RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12688
(222 letters)
>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 = 154 bits (392), Expect = 6e-49
Identities = 63/78 (80%), Positives = 68/78 (87%)
Query: 121 DTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRK 180
E +EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQN K YTC+ ++C IDKTQRK
Sbjct: 3 FGDEDLEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRK 62
Query: 181 RCPFCRFQKCLEVGMKLE 198
RCP+CRFQKCL VGMKLE
Sbjct: 63 RCPYCRFQKCLSVGMKLE 80
>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 = 144 bits (364), Expect = 8e-45
Identities = 40/72 (55%), Positives = 48/72 (66%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
+ LC VCGD SGYHYG+ +CE+CK FFKRT+Q Y+C A C I K +RK C CR
Sbjct: 4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACR 63
Query: 187 FQKCLEVGMKLE 198
F K L+VGM E
Sbjct: 64 FMKALKVGMLKE 75
>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 = 142 bits (359), Expect = 3e-44
Identities = 41/74 (55%), Positives = 52/74 (70%)
Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPF 184
+ +C +CGD+ SG HYG+ +CE CKGFFKRTV+ YTC + C IDK QR RC +
Sbjct: 3 FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQY 62
Query: 185 CRFQKCLEVGMKLE 198
CR+QKCL +GMK E
Sbjct: 63 CRYQKCLAMGMKRE 76
>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 = 142 bits (359), Expect = 3e-44
Identities = 43/69 (62%), Positives = 48/69 (69%)
Query: 130 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQK 189
C VCGD S HYG+ TCE CKGFFKRTVQ Y C+A + C +DK +R RC FCRFQK
Sbjct: 3 CAVCGDNASCQHYGVRTCEGCKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQK 62
Query: 190 CLEVGMKLE 198
CL VGM E
Sbjct: 63 CLAVGMVKE 71
>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 = 142 bits (359), Expect = 3e-44
Identities = 37/72 (51%), Positives = 43/72 (59%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
C VC D SGYHYG+ +CE CK FFKR++Q Y C A C IDK +RK C CR
Sbjct: 4 TRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACR 63
Query: 187 FQKCLEVGMKLE 198
+KC EVGM
Sbjct: 64 LRKCYEVGMMKG 75
>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 = 142 bits (359), Expect = 4e-44
Identities = 41/74 (55%), Positives = 51/74 (68%)
Query: 125 GIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPF 184
I + C VC DK SGYHYG+ CE CKGFF+R++Q VYTC +++C I+K R RC +
Sbjct: 2 RIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQY 61
Query: 185 CRFQKCLEVGMKLE 198
CR QKC EVGM E
Sbjct: 62 CRLQKCFEVGMSKE 75
>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 = 141 bits (358), Expect = 5e-44
Identities = 39/72 (54%), Positives = 48/72 (66%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
+C VC D+ SG HYG+LTC SCK FFKR V+ + Y C C IDK +RK CP CR
Sbjct: 2 SHMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACR 61
Query: 187 FQKCLEVGMKLE 198
++KCL+ GM LE
Sbjct: 62 YRKCLQAGMNLE 73
