RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6883
(414 letters)
>2hfh_A Genesis, HFH-2; HNF-3 homologues, winged helix protein; NMR {Rattus
norvegicus} SCOP: a.4.5.14
Length = 109
Score = 224 bits (572), Expect = 1e-73
Identities = 94/103 (91%), Positives = 98/103 (95%)
Query: 143 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDC 202
+VKPPYSYIALITMAILQSP KKLTLSGICEFI +RFPYYREKFPAWQNSIRHNLSLNDC
Sbjct: 1 MVKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDC 60
Query: 203 FVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTP 245
FVKIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKR+KR
Sbjct: 61 FVKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKRFKRLQ 103
>2c6y_A Forkhead box protein K2; transcription regulation, DNA-binding
domain, forkhead transcription factors, interleukin
enhancer binding factor; 2.4A {Homo sapiens} SCOP:
a.4.5.14 PDB: 1jxs_A 2a3s_A 2d2w_A
Length = 111
Score = 222 bits (569), Expect = 4e-73
Identities = 53/108 (49%), Positives = 67/108 (62%)
Query: 133 DSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNS 192
+Q G+ S KPPYSY LI AI +P K+LTL+GI I +PYYR WQNS
Sbjct: 4 TGGQQMGRGSDSKPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNS 63
Query: 193 IRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKR 240
IRHNLSLN F+K+PR PGKG++W +DP +E +F +RR R
Sbjct: 64 IRHNLSLNRYFIKVPRSQEEPGKGSFWRIDPASESKLIEQAFRKRRPR 111
>1vtn_C HNF-3/FORK head DNA-recognition motif; protein-DNA complex, double
helix, transcription-DNA complex; HET: DNA; 2.50A {Homo
sapiens} PDB: 1d5v_A
Length = 102
Score = 221 bits (565), Expect = 2e-72
Identities = 64/98 (65%), Positives = 77/98 (78%)
Query: 145 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 204
KPPYSYI+LITMAI Q+P K LTLS I ++IM FPYYRE WQNSIRH+LS NDCFV
Sbjct: 3 KPPYSYISLITMAIQQAPGKMLTLSEIYQWIMDLFPYYRENQQRWQNSIRHSLSFNDCFV 62
Query: 205 KIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYK 242
K+ R P PGKG+YW L P + +MF+NG +LRR+KR+K
Sbjct: 63 KVARSPDKPGKGSYWALHPSSGNMFENGCYLRRQKRFK 100
>2hdc_A Protein (transcription factor); structure, dyanamics, genesis,
winged helix protein, protein/DNA complex; HET: DNA; NMR
{Rattus norvegicus} SCOP: a.4.5.14
Length = 97
Score = 220 bits (564), Expect = 2e-72
Identities = 92/97 (94%), Positives = 94/97 (96%)
Query: 144 VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCF 203
VKPPYSYIALITMAILQSP KKLTLSGICEFI +RFPYYREKFPAWQNSIRHNLSLNDCF
Sbjct: 1 VKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCF 60
Query: 204 VKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKR 240
VKIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKR
Sbjct: 61 VKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKR 97
>1kq8_A HFH-1, hepatocyte nuclear factor 3 forkhead homolog 1, winged;
winged helix protein, structure, transcription; NMR
{Rattus norvegicus} SCOP: a.4.5.14
Length = 100
Score = 209 bits (533), Expect = 8e-68
Identities = 57/98 (58%), Positives = 72/98 (73%), Gaps = 1/98 (1%)
Query: 145 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 204
KPPYSYIALITMAI S +LTL+ I E++M +FP++R + W+NS+RHNLSLNDCFV
Sbjct: 2 KPPYSYIALITMAIRDSAGGRLTLAEINEYLMGKFPFFRGSYTGWRNSVRHNLSLNDCFV 61
