RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10745
(197 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 = 98.2 bits (244), Expect = 7e-27
Identities = 41/55 (74%), Positives = 49/55 (89%)
Query: 119 HGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173
G VNQLGGVF+NGRPLP+ +R +IVE+A +G+RPC ISRQLRVSHGCVSKIL+R
Sbjct: 2 QGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNR 56
Score = 85.9 bits (212), Expect = 4e-22
Identities = 37/70 (52%), Positives = 52/70 (74%)
Query: 13 RRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNV 72
RY ETGS + GVIGGSKP++AT + + I YKR +P MF+WEIR++L+ EG+C +
Sbjct: 55 NRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTA 114
Query: 73 PSVSSINRYI 82
PSVS+I+R +
Sbjct: 115 PSVSAISRLV 124
>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 = 99.1 bits (246), Expect = 7e-27
Identities = 49/58 (84%), Positives = 52/58 (89%)
Query: 116 SRSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173
HGG+NQLGG FVNGRPLP+VVRQRIV+LAH GVRPCDISRQLRVSHGCVSKIL R
Sbjct: 7 RSGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISRQLRVSHGCVSKILGR 64
Score = 83.4 bits (205), Expect = 9e-21
Identities = 54/70 (77%), Positives = 58/70 (82%)
Query: 13 RRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNV 72
RYYETGS + GVIGGSKPKVAT VV+ I YKR+NPTMFAWEIRDRLLAEG+C D V
Sbjct: 63 GRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYKRQNPTMFAWEIRDRLLAEGVCDNDTV 122
Query: 73 PSVSSINRYI 82
PSVSSINR I
Sbjct: 123 PSVSSINRII 132
>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 = 97.2 bits (241), Expect = 4e-26
Identities = 53/60 (88%), Positives = 54/60 (90%)
Query: 114 VASRSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173
+ HGGVNQLGGVFVNGRPLPDVVRQRIVELAH GVRPCDISRQLRVSHGCVSKIL R
Sbjct: 12 TSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGR 71
Score = 85.2 bits (210), Expect = 2e-21
Identities = 55/70 (78%), Positives = 58/70 (82%)
Query: 13 RRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNV 72
RYYETGS K GVIGGSKPKVAT VV+ IA YKR+NPTMFAWEIRDRLLAE +C D V
Sbjct: 70 GRYYETGSIKPGVIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTV 129
Query: 73 PSVSSINRYI 82
PSVSSINR I
Sbjct: 130 PSVSSINRII 139
>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 = 47.6 bits (112), Expect = 3e-07
Identities = 8/50 (16%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 36 APVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNV----PSVSSINRY 81
A + + +E+P A ++ L I ++ V + S ++++
Sbjct: 14 AHQKAVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQH 63
>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 = 43.3 bits (101), Expect = 2e-05
Identities = 31/191 (16%), Positives = 58/191 (30%), Gaps = 28/191 (14%)
Query: 25 VIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDR---LLAEGICSQDNVPSVSSINRY 81
+I T + + S + E F E+ L I ++ PS+ + Y
Sbjct: 54 IIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTR-MY 112
Query: 82 ITYVPIGHGGVNQLGGVFVNGRPLP-DVVRQRIVASRSHGGV--NQLGG----VFVNGRP 134
I + V+ R P +RQ ++ R V + + G
Sbjct: 113 IEQRDRLYNDNQVFAKYNVS-RLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVAL--- 168
Query: 135 LPDVVRQRIVELAHNG------VRPCD-----ISRQLRVSHGCVSKILSRESNLHNYRLV 183
DV V+ + ++ C+ + ++ + SR + N +L
Sbjct: 169 --DVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLR 226
Query: 184 REEGCFELSDL 194
EL L
Sbjct: 227 IHSIQAELRRL 237
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU,
homeo, protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 42.3 bits (98), Expect = 3e-05
Identities = 6/44 (13%), Positives = 15/44 (34%), Gaps = 4/44 (9%)
Query: 42 IASYKRENPTMFAWEIRDRLLAEGIC----SQDNVPSVSSINRY 81
+ E+P A I+ + I + S ++++
Sbjct: 21 VDRMLSEDPWRAAKMIKGYMQQHNIPQREVVDVTGLNQSHLSQH 64
