RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy556
(435 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 = 55.2 bits (132), Expect = 3e-08
Identities = 64/477 (13%), Positives = 145/477 (30%), Gaps = 133/477 (27%)
Query: 26 GSSLSTLLFAV---------FMNDIFHVINLPTRGLLFVDDLLLTIRGKILEQLGSRNPT 76
GS + + V IF +NL + +L + K+L Q+ +
Sbjct: 160 GSGKTWVALDVCLSYKVQCKMDFKIFW-LNL---KNCNSPETVLEMLQKLLYQIDPNWTS 215
Query: 77 LPLIMLNGNQLKFDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIVMLDYGSPIY 136
N +L+ + L R + K + N L +V+L+ +
Sbjct: 216 RSDHSSN-IKLRIHSIQAEL----RRLLKSKPYE-----------NCL-LVLLNVQNA-- 256
Query: 137 GSAKDHVIAKLNTEHHIGIRI--------VTGALRTSPVPSLYVESGIPPLVIRRQK-LL 187
N + +I VT L + + ++ L K LL
Sbjct: 257 -----KAWNAFN----LSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL 307
Query: 188 LNYV-TKIS-----ACPSNPVYNILFPTSLRRRLGIYEFTRTPKPLFVRF-RAIEAYVQE 240
L Y+ + +NP + S+R L ++ + + IE+ +
Sbjct: 308 LKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWK--HVNCDKLTTIIESSLNV 365
Query: 241 LDRCDMME-YKDLT--PPWSDDMSEVID-LWRNLTSNNIKLTFIWCPSHCGIEGNEEVDR 296
L+ + + + L+ PP + + ++ +W ++ +++ + N+
Sbjct: 366 LEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVV-----------NKLHKY 414
Query: 297 A-ANRDGHTQAINI--------CSPDDLKTMVKKL--------AYNNWQVLWNQTDP--- 336
+ + I+I ++ + + + +++ ++ D
Sbjct: 415 SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFY 474
Query: 337 ------LNKLKQ----------------IKPIISTWKTSQQSRRYDEVVLSRLRIGHTRV 374
L ++ ++ I T+ + L +L+ +
Sbjct: 475 SHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYI 534
Query: 375 T-HSYLFERTTPP----LCSCGENLLTVKHLLDCVHHAPVRSTLSSKPSLLDEPEGV 426
+ +ER L ENL+ K+ D + A L+ E E +
Sbjct: 535 CDNDPKYERLVNAILDFLPKIEENLICSKY-TDLLRIA-----------LMAEDEAI 579
Score = 35.6 bits (81), Expect = 0.038
Identities = 41/282 (14%), Positives = 74/282 (26%), Gaps = 110/282 (39%)
Query: 238 VQELDRCDMMEYKDLTPPWSD------DMSEVIDLWRNLTSNNIKLTFIWCPSHCGIEGN 291
E YKD+ + D D +V D+ +++ S
Sbjct: 11 TGEHQYQ----YKDILSVFEDAFVDNFDCKDVQDMPKSILS------------------K 48
Query: 292 EEVD---RAANRDGHTQAINICSPDDLKTMVKK-----LAYN-NW--------------- 327
EE+D + + T + + MV+K L N +
Sbjct: 49 EEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMM 108
Query: 328 --------QVLWNQTDPLNK---------------LKQIKP---II--------STWKTS 353
L+N K L +++P ++ TW
Sbjct: 109 TRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVAL 168
Query: 354 QQSRRYDEVVLSR-------LRIGHTRVTHSY------LFERTTPPLCSCGENLLTVKHL 400
V + L + + + L + P S ++ +K
Sbjct: 169 DVCL--SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLR 226
Query: 401 LDCVHHAPVRSTLSSKP---SL--LDE---PEGVKATNANVK 434
+ + +R L SKP L L + A N + K
Sbjct: 227 IHSIQAE-LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCK 267
Score = 31.7 bits (71), Expect = 0.57
Identities = 47/290 (16%), Positives = 83/290 (28%), Gaps = 75/290 (25%)
Query: 101 DRKMSWKQHVKYTKI-----KALTALNALKIVMLDYGSPIYGSAK-DHVIAKLNTEHHIG 154
D + Q+ +Y I A K V D I + DH+I + G
Sbjct: 8 DFETGEHQY-QYKDILSVFEDAFVDNFDCKDV-QDMPKSILSKEEIDHIIMSKDAVS--G 63
Query: 155 IRIVTGALRTSP--VPSLYVESGIPPLVIRRQKLLLNY---VTKISACPSNPVYNILFPT 209
+ L + + +VE + NY ++ I P
Sbjct: 64 TLRLFWTLLSKQEEMVQKFVEEVLRI----------NYKFLMSPIKTEQRQPSMMTRMYI 113
Query: 210 SLRRRLGIYEFTRTPKPLFV-RFRAIEAYVQELDRCDMMEYKDLTPPWSDDMSEVIDLWR 268
R RL Y + V R + Q L +L P
Sbjct: 114 EQRDRL--YNDNQVFAKYNVSRLQPYLKLRQAL--------LELRP-------------- 149
Query: 269 NLTSNNIKLTFIWCPSHCGIEG------------NEEVDRAANRDGH-TQAINICSPDDL 315
+ N+ + G+ G + +V + N SP+ +
Sbjct: 150 ---AKNVLI--------DGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETV 198
Query: 316 KTMVKKLAYNNWQVLWNQTDPLNKLKQIKPIISTWKTS-QQSRRYDEVVL 364
M++KL Y +++D + +K I +S+ Y+ +L
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL 248
>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 = 44.7 bits (105), Expect = 6e-05
