RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16683
(139 letters)
>1a6y_A Orphan nuclear receptor NR1D1; orphan receptor, DNA-binding,
reverb, REV- ERB, transcription regulation,
transcription/DNA complex; HET: DNA 5IU; 2.30A {Homo
sapiens} SCOP: g.39.1.2 PDB: 1ga5_A* 1hlz_A
Length = 94
Score = 98.6 bits (246), Expect = 3e-28
Identities = 39/80 (48%), Positives = 47/80 (58%)
Query: 1 MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKS 60
M CKVCG+ A+GFH+G CEGCK FF RS C N C I + NR C+
Sbjct: 6 MVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQ 65
Query: 61 CRLRKCLMVGMSKSGSRYGR 80
CR +KCL VGMS+ R+GR
Sbjct: 66 CRFKKCLSVGMSRDAVRFGR 85
>2nll_B Protein (thyroid hormone receptor); complex (transcription
regulation/DNA), DNA-binding, nuclear protein, zinc-
finger, multigene family; HET: DNA 5IU; 1.90A {Homo
sapiens} SCOP: g.39.1.2 PDB: 3m9e_A*
Length = 103
Score = 95.2 bits (237), Expect = 8e-27
Identities = 33/103 (32%), Positives = 54/103 (52%), Gaps = 1/103 (0%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRS-YNNLPSISECKNNNECIINKKNRTSCKS 60
++ C VCG+ A G+H+ TCEGCK FF R+ NL CK +C+I+K R C+
Sbjct: 1 DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQE 60
Query: 61 CRLRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQQAEQQTE 103
CR +KC+ VGM+ + + ++++ E+ +
Sbjct: 61 CRFKKCIYVGMATDLVLDDSKRLAKRKLIEENREKRRREELEK 103
>1hcq_A Protein (estrogen receptor); protein-DNA complex, complexed with
drug, transcription/DNA complex; HET: DNA; 2.40A {Homo
sapiens} SCOP: g.39.1.2 PDB: 1hcp_A 4aa6_A
Length = 84
Score = 94.0 bits (234), Expect = 2e-26
Identities = 38/80 (47%), Positives = 50/80 (62%), Gaps = 1/80 (1%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSC 61
+ C VC + A+G+H+G ++CEGCK+FF RS C N+C I+K R SC++C
Sbjct: 4 TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYM-CPATNQCTIDKNRRKSCQAC 62
Query: 62 RLRKCLMVGMSKSGSRYGRR 81
RLRKC VGM K G R RR
Sbjct: 63 RLRKCYEVGMMKGGIRKDRR 82
>2a66_A Orphan nuclear receptor NR5A2; protein-DNA complex, zinc finger,
DNA- binding domain, transcription factor, FTZ-F1,
C-terminal extension; 2.20A {Homo sapiens} PDB: 2ff0_A
Length = 113
Score = 94.4 bits (235), Expect = 2e-26
Identities = 36/101 (35%), Positives = 50/101 (49%), Gaps = 2/101 (1%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSC 61
+ C VCG+ +G+H+G TCE CK FF R+ N + C N C I+K R C C
Sbjct: 9 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYT-CIENQNCQIDKTQRKRCPYC 67
Query: 62 RLRKCLMVGMSKSGSRYGR-RSNWFKIHCLLQEQQQQAEQQ 101
R +KCL VGM R R R K + + + +Q+
Sbjct: 68 RFQKCLSVGMKLEAVRADRMRGGRNKFGPMYKRDRALKQQK 108
>1kb2_A Vitamin D3 receptor; VDR, nuclear receptor, protein-DNA complex,
transcription/DNA complex; 2.70A {Homo sapiens} SCOP:
g.39.1.2 PDB: 1kb4_A 1kb6_A 1ynw_A
Length = 110
Score = 94.5 bits (235), Expect = 2e-26
Identities = 36/102 (35%), Positives = 53/102 (51%), Gaps = 1/102 (0%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSC 61
+ C VCG+ A GFHF A TCEGCK FF RS + C N +C I K NR C++C
