RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12036
(236 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 = 44.1 bits (103), Expect = 2e-05
Identities = 38/251 (15%), Positives = 79/251 (31%), Gaps = 72/251 (28%)
Query: 5 KKYLSHLDTIHHMGIRLISRALKSSPVNSL--------YAESAILPLSVRRRLLFSNIIA 56
+ L+ D H+ ++ ++SS +N L + ++ P S +I
Sbjct: 338 RDGLATWDNWKHVNCDKLTTIIESS-LNVLEPAEYRKMFDRLSVFPPSA-------HIPT 389
Query: 57 KQEYYFASTNGSQISFMWIPSHSNIALNDKADQLAKNS------------INSKLLDFYI 104
+S +W + + ++L K S I S L+ +
Sbjct: 390 IL-----------LSLIWFDVIKSDVMVV-VNKLHKYSLVEKQPKESTISIPSIYLELKV 437
Query: 105 QDDLKNHLRKNIVKLYNDQWTNIQNNKLRTIKDNTTLWKTS--LRKIRNEE--ILLTRLR 160
+ + + L ++IV YN T ++ + D L+ I + E L +
Sbjct: 438 KLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMV- 496
Query: 161 IGHTRITHSYL---F--TKTPHPICTCGFPLTVKHIF-ECNKYKKFREKLSLPSIEIALS 214
+L F K H ++ + + YK + +
Sbjct: 497 ---------FLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPY------------IC 535
Query: 215 DNENMAEKTIK 225
DN+ E+ +
Sbjct: 536 DNDPKYERLVN 546
Score = 35.2 bits (80), Expect = 0.018
Identities = 24/158 (15%), Positives = 59/158 (37%), Gaps = 24/158 (15%)
Query: 15 HHMGIRLISRALKSSPVNSLYAESAILPLSVRRRL-LFSNIIAKQEY---YFASTNGSQI 70
HHM + + S++ ++ + + + +I++K+E + S
Sbjct: 5 HHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGT 64
Query: 71 SFM-WIPSHSNIALNDKADQLAKNSINSKLLDFY--IQDDLKNHLRK--NIVKLYNDQWT 125
+ W L K +++ + + L Y + +K R+ + ++Y +Q
Sbjct: 65 LRLFWT-------LLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRD 117
Query: 126 NIQNNKLRTIKDN-------TTLWKTSLRKIRNEEILL 156
+ N+ K N L + +L ++R + +L
Sbjct: 118 RLYNDNQVFAKYNVSRLQPYLKL-RQALLELRPAKNVL 154
Score = 32.5 bits (73), Expect = 0.14
Identities = 25/184 (13%), Positives = 58/184 (31%), Gaps = 50/184 (27%)
Query: 3 ANKKYLSHLDTIHHMGIRLISRALKSSPVNSLYAESAIL-PLSVRRRLLFSNIIAKQE-- 59
K+ +I I LK N +I+ ++ + ++I
Sbjct: 417 VEKQPKESTISIPS-----IYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471
Query: 60 YYF-------ASTNGSQ---------ISFMWIPS---HSNIALNDKADQLAKNSINSKLL 100
Y++ + + + F ++ H + A N A SI + L
Sbjct: 472 YFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWN------ASGSILNTLQ 525
Query: 101 DF-----YIQD----------DLKNHLRKNIVKLYNDQWTNIQNNKLRTIKDNTTLWKTS 145
YI D + + L K L ++T++ L ++ +++ +
Sbjct: 526 QLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMA--EDEAIFEEA 583
Query: 146 LRKI 149
+++
Sbjct: 584 HKQV 587
>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO
enzyme, structural genomics, protein structure
initiative; NMR {Desulfitobacterium hafniense dcb-2}
PDB: 2kw4_A
Length = 147
Score = 40.8 bits (96), Expect = 8e-05
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 69 QISFMWIPSHSNIALNDKADQLAKNSINSK 98
SF + +HS ND D AK+++ +
Sbjct: 109 IYSFEKVKAHSGNEFNDYVDMKAKSALGIR 138
>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability,
hydrogen exchange, cooperativity, hydrolase; 1.30A
{Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A
1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A
1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A
3aa5_X 1rbv_A ...
