RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5156
(389 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 = 54.5 bits (130), Expect = 4e-08
Identities = 61/402 (15%), Positives = 116/402 (28%), Gaps = 137/402 (34%)
Query: 2 LQNRFREIL-HENYKDFLKIYTDGSKDET----GVGCALII----------PQLNVTKRF 46
+Q R +L + Y++ L + + + + C +++ T
Sbjct: 230 IQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHI 289
Query: 47 TLNKYSSIF-HAELFSILQSLKNAKLLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIPH 105
+L+ +S E+ S+L K L+ + L + ++ NP I
Sbjct: 290 SLDHHSMTLTPDEVKSLL-----LKYLDCRP-----QDLPR-EVLTT----NPRRLSIIA 334
Query: 106 AELFSILQSLKNAELLNIKKVL-IISDSLSSFQAISNLYHPNPLVKEIQETYSSAQISIK 164
+ L + N + +N K+ II SL+ + P E ++ + ++S+
Sbjct: 335 ESIRDGLATWDNWKHVNCDKLTTIIESSLNVLE-------PA----EYRKMFD--RLSV- 380
Query: 165 FLWCPSHPCWYFWKRSSSQISIKFL---WCPSHVGISGNDQADTEAKKATSEPITNHSLL 221
F S+ I L W + K+ + N
Sbjct: 381 -----------F--PPSAHIPTILLSLIWF--------------DVIKSDVMVVVNKL-- 411
Query: 222 LEEMKSLAKKHFYQKWNTTWSNVNPNENKLR------RIKSTTTPWKTSSQKARLDEVCL 275
SL +K P E+ + +K + L
Sbjct: 412 --HKYSLVEKQ-------------PKESTISIPSIYLELK------VKLENEYAL----- 445
Query: 276 MRMRIGHTKITHSYLFKREERPICDSCHEPVT----VEHIILHCNKLR-------FRPP- 323
H I Y + D P HI H + FR
Sbjct: 446 ------HRSIVDHYNIPKTFDS--DDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVF 497
Query: 324 ---SFLGNSL--ANILSDNPDSISSLMRFLKQNNFLKHIGDS 360
FL + + + SI + ++ LK + +I D+
Sbjct: 498 LDFRFLEQKIRHDSTAWNASGSILNTLQQLK--FYKPYICDN 537
Score = 41.8 bits (97), Expect = 4e-04
Identities = 81/526 (15%), Positives = 152/526 (28%), Gaps = 176/526 (33%)
Query: 2 LQNRFREILHENYKDFLK-------------IYTDGSKDETGVGCALIIPQLNVTKR--- 45
Q ++++IL F+ I + D II +
Sbjct: 14 HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDH-------IIMSKDAVSGTLR 66
Query: 46 -FT--LNKYSSIFHAELFSILQSLKNAKLL--NIKKVLII-SDSLSSF-QAISNLYHPNP 98
F L+K + + +L+ N K L IK S + + LY+ N
Sbjct: 67 LFWTLLSKQEEMVQKFVEEVLR--INYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQ 124
Query: 99 LVKEI------PHAELFSILQSLKNAELLNI-------KKVLIISDSLSSFQ-------- 137
+ + P+ +L L L+ A+ + I K + + D S++
Sbjct: 125 VFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVAL-DVCLSYKVQCKMDFK 183
Query: 138 ----AISNLYHPNPLVKEIQETYSSAQISIKFLWCPSHPCWYFWKRSSSQISIKFL---- 189
+ N P +++ +Q+ QI + H + S Q ++ L
Sbjct: 184 IFWLNLKNCNSPETVLEMLQKLLY--QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK 241
Query: 190 ------------WCPSHVG---------ISGNDQADTEAKKA--TSEPITNH---SLLLE 223
++ + T+ A T+ +H +L +
Sbjct: 242 PYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPD 301
Query: 224 EMKSL---------------AKKH----------FYQKWNTTWSNV-NPNENKLRR-IKS 256
E+KSL + TW N + N +KL I+S
Sbjct: 302 EVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIES 361
Query: 257 TTTPWKTSSQKARLDEVCLMRMRIGHTKITHSYL-------FKREERPICDSCHEPVTVE 309
+ + + + D + + I L K + + + H+ VE
