RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16039
(586 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 = 54.1 bits (129), Expect = 1e-07
Identities = 87/596 (14%), Positives = 179/596 (30%), Gaps = 202/596 (33%)
Query: 43 YLSRHTDMLCRGTRIWRSLLTRSPLGLTRPQPVATHCCLGLTGRLSASVRQTARTPLSRA 102
Y+ + D L +++ + ++R QP +L ++ + L A
Sbjct: 112 YIEQR-DRLYNDNQVF------AKYNVSRLQPYL---------KLRQALLE-----LRPA 150
Query: 103 D---------VGRDSLRSAADRKDVIRFFFREEKREMGDK----KILFRKTLDEVLKWSQ 149
G+ + A DV + + + +M K + + + VL+
Sbjct: 151 KNVLIDGVLGSGKTWV--AL---DVCLSY--KVQCKMDFKIFWLNLKNCNSPETVLE--M 201
Query: 150 ANGLIFSTDPQKSVCVLFSRARNPSFPKLYYSGVELKFANSTKFLGLVWDSKLNWSLHIN 209
L++ DP SR+ D N L I+
Sbjct: 202 LQKLLYQIDPN-----WTSRS----------------------------DHSSNIKLRIH 228
Query: 210 YVKTRAAKALNALKMVCNKNYGVRRALLL---VFYKSFILPIFDYGC-VVYSSGKDHILK 265
++ L L + +K Y LL+ V F+ C ++ ++ +
Sbjct: 229 SIQAE----LRRL--LKSKPY--ENCLLVLLNVQNAK-AWNAFNLSCKILLTTRFKQVTD 279
Query: 266 RLNPIHNAGIRIATGALMTSP-----ICSLYVE----------SGIGPLSLR------RD 304
L+ I + ++ +P + Y++ P L RD
Sbjct: 280 FLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRD 339
Query: 305 KIIM----RYV------SKIGSCPSN--PA-HKELYHTNINVNDFPPNKPKP---LCVRI 348
+ ++V + I S + PA +++++ ++V FPP+ P L +
Sbjct: 340 GLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD-RLSV--FPPSAHIPTILLSLIW 396
Query: 349 KDMSDFLPLITDSEFVPFT---RPRPPWSFQVPSIDFSLHLDNKDNIPPIVFQQHFHDLV 405
D+ ++ ++ ++ + + +PSI L + ++ + H +
Sbjct: 397 FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLEN-------EYALHRSI 449
Query: 406 TNKYS-DSVLCFTDGSKTVNST-SCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLI 463
+ Y+ D ++ IG+ H + E M + ++
Sbjct: 450 VDHYNIPKTFDSDDLIPPYLDQYFYSH-IGH--HLKNIEH------PERMTLF----RMV 496
Query: 464 FLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITG 523
FL +F +LE K + W S G
Sbjct: 497 FL---DF----------------------------RFLEQKIRHDSTA--WNAS--GSIL 521
Query: 524 NELVDIAA-RNPITNITLKNCTSF--------DFRPNDDSYGTQCRYWSLLTYIMM 570
N L + + I N + DF P + +Y LL +M
Sbjct: 522 NTLQQLKFYKPYIC----DNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALM 573
>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 = 50.2 bits (120), Expect = 2e-07
Identities = 29/143 (20%), Positives = 48/143 (33%), Gaps = 16/143 (11%)
Query: 416 FTDGSKTVNS--TSCAYSIG---NQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNF 470
+TDGS + ++ + A L S +EL+A+ + L
Sbjct: 27 YTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALT---QALKMAEGKKL 83
Query: 471 TLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCG-----ITG 523
+ +DS A + + + L+A K L+ + CP H G
Sbjct: 84 NVYTDSRYAFATAHVHSEGREIKNKNEI-LALLKALFLPKRLSIIHCPGHQKGNSAEARG 142
Query: 524 NELVDIAARNPITNITLKNCTSF 546
N + D AAR L+ T
Sbjct: 143 NRMADQAAREAAMKAVLETSTLL 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 = 41.2 bits (97), Expect = 1e-04
Identities = 22/137 (16%), Positives = 40/137 (29%), Gaps = 22/137 (16%)
