RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1898
(230 letters)
>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX,
paired domain, DNA-binding protein, gene regulation/DNA
complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP:
a.4.1.5
Length = 128
Score = 167 bits (425), Expect = 1e-53
Identities = 100/124 (80%), Positives = 120/124 (96%), Gaps = 1/124 (0%)
Query: 86 GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145
VNQLGGVFINGRPLPN+IRLKIVEMAA G+RPCVISRQLRVSHGCVSKILNRYQETGSI
Sbjct: 4 RVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSI 63
Query: 146 RPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
RPGVIGGSKPR+ATP++E RIEEYK+++PG+FSWEIR++L++ +G+CD+++APSVS+ISR
Sbjct: 64 RPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIR-EGVCDRSTAPSVSAISR 122
Query: 206 LLRG 209
L+RG
Sbjct: 123 LVRG 126
>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription
factor, transcription/DNA complex; 2.25A {Homo sapiens}
SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A
Length = 149
Score = 165 bits (418), Expect = 2e-52
Identities = 86/126 (68%), Positives = 106/126 (84%), Gaps = 1/126 (0%)
Query: 84 SHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETG 143
GVNQLGGVF+NGRPLP+ +R +IVE+A GVRPC ISRQLRVSHGCVSKIL RY ETG
Sbjct: 17 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETG 76
Query: 144 SIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSI 203
SI+PGVIGGSKP+VATP V ++I EYK+ NP +F+WEIRDRL+ + +CD ++ PSVSSI
Sbjct: 77 SIKPGVIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLA-ERVCDNDTVPSVSSI 135
Query: 204 SRLLRG 209
+R++R
Sbjct: 136 NRIIRT 141
>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple
frequency, 3D NMR, induced FIT, alternative splicing,
developmental protein; NMR {Homo sapiens}
Length = 159
Score = 163 bits (412), Expect = 2e-51
Identities = 84/124 (67%), Positives = 105/124 (84%), Gaps = 1/124 (0%)
Query: 86 GVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145
G+NQLGG F+NGRPLP +R +IV++A GVRPC ISRQLRVSHGCVSKIL RY ETGSI
Sbjct: 12 GLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSI 71
Query: 146 RPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205
RPGVIGGSKP+VATP V ++I +YK+ NP +F+WEIRDRL+ +G+CD ++ PSVSSI+R
Sbjct: 72 RPGVIGGSKPKVATPKVVEKIGDYKRQNPTMFAWEIRDRLLA-EGVCDNDTVPSVSSINR 130
Query: 206 LLRG 209
++R
Sbjct: 131 IIRT 134
>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 = 70.3 bits (171), Expect = 3e-15
Identities = 7/63 (11%), Positives = 21/63 (33%), Gaps = 3/63 (4%)
Query: 160 PDVEKRIEEYKKTNPGIFSWEIRDRLVKQ---DGICDKNSAPSVSSISRLLRGGRRDDCD 216
+ +E + +P + ++ L + + + S +S+ L G
Sbjct: 14 AHQKAVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQ 73
Query: 217 RKN 219
++
Sbjct: 74 KRA 76
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 56.9 bits (136), Expect = 4e-10
Identities = 6/55 (10%), Positives = 18/55 (32%), Gaps = 3/55 (5%)
Query: 160 PDVEKRIEEYKKTNPGIFSWEIRDRLVK---QDGICDKNSAPSVSSISRLLRGGR 211
+ ++ +P + I+ + + + + S +S+ L G
Sbjct: 15 AEQRAEVDRMLSEDPWRAAKMIKGYMQQHNIPQREVVDVTGLNQSHLSQHLNKGT 69
>1u78_A TC3 transposase, transposable element TC3 transposase; transposon
DNA, bipartite DNA-binding, HTH- motif, DNA binding
protein/DNA complex; 2.69A {Caenorhabditis elegans}
SCOP: a.4.1.2 a.4.1.2
Length = 141
Score = 41.2 bits (96), Expect = 5e-05
Identities = 17/112 (15%), Positives = 39/112 (34%), Gaps = 14/112 (12%)
Query: 97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR 156
G L + R ++ M V +SR++ S C+ L G+ + + +
Sbjct: 4 GSALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGTSKR----APRRK 59
Query: 157 VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLR 208
+ E+ + + +IR+ L + S +I +++
Sbjct: 60 ALSVRDERNVIRAASNSCKTAR-DIRNEL---------QLSASKRTILNVIK 101
Score = 26.9 bits (59), Expect = 3.8
Identities = 25/137 (18%), Positives = 44/137 (32%), Gaps = 20/137 (14%)
Query: 53 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGV--------NQLGGVFINGRPLPNHI 104
G L + R ++ M V +SR++ S G R +
Sbjct: 4 GSALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGTSKRAPRRKALSV 63
Query: 105 RLK--IVEMAAAGVRPCVISRQLRVSHG---CVSKILNRYQETGSIRPGVIGGSKPRVAT 159
R + ++ A+ C +R +R ILN + +G I P ++
Sbjct: 64 RDERNVIRAAS---NSCKTARDIRNELQLSASKRTILNVIKRSGVIV-RQKLRPAPLLSA 119
