RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3393
(433 letters)
>2o4a_A DNA-binding protein SATB1; protein-DNA complex, transcription,
transcription/DNA complex; HET: DNA; 1.75A {Homo
sapiens} SCOP: a.35.1.7 PDB: 2o49_A*
Length = 93
Score = 131 bits (329), Expect = 2e-37
Identities = 27/85 (31%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 350 GELEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPK-PWSKLKSGRE 408
+ + E+ Q + ELKR I QA+FA+ R+QG LS++LR + P + +S
Sbjct: 2 SHMNTEVSSEIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLV 61
Query: 409 TFRRMWKWLQEPEFQRMSALRLAGN 433
R M +LQ PE +R +
Sbjct: 62 NLRAMQNFLQLPEAERDRIYQDERE 86
>1wiz_A DNA-binding protein SATB2; helix bundle, KIAA1034 protein,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: a.35.1.7
Length = 101
Score = 120 bits (301), Expect = 2e-33
Identities = 26/85 (30%), Positives = 43/85 (50%), Gaps = 1/85 (1%)
Query: 342 GAVSLGNSGELEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPK-PW 400
G+ + ++ Q++ ELKR S+ QA+FA+ R+QG LS++LR + P
Sbjct: 4 GSSGKPEPTNSSVEVSPDIYQQVRDELKRASVSQAVFARVAFNRTQGLLSEILRKEEDPR 63
Query: 401 SKLKSGRETFRRMWKWLQEPEFQRM 425
+ +S R M +L PE +R
Sbjct: 64 TASQSLLVNLRAMQNFLNLPEVERD 88
>1x2l_A CUT-like 2, homeobox protein CUX-2; CUT domain, human homeobox
protein CUX-2, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: a.35.1.7
Length = 101
Score = 116 bits (291), Expect = 6e-32
Identities = 33/92 (35%), Positives = 55/92 (59%), Gaps = 3/92 (3%)
Query: 342 GAVSLGNSGELEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWS 401
G+ G E E+++T E+A ++ +L +++I Q +F VL SQG++S++L PKPW
Sbjct: 4 GSSGAGPGAEEEQLDTAEIAFQVKEQLLKHNIGQRVFGHYVLGLSQGSVSEILARPKPWR 63
Query: 402 KLK-SGRETFRRMWKWLQEPEFQRMSALRLAG 432
KL G+E F +M ++L + Q + ALR
Sbjct: 64 KLTVKGKEPFIKMKQFLSDE--QNVLALRTIQ 93
>1wh6_A CUT-like 2, homeobox protein CUX-2; CUT domain, structural
genomics, riken structural genomics/proteomics
initiative, RSGI, transcription; NMR {Homo sapiens}
SCOP: a.35.1.7
Length = 101
Score = 115 bits (290), Expect = 7e-32
Identities = 34/85 (40%), Positives = 49/85 (57%), Gaps = 1/85 (1%)
Query: 348 NSGELEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKL-KSG 406
E++T EL +++ +L + I Q IF ++VL SQG++SD+L PKPWSKL + G
Sbjct: 10 ELYMYREVDTLELTRQVKEKLAKNGICQRIFGEKVLGLSQGSVSDMLSRPKPWSKLTQKG 69
Query: 407 RETFRRMWKWLQEPEFQRMSALRLA 431
RE F RM WL + Q + A
Sbjct: 70 REPFIRMQLWLSDQLGQAVGQQPGA 94
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 110 bits (275), Expect = 6e-29
Identities = 71/75 (94%), Positives = 74/75 (98%)
Query: 352 LEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFR 411
+EEINTKE+AQRI+ ELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFR
Sbjct: 1 MEEINTKEVAQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFR 60
Query: 412 RMWKWLQEPEFQRMS 426
RMWKWLQEPEFQRMS
Sbjct: 61 RMWKWLQEPEFQRMS 75
>1wh8_A CUT-like 2, homeobox protein CUX-2; CUT domain, structural
genomics, riken structural genomics/proteomics
