLLYAMDSYWHSRC 88
Query: 322 FFCSECAERTCDFDRTC 338
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
0.314 0.129 0.385
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: 5,280,641
Number of extensions: 314261
Number of successful extensions: 828
Number of sequences better than 10.0: 1
Number of HSP's gapped: 731
Number of HSP's successfully gapped: 175
Length of query: 353
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 258
Effective length of database: 4,049,298
Effective search space: 1044718884
Effective search space used: 1044718884
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 58 (26.5 bits)