Query: 160 PDVEKRIE---EYKKTN 173
KR+E T+
Sbjct: 120 DHKLKRLEFAKNNMGTH 136
>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 = 40.2 bits (93), Expect = 3e-04
Identities = 33/263 (12%), Positives = 78/263 (29%), Gaps = 82/263 (31%)
Query: 5 RMNQLGGVFINGRPLPNHIRLKIVEMAAAGRGSSC-----------QGRMNQLGGVF-IN 52
+ V I+G + G G + Q +M+ +F +N
Sbjct: 146 ELRPAKNVLIDG-------------VL--GSGKTWVALDVCLSYKVQCKMD--FKIFWLN 188
Query: 53 -GRPLPNHIRLKIVEMAAAGVRPCVISRQ---LRVSHGVNQLGGV---FINGRPLPN--- 102
L++++ + P SR + ++ + + +P N
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL 248
Query: 103 ---HIR-LKIVEMAAAGVRPCVISRQLRVSHGCVSKIL--NRYQETGSIRPGVIGGSKPR 156
+++ K + C KIL R++ + + +
Sbjct: 249 VLLNVQNAKAWNA---------------FNLSC--KILLTTRFK---QVTDFLSAATTTH 288
Query: 157 VATPDVEKRIEEYKKTNPGIFS-W-EIR-DRLVKQDGICDKNSAP-SVSSISRLLRGG-- 210
++ + + + + + R L ++ + N P +S I+ +R G
Sbjct: 289 ISLDHHSMTLTPDEVK--SLLLKYLDCRPQDLPRE--VLTTN--PRRLSIIAESIRDGLA 342
Query: 211 -----RRDDCDRKNHSIDGILEQ 228
+ +CD+ I+ L
Sbjct: 343 TWDNWKHVNCDKLTTIIESSLNV 365
>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 = 28.8 bits (63), Expect = 1.0
Identities = 9/39 (23%), Positives = 15/39 (38%), Gaps = 15/39 (38%)
Query: 163 EKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVS 201
EK + KK + +L D SAP+++
Sbjct: 18 EK--QALKKL-------QASLKLYADD------SAPALA 41
>3dfr_A Dihydrofolate reductase; oxido-reductase; HET: NDP MTX; 1.70A
{Lactobacillus casei} SCOP: c.71.1.1 PDB: 1ao8_A*
1bzf_A* 1dis_A* 1diu_A* 1lud_A* 2hm9_A* 2hqp_A* 2l28_A
2lf1_A*
Length = 162
Score = 27.9 bits (63), Expect = 2.1
Identities = 11/64 (17%), Positives = 19/64 (29%), Gaps = 19/64 (29%)
Query: 95 INGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSH-GC-----VSKILNRYQETGSIRPG 148
RPLP R + V++ Q G V+ + ++
Sbjct: 49 FPKRPLPE--RTNV-----------VLTHQEDYQAQGAVVVHDVAAVFAYAKQHLDQELV 95
Query: 149 VIGG 152
+ GG
Sbjct: 96 IAGG 99
>2nq5_A 5-methyltetrahydropteroyltriglutamate-- homocysteine
methyltransferase; structural genomics, target 6426D,
PSI; 1.90A {Streptococcus mutans} PDB: 3l7s_A 3l7r_A
3t0c_A
Length = 755
Score = 27.5 bits (61), Expect = 4.1
Identities = 16/50 (32%), Positives = 20/50 (40%), Gaps = 1/50 (2%)
Query: 120 VISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPD-VEKRIEE 168
VIS + SHG + + I GV PRV T + V IE
Sbjct: 652 VISIETSRSHGDIIESFETAVYPLGIGLGVYDIHSPRVPTKEEVVANIER 701
>3uvj_A Guanylate cyclase soluble subunit alpha-3; nitric oxide, structural
genomics, structural genomics conso SGC, CGMP
biosynthesis; 2.08A {Homo sapiens}
Length = 225
Score = 27.3 bits (61), Expect = 4.3
Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 14/69 (20%)
Query: 91 GGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKI---LNRYQETGSIRP 147
GG+ H +I MA + ++ HG K+ L+ +GS+
Sbjct: 71 GGLHKES---DTHAV-QIALMALKMMELS---DEVMSPHGEPIKMRIGLH----SGSVFA 119
Query: 148 GVIGGSKPR 156
GV+G PR
Sbjct: 120 GVVGVKMPR 128
>3u5c_N S27A, YS15, 40S ribosomal protein S13; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_O 3o30_G 3o2z_G 3u5g_N 3iz6_O
3jyv_O* 1ysh_E 1s1h_O
Length = 151
Score = 26.8 bits (59), Expect = 4.8
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 57 PNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGV 93
+ +IV+ A G+ P I LR +HGV Q +
Sbjct: 30 SESVIEQIVKYARKGLTPSQIGVLLRDAHGVTQARVI 66
>2xzm_O RPS13E; ribosome, translation; 3.93A {Tetrahymena thermophila}
PDB: 2xzn_O 1ysh_E 3jyv_O* 1s1h_O
Length = 153
Score = 25.6 bits (56), Expect = 9.5
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 57 PNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGV 93
P+ + V++A G+ P I LR HG+ Q+ +
Sbjct: 32 PSTVVDLSVKLAKKGLTPSQIGVILRDQHGIPQVRFL 68
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
0.321 0.140 0.419
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,717,932
Number of extensions: 232804
Number of successful extensions: 618
Number of sequences better than 10.0: 1
Number of HSP's gapped: 613
Number of HSP's successfully gapped: 25
Length of query: 230
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 140
Effective length of database: 4,188,903
Effective search space: 586446420
Effective search space used: 586446420
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 (21.8 bits)
S2: 56 (25.3 bits)