RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9595
(232 letters)
>3dxt_A JMJC domain-containing histone demethylation PROT; JMJD2D, histone
demethylase, H3K9, jumonji domain-CONT protein 2D,
oxidoreductase; 1.80A {Homo sapiens} PDB: 3dxu_A*
2w2i_A*
Length = 354
Score = 146 bits (369), Expect = 2e-42
Identities = 86/175 (49%), Positives = 118/175 (67%), Gaps = 4/175 (2%)
Query: 57 STIKTLLPVKQERKHEIMVFRPTYEEFKDFSKFITYMESQGAHKAGLAKVIPPPEWVPRK 116
T+K+ Q IM+F PT EEF DF K+I YMESQGAH+AGLAK+IPP EW R+
Sbjct: 2 ETMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARE 61
Query: 117 SGYSLDSSIGDMSIPAPICQVVTGKQGLYQQINIQKRQMTVREYGAMANKPRYATPKHFD 176
+ ++ ++ I P+ QV +G+ G++ Q + +K+ MTV EY +AN +Y TP H +
Sbjct: 62 TYDNIS----EILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQN 117
Query: 177 YEDLERKYWKNITYVSPIYGADVSGSITDEDVNVWNINHLGTILDYVNEDYGISI 231
+EDLERKYWKN Y SPIYGAD+SGS+ DE+ WN+ HLGTI D + ++ G+ I
Sbjct: 118 FEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVI 172
>2ox0_A JMJC domain-containing histone demethylation PROT; double-stranded
beta helix, demethylase, oxygenase, SGC, STR genomics,
structural genomics consortium, oxidoreductase; HET: MLY
ALY OGA; 1.95A {Homo sapiens} PDB: 2oq7_A* 2os2_A*
2ot7_A* 2oq6_A* 2vd7_A* 2ybk_A* 2ybp_A* 2ybs_A* 3njy_A*
3pdq_A* 3u4s_A* 2p5b_A* 2q8c_A* 2q8d_A* 2q8e_A* 2gp5_A*
2gp3_A* 2wwj_A* 2pxj_A* 2xml_A*
Length = 381
Score = 141 bits (355), Expect = 2e-40
Identities = 90/165 (54%), Positives = 122/165 (73%), Gaps = 4/165 (2%)
Query: 67 QERKHEIMVFRPTYEEFKDFSKFITYMESQGAHKAGLAKVIPPPEWVPRKSGYSLDSSIG 126
IM F PT EEF++FS++I Y+ESQGAH+AGLAKV+PP EW PR S +D
Sbjct: 30 LNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDID---- 85
Query: 127 DMSIPAPICQVVTGKQGLYQQINIQKRQMTVREYGAMANKPRYATPKHFDYEDLERKYWK 186
D+ IPAPI Q+VTG+ GL+ Q NIQK+ MTVRE+ +AN +Y TP++ ++E+LERKYWK
Sbjct: 86 DLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWK 145
Query: 187 NITYVSPIYGADVSGSITDEDVNVWNINHLGTILDYVNEDYGISI 231
N+T+ PIYGADV+G++ ++ V+ WNI L TILD V ++ GI+I
Sbjct: 146 NLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITI 190
>3opt_A DNA damage-responsive transcriptional repressor R; RPH1, histone
demethylase, catalytic core, oxidoreductase; HET: DNA
AKG; 2.20A {Saccharomyces cerevisiae} PDB: 3opw_A*
Length = 373
Score = 118 bits (295), Expect = 1e-31
Identities = 49/205 (23%), Positives = 82/205 (40%), Gaps = 49/205 (23%)
Query: 72 EIMVFRPTYEEFKDFSKFITYMESQGAHKAGLAKVIPPPEWVPRKSGYSLDSSIGDMSIP 131
+ VF+PTYE+F+DF + + G K+G+ KVIPP EW + ++ + I
Sbjct: 13 GVPVFKPTYEQFEDFYAYCKAINKYGM-KSGVVKVIPPKEWKDKLDLPYSAETLQKIKIK 71
Query: 132 APICQVVTGKQGLYQQINIQ---------------------------------------- 151
+PI Q ++G +GL+ N++
Sbjct: 72 SPIQQHISGNKGLFMVQNVEKNKTYNIIQWKDLSKDYVPPEDPKARRNSRKGSVSKSTKL 131