Query: 410 SDSVLCFTDGSKTVNSTSCAYSI---GNQVHAFKL------NKVNSVLSSELMAILLCVK 460
+TDGS + AY+ G + ++ E+ A L VK
Sbjct: 4 RTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVK 63
Query: 461 NLIFLPSTNFTLISDSMSALLAISN-CKNDH----PLVSLVYTTWLEAKDCGKNLNFVWC 515
L ++ D I+ + + + +F
Sbjct: 64 KASQLGV-KIRILHDYAG----IAFWATGEWKAKNEFTQAYAKLMNQYR---GIYSFEKV 115
Query: 516 PSHCGITGNELVDIAAR 532
+H G N+ VD+ A+
Sbjct: 116 KAHSGNEFNDYVDMKAK 132
>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 = 42.3 bits (99), Expect = 5e-04
Identities = 69/377 (18%), Positives = 112/377 (29%), Gaps = 135/377 (35%)
Query: 23 ENPSSCPPHRCPP--CSSTLS-PYLSRHTDMLCRGTRIWRSLLTRSPLGLTRPQPVATHC 79
ENPS+ P S +S P L + ++T LG T P + ++
Sbjct: 220 ENPSNTPD---KDYLLSIPISCP-LIGVIQLAH-------YVVTAKLLGFT-PGELRSYL 267
Query: 80 CLGLTGRLSASVRQTARTPLSRADVGRDSLRSAADRKDVIRFFFREEKREMGDKKILFR- 138
G TG V TA ++ D +S + + I F +G R
Sbjct: 268 K-GATGHSQGLV--TA-VAIAETD-SWESFFVSVRK--AITVLFF-----IG-----VRC 310
Query: 139 ------KTLD-EVLKWSQANGLIFSTDPQKSV-----CVLFSRAR--NPSFPKLYYSGVE 184
+L +L+ S N + P S+ + N P VE
Sbjct: 311 YEAYPNTSLPPSILEDSLENNEGVPS-PMLSISNLTQEQVQDYVNKTNSHLPA--GKQVE 367
Query: 185 LKFANSTKFLGLVWDSKLNWSLHINYVKTRAAKALNAL-----KMVCNKNYGVRRALL-- 237
+ N K N V + ++L L K R
Sbjct: 368 ISLVNGAK----------------NLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSE 411
Query: 238 --LVFYKSFILPIF-----DYGCVVYSSGKDHILKRLN-------------PIHN----A 273
L F F LP+ D I K L P+++ +
Sbjct: 412 RKLKFSNRF-LPVASPFHSHL----LVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGS 466
Query: 274 GIRIATGAL---MTSPICSLYVE--------------------SGIGPLSLR-RD----K 305
+R+ +G++ + I L V+ SG+G L+ R +D +
Sbjct: 467 DLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVR 526
Query: 306 IIMRYVSKIGSCPSNPA 322
+I+ G+ NP
Sbjct: 527 VIV-----AGTLDINPD 538
Score = 38.9 bits (90), Expect = 0.006
Identities = 82/550 (14%), Positives = 143/550 (26%), Gaps = 227/550 (41%)
Query: 10 SILPLALLTIQAPENPSS---------------CPPHRCPPCSSTLSPYLSR-HTDMLCR 53
ILP A + P++ P + L+ L+ L
Sbjct: 39 KILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYL-E 97
Query: 54 GTRI---WRSLLTRSPLGLTRPQPVATHCCLGLTGRLSASVRQTARTPLSRADVGRDSLR 110
G I LL + L + + + + ++A R A+ P + +L
Sbjct: 98 GNDIHALAAKLLQENDTTLVKTKEL-------IKNYITA--RIMAKRPFDKK--SNSALF 146
Query: 111 SAADRKDVIRFF------------FREEKREM--------------------------GD 132
A + + F EE R++ D
Sbjct: 147 RAVGEGNA-QLVAIFGGQGNTDDYF-EELRDLYQTYHVLVGDLIKFSAETLSELIRTTLD 204
Query: 133 KKILFRKTLDEVLKWSQANGLIFSTDPQKSVCVLFSRARNP-SFPKL-------YY---- 180
+ +F + L+ +L+W + + L P S P + Y
Sbjct: 205 AEKVFTQGLN-ILEW------LENPSNTPDKDYL---LSIPISCPLIGVIQLAHYVVTAK 254
Query: 181 -SGV---ELKF---ANSTKFLGLV----------WDS-------KLNWSLHINYVKTRA- 215
G EL+ + GLV W+S + I A
Sbjct: 255 LLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAY 314
Query: 216 ---AKALNALKMVCNKNYGVRRALLLVFYKSFILPIFDYGCVVYSSG--KDHILKRLN-- 268
+ + L+ N GV +L + S ++ + +N
Sbjct: 315 PNTSLPPSILEDSLENNEGVPSPMLSI------------------SNLTQEQVQDYVNKT 356