Query: 205 KIPREPGNP-GKGNYWTLDPMAEDMFDNGSFLRRRKRY 241
K+ R+P P GK NYW L+P +E F +G F RRR R
Sbjct: 62 KVLRDPSRPWGKDNYWMLNPNSEYTFADGVFRRRRYRL 99
>3g73_A Forkhead box protein M1; DNA-binding domain, forkhead transcription
factors, FOXM1, W helix; HET: DNA; 2.21A {Homo sapiens}
Length = 142
Score = 186 bits (473), Expect = 3e-58
Identities = 45/128 (35%), Positives = 62/128 (48%), Gaps = 5/128 (3%)
Query: 128 PGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK-F 186
PGP S + +PPYSY+A+I AI + K++TL I +I FPY++
Sbjct: 2 PGPSRPSASWQ-NSVSERPPYSYMAMIQFAINSTERKRMTLKDIYTWIEDHFPYFKHIAK 60
Query: 187 PAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPP 246
P W+NSIRHNLSL+D FV RE GK ++WT+ P A + P
Sbjct: 61 PGWKNSIRHNLSLHDMFV---RETSANGKVSFWTIHPSANRYLTLDQVFKPLDPGSPQLP 117
Query: 247 DFLLRDPH 254
+ L
Sbjct: 118 EHLESQQK 125
>2a07_F Forkhead box protein P2; double-helix, swapping, homodimer,
monomer, winged-helix, magnesium, transcription/DNA
complex; 1.90A {Homo sapiens} SCOP: a.4.5.14 PDB: 2as5_F
2kiu_A 3qrf_F
Length = 93
Score = 182 bits (465), Expect = 1e-57
Identities = 36/106 (33%), Positives = 56/106 (52%), Gaps = 13/106 (12%)
Query: 143 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDC 202
IV+PP++Y LI AI++S ++LTL+ I + F Y+R W+N++RHNLSL+ C
Sbjct: 1 IVRPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFAYFRRNAATWKNAVRHNLSLHKC 60
Query: 203 FVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDF 248
FV++ KG WT+D + +RR + P
Sbjct: 61 FVRVEN-----VKGAVWTVDE--------VEYQKRRSQKITGSPTL 93
>3coa_C Forkhead box protein O1; winged helix, forkhead domain, chromosomal
rearrangement; HET: DNA; 2.20A {Homo sapiens} PDB:
3co7_C* 2k86_A 2uzk_A
Length = 117
Score = 169 bits (430), Expect = 3e-52
Identities = 41/119 (34%), Positives = 58/119 (48%), Gaps = 10/119 (8%)
Query: 136 KQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK-----FPAWQ 190
K SY LIT AI S K+LTLS I E+++ PY+++K W+
Sbjct: 2 KSSSSRRNAWGNLSYADLITKAIESSAEKRLTLSQIYEWMVKSVPYFKDKGDSNSSAGWK 61
Query: 191 NSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFL 249
NSIRHNLSL+ F+++ E GK ++W L+P + +G RRR F
Sbjct: 62 NSIRHNLSLHSKFIRVQNE--GTGKSSWWMLNP---EGGKSGKSPRRRAASMDNNSKFA 115
>1e17_A AFX; DNA binding domain, winged helix; NMR {Homo sapiens} SCOP:
a.4.5.14
Length = 150
Score = 170 bits (431), Expect = 5e-52
Identities = 41/140 (29%), Positives = 64/140 (45%), Gaps = 10/140 (7%)
Query: 121 PTDGSISPGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFP 180
+ ++ G SY LI+ AI +P K+LTL+ I E+++ P
Sbjct: 16 RGSHMLEDPGAVTGPRKGGSRRNAWGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVP 75
Query: 181 YYREK-----FPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFL 235
Y+++K W+NSIRHNLSL+ F+K+ E GK ++W L+P + +G
Sbjct: 76 YFKDKGDSNSSAGWKNSIRHNLSLHSKFIKVHNEA--TGKSSWWMLNP---EGGKSGKAP 130
Query: 236 RRRKRYKRTPPDFLLRDPHA 255
RRR + L A
Sbjct: 131 RRRAASMDSSSKLLRGRSKA 150
>3bpy_A FORK head domain, forkhead transcription factor FOXO4, DNA binding
domain; forkhead BOX, winged helix; 1.87A {Homo sapiens}
SCOP: a.4.5.14
Length = 85
Score = 162 bits (413), Expect = 6e-50
Identities = 33/83 (39%), Positives = 51/83 (61%), Gaps = 7/83 (8%)
Query: 145 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPA-----WQNSIRHNLSL 199