Sbjct: 6 PRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFT-CPFNGDCRITKDNRRHCQAC 64
Query: 62 RLRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQQAEQQTE 103
RL++C+ +GM K + L +++++ +
Sbjct: 65 RLKRCVDIGMMKEFILTDEEVQRKREMILKRKEEEALKDSLR 106
>1lo1_A Steroid hormone receptor ERR2; estrogen related receptor 2, DNA
binding domain, HERR2, hormone nuclear receptor; NMR
{Homo sapiens} SCOP: g.39.1.2
Length = 98
Score = 92.9 bits (231), Expect = 5e-26
Identities = 36/80 (45%), Positives = 47/80 (58%), Gaps = 1/80 (1%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSC 61
+ C VCG+ A+G+H+G +CE CK+FF R+ S C NEC I K+ R SC++C
Sbjct: 4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYS-CPATNECEITKRRRKSCQAC 62
Query: 62 RLRKCLMVGMSKSGSRYGRR 81
R K L VGM K G R R
Sbjct: 63 RFMKALKVGMLKEGVRLDRV 82
>1dsz_A RAR-alpha, retinoic acid receptor alpha; RAR, nuclear receptor,
protein-DNA, transcription/DNA complex; HET: DNA; 1.70A
{Homo sapiens} SCOP: g.39.1.2 PDB: 1hra_A
Length = 86
Score = 92.4 bits (230), Expect = 7e-26
Identities = 35/79 (44%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSC 61
+ C VC + ++G+H+G CEGCK FF RS + C + CIINK R C+ C
Sbjct: 4 YKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYT-CHRDKNCIINKVTRNRCQYC 62
Query: 62 RLRKCLMVGMSKSGSRYGR 80
RL+KC VGMSK R R
Sbjct: 63 RLQKCFEVGMSKESVRNDR 81
>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex,
transcription/DNA complex; 3.10A {Rattus norvegicus}
SCOP: g.39.1.2
Length = 105
Score = 92.9 bits (231), Expect = 7e-26
Identities = 33/82 (40%), Positives = 46/82 (56%), Gaps = 1/82 (1%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSC 61
+TC +CG+ A+G H+GA TC CK FF R+ C + N+C I+K R +C SC
Sbjct: 7 QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYL-CASRNDCTIDKFRRKNCPSC 65
Query: 62 RLRKCLMVGMSKSGSRYGRRSN 83
RLRKC GM+ + + N
Sbjct: 66 RLRKCYEAGMTLGARKLKKLGN 87
>1cit_A NGFI-B, protein (orphan nuclear receptor NGFI-B); early immediate
response gene product, transcription factor, monomeric
protein-DNA complex; HET: DNA; 2.70A {Rattus
norvegicus} SCOP: g.39.1.2
Length = 89
Score = 92.0 bits (229), Expect = 9e-26
Identities = 32/76 (42%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLR 64
C VCG+ A+ H+G TCEGCK FF R+ C N +C ++K+ R C+ CR +
Sbjct: 3 CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYI-CLANKDCPVDKRRRNRCQFCRFQ 61
Query: 65 KCLMVGMSKSGSRYGR 80
KCL VGM K R
Sbjct: 62 KCLAVGMVKEVVRTDS 77
>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear
protein, receptor, transcription regulation, zinc,
EAR3, erbal3 tfcoup1; NMR {Homo sapiens}
Length = 89
Score = 92.0 bits (229), Expect = 1e-25
Identities = 37/80 (46%), Positives = 49/80 (61%), Gaps = 3/80 (3%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSY-NNLPSISECKNNNECIINKKNRTSCKS 60
C VCG+ ++G H+G FTCEGCKSFF RS NL C+ N C I++ +R C+
Sbjct: 7 GIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNL--TYTCRANRNCPIDQHHRNQCQY 64
Query: 61 CRLRKCLMVGMSKSGSRYGR 80
CRL+KCL VGM + + G
Sbjct: 65 CRLKKCLKVGMRREAVQRGS 84
