RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4559
(336 letters)
>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 = 47.2 bits (111), Expect = 5e-06
Identities = 52/350 (14%), Positives = 106/350 (30%), Gaps = 112/350 (32%)
Query: 13 ISMGDRLGPHVEAISGSTFSKDSWLKSQRKD----HKKIN-------------MTLLIKG 55
IS+ S K +L + +D N
Sbjct: 289 ISLDHHSMTLTPDEVKSLLLK--YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDN 346
Query: 56 WLSYMKNKKNITVLVSLIDL--------FVP-ALLPWQETVTVPSIKPLQKVLKIIDNNN 106
W +K + SL L F ++ P + +P+ +L +I +
Sbjct: 347 WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFP--PSAHIPT-----ILLSLIWFD- 398
Query: 107 CLFVHRQAGVRLNSQEAYDVACQGPIRPALLKEPVVYGLKCVHFKPPDFTIGNLYSALLP 166
+ + V + + +L+++ K +I ++Y
Sbjct: 399 -----------VIKSDVMVVVNK-LHKYSLVEK---------QPKESTISIPSIY----- 432
Query: 167 WQEAVLKITDNNCLFVCLFVHRQAGVRLNSQEAYDIARQGPIRPALLKEP--------VV 218
E +K+ + L HR N + +D L+ +
Sbjct: 433 -LELKVKLENEYAL------HRSIVDHYNIPKTFD-------SDDLIPPYLDQYFYSHIG 478
Query: 219 YGLKCVHFKPPDFTIEVHCIGEYEEF-LIRLIY-D---LGTKLRSAAICTSIQCIRFAQF 273
+ H K I E L R+++ D L K+R + + A
Sbjct: 479 H-----HLKN---------IEHPERMTLFRMVFLDFRFLEQKIRHDSTAWN------ASG 518
Query: 274 GLEHSLLR-KHWRVQHVIENIAHNETLVDKMDPMRPQLQSVNMTDSDSTD 322
+ ++L + K ++ ++ +N E LV+ + P+++ N+ S TD
Sbjct: 519 SILNTLQQLKFYK-PYICDNDPKYERLVNAILDFLPKIEE-NLICSKYTD 566
Score = 44.5 bits (104), Expect = 4e-05
Identities = 48/332 (14%), Positives = 92/332 (27%), Gaps = 90/332 (27%)
Query: 27 SGSTFSKDSWLKSQRKDHKKINMTLLIKGWLSYMKNKKNI----------TVLVS--LID 74
F+K + S+ + + K+ + L ++ KN+ T + +
Sbjct: 122 DNQVFAKYN--VSRLQPYLKL------RQALLELRPAKNVLIDGVLGSGKTWVALDVCLS 173
Query: 75 LFVPALLP----W----QETVTVPSIKPLQKVLKIIDNNNCLFVHRQAGVRLNSQEAYDV 126
V + W ++ LQK+L ID N + ++L
Sbjct: 174 YKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233
Query: 127 ACQGPIRPALLKEPVVYGLKCVHFKPPDFTIGNLYSALLP----WQEAVLKITDNNCLFV 182
L+ K + + LL + +C
Sbjct: 234 ----------LRR---------LLKSKPYE-----NCLLVLLNVQNAKAWNAFNLSCKI- 268
Query: 183 CLFVHRQAGV--RLNSQEAYDIARQGPIRPALLKEPVVYGLKCVHFKPPDFTIEVH---- 236
L R V L++ I+ E LK + +P D EV
Sbjct: 269 -LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNP 327
Query: 237 ----CIGE-YEEFLIRLIY--DLGTKLRSAAICTSIQCI-------RFAQFGL--EHS-- 278
I E + L + + I +S+ + F + + +
Sbjct: 328 RRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI 387
Query: 279 ---LLRKHWR--VQHVIENIA---HNETLVDK 302
LL W ++ + + H +LV+K
Sbjct: 388 PTILLSLIWFDVIKSDVMVVVNKLHKYSLVEK 419
>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 = 45.7 bits (109), Expect = 1e-05
Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 16/95 (16%)
Query: 192 VRLNSQEAYDIARQG-----PIRPALLKEPVVYGLKCVHFKPPDFTIEVHCI-GEYEEFL 245
++ ++ Y+ ARQG RP VY L + + + +E+HC G Y
