RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1178
(144 letters)
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex,
box H/ACA, snoRNP, pseudouridine synthase, RNA
modification; 1.95A {Methanocaldococcus jannaschii}
SCOP: b.122.1.1 d.265.1.2
Length = 357
Score = 193 bits (493), Expect = 3e-62
Identities = 60/139 (43%), Positives = 86/139 (61%), Gaps = 1/139 (0%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
M ELRR +SG E+D V L D+ DA + + DE LRRVI+P+E L K++++K
Sbjct: 217 MQELRRTKSGCFEEKD-AVYLQDLLDAYVFWKEDGDEEELRRVIKPMEYGLRHLKKVVVK 275
Query: 61 DSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGV 120
DSAV+A+C+GA + + G+ + GI E +++ + KGEAVA+ A M T + D GV
Sbjct: 276 DSAVDAICHGADVYVRGIAKLSKGIGKGETVLVETLKGEAVAVGKALMNTKEILNADKGV 335
Query: 121 VAKIKRVIMDRDTYPRKWG 139
++RV MDR TYPR W
Sbjct: 336 AVDVERVYMDRGTYPRMWK 354
>2aus_C Pseudouridine synthase; isomerase, structural protein,
isomerase-structural protein; 2.10A {Pyrococcus abyssi}
PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A*
2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A
Length = 334
Score = 192 bits (490), Expect = 6e-62
Identities = 53/138 (38%), Positives = 83/138 (60%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
M ELRR RSG E++ LVTLHD+ D + + + E +R+ I+P+E + +I +K
Sbjct: 197 MAELRRTRSGPFKEDETLVTLHDLVDYYHFWKEDGIEEYIRKAIQPMEKAVEHLPKIWIK 256
Query: 61 DSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGV 120
DSAV AV +GA + +PG+++ GI+ + + I++ K E VAL A M+T M G+
Sbjct: 257 DSAVAAVAHGANLTVPGIVKLNAGIKKGDLVAIMTLKDELVALGKAMMSTQEMIERSKGI 316
Query: 121 VAKIKRVIMDRDTYPRKW 138
+++V M RD YP+ W
Sbjct: 317 AVDVEKVFMPRDWYPKLW 334
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase,
pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces
cerevisiae} PDB: 3uai_A
Length = 400
Score = 188 bits (478), Expect = 1e-59
Identities = 94/144 (65%), Positives = 124/144 (86%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
M ELRR RSG SE D +VTLHD+ DA ++YD +DES LR +I+PLE LLVG+KRI++K
Sbjct: 213 MQELRRVRSGALSENDNMVTLHDVMDAQWVYDNTRDESYLRSIIQPLETLLVGYKRIVVK 272
Query: 61 DSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGV 120
DSAVNAVCYGA++M+PG+LRYE+GIE+ +EIV+++TKGEA+A+A+AQM+T +A+CDHGV
Sbjct: 273 DSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLASCDHGV 332
Query: 121 VAKIKRVIMDRDTYPRKWGLGPKS 144
VA +KR IM+RD YPR+WGLGP +
Sbjct: 333 VASVKRCIMERDLYPRRWGLGPVA 356
>3zv0_C H/ACA ribonucleoprotein complex subunit 4; cell cycle, RNP
assembly, X-linked dyskeratosis congenita; 2.80A
{Saccharomyces cerevisiae}
Length = 195
Score = 148 bits (375), Expect = 2e-46
Identities = 69/114 (60%), Positives = 93/114 (81%)
Query: 31 YDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEE 90
K + PLE LLVG+KRI++KDSAVNAVCYGA++M+PG+LRYE+GIE+ +E
Sbjct: 52 SSPLKRDLKSYISSGPLETLLVGYKRIVVKDSAVNAVCYGAKLMIPGLLRYEEGIELYDE 111
Query: 91 IVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRKWGLGPKS 144
IV+++TKGEA+A+A+AQM+T +A+CDHGVVA +KR IM+RD YPR+WGLGP +
Sbjct: 112 IVLITTKGEAIAVAIAQMSTVDLASCDHGVVASVKRCIMERDLYPRRWGLGPVA 165
>3d79_A PUA domain, putative uncharacterized protein PH0734; unknown
function; 1.73A {Pyrococcus horikoshii}
Length = 179
Score = 93.0 bits (231), Expect = 5e-25
Identities = 24/127 (18%), Positives = 55/127 (43%), Gaps = 6/127 (4%)
Query: 18 LVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPG 77
++ ++D + D + + E L +R+++ + AV + GA +M PG
Sbjct: 58 IILVNDKPMFIRRKDLIFPLVIALYNLSDEEDLRKWPRRVVVDEGAVPHILNGADVMAPG 117
Query: 78 VLRYEDGIEMDEEIVIVST-KGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPR 136
++ ++GI+ + + +V G +A+ +A M+ M + G K+ D +
Sbjct: 118 IVDADEGIKEGDFVFVVEEKYGRPLAIGIALMSGKVMKEKNRGKAVKVIHHARD-----K 172
Query: 137 KWGLGPK 143
W + +
Sbjct: 173 IWEVTAR 179
>1q7h_A Conserved hypothetical protein; structural genomics, MCSG, PSI, PR