>2han_B Ecdysone receptor; transcription regulation, transcription factor,
DNA-binding, nuclear protein, nuclear receptor, zinc
finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2
PDB: 1r0o_B 1r0n_B
Length = 119
Score = 93.0 bits (231), Expect = 1e-25
Identities = 33/102 (32%), Positives = 48/102 (47%), Gaps = 1/102 (0%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSC 61
+ C VCG+ A+G+H+ A TCEGCK FF RS CK C ++ R C+ C
Sbjct: 8 EELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYC-CKFGRACEMDMYMRRKCQEC 66
Query: 62 RLRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQQAEQQTE 103
RL+KCL VGM + + Q+++ +
Sbjct: 67 RLKKCLAVGMRPECVVPENQCAMKRREKKAQKEKDKMTTSPS 108
>1dsz_B RXR-alpha, retinoic acid receptor RXR-alpha; RAR, nuclear
receptor, protein-DNA, transcription/DNA complex; HET:
DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1by4_A*
1rxr_A 1r0n_A 1r0o_A 2nll_A*
Length = 85
Score = 90.9 bits (226), Expect = 3e-25
Identities = 29/79 (36%), Positives = 50/79 (63%), Gaps = 1/79 (1%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSC 61
C +CG+ ++G H+G ++CEGCK FF R+ + + C++N +C+I+K+ R C+ C
Sbjct: 5 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYT-CRDNKDCLIDKRQRNRCQYC 63
Query: 62 RLRKCLMVGMSKSGSRYGR 80
R +KCL +GM + + R
Sbjct: 64 RYQKCLAMGMKREAVQEER 82
>2han_A Protein ultraspiracle; transcription regulation, transcription
factor, DNA-binding, nuclear protein, nuclear receptor,
zinc finger; 1.95A {Drosophila melanogaster} SCOP:
g.39.1.2
Length = 93
Score = 90.9 bits (226), Expect = 3e-25
Identities = 31/79 (39%), Positives = 47/79 (59%), Gaps = 1/79 (1%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSC 61
C +CG+ A+G H+G ++CEGCK FF R+ + + C+ N CII+K+ R C+ C
Sbjct: 10 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYA-CRENRNCIIDKRQRNRCQYC 68
Query: 62 RLRKCLMVGMSKSGSRYGR 80
R +KCL GM + + R
Sbjct: 69 RYQKCLTCGMKREAVQEER 87
>3g9m_A Glucocorticoid receptor; glucocorticoid, DNA-binding, allostery,
lever ARM, transcription, hormone; HET: DNA; 1.61A
{Rattus norvegicus} PDB: 3g6p_A* 3g6q_B* 3g6r_B*
3g6u_A* 3g8u_A* 3g8x_A* 3g97_B* 3g99_A* 3g9i_A* 3g9j_A*
3fyl_A* 3g9o_B* 3g9p_B* 3g6t_A* 1r4o_A 1r4r_A 1glu_A*
1gdc_A 2gda_A 1rgd_A ...
Length = 90
Score = 90.6 bits (225), Expect = 4e-25
Identities = 30/80 (37%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSC 61
+ C VC + A+G H+G TC CK FF R+ + C N+CII+K R +C +C
Sbjct: 2 SHMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYL-CAGRNDCIIDKIRRKNCPAC 60
Query: 62 RLRKCLMVGMSKSGSRYGRR 81
R RKCL GM+ + ++
Sbjct: 61 RYRKCLQAGMNLEARKTKKK 80
>1ynw_B Retinoic acid receptor RXR-alpha, retinoid X receptor; VDR,
nuclear receptor, protein-DNA complex, transcripti
complex; 3.00A {Homo sapiens} SCOP: g.39.1.2
Length = 99
Score = 89.8 bits (223), Expect = 1e-24
Identities = 30/80 (37%), Positives = 50/80 (62%), Gaps = 3/80 (3%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSY-NNLPSISECKNNNECIINKKNRTSCKS 60
C +CG+ ++G H+G ++CEGCK FF R+ +L C++N +C+I+K+ R C+