Sbjct: 142 LKYQGKKLYEYARQGIEVPREARPI-----TVYELLFIRHEGNELELEIHCSKGTY---- 192
Query: 246 IR-LIYDLGTKLRSAAICTSIQCIRFAQFGLEHSL 279
IR +I DLG KL A ++ + +++ +E +
Sbjct: 193 IRTIIDDLGEKLGCGAHVIYLRRLAVSKYPVERMV 227
>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 = 45.7 bits (109), Expect = 1e-05
Identities = 21/95 (22%), Positives = 35/95 (36%), Gaps = 16/95 (16%)
Query: 192 VRLNSQEAYDIARQG-----PIRPALLKEPVVYGLKCVHFKPPDFTIEVHC-IGEYEEFL 245
+ + Y +AR+G P + ++ + V+ + D + V G Y
Sbjct: 120 KKYKGERLYKLAREGKIINLPPKRV-----KIFKIWDVNIEGRDVSFRVEVSPGTY---- 170
Query: 246 IR-LIYDLGTKLRSAAICTSIQCIRFAQFGLEHSL 279
IR L D+G KL A + +E SL
Sbjct: 171 IRSLCMDIGYKLGCGATAVELVRESVGPHTIEESL 205
>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 = 39.5 bits (93), Expect = 8e-04
Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 20/99 (20%)
Query: 192 VRLNSQEAYDIARQG-----PIRPALLKEPVVYGLKCVHFKP----PDFTIEVHC-IGEY 241
+++ + AY +ARQG RP + + + + D +E+ C G Y
Sbjct: 124 IKVGGRRAYRLARQGRSVQLEARPI-----RIDRFELLAARRRDQLIDIDVEIDCSSGTY 178
Query: 242 EEFLIR-LIYDLGTKLRSAAICTSIQCIRFAQFGLEHSL 279
IR L DLG L T+++ R +F L+ +
Sbjct: 179 ----IRALARDLGDALGVGGHVTALRRTRVGRFELDQAR 213
>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 = 29.1 bits (64), Expect = 1.3
Identities = 13/52 (25%), Positives = 18/52 (34%), Gaps = 27/52 (51%)
Query: 91 SIKPLQKVLKIIDNNNCLFVHRQAGVRLNSQEAYDVACQGPIRPAL-LKEPV 141
++K LQ LK L+ A D A PAL +K +
Sbjct: 21 ALKKLQASLK-------LY-------------ADDSA------PALAIKATM 46
Score = 26.8 bits (58), Expect = 8.2
Identities = 6/22 (27%), Positives = 11/22 (50%), Gaps = 4/22 (18%)
Query: 63 KKNITVLVSLIDLF----VPAL 80
K+ + L + + L+ PAL
Sbjct: 19 KQALKKLQASLKLYADDSAPAL 40
>3ll3_A Gluconate kinase; xylulose kinase, nysgx, ATP, ADP, xylulose,
transferase, structural genomics, PSI-2, protein
structure initiative; HET: ATP DXP XUL ADP; 2.00A
{Lactobacillus acidophilus} PDB: 3gbt_A*
Length = 504
Score = 27.9 bits (63), Expect = 5.6
Identities = 6/35 (17%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 27 SGSTFSKDSWLKSQRKDH-KKINMTLLIKGWLSYM 60
+ K WLK+++ + + + IK ++ +
Sbjct: 130 PMAPIYKLLWLKNKKTEVFSQAQKWIGIKEYIIFR 164
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
0.323 0.138 0.429
Gapped
Lambda K H
0.267 0.0787 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,150,550
Number of extensions: 298585
Number of successful extensions: 303
Number of sequences better than 10.0: 1
Number of HSP's gapped: 297
Number of HSP's successfully gapped: 10
Length of query: 336
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 242
Effective length of database: 4,077,219
Effective search space: 986686998
Effective search space used: 986686998
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (25.6 bits)