Query: 152 -----KRQMTVREYGAMANKPR---YATPKHFDYEDLERKYWKNITYVSPIYGADVSGSI 203
+ + ++ + + LE YWK + + +P+YGAD GSI
Sbjct: 132 KLKNFESSFNIDDFEQFRTEYTIDLSDFQNTERLKFLEEYYWKTLNFTTPMYGADTPGSI 191
Query: 204 TDEDVNVWNINHLGTILDYVNEDYG 228
E +NVWN+ L ILD++
Sbjct: 192 FPEGLNVWNVAKLPNILDHMETKVP 216
>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 = 35.8 bits (82), Expect = 0.011
Identities = 44/232 (18%), Positives = 75/232 (32%), Gaps = 90/232 (38%)
Query: 36 KKTKVVKEKAESGVQ-----EEGEVKSTIKT---LLPVKQERKHEIMVFRPTYEEFKDFS 87
K K+ KE E E+G + +T T L + E F
Sbjct: 1702 KTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLM------EKAAFE---------- 1745
Query: 88 KFITYMESQG-----AHKAGLAKVIPPPEWVPRKS-G-YS-LDSSIGDMSIPAPICQVVT 139
++S+G A AG S G Y+ L S MSI + + +VV
Sbjct: 1746 ----DLKSKGLIPADATFAGH-------------SLGEYAALASLADVMSIESLV-EVVF 1787
Query: 140 GKQGLYQQINIQKRQMTVREYGAMANKPRYATPKHFDYEDLERK---------------- 183
+G+ Q+ + + ++ YG +A P F E L+
Sbjct: 1788 -YRGMTMQVAVPRDELGRSNYGMIAINPG-RVAASFSQEALQYVVERVGKRTGWLVEIVN 1845
Query: 184 YWKNI---TYVSPIYGADVSGSITDEDVNVWNINHLGTILDYVNEDYGISID 232
Y N+ YV +G + ++ + +L+++ ID
Sbjct: 1846 Y--NVENQQYV-------AAGDLRA-------LDTVTNVLNFIKLQ---KID 1878
Score = 31.6 bits (71), Expect = 0.23
Identities = 27/116 (23%), Positives = 43/116 (37%), Gaps = 38/116 (32%)
Query: 96 QGAHKAG----------LAKVIPPPEWVPRKSGYSLDS---SIGDMSIPAPICQVV--TG 140
QG+ + G A+ + W R + D+ SI D+ I P+ + G
Sbjct: 1624 QGSQEQGMGMDLYKTSKAAQDV----W-NRADNHFKDTYGFSILDIVINNPVNLTIHFGG 1678
Query: 141 KQGLYQQINIQKRQMTVRE-YGAMANKPRYATPKHFDYEDLERKYWKNITYVSPIY 195
++G ++I RE Y AM + T D + K +K I S Y
Sbjct: 1679 EKG--KRI---------RENYSAMI----FETIV--DGKLKTEKIFKEINEHSTSY 1717
>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 = 34.1 bits (77), Expect = 0.041
Identities = 26/172 (15%), Positives = 49/172 (28%), Gaps = 66/172 (38%)
Query: 54 EVKSTIKTLLPVKQERKHEIM-----VFRPTY--EEFKDFSKF-----IT---------Y 92
+ +T V ++ I+ V P + F S F I
Sbjct: 339 DGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFD 398
Query: 93 MESQGA-------HKAGLAKVIPPPEWVPRKSGYSLDSSIGDMSIPAPICQVVTGKQGLY 145
+ HK L + + P++S S+ +Y
Sbjct: 399 VIKSDVMVVVNKLHKYSLVE-----KQ-PKESTISIP--------------------SIY 432
Query: 146 QQINIQKRQMTVREYGAMANK--PRYATPKHFDYEDL----ERKYWKN-ITY 190
++ ++ A+ Y PK FD +DL +Y+ + I +
Sbjct: 433 LELKVKLENEY-----ALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH 479
>3iz5_D 60S ribosomal protein L4 (L4P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_D
Length = 405
Score = 28.7 bits (63), Expect = 1.8
Identities = 14/83 (16%), Positives = 27/83 (32%), Gaps = 14/83 (16%)
Query: 9 EPSPPAKKKTKAAATGKGAKKKPRTPSKKTKVVKEKAESGVQEEGEVKSTIKTLLPVKQE 68
P +K A K + K + + + V+ G+
Sbjct: 334 NPYFGTARKMATLAEAARIKARKEKLDSKRTKLSPEEAAKVKAAGK-------------- 379