Sbjct: 3 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDL--TYTCRDNKDCLIDKRQRNRCQY 60
Query: 61 CRLRKCLMVGMSKSGSRYGR 80
CR +KCL +GM + + R
Sbjct: 61 CRYQKCLAMGMKREAVQEER 80
>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 = 95.9 bits (238), Expect = 2e-24
Identities = 29/82 (35%), Positives = 51/82 (62%), Gaps = 5/82 (6%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRS--YNNLPSISECKNNNECIINKKNRTSCK 59
C +CG+ ++G H+G ++CEGCK FF R+ + + C++N +C+I+K+ R C+
Sbjct: 137 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYT---CRDNKDCLIDKRQRNRCQ 193
Query: 60 SCRLRKCLMVGMSKSGSRYGRR 81
CR +KCL +GM + + R+
Sbjct: 194 YCRYQKCLAMGMKREAVQEERQ 215
>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding
domain, nuclear; zinc finger; 2.00A {Homo sapiens}
Length = 78
Score = 88.1 bits (219), Expect = 2e-24
Identities = 30/76 (39%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 5 CKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRLR 64
C +CG+ A G H+GA +C+GCK FF RS + C+ + +C+++K R C+ CRL+
Sbjct: 3 CAICGDRATGKHYGASSCDGCKGFFRRSVRK-NHMYSCRFSRQCVVDKDKRNQCRYCRLK 61
Query: 65 KCLMVGMSKSGSRYGR 80
KC GM K + R
Sbjct: 62 KCFRAGMKKEAVQNER 77
>3dzy_D Peroxisome proliferator-activated receptor gamma; 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_D* 3e00_D* 2env_A
Length = 419
Score = 90.9 bits (225), Expect = 1e-22
Identities = 38/100 (38%), Positives = 54/100 (54%), Gaps = 2/100 (2%)
Query: 1 MNQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKS 60
M C+VCG+ A+GFH+G CEGCK FF R+ + + + C I+KK+R C+
Sbjct: 49 MAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRL--KLIYDRCDLNCRIHKKSRNKCQY 106
Query: 61 CRLRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQQAEQ 100
CR +KCL VGMS + R+GR K L + +
Sbjct: 107 CRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAEISSDIDQL 146
>1z5x_E Ecdysone receptor ligand binding domain; ponasterone A, nuclear
receptor, ECR, USP, hormone/growth factor receptor
complex; HET: P1A; 3.07A {Bemisia tabaci}
Length = 310
Score = 35.9 bits (83), Expect = 0.002
Identities = 4/39 (10%), Positives = 11/39 (28%), Gaps = 1/39 (2%)
Query: 45 NNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRSN 83
+C + K+ + + + S G +
Sbjct: 20 EFQCAV-KRKEKKAQKDKDKPNSTTSCSPDGIKQEIDPQ 57
Score = 27.5 bits (61), Expect = 1.3
Identities = 7/70 (10%), Positives = 19/70 (27%), Gaps = 6/70 (8%)
Query: 42 CKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQ----- 96
+ + +K S SC + + + + + EQ++
Sbjct: 26 KRKEKKAQKDKDKPNSTTSCSPDGIKQEIDPQRLDTDSQLLSVNGVKPITPEQEELIHRL 85
Query: 97 -QAEQQTERT 105
+ + E
Sbjct: 86 VYFQNEYEHP 95
>1jae_A Alpha-amylase; glycosidase, carbohydrate metabolism,
4-glucan-4-glucanohydrolase, hydrolase; 1.65A {Tenebrio
molitor} SCOP: b.71.1.1 c.1.8.1 PDB: 1clv_A 1tmq_A
1viw_A*
Length = 471
Score = 29.7 bits (66), Expect = 0.30
Identities = 9/50 (18%), Positives = 19/50 (38%)
Query: 14 GFHFGAFTCEGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCRL 63
G T G +Y +P S ++ + N ++ + ++C L
