RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12035
(251 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 = 46.0 bits (108), Expect = 6e-06
Identities = 41/265 (15%), Positives = 83/265 (31%), Gaps = 75/265 (28%)
Query: 6 PILDYGCSIFMNANKKYLSHLDTIHHMGIRLISRALKSSPVNSL--------YAESAILP 57
P SI + + L+ D H+ ++ ++SS +N L + ++ P
Sbjct: 327 PRR---LSIIAESIRDGLATWDNWKHVNCDKLTTIIESS-LNVLEPAEYRKMFDRLSVFP 382
Query: 58 LSVRRRLLFSNIIAKQEYYFASTNGSQISFMWIPSHSNIALNDKADQLAKNS-------- 109
S +I +S +W + + ++L K S
Sbjct: 383 PSA-------HIPTIL-----------LSLIWFDVIKSDVMVV-VNKLHKYSLVEKQPKE 423
Query: 110 ----INSKLLDFYIQDDLKNHLRKNIVKLYNDQWTNIQNNKLRTIKDNTTLWKTS--LRK 163
I S L+ ++ + + L ++IV YN T ++ + D L+
Sbjct: 424 STISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKN 483
Query: 164 IRNEE--ILLTRLRIGHTRITHSYL---F--TKTPHPICTCGFPLTVKHIF-ECNKYKKF 215
I + E L + +L F K H ++ + + YK +
Sbjct: 484 IEHPERMTLFRMV----------FLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPY 533
Query: 216 REKLSLPSIEIALSDNENMAEKTIK 240
+ DN+ E+ +
Sbjct: 534 ------------ICDNDPKYERLVN 546
Score = 32.5 bits (73), Expect = 0.15
Identities = 25/184 (13%), Positives = 58/184 (31%), Gaps = 50/184 (27%)
Query: 18 ANKKYLSHLDTIHHMGIRLISRALKSSPVNSLYAESAIL-PLSVRRRLLFSNIIAKQE-- 74
K+ +I I LK N +I+ ++ + ++I
Sbjct: 417 VEKQPKESTISIPS-----IYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471
Query: 75 YYF-------ASTNGSQ---------ISFMWIPS---HSNIALNDKADQLAKNSINSKLL 115
Y++ + + + F ++ H + A N A SI + L
Sbjct: 472 YFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWN------ASGSILNTLQ 525
Query: 116 DF-----YIQD----------DLKNHLRKNIVKLYNDQWTNIQNNKLRTIKDNTTLWKTS 160
YI D + + L K L ++T++ L ++ +++ +
Sbjct: 526 QLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMA--EDEAIFEEA 583
Query: 161 LRKI 164
+++
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 = 41.2 bits (97), Expect = 6e-05
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 84 QISFMWIPSHSNIALNDKADQLAKNSINSK 113
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 = 2e-04
Identities = 10/33 (30%), Positives = 20/33 (60%)
Query: 84 QISFMWIPSHSNIALNDKADQLAKNSINSKLLD 116
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 = 0.001
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 84 QISFMWIPSHSNIALNDKADQLAKNSIN 111
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 = 37.1 bits (87), Expect = 0.002
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 84 QISFMWIPSHSNIALNDKADQLAKNSINSK 113
QI + W+ H+ A N++ DQLA+ + +
Sbjct: 117 QIDWRWVKGHAGHAENERCDQLARAAAEAN 146
>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 = 38.5 bits (89), Expect = 0.002
Identities = 39/214 (18%), Positives = 68/214 (31%), Gaps = 91/214 (42%)
Query: 2 AYTQP-ILDYGCSIFMNANKKYLSHLDTIHHMGIRLISRALKS---SPVNSLYA-----E 52
+TQP + + F LKS P ++ +A E
Sbjct: 1730 QFTQPALTLMEKAAF-----------------------EDLKSKGLIPADATFAGHSLGE 1766
Query: 53 -SA------ILPLS-----VRRR-LLFSNIIAKQE-----YYFASTNGSQISFMWIPSHS 94
+A ++ + V R + + + E Y + N +++ S S
Sbjct: 1767 YAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVA----ASFS 1822
Query: 95 NIALNDKADQLAKNSINSKLLDFYIQDDLKNHLRKNIVKLYN---------------DQW 139
AL +++ K + + ++ IV YN D
Sbjct: 1823 QEALQYVVERVGKRT------GWLVE----------IVN-YNVENQQYVAAGDLRALDTV 1865
Query: 140 TNIQN-NKLRTIKDNTTLWKT-SLRKIRNEEILL 171
TN+ N KL+ I D L K+ SL ++ E L
Sbjct: 1866 TNVLNFIKLQKI-DIIELQKSLSLEEV--EGHLF 1896
Score = 35.4 bits (81), Expect = 0.016
Identities = 38/240 (15%), Positives = 75/240 (31%), Gaps = 78/240 (32%)
Query: 20 KKYLSHL-DTIHHMGIRLISRALKSSPVNSLYAESAILPLSVRRRLLFSNIIAKQEYYFA 78