Query: 69 RKHEIMVFRPTYEEFKDFSKFIT 91
++ M+ Y EF +FSK++
Sbjct: 380 AWYKTMISDSDYAEFDNFSKWLG 402
>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling
protein; 2.85A {Arabidopsis thaliana}
Length = 338
Score = 28.4 bits (63), Expect = 1.8
Identities = 21/110 (19%), Positives = 39/110 (35%), Gaps = 5/110 (4%)
Query: 112 WVPRKSGYSLDSSIGDMSIP--APICQVVTGKQGLYQQINIQKRQMTVREYGAMANKPRY 169
V + Y + + ++P A + V + + MTV E A++ +
Sbjct: 125 HVGWELAYGKEGNFSFPNVPPMADLLYEVEVIGFDETKEGKARSDMTVEERIGAADRRKM 184
Query: 170 ATPKHF---DYEDLERKYWKNITYVSPIYGADVSGSITDEDVNVWNINHL 216
F E+ ++Y I Y+ + + G D + V N HL
Sbjct: 185 DGNSLFKEEKLEEAMQQYEMAIAYMGDDFMFQLYGKYQDMALAVKNPCHL 234
>1kxf_A Sindbis virus capsid protein; chymotrypsin-like serine proteinase,
wild type, viral protein; 2.38A {Sindbis virus} SCOP:
b.47.1.3 PDB: 1ld4_A 3j0f_A
Length = 264
Score = 28.2 bits (62), Expect = 1.9
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 2/59 (3%)
Query: 10 PSPPAKKKTKAAATGKGAKKKPRTPSKKTKVVKEKAESGVQEEGEVKSTIKTLLPVKQE 68
P PP ++K +A KK KK + K + G ++ +K L VK E
Sbjct: 65 PRPPPRQKKQAPKQPPKPKKPKPQEKKKKQ--PAKTKPGKRQRMALKLEADRLFDVKNE 121
>4ask_A Lysine-specific demethylase 6B; oxidoreductase, KDM6B, GSK-J1,
inhibitor, lysine specific HI demethylase; HET: K0I;
1.86A {Homo sapiens} PDB: 2xue_A*
Length = 510
Score = 27.5 bits (60), Expect = 4.6
Identities = 27/220 (12%), Positives = 56/220 (25%), Gaps = 26/220 (11%)
Query: 1 GASSSEDFEPSPPAKKKTKAAATGKGAKKKPRTPSKKTKVVKEKAESGVQEEGEVKSTIK 60
G P+ K K K P TPS + ++ + +
Sbjct: 14 GKFRESYLSPAQSVKPKINTEEKLPREKLNPPTPSIYLESKRDAFSPVLLQ--------- 64
Query: 61 TLLPVKQERKHEIMVFRPTYEEFK-DFSKFITYMESQGAHKAGLAKVIPPPEWVPRKSGY 119
+ ++ I V R + + F T + + + + V + S
Sbjct: 65 ----FCTDPRNPITVIRGLAGSLRLNLGLFSTKTLVEASGE----HTVEVRTQVQQPSDE 116
Query: 120 SLDSSIGDMSIPAPICQVVTGKQGLYQQINIQKRQMTVREYGAMANKPRYATPKHFDYED 179
+ D + G I Y Q Q +++E + + + + D
Sbjct: 117 NWDLT-GTRQIWPCESSRSHTTIAKYAQYQASSFQESLQEE-------KESEDEESEEPD 168
Query: 180 LERKYWKNITYVSPIYGADVSGSITDEDVNVWNINHLGTI 219
+ + G+ D L +
Sbjct: 169 STTGTPPSSAPDPKNHHIIKFGTNIDLSDAKRWKPQLQEL 208
>2xcl_A Phosphoribosylamine--glycine ligase; GAR-SYN, ATP-grAsp, metal
binding; HET: ANP; 2.10A {Bacillus subtilis} PDB:
2xd4_A*
Length = 422
Score = 27.0 bits (61), Expect = 5.0
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 10/42 (23%)
Query: 69 RKHEIMVFRPT--YEEFKDFSKFITYMESQGAH---KA-GLA 104
+K++I PT YE F F + Y++ +GA KA GLA
Sbjct: 111 KKYDI----PTAEYETFTSFDEAKAYVQEKGAPIVIKADGLA 148
>2yrx_A Phosphoribosylglycinamide synthetase; glycinamide ribonucleotide
synthetase, GAR synthetase; HET: AMP; 1.90A {Geobacillus
kaustophilus} PDB: 2yrw_A* 2ys6_A* 2ys7_A
Length = 451
Score = 27.1 bits (61), Expect = 5.6
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 10/42 (23%)