>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 = 141 bits (358), Expect = 6e-44
Identities = 43/79 (54%), Positives = 52/79 (65%)
Query: 120 PDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQR 179
G + LC +CGD+ SG HYG+ +CE CKGFFKRTV+ Y C R+C IDK QR
Sbjct: 3 NHPLSGSKHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACRENRNCIIDKRQR 62
Query: 180 KRCPFCRFQKCLEVGMKLE 198
RC +CR+QKCL GMK E
Sbjct: 63 NRCQYCRYQKCLTCGMKRE 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 = 141 bits (356), Expect = 1e-43
Identities = 38/72 (52%), Positives = 47/72 (65%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
++ C +CGD+ SG HYG LTC SCK FFKR + K+ Y C + C IDK +RK CP CR
Sbjct: 7 QKTCLICGDEASGAHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCR 66
Query: 187 FQKCLEVGMKLE 198
+KC E GM L
Sbjct: 67 LRKCYEAGMTLG 78
>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 = 141 bits (356), Expect = 2e-43
Identities = 30/75 (40%), Positives = 49/75 (65%)
Query: 124 EGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCP 183
+ +C VCGD+ +G+H+ +TCE CKGFF+R+++ K ++TC C I K R+ C
Sbjct: 3 RNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQ 62
Query: 184 FCRFQKCLEVGMKLE 198
CR ++C+++GM E
Sbjct: 63 ACRLKRCVDIGMMKE 77
>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 = 139 bits (351), Expect = 8e-43
Identities = 41/72 (56%), Positives = 52/72 (72%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
+ +C +CGD+ SG HYG+ +CE CKGFFKRTV+ YTC + C IDK QR RC +CR
Sbjct: 3 KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCR 62
Query: 187 FQKCLEVGMKLE 198
+QKCL +GMK E
Sbjct: 63 YQKCLAMGMKRE 74
>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 = 138 bits (350), Expect = 2e-42
Identities = 41/72 (56%), Positives = 50/72 (69%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCR 186
EELC VCGD+ SGYHY LTCE CKGFF+R+V VY C R+C +D R++C CR
Sbjct: 8 EELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECR 67
Query: 187 FQKCLEVGMKLE 198
+KCL VGM+ E
Sbjct: 68 LKKCLAVGMRPE 79
>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 = 137 bits (347), Expect = 2e-42
Identities = 40/77 (51%), Positives = 50/77 (64%)
Query: 122 TKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKR 181
+ C VCGDK SG HYG TCE CK FFKR+V+ YTC A R+C ID+ R +
Sbjct: 2 SSGSSGIECVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQ 61
Query: 182 CPFCRFQKCLEVGMKLE 198
C +CR +KCL+VGM+ E
Sbjct: 62 CQYCRLKKCLKVGMRRE 78
>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 = 137 bits (346), Expect = 4e-42
Identities = 40/74 (54%), Positives = 50/74 (67%), Gaps = 2/74 (2%)
Query: 127 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNK--KVYTCVAERSCHIDKTQRKRCPF 184
+ELC VCGDK +GYHY +TCE CKGFF+RT+Q Y+C E C IDK R +C
Sbjct: 1 DELCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQE 60
Query: 185 CRFQKCLEVGMKLE 198
CRF+KC+ VGM +
Sbjct: 61 CRFKKCIYVGMATD 74
>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 = 136 bits (344), Expect = 8e-42