Sbjct: 362 SLNVLEPAEYRKMFDRLSVFPP---SAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVE 418
Query: 310 ---------------------------H--IILHCNKLR------FRPP-------SFLG 327
H I+ H N + PP S +G
Sbjct: 419 KQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIG 478
Query: 328 NSLANI-LSDNPDSISSL---MRFLKQNNFLKHIGDS-TANAPVPN 368
+ L NI + + RFL+Q ++H + A+ + N
Sbjct: 479 HHLKNIEHPERMTLFRMVFLDFRFLEQK--IRHDSTAWNASGSILN 522
>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 = 48.5 bits (115), Expect = 3e-06
Identities = 72/440 (16%), Positives = 120/440 (27%), Gaps = 194/440 (44%)
Query: 6 FREI--LHENYKDFL----------------------KIYTDG--------SKDET---- 29
F E+ L++ Y + K++T G + T
Sbjct: 170 FEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKD 229
Query: 30 -----GVGCALI-IPQL----NVTKRFTLNKYSSIFHAELFSILQSLKNAKLLNIKKVL- 78
+ C LI + QL K EL S L+ + + ++
Sbjct: 230 YLLSIPISCPLIGVIQLAHYVVTAKLLGFT------PGELRSYLKGA----TGHSQGLVT 279
Query: 79 --II--SDSLSSF-----QAISNLYH-----------------------------PNPL- 99
I +DS SF +AI+ L+ P+P+
Sbjct: 280 AVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPML 339
Query: 100 -VKEIPHAELFSILQSLKNAELLNIKKVLIISDSL--SSFQAI-----SNLYHPNPLVKE 151
+ + ++ + N+ L K+V I SL + + +LY N +++
Sbjct: 340 SISNLTQEQVQDYVNKT-NSHLPAGKQVEI---SLVNGAKNLVVSGPPQSLYGLNLTLRK 395
Query: 152 IQETYSSAQISIKFLWCPSHPCWYFWKRSSSQ----ISIKFLWCPSHVGISGNDQADTEA 207
+ Q I F S+ S +FL
Sbjct: 396 AKAPSGLDQSRIPF----------------SERKLKFSNRFL------------------ 421
Query: 208 KKATSEPITN--HSLLLEEMKSLAKKHFYQKWNTTWSNVNPNENKLRR-IKSTTTPWKTS 264
P+ + HS LL L K + NV+ N ++ + T
Sbjct: 422 ------PVASPFHSHLLVPASDLINKDLVKN------NVSFNAKDIQIPVYDTFD-GS-- 466
Query: 265 SQKARLDEVCLMRMRIGHTKITHSYLFKREERPICDS-CHEPV----TVEHIILHCNKLR 319
D +R+ I+ I D PV T + H L
Sbjct: 467 ------D------LRVLSGSISER---------IVDCIIRLPVKWETTTQFKATHI--LD 503
Query: 320 FRPPSFLGNSLANILSDNPD 339
F P G L + N D
Sbjct: 504 FGPGGASG--LGVLTHRNKD 521
Score = 42.3 bits (99), Expect = 3e-04
Identities = 75/431 (17%), Positives = 128/431 (29%), Gaps = 151/431 (35%)
Query: 2 LQNRFREILHENYKD----------------FLKIYTDGSKDETGVGCALIIPQLNVTKR 45
LQ +F +IL E + FL Y + + VG Q +
Sbjct: 33 LQEQFNKILPEPTEGFAADDEPTTPAELVGKFLG-YVSSLVEPSKVG------QFDQVLN 85
Query: 46 FTLNKYSSIF------HAELFSILQSLKNAKLLNIKKVLIISDSLSSFQAISNLYHPNPL 99
L ++ + + HA +LQ + L+ K+++ + A P
Sbjct: 86 LCLTEFENCYLEGNDIHALAAKLLQE-NDTTLVKTKELI-----KNYITARIMAKRPFD- 138
Query: 100 VKEIPHAELFSILQSLKNAELLNIKKVLIISDSLSSF--QAISNLYHPNPLVKEIQETYS 157
K+ A LF + NA+L+ I F Q ++ Y +E+++ Y
Sbjct: 139 -KKSNSA-LFRAVGE-GNAQLVAI------------FGGQGNTDDY-----FEELRDLYQ 178
Query: 158 SAQISIKFLWCPSHPCWYFWKRSSSQISIKFL---------WCPSHVGISGNDQA-DTEA 207
+ + + L S + + + + + W + D +
Sbjct: 179 TYHVLVGDLIKFSAET--LSELIRTTLDAEKVFTQGLNILEW------LENPSNTPDKDY 230
Query: 208 KKATSEPITNHSLLLEEMKSLAKKHFYQKWNTTWSNVNPNENKLR-RIKSTTTPWK---- 262
S PI S L + LA H+ P E LR +K T +