Query: 69 RKHEIMVFRPT--YEEFKDFSKFITYMESQGAH---KA-GLA 104
+K+ I PT + F + + Y+E +GA KA GLA
Sbjct: 132 KKYGI----PTADHAAFTSYEEAKAYIEQKGAPIVIKADGLA 169
>2yw2_A Phosphoribosylamine--glycine ligase; glycinamide ribonucleotide
synthetase, GAR synthetase, ATP B purine nucleotide
biosynthetic pathway; HET: ATP; 1.80A {Aquifex aeolicus}
PDB: 2yya_A
Length = 424
Score = 27.0 bits (61), Expect = 5.8
Identities = 19/42 (45%), Positives = 22/42 (52%), Gaps = 10/42 (23%)
Query: 69 RKHEIMVFRPT--YEEFKDFSKFITYMESQGAH---KA-GLA 104
+K+ I PT YE F DF K Y+E GA KA GLA
Sbjct: 111 KKYGI----PTARYEVFTDFEKAKEYVEKVGAPIVVKADGLA 148
>1vkz_A Phosphoribosylamine--glycine ligase; TM1250, structural GENO JCSG,
protein structure initiative, PSI, joint center for S
genomics; 2.30A {Thermotoga maritima} SCOP: b.84.2.1
c.30.1.1 d.142.1.2
Length = 412
Score = 27.1 bits (61), Expect = 6.1
Identities = 9/42 (21%), Positives = 16/42 (38%), Gaps = 10/42 (23%)
Query: 69 RKHEIMVFRPT--YEEFKDFSKFITYMESQGAH---KA-GLA 104
+K+ I T +E + + ++ KA GLA
Sbjct: 115 KKYGI----RTARFEVAETPEELREKIKKFSPPYVIKADGLA 152
>2qqo_A Neuropilin-2; VEGF receptor, semaphorin receptor, calcium-binding
domain, developmental protein, differentiation,
glycoprotein, membr neurogenesis; 2.30A {Homo sapiens}
Length = 460
Score = 27.0 bits (59), Expect = 6.4
Identities = 9/38 (23%), Positives = 15/38 (39%), Gaps = 1/38 (2%)
Query: 88 KFITYMESQGAHKAGLAKVIPPPEWVPR-KSGYSLDSS 124
K + + QGA + +V + K YSL+
Sbjct: 355 KTVKGVIIQGARGGDSITAVEARAFVRKFKVSYSLNGK 392
>3mjf_A Phosphoribosylamine--glycine ligase; structural genomics, CEN
structural genomics of infectious diseases, csgid; HET:
MSE PGE; 1.47A {Yersinia pestis} PDB: 1gso_A
Length = 431
Score = 26.7 bits (60), Expect = 6.6
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 10/42 (23%)
Query: 69 RKHEIMVFRPT--YEEFKDFSKFITYMESQGAH---KA-GLA 104
+H I P+ Y+ F D + Y+ +GA KA GLA
Sbjct: 116 ARHNI----PSAEYQNFTDVEAALAYVRQKGAPIVIKADGLA 153
>1p8j_A Furin precursor; prohormone convertase, SPC1, PACE, P-domain; HET:
DKA AR7 NAG FUL BMA MAN GAL FUC; 2.60A {Mus musculus}
SCOP: b.18.1.20 c.41.1.1
Length = 471
Score = 27.0 bits (59), Expect = 6.6
Identities = 8/58 (13%), Positives = 13/58 (22%), Gaps = 2/58 (3%)
Query: 175 FDY--EDLERKYWKNITYVSPIYGADVSGSITDEDVNVWNINHLGTILDYVNEDYGIS 230
+ DL Y ++ D T + N G + N
Sbjct: 49 IEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGV 106
>2qk4_A Trifunctional purine biosynthetic protein adenosi; purine
synthesis, enzyme, protein-ATP complex, structural GE
structural genomics consortium, SGC; HET: ATP; 2.45A
{Homo sapiens}
Length = 452
Score = 26.7 bits (60), Expect = 7.2
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 11/43 (25%)
Query: 69 RKHEIMVFRPT--YEEFKDFSKFITYMESQGAH----KA-GLA 104