Identities = 38/78 (48%), Positives = 49/78 (62%), Gaps = 1/78 (1%)
Query: 122 TKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYT-CVAERSCHIDKTQRK 180
G+ LC VCGD SG+HYG+L CE CKGFF+R++Q Y C+ +C I + R
Sbjct: 2 KLNGMVLLCKVCGDVASGFHYGVLACEGCKGFFRRSIQQNIQYKRCLKNENCSIVRINRN 61
Query: 181 RCPFCRFQKCLEVGMKLE 198
RC CRF+KCL VGM +
Sbjct: 62 RCQQCRFKKCLSVGMSRD 79
>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain,
nuclear; zinc finger; 2.00A {Homo sapiens}
Length = 78
Score = 135 bits (342), Expect = 1e-41
Identities = 33/70 (47%), Positives = 48/70 (68%)
Query: 129 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQ 188
LC +CGD+ +G HYG +C+ CKGFF+R+V+ +Y+C R C +DK +R +C +CR +
Sbjct: 2 LCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLK 61
Query: 189 KCLEVGMKLE 198
KC GMK E
Sbjct: 62 KCFRAGMKKE 71
>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 = 135 bits (341), Expect = 1e-37
Identities = 61/168 (36%), Positives = 83/168 (49%), Gaps = 4/168 (2%)
Query: 35 SAATGAQTPQMQHSNNDTQSSQLSPML--GNNTSASAGGAGYNFNNMVDNSYLFQSPGGG 92
S G +P HS T SS ++ M + S+ G + + SP
Sbjct: 41 SLGPGIGSPGQLHSPISTLSSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLS 100
Query: 93 STNMDLSSAGISYHPFHTSTIAATPEHPDTKE--GIEELCPVCGDKVSGYHYGLLTCESC 150
S +SS+ P + + P HP + +C +CGD+ SG HYG+ +CE C
Sbjct: 101 SPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNMASFTKHICAICGDRSSGKHYGVYSCEGC 160
Query: 151 KGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLE 198
KGFFKRTV+ YTC + C IDK QR RC +CR+QKCL +GMK E
Sbjct: 161 KGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKRE 208
>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 = 118 bits (296), Expect = 1e-31
Identities = 42/112 (37%), Positives = 57/112 (50%), Gaps = 2/112 (1%)
Query: 87 QSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELCPVCGDKVSGYHYGLLT 146
+ + + A Y+ T E P + C VCGDK SG+HYG+
Sbjct: 11 DDDKMYQSAIKVEPASPPYYSEKTQLYNKPHEEPSNS-LMAIECRVCGDKASGFHYGVHA 69
Query: 147 CESCKGFFKRTVQNKKVYTCVAERSCHIDKTQRKRCPFCRFQKCLEVGMKLE 198
CE CKGFF+RT++ K +Y + +C I K R +C +CRFQKCL VGM
Sbjct: 70 CEGCKGFFRRTIRLKLIYDR-CDLNCRIHKKSRNKCQYCRFQKCLAVGMSHN 120
>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 = 38.1 bits (88), Expect = 8e-04
Identities = 12/47 (25%), Positives = 15/47 (31%), Gaps = 11/47 (23%)
Query: 115 ATPEHPDTKEG-------IEELCPVCGDK----VSGYHYGLLTCESC 150
T E D + G I CP C V + G + C C
Sbjct: 2 MTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALC 48
>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 = 35.6 bits (82), Expect = 0.008
Identities = 5/30 (16%), Positives = 10/30 (33%), Gaps = 1/30 (3%)
Query: 166 CVAERSCHIDKTQRKRCPFCRFQKCLEVGM 195
V E C + K + K+ + +
Sbjct: 17 VVPEFQCAV-KRKEKKAQKDKDKPNSTTSC 45
Score = 33.6 bits (77), Expect = 0.039
Identities = 9/52 (17%), Positives = 15/52 (28%)
Query: 169 ERSCHIDKTQRKRCPFCRFQKCLEVGMKLEVSSQSTHGVVVIWSPHSPSISE 220
E+ DK + C + + + S V P +P E