Sbjct: 231 --LLSIPI---SCPLIGVIQLA--HYVVTAKL--LGFTPGE--LRSYLKGATGHSQGLVT 279
Query: 263 -----TSSQKARLDEVCLMRMRIGHTKITHSYLFK---REERPICDSCHE--PVTVEHII 312
+ + + LF R C+E P T
Sbjct: 280 AVAIAETDSWESFFVSVRKAITV---------LFFIGVR--------CYEAYPNT----- 317
Query: 313 LHCNKLRFRPPSFLGNSLANILSDNPDSISSLM---RFLKQNNFLKHIGDSTANAPVP-- 367
PPS L +SL +N + + S M L Q ++ N+ +P
Sbjct: 318 -------SLPPSILEDSL-----ENNEGVPSPMLSISNLTQEQVQDYVNK--TNSHLPAG 363
Query: 368 --------NGA 370
NGA
Sbjct: 364 KQVEISLVNGA 374
Score = 29.6 bits (66), Expect = 2.2
Identities = 7/46 (15%), Positives = 23/46 (50%), Gaps = 6/46 (13%)
Query: 326 LGNSLANILSDNPDSISSLM-----RFLKQNNFLKHIGDSTANAPV 366
G S+ +I+ +NP +++ + +++ N+ I ++ + +
Sbjct: 1657 YGFSILDIVINNPVNLTIHFGGEKGKRIRE-NYSAMIFETIVDGKL 1701
>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 = 39.1 bits (91), Expect = 7e-04
Identities = 29/111 (26%), Positives = 50/111 (45%), Gaps = 11/111 (9%)
Query: 20 IYTDGS-KDETGVGCA--LIIPQLNVTKRFTLNKYSSIFHAELFSILQSLKNAKLLNIKK 76
YTDGS + G A + + V L +S AEL ++ Q+LK A+ KK
Sbjct: 26 WYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAE---GKK 82
Query: 77 VLIISDSLSSFQAISNLYHPNPLVKEIPHAELF-SILQSLKNAELLNIKKV 126
+ + +DS +F H + +EI + ++L++L + L+I
Sbjct: 83 LNVYTDSRYAFATA----HVHSEGREIKNKNEILALLKALFLPKRLSIIHC 129
Score = 36.0 bits (83), Expect = 0.007
Identities = 24/122 (19%), Positives = 39/122 (31%), Gaps = 27/122 (22%)
Query: 106 AELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIQETYSSAQISIKF 165
AEL ++ Q+L ++ KK+ + +DS +I K
Sbjct: 66 AELIALTQAL---KMAEGKKLNVYTDSRY-------------AFATAHVHSEGREIKNKN 109
Query: 166 LWCPSHPCWYFWKRSSSQISIKFLWCPSHVG-----ISGNDQADTEAKKATSEPITNHSL 220
K + + CP H GN AD A++A + + S
Sbjct: 110 EI------LALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLETST 163
Query: 221 LL 222
LL
Sbjct: 164 LL 165
>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 = 37.3 bits (87), Expect = 0.002
Identities = 19/118 (16%), Positives = 31/118 (26%), Gaps = 33/118 (27%)
Query: 106 AELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHP-----NPLVKEIQETYSSAQ 160
E+ + L ++K A K+ I+ D I+ N + +
Sbjct: 53 GEIAAALYAVKKA-SQLGVKIRILHDY----AGIAFWATGEWKAKNEFTQAYAK------ 101
Query: 161 ISIKFLWCPSHPCWYFWKRSSSQISIKFLWCPSHVGISGNDQADTEAKKATSEPITNH 218
+ F +H G ND D +AK A H
Sbjct: 102 ---------------LMNQYRGIY--SFEKVKAHSGNEFNDYVDMKAKSALGIRDLEH 142
>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded
RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus
tokodaii} PDB: 3aly_A
Length = 149
Score = 35.8 bits (83), Expect = 0.007
Identities = 13/77 (16%), Positives = 25/77 (32%), Gaps = 10/77 (12%)
Query: 18 LKIYTDGSKDETGVGC-----ALIIPQLNVTKRFTLNKYSSIFH-----AELFSILQSLK 67
+ Y DG + G +I + + L + + AE ++ ++
Sbjct: 2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLME 61
Query: 68 NAKLLNIKKVLIISDSL 84
L I +I DS
Sbjct: 62 TMLRLGISSPIIKGDSQ 78
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 34.5 bits (80), Expect = 0.020