+H I PT ++ F + +++ S KA GLA
Sbjct: 137 DRHGI----PTAQWKAFTKPEEACSFILSADFPALVVKASGLA 175
>3lp8_A Phosphoribosylamine-glycine ligase; ssgcid, NIH, niaid, SBRI, UW,
emerald biostructures, ALS collaborative
crystallography; 2.15A {Ehrlichia chaffeensis}
Length = 442
Score = 26.7 bits (60), Expect = 7.8
Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 10/42 (23%)
Query: 69 RKHEIMVFRPT--YEEFKDFSKFITYMESQGAH---KA-GLA 104
++ I PT Y F D + +++ KA GLA
Sbjct: 132 MRYGI----PTAKYGYFVDTNSAYKFIDKHKLPLVVKADGLA 169
>3ujh_A Glucose-6-phosphate isomerase; ssgcid, structural genomics, seattle
structural genomics CEN infectious disease; HET: G6Q;
2.10A {Toxoplasma gondii}
Length = 567
Score = 26.9 bits (60), Expect = 7.9
Identities = 7/22 (31%), Positives = 13/22 (59%), Gaps = 6/22 (27%)
Query: 111 EWVPRKSG--YSLDSSIGDMSI 130
+WV G YS+ S++G + +
Sbjct: 276 DWV----GGRYSVTSAVGILPL 293
>3qsd_A Cathepsin B-like peptidase (C01 family); cysteine peptidase,
digestive tract, hydrolase-hydrolase INH complex; HET:
074; 1.30A {Schistosoma mansoni} PDB: 3s3q_A* 3s3r_A*
Length = 254
Score = 26.4 bits (59), Expect = 8.1
Identities = 7/23 (30%), Positives = 9/23 (39%), Gaps = 4/23 (17%)
Query: 172 PKHFDYEDLERKYWKNITYVSPI 194
P FD RK W ++ I
Sbjct: 4 PSSFDS----RKKWPRCKSIATI 22
>2ip4_A PURD, phosphoribosylamine--glycine ligase; GAR synthetase, purine
nucleotid structural genomics, NPPSFA; 2.80A {Thermus
thermophilus}
Length = 417
Score = 26.3 bits (59), Expect = 9.4
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 10/42 (23%)
Query: 69 RKHEIMVFRPT--YEEFKDFSKFITYMESQGAH---KA-GLA 104
++ I PT Y F++ + + Y+E G K GLA
Sbjct: 110 ERYGI----PTARYRVFREPLEALAYLEEVGVPVVVKDSGLA 147
>4a17_O RPL19, 60S ribosomal protein L5; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila}
Length = 185
Score = 26.2 bits (57), Expect = 9.5
Identities = 14/79 (17%), Positives = 27/79 (34%), Gaps = 9/79 (11%)
Query: 28 KKKP---RTPSKKTKVVKEKAESGVQEEGEVKSTIKTLLPVKQERKHEIMVFRPTYEEFK 84
K+ + S+ ++ K + G+ K T +P K V R +++
Sbjct: 51 MKRSTVIHSRSRARAFLEAKRKGRHTGSGKRKGTRNARMPTKVLWMRRQRVLRRLLRKYR 110
Query: 85 DFSKFIT------YMESQG 97
K Y+ S+G
Sbjct: 111 AAKKIDKHQYHEFYLGSKG 129
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
0.311 0.130 0.378
Gapped
Lambda K H
0.267 0.0478 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,584,931
Number of extensions: 210127
Number of successful extensions: 347
Number of sequences better than 10.0: 1
Number of HSP's gapped: 342
Number of HSP's successfully gapped: 34
Length of query: 232
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 142
Effective length of database: 4,188,903
Effective search space: 594824226
Effective search space used: 594824226
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 (21.8 bits)
S2: 56 (26.0 bits)