Sbjct: 101 TGMNGVGTSGSSADHDGMNYPAVPYGSGDFHSPCEVNNYQDADNVRNCEL 150
>2hc4_A Vitamin D receptor; alpha helical sandwich, gene regulation; HET:
VDX; 2.20A {Danio rerio} PDB: 2hbh_A* 2hcd_A* 3dr1_A*
3o1d_A* 3o1e_A*
Length = 302
Score = 29.4 bits (66), Expect = 0.35
Identities = 3/29 (10%), Positives = 7/29 (24%)
Query: 55 RTSCKSCRLRKCLMVGMSKSGSRYGRRSN 83
+ R R + G + +
Sbjct: 26 DSYSDFVRFRPPVREGPVTRSASRAASLH 54
>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 = 0.36
Identities = 6/26 (23%), Positives = 11/26 (42%), Gaps = 4/26 (15%)
Query: 94 QQQQAEQQTERTKLGHPD----LLLK 115
++Q ++ KL D L +K
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIK 43
>1a0i_A DNA ligase; DNA replication; HET: DNA ATP; 2.60A {Enterobacteria
phage T7} SCOP: b.40.4.6 d.142.2.1
Length = 348
Score = 29.2 bits (65), Expect = 0.40
Identities = 6/22 (27%), Positives = 11/22 (50%), Gaps = 3/22 (13%)
Query: 71 MSKS-GSRY--GRRSNWFKIHC 89
+ K Y G++S W+K+
Sbjct: 219 IVKDPMCIYKRGKKSGWWKMKP 240
>3od8_A Poly [ADP-ribose] polymerase 1; protein-DNA complex, PARP zinc
finger, DNA binding protein-D complex; 2.40A {Homo
sapiens} PDB: 3oda_A
Length = 116
Score = 28.0 bits (62), Expect = 0.51
Identities = 15/59 (25%), Positives = 21/59 (35%), Gaps = 10/59 (16%)
Query: 52 KKNRTSCKSCR-------LRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQQAEQQTE 103
K R SCK C LR +MV +S G+ +W+ C + E
Sbjct: 35 KSGRASCKKCSESIPKDSLRMAIMV---QSPMFDGKVPHWYHFSCFWKVGHSIRHPDVE 90
>2dmj_A Poly (ADP-ribose) polymerase family, member 1; zinc finger, PARP-1,
ADPRT, NAD(+) ADP-ribosyltransferase 1, poly(ADP-ribose)
synthetase 1; NMR {Homo sapiens}
Length = 106
Score = 27.9 bits (62), Expect = 0.54
Identities = 15/59 (25%), Positives = 21/59 (35%), Gaps = 10/59 (16%)
Query: 52 KKNRTSCKSCR-------LRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQQAEQQTE 103
K R SCK C LR +MV +S G+ +W+ C + E
Sbjct: 22 KSGRASCKKCSESIPKDSLRMAIMV---QSPMFDGKVPHWYHFSCFWKVGHSIRHPDVE 77
>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 = 28.7 bits (63), Expect = 0.71
Identities = 11/105 (10%), Positives = 26/105 (24%), Gaps = 30/105 (28%)
Query: 38 SISECKNNNECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGRRSNWFK--IHCLLQEQQ 95
++ C + + + S S R + + + LL+ +
Sbjct: 188 NLKNCNSPETVLEMLQKL-----LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKP 242
Query: 96 QQAEQQTERTKLGHPDLLLKLD---------KFTNN-NTIVTNNN 130
+ + LL L F + ++T
Sbjct: 243 -------------YENCLLVLLNVQNAKAWNAFNLSCKILLTTRF 274
>1v9x_A Poly (ADP-ribose) polymerase; PARP, DNA repair, inflammation,
cell death, structural genomics; NMR {Arabidopsis
thaliana}
Length = 114
Score = 27.2 bits (60), Expect = 1.2
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 10/52 (19%)
Query: 52 KKNRTSCKSCR-------LRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQ 96
K +R+SCK+C+ R +V +S G W C+L++ +Q
Sbjct: 17 KSSRSSCKTCKSVINKENFRLGKLV---QSTHFDGIMPMWNHASCILKKTKQ 65
>4fsd_A Arsenic methyltransferase; rossmann fold; 1.75A {Cyanidioschyzon
SP} PDB: 4fr0_A* 4fs8_A 3p7e_A 3qnh_A 3qhu_A