initiative, RSGI, transcription; NMR {Homo sapiens}
SCOP: a.35.1.7
Length = 111
Score = 107 bits (269), Expect = 1e-28
Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 353 EEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLK-SGRETFR 411
E++T + +R+ L ++ Q +F + +L +QG++SDLL PKPW KL GRE F
Sbjct: 25 PELDTYSITKRVKEVLTDNNLGQRLFGESILGLTQGSVSDLLSRPKPWHKLSLKGREPFV 84
Query: 412 RMWKWLQEPEFQRM 425
RM WL +P
Sbjct: 85 RMQLWLNDPHNVEK 98
>1yse_A DNA-binding protein SATB1; all helical, DNA-binding domain, T-cell
development; NMR {Homo sapiens} SCOP: a.35.1.7
Length = 141
Score = 105 bits (261), Expect = 3e-27
Identities = 28/86 (32%), Positives = 42/86 (48%), Gaps = 1/86 (1%)
Query: 345 SLGNSGELEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPK-PWSKL 403
L + E+ Q + ELKR I QA+FA+ R+QG LS++LR + P +
Sbjct: 11 PLEQQVSTNTEVSSEIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTAS 70
Query: 404 KSGRETFRRMWKWLQEPEFQRMSALR 429
+S R M +LQ PE +R +
Sbjct: 71 QSLLVNLRAMQNFLQLPEAERDRIYQ 96
>2csf_A DNA-binding protein SATB2; CUT domain, special AT-rich
sequence-binding protein 2, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: a.35.1.7
Length = 101
Score = 100 bits (248), Expect = 7e-26
Identities = 24/95 (25%), Positives = 41/95 (43%), Gaps = 5/95 (5%)
Query: 342 GAVSLGNSGELEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLR---NPK 398
G+ T + I E+KR + QA+FA+ +SQG L +LLR NP
Sbjct: 4 GSSGPIKVDGANINITAAIYDEIQQEMKRAKVSQALFAKVAANKSQGWLCELLRWKENPS 63
Query: 399 PWSKLKSGRETFRRMWKWLQEPEFQRMSALRLAGN 433
P + ++ E + ++L P+ +R +
Sbjct: 64 PEN--RTLWENLCTIRRFLNLPQHERDVIYEEESS 96
>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 = 52.4 bits (125), Expect = 2e-07
Identities = 47/260 (18%), Positives = 84/260 (32%), Gaps = 70/260 (26%)
Query: 194 NGLST--IVITQ---ENSPLSPQSTY---SQ------NGLNSPQKSLSPNSYDSPYNQRD 239
+ ST + ++ E+ L P +++ SQ L P + + + D P +
Sbjct: 2 DAYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAAD--DEPTTPAE 59
Query: 240 LVDRSVLGGGSQSPTLSPNE-GSLHSSPTTLVTNFQGAATIPTMNGITTITPHTVVVS-P 297
LV + + G S + P++ G +T F+ N I H +
Sbjct: 60 LVGKFL---GYVSSLVEPSKVGQFDQVLNLCLTEFE--NCYLEGNDI-----HALAAKLL 109
Query: 298 QTSP-----QHSLISNQLQRSDSPGPPKIISQQTATLTLKTVTPTNAVVGAVSL------ 346
Q + LI N + P +A G L
Sbjct: 110 QENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFR-------AVGEGNAQLVAIFGG 162
Query: 347 -GNSGE-LEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLK 404
GN+ + EE+ ++L Y ++ S TLS+L+R K+
Sbjct: 163 QGNTDDYFEEL--RDL----------YQTYHV-LVGDLIKFSAETLSELIRTTLDAEKV- 208
Query: 405 SGRETFRR---MWKWLQEPE 421
F + + +WL+ P
Sbjct: 209 -----FTQGLNILEWLENPS 223
Score = 45.0 bits (106), Expect = 4e-05
Identities = 50/289 (17%), Positives = 76/289 (26%), Gaps = 96/289 (33%)
Query: 91 SVASIMDSSEFRNLHAEPTYQTLTNVNGRLSPPGYSPSSSYATLTPLQPLPPI------- 143
A + L AE + N+ L P +P Y P+ P I
Sbjct: 190 FSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPIS-CPLIGVIQLAH 248
Query: 144 ------------STMSDKFAYGHTGNVTG--------------SF-----TVMQNNIGLG 172