+ Y + D I L + ++ + L++ L + ++Y
Sbjct: 178 QTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQG----LNILEWLENPSNTPDKDY-LL 232
Query: 79 STNGSQISFMWIPSHSNIALNDKADQLAKNSINSKLLDFYIQDDLKNHLR------KNIV 132
S IS P I + QLA + +KLL + +L+++L+ + +V
Sbjct: 233 S---IPISC---PL---IGVI----QLAHYVVTAKLLG-FTPGELRSYLKGATGHSQGLV 278
Query: 133 K----LYNDQWTNIQNNKLRTIK-------------DNTTLWKTSLRK-IRNEEILLTRL 174
D W + + + I NT+L + L + N E
Sbjct: 279 TAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNE------ 332
Query: 175 RIGHTRITHSYLFTKTPHPICTC-GFPLTV--KHIFECNKYKKFREKLSLPS---IEIAL 228
P P+ + ++ + N + LP+ +EI+L
Sbjct: 333 --------------GVPSPMLSISNLTQEQVQDYVNKTNSH--------LPAGKQVEISL 370
Score = 33.9 bits (77), Expect = 0.050
Identities = 34/201 (16%), Positives = 55/201 (27%), Gaps = 89/201 (44%)
Query: 15 FMNANKKYLSHLDTIHHMGIRLISRALKSSPVNSLYAESAIL----------P---LSVR 61
F + +K ++ L +G+R ++ P SL +IL P LS+
Sbjct: 292 FFVSVRKAITVL---FFIGVR----CYEAYPNTSL--PPSILEDSLENNEGVPSPMLSIS 342
Query: 62 ---RRLLFSNIIAKQEYYFASTNGSQISFMWIP--SHSNIALNDKADQLAKNSINSKLLD 116
+ + + TN +P I+L +N
Sbjct: 343 NLTQEQVQDYV--------NKTNSH------LPAGKQVEISL-----------VNGA--K 375
Query: 117 FYI-----QD--DLKNHLRKNIVKLYNDQWTNIQNNKLRTIKDNTTLWKTSLRKIRNEEI 169
+ Q L LRK DQ R S RK++
Sbjct: 376 NLVVSGPPQSLYGLNLTLRKAKAPSGLDQS--------RI--------PFSERKLK---- 415
Query: 170 LLTR-LRIG---HTRITHSYL 186
R L + H+ L
Sbjct: 416 FSNRFLPVASPFHS----HLL 432
Score = 32.3 bits (73), Expect = 0.16
Identities = 16/77 (20%), Positives = 27/77 (35%), Gaps = 17/77 (22%)
Query: 172 TR-LRIGHTRITHSYLFTKTPHPICTCGFPLTVKHIFECNKYKKFREKLSLPSIEIALSD 230
TR L + H + H L P ++F + L P+ A +D
Sbjct: 6 TRPLTLSHGSLEHVLL---VPTAS----------FFIASQLQEQFNKILPEPTEGFA-AD 51
Query: 231 NE--NMAEKTIKYMKMI 245
+E AE K++ +
Sbjct: 52 DEPTTPAELVGKFLGYV 68
>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 = 36.8 bits (86), Expect = 0.002
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 84 QISFMWIPSHSNIALNDKADQLAKNSINSKLL 115
++ 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 = 36.0 bits (84), Expect = 0.004
Identities = 6/30 (20%), Positives = 16/30 (53%)
Query: 84 QISFMWIPSHSNIALNDKADQLAKNSINSK 113
++ 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 = 35.5 bits (83), Expect = 0.005
Identities = 9/30 (30%), Positives = 18/30 (60%)
Query: 84 QISFMWIPSHSNIALNDKADQLAKNSINSK 113
+++F + HS+ N +AD+LA+ +I
Sbjct: 116 RVTFHKVKGHSDNPYNSRADELARLAIKEN 145
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 33.6 bits (76), Expect = 0.035
Identities = 6/51 (11%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 120 QDDLKNHLRKNIVKLYNDQWTNIQNNKLRTIKDNTTLWKTSLRKIRNEEIL 170
+ + + +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 = 32.9 bits (75), Expect = 0.051
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 84 QISFMWIPSHS-----NIALNDKADQLAKNSINSKLLD 116
++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 = 7.5
Identities = 8/29 (27%), Positives = 10/29 (34%), Gaps = 2/29 (6%)
Query: 208 ECNKYKKFREKLSL--PSIEIALSDNENM 234
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
0.321 0.134 0.394
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: 3,688,513
Number of extensions: 204956
Number of successful extensions: 414
Number of sequences better than 10.0: 1
Number of HSP's gapped: 407
Number of HSP's successfully gapped: 26
Length of query: 251
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 160
Effective length of database: 4,160,982
Effective search space: 665757120
Effective search space used: 665757120
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)