Sbjct: 29 EKKAQKDKDKPNSTTSCSPDGIKQEIDPQRLDTDSQLLSVNGVKPITPEQEE 80
>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 = 35.2 bits (81), Expect = 0.012
Identities = 10/52 (19%), Positives = 18/52 (34%), Gaps = 5/52 (9%)
Query: 173 HIDKTQRKRCPFCRFQKCLEVGMKLEVSSQ--STHGVVVIWSPHSPSISENL 222
D + F RF+ + G +S+ S H + S E++
Sbjct: 23 TYDDSY---SDFVRFRPPVREGPVTRSASRAASLHSLSDASSDSFNHSPESV 71
>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 = 31.7 bits (71), Expect = 0.20
Identities = 30/137 (21%), Positives = 39/137 (28%), Gaps = 50/137 (36%)
Query: 4 MSQIHEN---ILDLVQ----------RCK----KRKKLKPKTPIQQLLSAATGAQTPQMQ 46
S+ +EN +L VQ CK R K + LSAAT
Sbjct: 239 KSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFK-----QVTDFLSAATTTHISLDH 293
Query: 47 HSNNDTQSSQLSPMLGNNTSASAGGAGYNFNNMVDNSYLFQSPGGGSTNMDLSSAGISYH 106
HS T S +L YL P DL ++ +
Sbjct: 294 HSMTLTPDEVKS-LLLK--------------------YLDCRPQ------DLPREVLTTN 326
Query: 107 PFHTSTIAA-TPEHPDT 122
P S IA + T
Sbjct: 327 PRRLSIIAESIRDGLAT 343
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 31.6 bits (71), Expect = 0.23
Identities = 20/112 (17%), Positives = 29/112 (25%), Gaps = 13/112 (11%)
Query: 13 DLVQRCKKRKKLKPKTPIQQLLSAAT-------GAQTPQMQHSNND------TQSSQLSP 59
D+ T + L + GA TP + D ++ SP
Sbjct: 1448 DIYLDQDMLMNYSLGTAVPTLAGSGMGTSQLPEGAGTPYERSPMVDSGFVGSPDAAAFSP 1507
Query: 60 MLGNNTSASAGGAGYNFNNMVDNSYLFQSPGGGSTNMDLSSAGISYHPFHTS 111
++ + G Y QSPG S S G S
Sbjct: 1508 LVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYS 1559
Score = 27.0 bits (59), Expect = 6.7
Identities = 16/74 (21%), Positives = 23/74 (31%)
Query: 34 LSAATGAQTPQMQHSNNDTQSSQLSPMLGNNTSASAGGAGYNFNNMVDNSYLFQSPGGGS 93
S G Q+P + S + + +S G + SY SP
Sbjct: 1528 ASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPSYSP 1587
Query: 94 TNMDLSSAGISYHP 107
T+ S SY P
Sbjct: 1588 TSPSYSPTSPSYSP 1601
>1on3_A Methylmalonyl-COA carboxyltransferase 12S subunit; domain
duplication, multienzyme complex, transcarboxylase; HET:
MCA; 1.90A {Propionibacterium freudenreichii} SCOP:
c.14.1.4 c.14.1.4 PDB: 1on9_A*
Length = 523
Score = 30.6 bits (70), Expect = 0.44
Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 9/36 (25%)
Query: 56 QLSPMLGNNTSASAGGAGYN-----FNNMVDNSYLF 86
Q++ + G AGGA Y+ F M +++F
Sbjct: 170 QIAIIAG----PCAGGASYSPALTDFIIMTKKAHMF 201
>1nkw_1 50S ribosomal protein L33; ribosome, large subunit, X- RAY
structure, peptidyl-transferase, peptide bond formation;
3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB:
1sm1_1* 1yl3_6 2b66_6 2b9n_6 2b9p_6
Length = 82
Score = 28.6 bits (64), Expect = 0.49
Identities = 7/43 (16%), Positives = 15/43 (34%), Gaps = 10/43 (23%)
Query: 145 LTCESCKGFFKRTVQNKKVYTCVAERSCHIDK-TQRKRCPFCR 186
+ + GF+ T +N++ K +K P +
Sbjct: 39 MESSAGTGFYYTTTKNRRNTQ---------AKLELKKYDPVAK 72
>2zjr_1 50S ribosomal protein L33; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: g.41.8.6 PDB: 1nwx_1* 1xbp_1* 2zjp_1*
2zjq_1 1nwy_1 3cf5_1* 3dll_1* 3pio_1* 3pip_1* 1pnu_1