Identities = 46/269 (17%), Positives = 86/269 (31%), Gaps = 81/269 (30%)
Query: 19 LENGLVQGS-SLSTLLFAVF--MNDIF-HVINLPTRGLLFVDDLLLTIRGKILEQLGSRN 74
L +G ++ + T F + + + F ++ PT G DD
Sbjct: 11 LSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFA-ADD----------------E 53
Query: 75 PTLPLIMLNGNQLKFDNTAKFLGLIWDRKMSWKQHVKYTKIKALTALNALKIVMLDYGSP 134
PT P +L KFLG + + + ++ ++ L + L+ G+
Sbjct: 54 PTTPA------EL----VGKFLGYV-SSLVEPSKVGQFDQV-LNLCLTEFENCYLE-GND 100
Query: 135 IYGSAKDH-VIAKLNTEHHIGIRIVTGALRTSPVPSLYVESGI---PPLVIRRQKLLLNY 190
I H + AKL E+ + ++ Y+ + I P + L
Sbjct: 101 I------HALAAKLLQENDTTLVKTKELIKN------YITARIMAKRPFDKKSNSALFRA 148
Query: 191 VTKISACPSNPVYNILF----PTS-----LRRRLGIYEFTRTPKPLFVRF-RAIEAYVQE 240
V + +A + I F T LR +Y+ T L + + E
Sbjct: 149 VGEGNA----QLVAI-FGGQGNTDDYFEELRD---LYQ---TYHVLVGDLIKFSAETLSE 197
Query: 241 LDRCDMMEYKDLTPPWSDDMSEVIDL--W 267
L R T ++ +++ W
Sbjct: 198 LIRT--------TLDAEKVFTQGLNILEW 218
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 41.4 bits (98), Expect = 1e-04
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 264 IDLWRNL--TSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
+ + L + + + ++ P H G GNEE DR A
Sbjct: 109 KEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLARE 147
>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 = 39.3 bits (92), Expect = 5e-04
Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 5/46 (10%)
Query: 264 IDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANRDGHTQAINI 309
+ + +F +H G E N+ VD A A+ I
Sbjct: 97 QAYAKLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAK-----SALGI 137
>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 = 36.0 bits (84), Expect = 0.007
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 265 DLWRNL---TSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
DL + K+ W P+H GI GNE+VD+ +
Sbjct: 105 DLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA 143
>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 = 34.8 bits (81), Expect = 0.017
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 264 IDLWRNL--TSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
+DLW+ L ++ + W H G NE D A
Sbjct: 101 VDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARA 139
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 34.8 bits (81), Expect = 0.018
Identities = 10/39 (25%), Positives = 15/39 (38%), Gaps = 2/39 (5%)
Query: 264 IDLWRNL--TSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
IDLW+ + + ++TF H N D A
Sbjct: 102 IDLWQEILKLTTLHRVTFHKVKGHSDNPYNSRADELARL 140
>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 = 34.8 bits (80), Expect = 0.020
Identities = 11/48 (22%), Positives = 16/48 (33%), Gaps = 8/48 (16%)
Query: 261 SEVIDLWRNL---TSNNIKLTFIWCPSHCG-----IEGNEEVDRAANR 300
+ + L +L+ I CP H GN D+AA
Sbjct: 105 IKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAARE 152
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 34.9 bits (81), Expect = 0.021
Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 264 IDLWRNL--TSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
DLW L ++ F + H G NE VDR A R
Sbjct: 106 RDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARR 144
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 33.7 bits (78), Expect = 0.048
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 264 IDLWRNL--TSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
+DLW+ L + ++ + W H G NE D+ A
Sbjct: 103 VDLWKRLDKAAQLHQIDWRWVKGHAGHAENERCDQLARA 141
>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI,
nonnucleoside inhibitor, AIDS, HIV, rilpivirine,
diarylpyrimidine, DAPY, DNA recombination; HET: T27;
1.80A {Human immunodeficiency virus 1} PDB: 3is9_A*
3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A
1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A*
2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...