Length = 383
Score = 27.7 bits (61), Expect = 1.5
Identities = 5/47 (10%), Positives = 8/47 (17%), Gaps = 16/47 (34%)
Query: 2 NQTCKVCGEPAA----------------GFHFGAFTCEGCKSFFGRS 32
+ +V A H G F +
Sbjct: 315 EKPVRVDRNTAEIIRHSRLHQWFSVSAEQQHMGLFKANDSYALLHAP 361
>4av1_A Poly [ADP-ribose] polymerase 1; transferase, PARP1, DNA-binding
domain, DBD, DNA repair, CAN poly- ADP(ribosyl)ation;
3.10A {Homo sapiens} PDB: 2l30_A
Length = 223
Score = 27.5 bits (60), Expect = 1.5
Identities = 14/59 (23%), Positives = 19/59 (32%), Gaps = 10/59 (16%)
Query: 52 KKNRTSCKSCR-------LRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQQAEQQTE 103
K R SCK C LR +MV G+ +W+ C + E
Sbjct: 36 KSGRASCKKCSESIPKDSLRMAIMVQSPMFD---GKVPHWYHFSCFWKVGHSIRHPDVE 91
Score = 25.2 bits (54), Expect = 9.5
Identities = 16/104 (15%), Positives = 33/104 (31%), Gaps = 9/104 (8%)
Query: 23 EGCKSFFGRSYNNLPSISECKNNNECIINKKNRTSCKSCR-------LRKCLMVGMSKSG 75
E + + K NR++CK C +R + +
Sbjct: 111 EAGGVTGKGQDGIGSKAEKTLGDFAAEYAKSNRSTCKGCMEKIEKGQVRLSKKM-VDPEK 169
Query: 76 SRYGRRSNWFKIHCLLQEQQQ-QAEQQTERTKLGHPDLLLKLDK 118
+ G W+ C ++ +++ + ++L LL DK
Sbjct: 170 PQLGMIDRWYHPGCFVKNREELGFRPEYSASQLKGFSLLATEDK 213
>2cs2_A Poly [ADP-ribose] polymerase-1; DNA BIND, DNA repair, necrosis,
apoptosis, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 134
Score = 27.0 bits (59), Expect = 1.7
Identities = 10/52 (19%), Positives = 22/52 (42%), Gaps = 8/52 (15%)
Query: 52 KKNRTSCKSCR-------LRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQ 96
K NR++CK C +R + + + G W+ C ++ +++
Sbjct: 24 KSNRSTCKGCMEKIEKGQVRLSKKM-VDPEKPQLGMIDRWYHPGCFVKNREE 74
>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 = 27.3 bits (60), Expect = 2.0
Identities = 20/121 (16%), Positives = 35/121 (28%), Gaps = 23/121 (19%)
Query: 23 EGCKSFFGRSYNNLPSISECKNNN--ECIINKKNRTSCKSCRLRKCLMVGMSKSGSRYGR 80
+ F +Y SI + NN I+ K R+R+ M G+
Sbjct: 1647 NRADNHFKDTYGF--SILDIVINNPVNLTIHF---GGEKGKRIRENYS-AMIFETIVDGK 1700
Query: 81 RSNWFKIHCLLQEQQQQAEQQTERTKLGHPDLLLKLDKFTNNNT---IVTNNNLILQLLQ 137
K + +E + + T LL T T + + L+
Sbjct: 1701 ----LKTEKIFKEINEHSTSYT----FRSEKGLLSA---T-QFTQPALTLMEKAAFEDLK 1748
Query: 138 N 138
+
Sbjct: 1749 S 1749
>1uw0_A DNA ligase III; DNA repair, zinc finger, PARP-like finger, cell
division, DNA replication, nuclear protein; HET: DNA;
NMR {Homo sapiens} SCOP: g.39.1.12
Length = 117
Score = 26.6 bits (58), Expect = 2.2
Identities = 10/53 (18%), Positives = 20/53 (37%), Gaps = 8/53 (15%)
Query: 52 KKNRTSCKSCR-------LRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQQ 97
K+ CK C+ R +V + G W+ I C+ ++ ++
Sbjct: 12 KRGTAGCKKCKEKIVKGVCRIGKVV-PNPFSESGGDMKEWYHIKCMFEKLERA 63
>3odc_A Poly [ADP-ribose] polymerase 1; protein-DNA complex, PARP zinc
finger, DNA binding protein-D complex; 2.80A {Homo
sapiens} PDB: 3ode_A 2l31_A
Length = 111
Score = 26.1 bits (57), Expect = 2.5
Identities = 10/52 (19%), Positives = 22/52 (42%), Gaps = 8/52 (15%)
Query: 52 KKNRTSCKSCR-------LRKCLMVGMSKSGSRYGRRSNWFKIHCLLQEQQQ 96