Length = 155
Score = 39.4 bits (93), Expect = 3e-04
Identities = 10/33 (30%), Positives = 20/33 (60%)
Query: 69 QISFMWIPSHSNIALNDKADQLAKNSINSKLLD 101
QI + W+ H+ N++AD+LA+ + + L+
Sbjct: 115 QIKWEWVKGHAGHPENERADELARAAAMNPTLE 147
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 37.2 bits (87), Expect = 0.002
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 69 QISFMWIPSHSNIALNDKADQLAKNSIN 96
I +M +P HS N++AD+LA+
Sbjct: 123 DIQWMHVPGHSGFIGNEEADRLAREGAK 150
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 36.7 bits (86), Expect = 0.002
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 69 QISFMWIPSHSNIALNDKADQLAKNSINSK 98
QI + W+ H+ A N++ DQLA+ + +
Sbjct: 117 QIDWRWVKGHAGHAENERCDQLARAAAEAN 146
>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase,
hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} PDB:
3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A
Length = 150
Score = 36.4 bits (85), Expect = 0.002
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 69 QISFMWIPSHSNIALNDKADQLAKNSINSKLL 100
++ W+P+H I N++ D+L I L
Sbjct: 119 KVYLAWVPAHKGIGGNEQVDKLVSAGIRKVLF 150
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 35.6 bits (83), Expect = 0.005
Identities = 6/30 (20%), Positives = 16/30 (53%)
Query: 69 QISFMWIPSHSNIALNDKADQLAKNSINSK 98
++ F ++ H+ N++ D+ A+ S+
Sbjct: 120 RVRFHFVKGHTGHPENERVDREARRQAQSQ 149
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 35.2 bits (82), Expect = 0.005
Identities = 9/30 (30%), Positives = 18/30 (60%)
Query: 69 QISFMWIPSHSNIALNDKADQLAKNSINSK 98
+++F + HS+ N +AD+LA+ +I
Sbjct: 116 RVTFHKVKGHSDNPYNSRADELARLAIKEN 145
>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 = 38/240 (15%), Positives = 75/240 (31%), Gaps = 78/240 (32%)
Query: 5 KKYLSHL-DTIHHMGIRLISRALKSSPVNSLYAESAILPLSVRRRLLFSNIIAKQEYYFA 63
+ Y + D I L + ++ + L++ L + ++Y
Sbjct: 178 QTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQG----LNILEWLENPSNTPDKDY-LL 232
Query: 64 STNGSQISFMWIPSHSNIALNDKADQLAKNSINSKLLDFYIQDDLKNHLR------KNIV 117
S IS P I + QLA + +KLL + +L+++L+ + +V
Sbjct: 233 S---IPISC---PL---IGVI----QLAHYVVTAKLLG-FTPGELRSYLKGATGHSQGLV 278
Query: 118 K----LYNDQWTNIQNNKLRTIK-------------DNTTLWKTSLRK-IRNEEILLTRL 159
D W + + + I NT+L + L + N E
Sbjct: 279 TAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNE------ 332
Query: 160 RIGHTRITHSYLFTKTPHPICTC-GFPLTV--KHIFECNKYKKFREKLSLPS---IEIAL 213
P P+ + ++ + N + LP+ +EI+L
Sbjct: 333 --------------GVPSPMLSISNLTQEQVQDYVNKTNSH--------LPAGKQVEISL 370
Score = 32.3 bits (73), Expect = 0.13
Identities = 16/77 (20%), Positives = 27/77 (35%), Gaps = 17/77 (22%)
Query: 157 TR-LRIGHTRITHSYLFTKTPHPICTCGFPLTVKHIFECNKYKKFREKLSLPSIEIALSD 215
TR L + H + H L P ++F + L P+ A +D
Sbjct: 6 TRPLTLSHGSLEHVLL---VPTAS----------FFIASQLQEQFNKILPEPTEGFA-AD 51
Query: 216 NE--NMAEKTIKYMKMI 230
+E AE K++ +
Sbjct: 52 DEPTTPAELVGKFLGYV 68
Score = 30.8 bits (69), Expect = 0.49
Identities = 31/185 (16%), Positives = 48/185 (25%), Gaps = 86/185 (46%)
Query: 16 HMGIRLISRALKSSPVNSLYAESAIL----------P---LSVR---RRLLFSNIIAKQE 59
+G+R ++ P SL +IL P LS+ + + +
Sbjct: 305 FIGVR----CYEAYPNTSL--PPSILEDSLENNEGVPSPMLSISNLTQEQVQDYV----- 353
Query: 60 YYFASTNGSQISFMWIP--SHSNIALNDKADQLAKNSINSKLLDFYI-----QD--DLKN 110
TN +P I+L +N + Q L
Sbjct: 354 ---NKTNSH------LPAGKQVEISL-----------VNGA--KNLVVSGPPQSLYGLNL 391
Query: 111 HLRKNIVKLYNDQWTNIQNNKLRTIKDNTTLWKTSLRKIRNEEILLTR-LRIG---HTRI 166
LRK DQ R S RK++ R L + H+
Sbjct: 392 TLRKAKAPSGLDQS--------RI--------PFSERKLK----FSNRFLPVASPFHS-- 429
Query: 167 THSYL 171
L
Sbjct: 430 --HLL 432
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.8 bits (74), Expect = 0.048
Identities = 6/51 (11%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 105 QDDLKNHLRKNIVKLYNDQWTNIQNNKLRTIKDNTTLWKTSLRKIRNEEIL 155
+ + + +K++ ++W Q+ ++ K N + + + + +I+
Sbjct: 109 EQEWREKAKKDL-----EEWNQRQSEQVEKNKINNRIADKAFYQQPDADII 154
>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV,
RNAse H, reverse transcriptase, transcription; 1.50A
{Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A
3v1r_A* 2hb5_A
Length = 165
Score = 32.5 bits (74), Expect = 0.057
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 69 QISFMWIPSHS-----NIALNDKADQLAKNSINSKLLD 101
++S + P H N ADQ A+ + +L+
Sbjct: 123 RLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLE 160
>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 = 26.5 bits (57), Expect = 6.6
Identities = 8/29 (27%), Positives = 10/29 (34%), Gaps = 2/29 (6%)
Query: 193 ECNKYKKFREKLSL--PSIEIALSDNENM 219
E KK + L L AL+ M
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKATM 46
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 0.133 0.388
Gapped
Lambda K H
0.267 0.0610 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,454,224
Number of extensions: 190902
Number of successful extensions: 374
Number of sequences better than 10.0: 1
Number of HSP's gapped: 369
Number of HSP's successfully gapped: 26
Length of query: 236
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 145
Effective length of database: 4,160,982
Effective search space: 603342390
Effective search space used: 603342390
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 (21.9 bits)
S2: 56 (25.6 bits)