SY LI+ AI +P K+LTL+ I E+++ PY+++K + W+NSIRHNLSL
Sbjct: 5 WGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSL 64
Query: 200 NDCFVKIPREPGNPGKGNYWTLD 222
+ F+K+ E GK ++W L+
Sbjct: 65 HSKFIKVHNEA--TGKSSWWMLN 85
>3l2c_A Forkhead box protein O4; winged helix, transcription-DNA COMP;
1.87A {Homo sapiens} PDB: 3co6_C*
Length = 110
Score = 161 bits (410), Expect = 3e-49
Identities = 35/109 (32%), Positives = 55/109 (50%), Gaps = 7/109 (6%)
Query: 123 DGSISPGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYY 182
+ ++ G SY LI+ AI +P K+LTL+ I E+++ PY+
Sbjct: 2 SHMLEDPGAVTGPRKGGSRRNAWGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYF 61
Query: 183 REK-----FPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAE 226
++K W+NSIRHNLSL+ F+K+ E GK ++W L+P
Sbjct: 62 KDKGDSNSSAGWKNSIRHNLSLHSKFIKVHNEA--TGKSSWWMLNPEGG 108
>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 = 41.2 bits (96), Expect = 7e-04
Identities = 62/386 (16%), Positives = 99/386 (25%), Gaps = 149/386 (38%)
Query: 13 HSPHLLP-QPHHTGPRTSFDSPLDLRG-----APHPGDMYLRGAP------------HPG 54
+ L F L++ + P YL P H
Sbjct: 191 SAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYV 250
Query: 55 DMCNLSSPSPSSEDDSDADINVESDDGDEQGM-------KSDDGDEQGMSNVRRNI---- 103
L +P ++ G QG+ ++D + +VR+ I
Sbjct: 251 VTAKLLGFTPGELRSY-----LKGATGHSQGLVTAVAIAETDSWESF-FVSVRKAITVLF 304
Query: 104 ---AEFHKHFSNCE---SDVNGCPTDGSISPGP----EGDSDKQ-----DGKNSIVKPPY 148
++ + N S + + P P + +Q + NS + P
Sbjct: 305 FIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHL-PAG 363
Query: 149 S--YIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKI 206
I+L+ K L +SG P S+ LN K
Sbjct: 364 KQVEISLV-----NGA-KNLVVSG---------------PPQ---SLYG---LNLTLRKA 396
Query: 207 PREPGNPGKGNYWTLD----PMAEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMASFL 262
G LD P +E RK F R FL
Sbjct: 397 KAPSG---------LDQSRIPFSE-----------RK------LKFSNR---------FL 421
Query: 263 G-SDPYHHGLLPHSLQHGGFSFMSP-LPPAVPLLPPSELARIQLGLNLLSNQSLPCKPVP 320
+ P+H S L PA L+ +L + + + + + PV
Sbjct: 422 PVASPFH----------------SHLLVPASDLI-NKDLVKNNV---SFNAKDIQI-PV- 459
Query: 321 LTSSSSRNTHIQKDKCSAVFSIDSLI 346
+T D SI I
Sbjct: 460 ------YDTFDGSDLRVLSGSISERI 479
Score = 30.0 bits (67), Expect = 1.7
Identities = 25/147 (17%), Positives = 46/147 (31%), Gaps = 31/147 (21%)
Query: 269 HGLLPHSLQHGGFSFMSPLPPAVPLLPPSELARIQLGLNL------LSNQSLPCKPVPLT 322
+ P +L HG + +P A + + Q L + P P L
Sbjct: 4 YSTRPLTLSHGSLEHVLLVPTA--SFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELV 61
Query: 323 SS-----SSRNTHIQKDKCSAVFSIDSLIGKNEFEKS----------AEKLDSDSEHSIS 367
SS ++ K + +L EFE A KL +++ ++
Sbjct: 62 GKFLGYVSSL---VEPSKVGQFDQVLNLC-LTEFENCYLEGNDIHALAAKLLQENDTTLV 117
Query: 368 KDK--CSAVFSIDSLIGK--NEFEKSA 390
K K + + + ++ SA
Sbjct: 118 KTKELIKNYITARIMAKRPFDKKSNSA 144
>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 = 30.3 bits (67), Expect = 0.61
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 6/25 (24%)
Query: 387 EKSA-EKLDSDSEHSISVNRSPDSA 410
EK A +KL + S+ + + DSA
Sbjct: 18 EKQALKKLQA----SLKL-YADDSA 37
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.1 bits (67), Expect = 0.86
Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 11/64 (17%)