Identities = 9/41 (21%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 177 WKR---SSSQISIKFLWCPSHVGISGNDQADTEAKKATSEP 214
+ + + I+++ P H G GN++AD A++ +
Sbjct: 112 FVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAREGAKQS 152
>3v2d_F 50S ribosomal protein L4; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2hgq_F 2hgj_F 2hgu_F 2j03_F 2jl6_F 2jl8_F 2v47_F 2v49_F
2wdi_F 2wdj_F 2wdl_F 2wdn_F 2wh2_F 2wh4_F 2wrj_F 2wrl_F
2wro_F 2wrr_F 2x9s_F 2x9u_F ...
Length = 210
Score = 31.1 bits (71), Expect = 0.39
Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 13/79 (16%)
Query: 61 SILQSLKNAKLLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIPHAELFSILQSLKNA-E 119
L K A L + VL+++ + +A NL P V + L N +
Sbjct: 138 EFLAWAKEAGLDGSESVLLVTGNELVRRAARNL----PWVVTLAPEGL--------NVYD 185
Query: 120 LLNIKKVLIISDSLSSFQA 138
++ +++++ D+ FQ
Sbjct: 186 IVRTERLVMDLDAWEVFQN 204
>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 293
Score = 31.4 bits (71), Expect = 0.41
Identities = 11/81 (13%), Positives = 28/81 (34%), Gaps = 15/81 (18%)
Query: 61 SILQSLKNAKLLNIKKVLIISDSLSS--FQAISNLYHPNPLVKEIPHAELFSILQSLKNA 118
+ +++ L +K L L ++ N+ +K + L N
Sbjct: 189 DFIAAMQRWGLDPAEKSLFFLMDLVENVEKSGRNI----RTLKLLTPRSL--------NL 236
Query: 119 -ELLNIKKVLIISDSLSSFQA 138
++LN +K++ ++
Sbjct: 237 FDVLNAEKLVFTEGTIQYLNQ 257
>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 = 30.7 bits (68), Expect = 0.44
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 11/38 (28%)
Query: 178 KRSSSQI--SIKFLWCPSHVGISGNDQADTEAKKATSE 213
K++ ++ S+K L+ D A A KAT E
Sbjct: 19 KQALKKLQASLK-LYAD--------DSAPALAIKATME 47
Score = 29.1 bits (64), Expect = 1.5
Identities = 11/49 (22%), Positives = 17/49 (34%), Gaps = 24/49 (48%)
Query: 116 KNAELLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIQETYSSAQISIK 164
K A +KK + SL LY + S+ ++IK
Sbjct: 19 KQA----LKK---LQASL-------KLYADD----------SAPALAIK 43
Score = 27.6 bits (60), Expect = 5.3
Identities = 9/34 (26%), Positives = 12/34 (35%), Gaps = 16/34 (47%)
Query: 67 KNAKLLNIKKVLIISDSLSSFQAISNLYHPN--P 98
K A +KK + SL LY + P
Sbjct: 19 KQA----LKK---LQASL-------KLYADDSAP 38
Score = 27.2 bits (59), Expect = 7.3
Identities = 11/42 (26%), Positives = 12/42 (28%), Gaps = 21/42 (50%)
Query: 2 LQNRFREILHENYKDFLKIYTDGSKDETGVGCALIIPQLNVT 43
LQ LK+Y D S AL I T
Sbjct: 25 LQAS------------LKLYADDSAP------ALAI---KAT 45
>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 = 30.6 bits (70), Expect = 0.46
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 186 IKFLWCPSHVGISGNDQADTEAKKA 210
+ W P+H GI GN+Q D
Sbjct: 120 VYLAWVPAHKGIGGNEQVDKLVSAG 144
>2zjr_C 50S ribosomal protein L4; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: c.22.1.1 PDB: 1j5a_K* 1jzy_K* 1jzz_K*
1k01_K* 1nkw_C 1sm1_C* 2zjp_C* 2zjq_C 1jzx_K 3cf5_C*
3dll_C* 3pio_C* 3pip_C* 1nwy_C* 1nwx_C* 1xbp_C* 1pnu_C
1pny_C 1vor_F 1vou_F ...