structure initiative; 2.10A {Thermoplasma acidophilum
dsm 1728} SCOP: b.122.1.1 d.17.6.2
Length = 153
Score = 83.3 bits (206), Expect = 2e-21
Identities = 19/99 (19%), Positives = 38/99 (38%), Gaps = 5/99 (5%)
Query: 44 IRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVAL 103
+ L + + + A + G+ + PG++ +D I + I + S+KG +A+
Sbjct: 60 VYLLNYRNPSRNIVTVDEGAEPHILNGSDLFAPGIVSMDDSIRKGDMIFVKSSKGYFIAV 119
Query: 104 ALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRKWGLGP 142
+A+M + G A+I D P
Sbjct: 120 GMAEMDAGEVMATKRGKAARIIHFPGDEL-----IRAFP 153
>3r90_A Malignant T cell-amplified sequence 1; structural genomics
consortium, surface entropy reduction, S binding
protein; 1.70A {Homo sapiens}
Length = 188
Score = 75.8 bits (186), Expect = 4e-18
Identities = 18/123 (14%), Positives = 40/123 (32%), Gaps = 10/123 (8%)
Query: 26 DAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGI 85
+ L+ + ++ + R L + A+ V GA IM PG+ +
Sbjct: 65 NGELLFFRQREGPFYPTL-RLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKL 123
Query: 86 EMDEEIVIVS----TKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRKWGLG 141
IV+ A+ + + +M+ + + G+ + + D W +
Sbjct: 124 YPAAVDTIVAIMAAGAAHALCVGVMKMSAEDIEKVNKGIGIENIHYLND-----GLWHMK 178
Query: 142 PKS 144
Sbjct: 179 TYK 181
>2q07_A Uncharacterized protein AF0587; monomer, structural genomics,
PSI-2, protein structure initiative; 2.04A
{Archaeoglobus fulgidus dsm 4304} SCOP: b.122.1.1
c.18.1.4 d.17.6.5
Length = 306
Score = 45.6 bits (107), Expect = 1e-06
Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 2/62 (3%)
Query: 73 IMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRD 132
I GVLR ++ I ++ +V + LA M+ MA + G+ +KR +
Sbjct: 244 IFAGGVLRADEKIRPNDVVVFH--NSRIFGVGLAAMSGKEMAGSEKGIAINVKRKFSEGH 301
Query: 133 TY 134
+
Sbjct: 302 HH 303
>2cx0_A Hypothetical protein APE0525; PUA domain, structural genomics,
NPPSFA, national project on structural and functional
analyses; 1.80A {Aeropyrum pernix} SCOP: b.122.1.1
d.17.6.4 PDB: 2cx1_A* 1zs7_A
Length = 187
Score = 44.1 bits (104), Expect = 2e-06
Identities = 16/93 (17%), Positives = 35/93 (37%), Gaps = 10/93 (10%)
Query: 56 RIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVS-TKGEAVALALAQMTTSTMA 114
+++ A A+ GA +M+PGV+ E + + + V + +A++ +S +
Sbjct: 94 VVLVDKGAAIALAKGAHLMIPGVVGVEGSFTRGDVVAALYHETRTPVMVGVAEVDSSALE 153
Query: 115 TC----DHGVVAKIKRVIMDRDTYPRKWGLGPK 143
G + + D W L +
Sbjct: 154 KLYREKARGRAVRRVHRLGD-----ALWELAQE 181
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation,
lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima}
SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A
Length = 309
Score = 41.1 bits (97), Expect = 4e-05
Identities = 28/135 (20%), Positives = 56/135 (41%), Gaps = 17/135 (12%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
+EL R G + E+ + + + + I PLE L R+++
Sbjct: 188 AVELVRESVGPHTIEES-LNVFEA-----------APEEIENRIIPLEKCLEWLPRVVVH 235
Query: 61 DSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMAT----C 116
+ + G+QI L + + DG + E + + + +G +ALA A+ +S + T
Sbjct: 236 QESTKMILNGSQIHLEMLKEW-DGFKKGEVVRVFNEEGRLLALAEAERNSSFLETLRKHE 294
Query: 117 DHGVVAKIKRVIMDR 131
+ V +++V R
Sbjct: 295 RNERVLTLRKVFNTR 309
>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 = 40.0 bits (93), Expect = 1e-04
Identities = 25/159 (15%), Positives = 46/159 (28%), Gaps = 58/159 (36%)
Query: 3 ELRRNRSGIQSE--EDGLVT----LHDIKDAMYLYDQHKDESLLR--------------- 41
+R N S + E DG + +I + Y ++ LL
Sbjct: 1683 RIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKA 1742
Query: 42 --RVIR-----PLEGLLVGHKRIILKDS-----AVNAVCYGAQIMLPGVLRYEDGIEMDE 89
++ P + GH S A+ V+ E +E
Sbjct: 1743 AFEDLKSKGLIPADATFAGH-------SLGEYAAL--ASLA------DVMSIESLVE--- 1784
Query: 90 EIVIVSTKGEAVALALAQ----MTTSTMATCDHGVVAKI 124
+V +G + +A+ + + M + G VA
Sbjct: 1785 ---VVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAAS 1820