>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 = 37.7 bits (87), Expect = 6e-04
Identities = 10/50 (20%), Positives = 20/50 (40%)
Query: 132 GRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYR 181
G L D R ++ + V ++SR++ S C+ L + +
Sbjct: 4 GSALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGTSK 53
>3hef_A Gene 1 protein; bacteriophage SF6, terminase small subunit GP1,
GP1 octameric assembly, GP1 channel, DNA recognition,
DNA packaging; 1.65A {Enterobacteria phage SF6}
Length = 143
Score = 29.3 bits (65), Expect = 0.52
Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 8/45 (17%)
Query: 46 KRENPTMFAWEIRDR---LLAEG-----ICSQDNVPSVSSINRYI 82
K P+ + E+ D LL+ G +C + +P S++ R++
Sbjct: 9 KAGRPSDYMPEVADDICSLLSSGESLLKVCKRPGMPDKSTVFRWL 53
>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 = 29.1 bits (65), Expect = 0.63
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 136 PDVVRQRIVELAHNGVRPCDISRQLRVSHG 165
+ V ++IV+ A G+ P I LR +HG
Sbjct: 30 SESVIEQIVKYARKGLTPSQIGVLLRDAHG 59
>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription
factor DNA complex, pore, stem cells; HET: DNA; 2.80A
{Mus musculus} PDB: 1ocp_A
Length = 155
Score = 28.9 bits (64), Expect = 0.63
Identities = 20/120 (16%), Positives = 38/120 (31%), Gaps = 27/120 (22%)
Query: 53 FAWEIRDRLLAEGICSQD----------NVPSVSSINRY----------ITYVPIGH--- 89
FA ++ + + G D V S ++I+R+ P+
Sbjct: 15 FAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEALQLSLKNMSKLRPLLEKWV 74
Query: 90 -GGVNQLGGVFVNGRPLPDVVRQRIVASRSHGGVNQLGGVFVNGRPLPDVVRQRIVELAH 148
N ++ R+R S + L +F+ P P Q+I +A+
Sbjct: 75 EEADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLK-SPKPS--LQQITHIAN 131
>2xzm_O RPS13E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_O 1ysh_E 3jyv_O* 1s1h_O
Length = 153
Score = 28.3 bits (63), Expect = 0.95
Identities = 12/30 (40%), Positives = 14/30 (46%)
Query: 136 PDVVRQRIVELAHNGVRPCDISRQLRVSHG 165
P V V+LA G+ P I LR HG
Sbjct: 32 PSTVVDLSVKLAKKGLTPSQIGVILRDQHG 61
>2qtw_B Proprotein convertase subtilisin/kexin type 9; coronary heart
disease, hypercholest low density lipoprotein receptor,
autocatalytic cleavage; HET: NAG; 1.90A {Homo sapiens}
PDB: 3m0c_B 3bps_A 3gcw_A 3gcx_A 3p5b_A 3p5c_A 2pmw_B
3h42_B 2w2n_A 2w2m_A 2w2p_A 2w2q_A 2xtj_A 2w2o_A
Length = 546
Score = 29.1 bits (65), Expect = 1.0
Identities = 21/128 (16%), Positives = 34/128 (26%), Gaps = 10/128 (7%)
Query: 34 ATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYIT-----YVP-- 86
A A V A P + E+R RL+ N R +T +P
Sbjct: 236 AAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPS 295
Query: 87 IGHGGVNQLGGVFVNGRPLPDVVRQRIVASRSHGGVNQLGGVFVNGRPL---PDVVRQRI 143
G + P + I + +G+ + ++
Sbjct: 296 THGAGWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKL 355
Query: 144 VELAHNGV 151
V AHN
Sbjct: 356 VCRAHNAF 363
>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 = 28.5 bits (63), Expect = 1.6
Identities = 31/205 (15%), Positives = 57/205 (27%), Gaps = 71/205 (34%)
Query: 1 PTPQLLTPFLCPRRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFA------ 54
T + T L + Y + K + + + A+ N + A
Sbjct: 113 DTTLVKTKELI-KNYITA----RIMAKRPFDKKSNSALFRAVGE---GNAQLVAIFGGQG 164
Query: 55 -----W-EIRDRLLAEGICSQDNVPSVSSINRYITYVPIGHGGVNQLGGVFVNGRPLPDV 108
+ E+RD Y TY + V L + + L ++
Sbjct: 165 NTDDYFEELRDL--------------------YQTYHVL----VGDL--IKFSAETLSEL 198
Query: 109 VRQRIVASRSHGGVNQLGGVFVNGRPLPDV--------------VRQRIVELAH------ 148
+R + A + + N PD V Q LAH
Sbjct: 199 IRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQ----LAHYVVTAK 254
Query: 149 -NGVRPCDISRQLRVSHGCVSKILS 172
G P ++ L+ + G +++
Sbjct: 255 LLGFTPGELRSYLKGATGHSQGLVT 279
>2p4e_P Proprotein convertase subtilisin/kexin type 9; protease, LDL