Length = 205
Score = 30.3 bits (69), Expect = 0.84
Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 13/79 (16%)
Query: 61 SILQSLKNAKLLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIPHAELFSILQSLKNA-E 119
+ + K L +KVL+++D ++ +A N+ V +P A + N +
Sbjct: 132 NFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSW----VSVLPVAGV--------NVYD 179
Query: 120 LLNIKKVLIISDSLSSFQA 138
+L +++I + +L +
Sbjct: 180 ILRHDRLVIDAAALEIVEE 198
>3r8s_E 50S ribosomal protein L4; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_C
1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E
2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E*
2qbk_E* 2qov_E 2qox_E 2qoz_E* ...
Length = 201
Score = 29.9 bits (68), Expect = 0.91
Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 15/72 (20%)
Query: 70 KLLNIKKVLIISDSLSS--FQAISNLYHPNPLVKEIPHAELFSILQSLKNA-ELLNIKKV 126
K + ++ VLII+ L F A NL+ V + + L+ KV
Sbjct: 139 KDMALEDVLIITGELDENLFLAARNLHK----VDVRDATGI--------DPVSLIAFDKV 186
Query: 127 LIISDSLSSFQA 138
++ +D++ +
Sbjct: 187 VMTADAVKQVEE 198
>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal
domain, fusion protein, maltose binding protein, HYDR;
HET: MLR TAR; 2.25A {Mycobacterium tuberculosis}
Length = 141
Score = 29.2 bits (66), Expect = 1.1
Identities = 13/77 (16%), Positives = 22/77 (28%), Gaps = 16/77 (20%)
Query: 18 LKIYTDGSKD----ETGVGCALIIPQLNVTKRFTLNKYSSIFH-------AELFSILQSL 66
+ I DG G G + + S AE ++ L
Sbjct: 4 VVIEADGGSRGNPGPAGYGAVVWTADHSTVLA-----ESKQAIGRATNNVAEYRGLIAGL 58
Query: 67 KNAKLLNIKKVLIISDS 83
+A L + ++ DS
Sbjct: 59 DDAVKLGATEAAVLMDS 75
>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 = 30.1 bits (68), Expect = 1.5
Identities = 22/104 (21%), Positives = 40/104 (38%), Gaps = 36/104 (34%)
Query: 106 AELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHP----NPLVKEI-QETYSSAQ 160
EL +I +L+++ +V I++DS + I P + LV +I ++ +
Sbjct: 479 TELQAIYLALQDSG----LEVNIVTDSQYALGIIQA--QPDKSESELVNQIIEQLIKKEK 532
Query: 161 ISIKFLWCPSHPCWYFWKRSSSQISIKFLWCPSHVGISGNDQAD 204
+ + W P+H GI GN+Q D
Sbjct: 533 VYLA-------------------------WVPAHKGIGGNEQVD 551
>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 = 29.0 bits (66), Expect = 1.5
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 177 WKR---SSSQISIKFLWCPSHVGISGNDQADTEAKKATSEP 214
W+R + Q IK+ W H G N++AD A+ A P
Sbjct: 104 WQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNP 144
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 28.6 bits (65), Expect = 1.8
Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 3/41 (7%)
Query: 177 WKR---SSSQISIKFLWCPSHVGISGNDQADTEAKKATSEP 214
W+ ++ + F H N +AD A+ A E
Sbjct: 105 WQEILKLTTLHRVTFHKVKGHSDNPYNSRADELARLAIKEN 145
>1esx_A VPR protein; helix, amphipatic, turn, viral protein; NMR
{Synthetic} SCOP: j.11.1.1 PDB: 1m8l_A 1vpc_A 1x9v_A