1pny_1 1vor_3 1vou_3 1vow_3 1voy_3 1vp0_3
Length = 55
Score = 26.8 bits (60), Expect = 1.0
Identities = 7/43 (16%), Positives = 15/43 (34%), Gaps = 10/43 (23%)
Query: 145 LTCESCKGFFKRTVQNKKVYTCVAERSCHIDK-TQRKRCPFCR 186
+ + GF+ T +N++ K +K P +
Sbjct: 12 MESSAGTGFYYTTTKNRRNTQ---------AKLELKKYDPVAK 45
>3h6z_A Polycomb protein SFMBT; MBT, MBR repeat, aromatic CAGE, chromatin
regulator, DNA-BIN metal-binding, nucleus, repressor,
transcription; HET: MLZ SUC; 2.80A {Drosophila
melanogaster}
Length = 447
Score = 29.2 bits (65), Expect = 1.0
Identities = 12/39 (30%), Positives = 17/39 (43%)
Query: 180 KRCPFCRFQKCLEVGMKLEVSSQSTHGVVVIWSPHSPSI 218
P C L VGMK+EV + + VI +P+
Sbjct: 26 PHAPGCEVWDNLGVGMKVEVENTDCDSIEVIQPGQTPTS 64
>3u50_C Telomerase-associated protein 82; TEB1, processivity factor, DNA
BIND protein; 2.50A {Tetrahymena thermophila}
Length = 172
Score = 28.1 bits (62), Expect = 1.7
Identities = 9/22 (40%), Positives = 10/22 (45%)
Query: 130 CPVCGDKVSGYHYGLLTCESCK 151
C G V YH CESC+
Sbjct: 45 CTCQGKSVLKYHGDSFFCESCQ 66
>3feo_A MBT domain-containing protein 1; MBTL1, structural genomics,
structural genomics consortium, metal-binding, nucleus,
zinc-finger; 2.50A {Homo sapiens}
Length = 437
Score = 28.1 bits (62), Expect = 2.6
Identities = 6/33 (18%), Positives = 13/33 (39%), Gaps = 1/33 (3%)
Query: 180 KRCPFCRFQKCLEVGMKLEV-SSQSTHGVVVIW 211
K P + +++EV ++ + V W
Sbjct: 32 KHAPMGTCWGDISENVRVEVPNTDCSLPTKVFW 64
>1vq8_B 50S ribosomal protein L3P; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: b.43.3.2 PDB: 1vq4_B*
1vq5_B* 1vq6_B* 1vq7_B* 1s72_B* 1vq9_B* 1vqk_B* 1vql_B*
1vqm_B* 1vqn_B* 1vqo_B* 1vqp_B* 1yhq_B* 1yi2_B* 1yij_B*
1yit_B* 1yj9_B* 1yjn_B* 1yjw_B* 2otj_B* ...
Length = 338
Score = 28.1 bits (62), Expect = 2.7
Identities = 5/14 (35%), Positives = 9/14 (64%)
Query: 151 KGFFKRTVQNKKVY 164
G+ +RT NK++
Sbjct: 258 TGYHQRTELNKRLI 271
>3zr5_A Galactocerebrosidase; hydrolase, GALC, glycosyl hydrolase, krabbe
disease, TIM BAR lectin domain; HET: NAG; 2.10A {Mus
musculus} PDB: 3zr6_A*
Length = 656
Score = 27.9 bits (61), Expect = 2.8
Identities = 9/55 (16%), Positives = 16/55 (29%)
Query: 62 GNNTSASAGGAGYNFNNMVDNSYLFQSPGGGSTNMDLSSAGISYHPFHTSTIAAT 116
G F + SY + GG A ++ ++T T+
Sbjct: 554 NKGGILIRSATGVFFWIFANGSYRVTADLGGWITYASGHADVTAKRWYTLTLGIK 608
>2odv_A Plectin 1, HD1; plakin domain, spectrin repeat, cytoskeleton,
hemidesmosomes epidermolysis bullosa, structural
protein; 2.05A {Homo sapiens} PDB: 2odu_A
Length = 235
Score = 27.4 bits (60), Expect = 3.6
Identities = 5/30 (16%), Positives = 13/30 (43%)
Query: 4 MSQIHENILDLVQRCKKRKKLKPKTPIQQL 33
+ ++H+ ++ + R K P Q+
Sbjct: 206 VYRLHKRLVAIRTEYNLRLKAGVAAPATQV 235
>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein
structure initiative, midwest center for structural
genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP:
e.59.1.1
Length = 309
Score = 27.1 bits (59), Expect = 5.7
Identities = 13/80 (16%), Positives = 23/80 (28%), Gaps = 14/80 (17%)
Query: 107 PFHTSTIAATPEHPDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTC 166
+ + E + LCP CG S G++ + + +C
Sbjct: 162 VAWSHWLLGLEEGAVVETESRTLCPACG---SPPMAGMIRQGGKE-------TGLRYLSC 211
Query: 167 VAERSCHID-KTQRKRCPFC 185
C + R +C C
Sbjct: 212 SL---CACEWHYVRIKCSHC 228
>2x24_A Acetyl-COA carboxylase; fatty acid biosynthesis, ligase, lipid
synthesis; HET: X24; 2.40A {Bos taurus} PDB: 3ff6_A*
3tdc_A*
Length = 793
Score = 27.1 bits (60), Expect = 6.1
Identities = 6/40 (15%), Positives = 13/40 (32%), Gaps = 5/40 (12%)
Query: 52 TQSSQLSPMLGNNTSASAGGAGY-----NFNNMVDNSYLF 86
+Q + + + G Y V+NS++
Sbjct: 254 SQDYDEIVTISMVSCRALGIGAYLVRLGQRVIQVENSHII 293
>4a17_B RPL3, ribosomal protein L3; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_B 4a1c_B 4a1e_B
Length = 391
Score = 26.7 bits (58), Expect = 7.8
Identities = 13/48 (27%), Positives = 15/48 (31%), Gaps = 5/48 (10%)
Query: 151 KGFFKRTVQNKKVYTCVAERSCH-----IDKTQRKRCPFCRFQKCLEV 193
G+ RT NKKVY D T + P F V
Sbjct: 268 LGYHHRTETNKKVYRVGKGDDASNASTAGDVTDKAITPLGGFPHYGVV 315
>6rlx_A Relaxin, A-chain; hormone(muscle relaxant); 1.50A {Homo sapiens}
SCOP: g.1.1.1
Length = 26
Score = 23.5 bits (50), Expect = 8.5
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 162 KVYTCVAERSCHIDKTQRKRCPFC 185
++Y+ +A + CH+ T+R FC
Sbjct: 1 ELYSALANKCCHVGCTKRSLARFC 24
>1e4u_A Transcriptional repressor NOT4; gene regulation, transcriptional
control; NMR {Homo sapiens} SCOP: g.44.1.1 PDB: 1ur6_B
Length = 78
Score = 24.7 bits (53), Expect = 8.9
Identities = 17/70 (24%), Positives = 21/70 (30%), Gaps = 18/70 (25%)
Query: 119 HPDTKEGIEELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKVYTCVAERSC--HIDK 176
PD KE E CP+C + + C C R C I
Sbjct: 4 SPDAKEDPVE-CPLCMEPLEIDDINFFPCTCG------------YQIC---RFCWHRIRT 47
Query: 177 TQRKRCPFCR 186
+ CP CR
Sbjct: 48 DENGLCPACR 57
>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 = 26.3 bits (57), Expect = 9.6
Identities = 23/105 (21%), Positives = 33/105 (31%), Gaps = 23/105 (21%)
Query: 84 YLFQSPGGGSTNMDLSSAGISYHPFHTSTIAATPEHPDTKEGIEELCPVCGDKVSGYHYG 143
YLF P G + N DL+ H E +LC +C +
Sbjct: 291 YLF--PDGRNQNPDLTGLCEPTPQDHIKVTQEQYELYCEMGSTFQLCKICAENDKD---- 344
Query: 144 LLTCESCKGFFKRTVQNKKVYTCVAERSC--HIDKTQRKRCPFCR 186
+ E C C SC +++ + CPFCR
Sbjct: 345 -VKIEPCGHLM-----------C---TSCLTSWQESEGQGCPFCR 374
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
0.316 0.129 0.392
Gapped
Lambda K H
0.267 0.0522 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,192,408
Number of extensions: 173056
Number of successful extensions: 642
Number of sequences better than 10.0: 1
Number of HSP's gapped: 630
Number of HSP's successfully gapped: 82
Length of query: 222
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 132
Effective length of database: 4,188,903
Effective search space: 552935196
Effective search space used: 552935196
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.4 bits)