Query: 348 KNEFEKSAEKLDSDSEHSISKDKCSAVFSIDSLIGKNEFEKS-AEKLDSDSEHSISVNRS 406
+ E K ++LD+ S+ + + A ++ E+ + +E++ E + NR
Sbjct: 91 REEQRKRLQELDAASKVMEQEWREKAKKDLE------EWNQRQSEQV----EKNKINNRI 140
Query: 407 PDSA 410
D A
Sbjct: 141 ADKA 144
>1sfe_A ADA O6-methylguanine-DNA methyltransferase; enzyme, nucleic acid
binding DNA repair protein, DNA-binding protein; 2.10A
{Escherichia coli} SCOP: a.4.2.1 c.55.7.1
Length = 180
Score = 28.7 bits (65), Expect = 2.6
Identities = 6/16 (37%), Positives = 7/16 (43%)
Query: 25 GPRTSFDSPLDLRGAP 40
T PLD+RG
Sbjct: 81 QRDTPLTLPLDIRGTA 96
>3a7n_A UDG, uracil-DNA glycosylase; UNG-UGI interactions, UNG-DNA complex,
citrate AS protein LI ligand binding, inhibitor design;
HET: FLC; 1.95A {Mycobacterium tuberculosis H37RV} PDB:
2zhx_A*
Length = 238
Score = 28.7 bits (65), Expect = 3.0
Identities = 12/41 (29%), Positives = 14/41 (34%), Gaps = 17/41 (41%)
Query: 262 LGSDPYH-----HGLLPHSLQHGGFSFMSPLPPAVPLLPPS 297
+G DPY GL FS + P V P S
Sbjct: 76 VGQDPYPTPGHAVGL--------SFS----VAPDVRPWPRS 104
>2owr_A UDG, uracil-DNA glycosylase; uracil-DNA glycosylase fold in the
core: 3 layers (A/B/A); HET: EPE; 2.30A {Vaccinia virus}
PDB: 2owq_A 3nt7_C
Length = 218
Score = 27.6 bits (62), Expect = 6.6
Identities = 14/76 (18%), Positives = 22/76 (28%), Gaps = 18/76 (23%)
Query: 221 LDPMAEDMFDNGSFLRRRKRYKRTPP--DFL--LRDPHAAAMASFLGSDPYH---HGLLP 273
+ + E + S+L R + P F L+ P G DPY G+
Sbjct: 23 MSQLVEFYNEVASWLLRDETS---PIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGV-- 77
Query: 274 HSLQHGGFSFMSPLPP 289
F +
Sbjct: 78 ------PFESPNFTKK 87
>4e4u_A Mandalate racemase/muconate lactonizing enzyme; mandelate racemase,
aldolase, structural genomics, biology; 1.35A
{Unidentified}
Length = 412
Score = 27.6 bits (62), Expect = 7.4
Identities = 14/80 (17%), Positives = 22/80 (27%), Gaps = 23/80 (28%)
Query: 170 GICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPG-------------NPGKG 216
I E IM+ ++ E + D ++ EPG P G
Sbjct: 331 LIQESIMTWGGFHAEVVK-------TPIRWEDGYIIPSNEPGLGIELDMDVVKRHTPYTG 383
Query: 217 NYWTLDPMAED--MFDNGSF 234
L M E + +
Sbjct: 384 ERLHL-QMGEHPVDVKDLAP 402
>2j8x_A Uracil-DNA glycosylase; hydrolase-inhibitor complex,
hydrolase/inhibitor complex, EB repair, lytic protein,
epstein-BARR virus; 2.3A {Epstein-barr virus} SCOP:
c.18.1.1
Length = 231
Score = 27.2 bits (61), Expect = 8.2
Identities = 14/40 (35%), Positives = 17/40 (42%), Gaps = 17/40 (42%)
Query: 262 LGSDPYH----HGLLPHSLQHGGFSFMSPLPPAVPLLPPS 297
LG DPYH +GL FS + P +PPS
Sbjct: 64 LGQDPYHGGQANGL--------AFS----VAYGFP-VPPS 90
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 0.133 0.404
Gapped
Lambda K H
0.267 0.0796 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,405,191
Number of extensions: 385195
Number of successful extensions: 603
Number of sequences better than 10.0: 1
Number of HSP's gapped: 586
Number of HSP's successfully gapped: 29
Length of query: 414
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 318
Effective length of database: 4,021,377
Effective search space: 1278797886
Effective search space used: 1278797886
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 (21.9 bits)
S2: 58 (26.0 bits)