receptor, LDL, endocytosis, hydrol; 1.98A {Homo sapiens}
Length = 692
Score = 28.4 bits (63), Expect = 1.6
Identities = 21/128 (16%), Positives = 34/128 (26%), Gaps = 10/128 (7%)
Query: 34 ATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYIT-----YVP-- 86
A A V A P + E+R RL+ N R +T +P
Sbjct: 388 AAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPS 447
Query: 87 IGHGGVNQLGGVFVNGRPLPDVVRQRIVASRSHGGVNQLGGVFVNGRPL---PDVVRQRI 143
G + P + I + +G+ + ++
Sbjct: 448 THGAGWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKL 507
Query: 144 VELAHNGV 151
V AHN
Sbjct: 508 VCRAHNAF 515
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex,
helix-turn-helix (HTH), DNA-binding, homeobox, nucleus,
transcription regulation; 2.51A {Homo sapiens}
Length = 151
Score = 27.3 bits (60), Expect = 2.0
Identities = 14/93 (15%), Positives = 31/93 (33%), Gaps = 7/93 (7%)
Query: 53 FAWEIRDRLLAEGICSQDNV---PSVSSINRYITYVPIGHGGVNQLGGVFVNGRPLPDVV 109
FA + R L+ G+ +Q V + + Y + I + + + L V+
Sbjct: 9 FAKNFKIRRLSLGL-TQTQVGQAMTATEGPAY-SQSAISRFEKLDIT--PKSAQKLKPVL 64
Query: 110 RQRIVASRSHGGVNQLGGVFVNGRPLPDVVRQR 142
+ + + Q + G ++R
Sbjct: 65 EKWLNEAELRNQEGQQNLMEFVGGEPSKKRKRR 97
>1qw9_A Arabinosidase, alpha-L-arabinofuranosidase; hydrolase; HET: KHP;
1.20A {Geobacillus stearothermophilus} SCOP: b.71.1.2
c.1.8.3 PDB: 1pz2_A* 1qw8_A* 1pz3_A
Length = 502
Score = 28.0 bits (61), Expect = 2.5
Identities = 24/94 (25%), Positives = 37/94 (39%), Gaps = 12/94 (12%)
Query: 74 SVSSINRYITYVPIGHGGVNQLGGVFVNGRPLPDV--VRQRIVA---------SRSHGGV 122
++ I++ I I H G GG++ G P D RQ ++ R GG
Sbjct: 15 KIAEIDKRIYGSFIEHLGRAVYGGIYEPGHPQADENGFRQDVIELVKELQVPIIRYPGGN 74
Query: 123 NQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDI 156
G + +G P R R ++LA V +I
Sbjct: 75 FVSGYNWEDGVG-PKEQRPRRLDLAWKSVETNEI 107
>1yvw_A PRA-PH, phosphoribosyl-ATP pyrophosphatase; helix bundle, histidine
biosynthesis, structural genomics, PSI, protein
structure initiative; 2.60A {Bacillus cereus} SCOP:
a.204.1.4
Length = 115
Score = 26.5 bits (59), Expect = 2.7
Identities = 8/33 (24%), Positives = 17/33 (51%)
Query: 143 IVELAHNGVRPCDISRQLRVSHGCVSKILSRES 175
V LA + D+ R+++ +G +S++ R
Sbjct: 71 FVLLAEKNIALEDVMREVKERNGKLSRVGDRRE 103
>1ctt_A Cytidine deaminase; hydrolase; HET: DHZ; 2.20A {Escherichia coli}
SCOP: c.97.1.1 c.97.1.1 PDB: 1aln_A* 1af2_A* 1ctu_A*
Length = 294
Score = 27.3 bits (60), Expect = 3.6
Identities = 9/36 (25%), Positives = 14/36 (38%)
Query: 131 NGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGC 166
G PD+ R + E A + D + + GC
Sbjct: 250 KGYDYPDIQRAVLAEKADAPLIQWDATSATLKALGC 285
>2csw_A Ubiquitin ligase protein RNF8; 11-stranded beta sandwich, ring
finger protein 8, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: b.26.1.2
Length = 145
Score = 25.7 bits (56), Expect = 8.4
Identities = 14/67 (20%), Positives = 20/67 (29%), Gaps = 6/67 (8%)
Query: 97 GVFVNGRPLPDVVRQRIVASRSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDI 156
GV++N L + I G QLG N + E + PC
Sbjct: 84 GVWLNRARLEPLRVYSI----HQGDYIQLGVPLENKE--NAEYEYEVTEEDWETIYPCLS 137
Query: 157 SRQLRVS 163
+ S
Sbjct: 138 PKSGPSS 144
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 0.424
Gapped
Lambda K H
0.267 0.0612 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,182,527
Number of extensions: 194302
Number of successful extensions: 503
Number of sequences better than 10.0: 1
Number of HSP's gapped: 500
Number of HSP's successfully gapped: 27
Length of query: 197
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 108
Effective length of database: 4,216,824
Effective search space: 455416992
Effective search space used: 455416992
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: 55 (25.2 bits)