Length = 96
Score = 27.8 bits (62), Expect = 1.9
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 221 LLEEMKSLAKKHFYQKW 237
LLEE+K+ A +HF + W
Sbjct: 22 LLEELKNEAVRHFPRIW 38
>1gxj_A SMC, chromosome segregation SMC protein; SMC dimerisation domain,
anti parallel coiled coil, SMC proteins; 2.0A
{Thermotoga maritima} SCOP: d.215.1.1 PDB: 1gxk_A
Length = 186
Score = 29.1 bits (66), Expect = 2.0
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 326 LGNSLANILSDNPDSISSLMRFLKQNN 352
LG + NI+ N D+ +++ FLKQN
Sbjct: 54 LGGTAQNIVVRNVDTAKAIVEFLKQNE 80
>1ceu_A Protein (HIV-1 regulatory protein N-terminal domain VPR); helical
domain, amphipaticity, viral protein; NMR {Synthetic}
SCOP: j.11.1.1 PDB: 1fi0_A
Length = 51
Score = 26.5 bits (59), Expect = 2.0
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 221 LLEEMKSLAKKHFYQKW 237
LLEE+K+ A +HF + W
Sbjct: 22 LLEELKNEAVRHFPRIW 38
>3nwc_A SMC protein; structural maintenance of chromosomes (SMC), SMC hinge
domai dimerization, DNA binding, cell cycle; 1.70A
{Pyrococcus furiosus}
Length = 189
Score = 28.4 bits (64), Expect = 2.9
Identities = 6/27 (22%), Positives = 15/27 (55%)
Query: 326 LGNSLANILSDNPDSISSLMRFLKQNN 352
LGN N++ ++ +++LK++
Sbjct: 59 LGNRADNVVVEDELVAEKAIKYLKEHK 85
>1gxl_A SMC, chromosome segregation SMC protein; SMC dimerisation domain,
anti parallel coiled coil, SMC proteins; 3.0A
{Thermotoga maritima} SCOP: d.215.1.1
Length = 213
Score = 28.4 bits (64), Expect = 3.5
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 326 LGNSLANILSDNPDSISSLMRFLKQNN 352
LG + NI+ N D+ +++ FLKQN
Sbjct: 66 LGGTAQNIVVRNVDTAKAIVEFLKQNE 92
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 27.9 bits (63), Expect = 3.6
Identities = 8/41 (19%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 177 WKR---SSSQISIKFLWCPSHVGISGNDQADTEAKKATSEP 214
W+ + + ++F + H G N++ D EA++
Sbjct: 109 WEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQ 149
>2r3s_A Uncharacterized protein; methyltransferase domain, structural
genomics, joint center structural genomics, JCSG,
protein structure initiative; HET: MSE; 2.15A {Nostoc
punctiforme}
Length = 335
Score = 28.5 bits (64), Expect = 3.8
Identities = 5/37 (13%), Positives = 10/37 (27%)
Query: 330 LANILSDNPDSISSLMRFLKQNNFLKHIGDSTANAPV 366
LA + + L +L F+ +
Sbjct: 45 LAQKCQTSERGMRMLCDYLVIIGFMTKQAEGYRLTSD 81
>3av4_A DNA (cytosine-5)-methyltransferase 1; CXXC-type zinc
finger/C5-methyltransferase family; HET: DNA; 2.75A {Mus
musculus} PDB: 3av5_A* 3av6_A*
Length = 1330
Score = 28.8 bits (63), Expect = 4.2
Identities = 19/112 (16%), Positives = 32/112 (28%), Gaps = 5/112 (4%)
Query: 194 HVGISGNDQADTEAKKATSEPITNHSLLLEEMKSLAKKHFYQKWNTTWSNVNPNENKLRR 253
H + + K E S + + LA Q+ T E
Sbjct: 269 HAQFVVSQVESYDEAKDDDETPIFLSPCMRALIHLAGVSLGQRRATRRVMGATKEKDKAP 328