K NR++CK C +R + + + G W+ C ++ +++
Sbjct: 16 KSNRSTCKGCMEKIEKGQVRLSKKM-VDPEKPQLGMIDRWYHPGCFVKNREE 66
>2e2z_A TIM15; protein import, zinc finger, protein transport, chaperone
regulator; NMR {Saccharomyces cerevisiae}
Length = 100
Score = 25.8 bits (56), Expect = 3.4
Identities = 10/59 (16%), Positives = 20/59 (33%), Gaps = 9/59 (15%)
Query: 4 TCKVCGEPAA------GFHFGA--FTCEGCKSFFGRSYNNLPSISECKNNNECIINKKN 54
TCK C ++ + G +C CK + ++L + E ++
Sbjct: 15 TCKKCNTRSSHTMSKQAYEKGTVLISCPHCKVRHLIA-DHLKIFHDHHVTVEQLMKANG 72
>3ial_A Prolyl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase,
AARS, prors, cysrs, RS, translation, ATP-binding,
nucleotide-binding; HET: PR8; 2.20A {Giardia lamblia
atcc 50803}
Length = 518
Score = 26.3 bits (58), Expect = 4.6
Identities = 7/32 (21%), Positives = 12/32 (37%), Gaps = 11/32 (34%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSY 33
+ C + G+PA C + +SY
Sbjct: 498 GEVCALSGKPAV-----------CYMYCAKSY 518
>3cxl_A N-chimerin; SH2, RHO-GAP, structural genomics consortium, SGC,
gtpas activation, metal-binding, phorbol-ester binding,
SH2 domai finger; 2.60A {Homo sapiens} PDB: 1xa6_A
Length = 463
Score = 26.0 bits (57), Expect = 4.9
Identities = 5/24 (20%), Positives = 6/24 (25%)
Query: 3 QTCKVCGEPAAGFHFGAFTCEGCK 26
C+ C G C C
Sbjct: 221 HWCEYCANFMWGLIAQGVKCADCG 244
>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 = 25.8 bits (56), Expect = 5.7
Identities = 6/27 (22%), Positives = 6/27 (22%), Gaps = 4/27 (14%)
Query: 3 QTCKVCGEPAAGFHF----GAFTCEGC 25
TC C G C C
Sbjct: 22 LTCPECKVYPPKIVERFSEGDVVCALC 48
>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear
receptor, structural proteomic europe, spine,
structural genomics; 2.70A {Homo sapiens} SCOP:
a.123.1.1 PDB: 1z5x_U* 2q60_A
Length = 282
Score = 25.5 bits (56), Expect = 6.9
Identities = 2/27 (7%), Positives = 7/27 (25%), Gaps = 3/27 (11%)
Query: 55 RTSCKSCRLRKCLMVGMSKSGSRYGRR 81
S + + + + R+
Sbjct: 7 HHHHSSGLVPR---GSHKREAVQEERQ 30
>1hc7_A Prolyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP + L-proline
+ tRNA(Pro) AMP + PPI + L-prolyl-tRNA(Pro); 2.43A
{Thermus thermophilus} SCOP: c.51.1.1 d.68.5.1 d.104.1.1
PDB: 1h4q_A* 1h4t_A 1h4s_A
Length = 477
Score = 25.4 bits (56), Expect = 9.1
Identities = 8/32 (25%), Positives = 12/32 (37%), Gaps = 9/32 (28%)
Query: 2 NQTCKVCGEPAAGFHFGAFTCEGCKSFFGRSY 33
C CG P+A G + F ++Y
Sbjct: 455 EGFCVRCGRPSAY---------GKRVVFAKAY 477
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
0.320 0.133 0.419
Gapped
Lambda K H
0.267 0.0528 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,958,806
Number of extensions: 100326
Number of successful extensions: 393
Number of sequences better than 10.0: 1
Number of HSP's gapped: 372
Number of HSP's successfully gapped: 93
Length of query: 139
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 55
Effective length of database: 4,356,429
Effective search space: 239603595
Effective search space used: 239603595
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.3 bits)