+ G TG+ G SF + +G
Sbjct: 249 YVVTAKLLGFTPGELRSYLK-GATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIG 307
Query: 173 INSHYTYDKIQMSPPQ-HYSPNNGLSTIVITQENSPLSPQSTYSQNGLNSPQ-------- 223
+ + Y + P S N E P SP S + L Q
Sbjct: 308 VRCYEAYPNTSLPPSILEDSLENN--------EGVP-SPML--SISNLTQEQVQDYVNKT 356
Query: 224 -KSLSPNS--YDSPYNQRDLVDRSVLGGGSQSPTLSPNEGSLHSSPTTLVTNFQGAATIP 280
L S N + V+ G P SL+ L + A
Sbjct: 357 NSHLPAGKQVEISLVNGAKNL---VVSG---PPQ------SLYG----LNLTLRKAKAPS 400
Query: 281 TMNGITTITPHT---VVVS----PQTSPQHS--------LISNQLQRSD 314
++ + P + + S P SP HS LI+ L +++
Sbjct: 401 GLD--QSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNN 447
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation,
DNA-binding, POU domain, diabetes, disease mutation,
MODY3, transcription/DNA comple; 2.60A {Homo sapiens}
SCOP: a.4.1.1 a.35.1.1
Length = 194
Score = 42.6 bits (99), Expect = 8e-05
Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 4/75 (5%)
Query: 351 ELEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETF 410
L + + +A+ + + L++++IPQ +Q LS L P K
Sbjct: 22 TLLQEDPWRVAKMVKSYLQQHNIPQREVVD-TTGLNQSHLSQHLNKGTPMKTQKRAA--- 77
Query: 411 RRMWKWLQEPEFQRM 425
W ++ E +
Sbjct: 78 LYTWYVRKQREVAQQ 92
>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 = 38.9 bits (90), Expect = 0.003
Identities = 41/210 (19%), Positives = 70/210 (33%), Gaps = 27/210 (12%)
Query: 121 SPPGYSPSSSYATLTPLQPLPPISTMSDKFAYGHTGNVTGSFTVMQNNIGLGINSHYTYD 180
S PG+SP+S + T P + S + S++ + S+
Sbjct: 1538 SSPGFSPTSPTYSPTSPAYSPTSPSYSP--TSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1595
Query: 181 KIQMSPPQHYSPNNGLSTIVITQENSPLSPQSTYSQNGLN---------SPQKSLSPNSY 231
YSP + SP SP + + + SP S + SY
Sbjct: 1596 PSYSPTSPSYSPT--------SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1647
Query: 232 DSPYNQRDLVDRSVLGGGSQSPTLSPNEGSLHSSPTTLVTNFQGAATIPTMNGITTITPH 291
SP + + SP+ SP S SPT+ + + PT + +P
Sbjct: 1648 -SPTSPS--YSPTSPAYSPTSPSYSPT--SPSYSPTSPSYSPTSPSYSPTSPNYSPTSPS 1702
Query: 292 TVVVSPQ---TSPQHSLISNQLQRSDSPGP 318
SP SP +S ++ + +++
Sbjct: 1703 YSPTSPGYSPGSPAYSPKQDEQKHNENENS 1732
>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 = 37.1 bits (85), Expect = 0.011
Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 14/85 (16%)
Query: 336 PTNAVVGAVSLGNSGELEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLR 395
V V E+ IN K L I E ++ S+ ++ + R + L
Sbjct: 75 QEEMVQKFV-----EEVLRINYKFLMSPIKTEQRQPSMMTRMYIE---QRDR-----LYN 121
Query: 396 NPKPWSKLKSGR-ETFRRMWKWLQE 419
+ + ++K R + + ++ + L E
Sbjct: 122 DNQVFAKYNVSRLQPYLKLRQALLE 146
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 35.4 bits (81), Expect = 0.043
Identities = 33/178 (18%), Positives = 57/178 (32%), Gaps = 16/178 (8%)
Query: 146 MSDKFAYGHTGNVTGSFTVMQNNIGLGINSHYTYDKIQMSPPQHYSPNNGLSTIVITQEN 205
M ++ G + + + G + Y + SP+ + ++ +
Sbjct: 1455 MLMNYSLGTAVPTLAGSGMGTSQLPEGAGTPYERSP-MVDSGFVGSPDAAAFSPLVQGGS 1513
Query: 206 SPLSPQSTYSQNGLNSPQKSLSPNSYDSPYNQRDLVDRSVLGGGSQSPTLSPNEGSLHSS 265
Y G SP SP G G SP+ SP+ +S