Length = 557
Score = 32.8 bits (75), Expect = 0.21
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 281 WCPSHCGIEGNEEVDR 296
W P+H GI GNE+VD+
Sbjct: 537 WVPAHKGIGGNEQVDK 552
>3kyl_A Telomerase reverse transcriptase; reverse transcriptase; 2.70A
{Tribolium castaneum} PDB: 3du5_A 3du6_A
Length = 596
Score = 31.8 bits (71), Expect = 0.43
Identities = 18/127 (14%), Positives = 37/127 (29%), Gaps = 15/127 (11%)
Query: 20 ENGLVQGSSLSTLLFAVFMNDI----FHVINLPTRGLLFVDDLLLTIRGK--------IL 67
+GL+QG LS L ++M + F ++ VDD ++
Sbjct: 303 NHGLLQGDPLSGCLCELYMAFMDRLYFSNLDKDAFIHRTVDDYFFCSPHPHKVYDFELLI 362
Query: 68 EQLGSRNPTLPLIMLNGNQLKFDNTAKFLGLIWDRKM--SWKQHVKYTKIKALTALNALK 125
+ + NPT L ++ + + G I++ + +
Sbjct: 363 KGVYQVNPTKTRTNLPTHRHP-QDEIPYCGKIFNLTTRQVRTLYKLPPNYEIRHKFKLWN 421
Query: 126 IVMLDYG 132
Sbjct: 422 FNNQISD 428
>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug
design, transferase; 2.35A {Human immunodeficiency virus
2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B
Length = 555
Score = 30.5 bits (69), Expect = 1.2
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 281 WCPSHCGIEGNEEVDR 296
W P+H GI GN+EVD
Sbjct: 534 WVPAHKGIGGNQEVDH 549
>2dre_A Water-soluble chlorophyll protein; beta-trefoil, tetramer, plant,
singlet oxygen, photooxidation, chlorophyll carrier;
HET: CLA; 2.00A {Lepidium virginicum}
Length = 180
Score = 28.9 bits (64), Expect = 2.0
Identities = 5/46 (10%), Positives = 15/46 (32%), Gaps = 2/46 (4%)
Query: 193 KISACPSNPVYNILFPTSLRRRLGIY--EFTRTPKPLFVRFRAIEA 236
K+ + ++ SL + + ++FR ++
Sbjct: 135 KLVRYDNGEGKSVGSTKSLWGPALVLNDDDDSDENAFPIKFREVDT 180
>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 = 28.4 bits (62), Expect = 2.6
Identities = 6/28 (21%), Positives = 13/28 (46%), Gaps = 6/28 (21%)
Query: 155 IRIVTGALRTSPVPSLYVESGIPPLVIR 182
++ + +L+ LY + P L I+
Sbjct: 22 LKKLQASLK------LYADDSAPALAIK 43
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 0.137 0.419
Gapped
Lambda K H
0.267 0.0802 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,733,017
Number of extensions: 406407
Number of successful extensions: 634
Number of sequences better than 10.0: 1
Number of HSP's gapped: 629
Number of HSP's successfully gapped: 17
Length of query: 435
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 339
Effective length of database: 4,021,377
Effective search space: 1363246803
Effective search space used: 1363246803
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: 59 (26.4 bits)