Query: 254 IKSTTTPWKTSSQKARLDEVCLMRMRIGHTKITHSYLFKREERPICDSCHEP 305
K+TTT ++ + + K KR +C+ C +P
Sbjct: 329 TKATTTK-----LVYQIFDTFFSEQIEKYDKEDKENAMKRRRCGVCEVCQQP 375
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 27.5 bits (62), Expect = 5.4
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 177 WKR---SSSQISIKFLWCPSHVGISGNDQADTEAKKA 210
WKR ++ I + W H G + N++ D A+ A
Sbjct: 106 WKRLDKAAQLHQIDWRWVKGHAGHAENERCDQLARAA 142
>2e4u_A Metabotropic glutamate receptor 3; G-protein-coupled receptor,
neuron, central nerve system, SI protein; HET: NAG GLU;
2.35A {Rattus norvegicus} PDB: 2e4v_A* 2e4w_A* 2e4x_A*
2e4y_A*
Length = 555
Score = 28.2 bits (63), Expect = 5.8
Identities = 5/43 (11%), Positives = 13/43 (30%)
Query: 54 IFHAELFSILQSLKNAKLLNIKKVLIISDSLSSFQAISNLYHP 96
+ + + A +N + SD + ++I
Sbjct: 249 VLFMRSDDSRELIAAANRVNASFTWVASDGWGAQESIVKGSEH 291
>1bdg_A Hexokinase; phosphotransferase; HET: GLC; 2.60A {Schistosoma
mansoni} SCOP: c.55.1.3 c.55.1.3
Length = 451
Score = 28.0 bits (62), Expect = 5.9
Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 1 MLQNRFREILHENYKDFLKIYTDGSKDETGVGCALI 36
+ + ++ +N + L++ DGS G G A I
Sbjct: 412 RMTDMVDKLKPKNTRFCLRLSEDGS----GKGAAAI 443
>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 = 27.8 bits (62), Expect = 7.5
Identities = 23/104 (22%), Positives = 37/104 (35%), Gaps = 36/104 (34%)
Query: 106 AELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHP----NPLVKEI-QETYSSAQ 160
AEL + +L ++ KV II DS +++ P + +V +I +E
Sbjct: 476 AELEAFAMALTDSG----PKVNIIVDSQYVMGIVAS--QPTESESKIVNQIIEEMIKKEA 529
Query: 161 ISIKFLWCPSHPCWYFWKRSSSQISIKFLWCPSHVGISGNDQAD 204
I + W P+H GI GN + D
Sbjct: 530 IYVA-------------------------WVPAHKGIGGNQEVD 548
>1w9y_A 1-aminocyclopropane-1-carboxylate oxidase 1; oxygenase, 2OG
oxygenase, ACCO, ACC oxidase; 2.1A {Petunia hybrida}
SCOP: b.82.2.1 PDB: 1wa6_X
Length = 319
Score = 27.2 bits (61), Expect = 9.9
Identities = 6/60 (10%), Positives = 23/60 (38%), Gaps = 13/60 (21%)
Query: 215 ITNH---SLLLEEMKSLAKKHFYQKWNTTWSNVNPNENKLRRIKSTTTPWKTSSQKARLD 271
+ NH +++ ++ + K H+ + E + + + ++ ++ +D
Sbjct: 36 LVNHGIPREVMDTVEKMTKGHYKK----------CMEQRFKELVASKALEGVQAEVTDMD 85
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 0.408
Gapped
Lambda K H
0.267 0.0759 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,719,243
Number of extensions: 318172
Number of successful extensions: 984
Number of sequences better than 10.0: 1
Number of HSP's gapped: 966
Number of HSP's successfully gapped: 65
Length of query: 389
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 294
Effective length of database: 4,049,298
Effective search space: 1190493612
Effective search space used: 1190493612
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: 58 (26.1 bits)