Sbjct: 1514 EGREGFGDYGLLGAASP-----YKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTS 1568
Query: 266 PTTLVTNFQGAATIPTMNGITTITPHTVVVSPQTSPQHSLISNQLQRSD---SPGPPK 320
P + ++ + T P+ +P + SP TSP +S S + SP P
Sbjct: 1569 PAYMPSSPSYSPTSPSY------SPTSPSYSP-TSPSYSPTSPSYSATSPSYSPTSPS 1619
>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 = 30.7 bits (68), Expect = 0.57
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 4/27 (14%)
Query: 358 KELAQRISAELKRY---SIPQ-AIFAQ 380
K+ +++ A LK Y S P AI A
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKAT 45
Score = 29.9 bits (66), Expect = 0.91
Identities = 6/22 (27%), Positives = 9/22 (40%), Gaps = 2/22 (9%)
Query: 111 QTLTNVNGRLSPPGYSPSSSYA 132
Q L + L Y+ S+ A
Sbjct: 20 QALKKLQASLKL--YADDSAPA 39
>1ffk_I Ribosomal protein L15E; ribosome assembly, RNA-RNA, protein-RNA,
protein-protein; 2.40A {Haloarcula marismortui} SCOP:
d.12.1.2
Length = 194
Score = 28.3 bits (63), Expect = 3.4
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 3/30 (10%)
Query: 400 WSKLKSG--RETFR-RMWKWLQEPEFQRMS 426
W + G E R+ KW +EP R+
Sbjct: 12 WKRPYEGYVGELMWHRLQKWRREPAVVRIP 41
>1ses_A Seryl-tRNA synthetase; ligase; HET: AHX AMP; 2.50A {Thermus
thermophilus} SCOP: a.2.7.1 d.104.1.1 PDB: 1ser_A*
1set_A* 1sry_A
Length = 421
Score = 28.6 bits (65), Expect = 4.6
Identities = 11/64 (17%), Positives = 19/64 (29%), Gaps = 14/64 (21%)
Query: 3 MAEDGSLSEEIDNAAHARMSAISRSVVPALVPIPHDALDLGSN--HSS---GKDDDNESI 57
+A +L EE + + L+ +P G ++ N I
Sbjct: 70 IARGKALGEEAK-RLEEALREKEARLEALLLQVP--------LPPWPGAPVGGEEANREI 120
Query: 58 KTEG 61
K G
Sbjct: 121 KRVG 124
>2q3z_A Transglutaminase 2; transglutaminase 2, tissue transglutaminase,
TG2, transferas; 2.00A {Homo sapiens} SCOP: b.1.18.9
b.1.5.1 b.1.5.1 d.3.1.4 PDB: 1kv3_A 3ly6_A*
Length = 687
Score = 27.7 bits (61), Expect = 8.8
Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 5/60 (8%)
Query: 292 TVVVSPQTSPQHS---LISNQLQRSDSPGPP--KIISQQTATLTLKTVTPTNAVVGAVSL 346
T V +P L+ + G ++ QQ TL+L+ TP NA +G L
Sbjct: 58 TFSVVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRL 117
>3zrh_A Ubiquitin thioesterase zranb1; hydrolase, deubiquitinating enzyme,
WNT signaling, ovarian T domain; 2.23A {Homo sapiens}
Length = 454
Score = 27.4 bits (60), Expect = 9.6
Identities = 5/24 (20%), Positives = 6/24 (25%)
Query: 400 WSKLKSGRETFRRMWKWLQEPEFQ 423
L F WK + Q
Sbjct: 224 HDSLHDCSHWFYTRWKDWESWYSQ 247
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
0.309 0.126 0.355
Gapped
Lambda K H
0.267 0.0506 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,218,920
Number of extensions: 360111
Number of successful extensions: 687
Number of sequences better than 10.0: 1
Number of HSP's gapped: 670
Number of HSP's successfully gapped: 31
Length of query: 433
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 337
Effective length of database: 4,021,377
Effective search space: 1355204049
Effective search space used: 1355204049
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 59 (27.0 bits)