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop,
lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli}
SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A
Length = 327
Score = 39.5 bits (93), Expect = 1e-04
Identities = 21/133 (15%), Positives = 46/133 (34%), Gaps = 19/133 (14%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMY--LYDQHKDESLLRRVIRPLEGLLVGHKRII 58
+I LRR E VTL +++ + LL ++ P++ + +
Sbjct: 210 VIYLRRLAVSKYPVERM-VTLEHLRELVEQAEQQDIPAAELLDPLLMPMDSPASDYPVVN 268
Query: 59 LKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDH 118
L ++ G + G E +V V+ + + ++ D
Sbjct: 269 LPLTSSVYFKNGNPVRTSGAP--------LEGLVRVTEGENGKFIGMGEID-------DE 313
Query: 119 GVVAKIKRVIMDR 131
G V +R++++
Sbjct: 314 GRV-APRRLVVEY 325
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification,
structural genomics, PSI, structure initiative; 1.90A
{Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2
Length = 316
Score = 34.1 bits (79), Expect = 0.009
Identities = 18/104 (17%), Positives = 29/104 (27%), Gaps = 22/104 (21%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
+ LRR R G + +L D+ + E L+ R L
Sbjct: 196 VTALRRTRVGRFELDQA-RSLDDL------------AERPALSLSLDEACLLMFARRDLT 242
Query: 61 DSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALA 104
+ +A G + G+ D G +AL
Sbjct: 243 AAEASAAANGRSLPAVGI---------DGVYAACDADGRVIALL 277
>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 = 29.4 bits (65), Expect = 0.45
Identities = 13/103 (12%), Positives = 27/103 (26%), Gaps = 32/103 (31%)
Query: 1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
+ +L + + ++ +++ I YL + LE H+ I+
Sbjct: 408 VNKLHKYSLVEKQPKESTISIPSI----YL-----------ELKVKLENEYALHRSIVDH 452
Query: 61 DSAVNAVCYGAQIMLPGVLRYEDG------------IEMDEEI 91
+ I D IE E +
Sbjct: 453 YNIPKTFDSDDLIPPY-----LDQYFYSHIGHHLKNIEHPERM 490
>1iq8_A Archaeosine tRNA-guanine transglycosylase; (alpha/beta)8 barrel,
riken structural genomics/proteomics initiative, RSGI;
2.20A {Pyrococcus horikoshii} SCOP: b.122.1.1 c.1.20.1
d.17.6.1 PDB: 1it7_A* 1it8_A* 1j2b_A
Length = 582
Score = 27.7 bits (62), Expect = 1.4
Identities = 14/71 (19%), Positives = 32/71 (45%)
Query: 56 RIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMAT 115
R+++ A G + V+ + GI +E+++V+ E +A A ++ M
Sbjct: 509 RVVVNKEAEPFARKGKDVFAKFVIFADPGIRPYDEVLVVNENDELLATGQALLSGREMIV 568
Query: 116 CDHGVVAKIKR 126
+G K+++
Sbjct: 569 FQYGRAVKVRK 579
>2bw2_A Bypass of forespore C; sporulation, signaling protein, BOFC, sigmak
checkpoint; NMR {Bacillus subtilis}
Length = 140
Score = 27.0 bits (59), Expect = 1.8
Identities = 15/85 (17%), Positives = 31/85 (36%), Gaps = 6/85 (7%)
Query: 10 GIQSEEDGLVTLHDIKDAMYLY------DQHKDESLLRRVIRPLEGLLVGHKRIILKDSA 63
G S E + + D Y +Q K L R+ + + L + I + D+
Sbjct: 22 GDVSIEHKHEKVFSMDDFWAAYAGWTLVEQKKGYVLFRKQMDDISPLSKVNGYIGVSDNG 81
Query: 64 VNAVCYGAQIMLPGVLRYEDGIEMD 88
V + +G ++ I+++
Sbjct: 82 VISTFHGRPEPASEPIQSFFQIDLE 106
>1ha0_A Protein (hemagglutinin precursor); glycoprotein, membrane-fusion
precursor, virus/viral protein protein; HET: NAG BMA
MAN; 2.80A {Influenza a virus} SCOP: b.19.1.2 h.3.1.1
Length = 494
Score = 26.9 bits (59), Expect = 3.1
Identities = 6/23 (26%), Positives = 14/23 (60%)
Query: 20 TLHDIKDAMYLYDQHKDESLLRR 42
+ I++ Y +D +++E+L R
Sbjct: 469 CIESIRNGTYDHDVYRNEALNNR 491
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
0.320 0.137 0.392
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,263,416
Number of extensions: 134846
Number of successful extensions: 446
Number of sequences better than 10.0: 1
Number of HSP's gapped: 441
Number of HSP's successfully gapped: 19
Length of query: 144
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 59
Effective length of database: 4,328,508
Effective search space: 255381972
Effective search space used: 255381972
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: 52 (23.7 bits)