Query: 269 ----PIHNAGIRIA----------TGALMTSPICSLY----------VESGIG----PLS 300
P + I+ +G P SLY SG+ P S
Sbjct: 357 NSHLPAGKQ-VEISLVNGAKNLVVSG-----PPQSLYGLNLTLRKAKAPSGLDQSRIPFS 410
Query: 301 LRRDKIIMRYVSKIGSCPSNPAHKELYHTNINVNDFPPNKPKPLCVRIKDMSDFLPLITD 360
R+ K R++ + + P +H+ L + LI
Sbjct: 411 ERKLKFSNRFL-PV-ASP--------FHS-------------HL------LVPASDLINK 441
Query: 361 ---SEFVPFTRPRPPWSFQVPSIDFSLHLDNKD------NIPPIVFQQHFHDLV----TN 407
V F Q+P D D D +I + V T
Sbjct: 442 DLVKNNVSFNAK----DIQIPVYDTF---DGSDLRVLSGSISERIVDCIIRLPVKWETTT 494
Query: 408 KYSDS-VLCF 416
++ + +L F
Sbjct: 495 QFKATHILDF 504
Score = 32.3 bits (73), Expect = 0.51
Identities = 28/172 (16%), Positives = 48/172 (27%), Gaps = 52/172 (30%)
Query: 326 LYHTNINVNDFP-PNKPKPLCVRIKDMSDF---LPLITDSEFVPFTRPRPPWS------- 374
L H ++ P + ++++ F LP T+ F P +
Sbjct: 11 LSHGSLEH-VLLVPTASFFIASQLQE--QFNKILPEPTEG----FAADDEPTTPAELVGK 63
Query: 375 FQVPSIDFSLHLDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGN 434
F + + L F ++ + F + Y GN
Sbjct: 64 F----LGYVSSLVEPSK------VGQFDQVLNL----CLTEFEN----------CYLEGN 99
Query: 435 QVHAFKLNKVNSVLSSELMAILLCVKNLI--FLPS---TNFTLISDSMSALL 481
+HA L E L+ K LI ++ + S SAL
Sbjct: 100 DIHALAAK-----LLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALF 146
>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 = 37.8 bits (88), Expect = 0.008
Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 10/81 (12%)
Query: 450 SELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDCG 507
+EL AI L +++ +++DS AL I K++ LV+ + L K+
Sbjct: 479 TELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI-IEQLIKKE-- 531
Query: 508 KNLNFVWCPSHCGITGNELVD 528
+ W P+H GI GNE VD
Sbjct: 532 -KVYLAWVPAHKGIGGNEQVD 551
>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 = 34.3 bits (79), Expect = 0.13
Identities = 17/81 (20%), Positives = 37/81 (45%), Gaps = 10/81 (12%)
Query: 450 SELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDCG 507
+EL A + + + +I DS + +++ +++ +V+ + + K+
Sbjct: 476 AELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQPTESESKIVNQI-IEEMIKKE-- 528
Query: 508 KNLNFVWCPSHCGITGNELVD 528
+ W P+H GI GN+ VD
Sbjct: 529 -AIYVAWVPAHKGIGGNQEVD 548
>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 = 32.1 bits (74), Expect = 0.19
Identities = 11/30 (36%), Positives = 14/30 (46%)
Query: 509 NLNFVWCPSHCGITGNELVDIAARNPITNI 538
+ W P+H GI GNE VD I +
Sbjct: 119 KVYLAWVPAHKGIGGNEQVDKLVSAGIRKV 148
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 30.6 bits (70), Expect = 0.67
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 509 NLNFVWCPSHCGITGNELVDIAARN 533
++ ++ P H G GNE D AR
Sbjct: 123 DIQWMHVPGHSGFIGNEEADRLARE 147
>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 = 30.2 bits (69), Expect = 0.97
Identities = 11/34 (32%), Positives = 15/34 (44%)
Query: 509 NLNFVWCPSHCGITGNELVDIAARNPITNITLKN 542
+ + W H G NE D AR N TL++
Sbjct: 115 QIKWEWVKGHAGHPENERADELARAAAMNPTLED 148
>1ncn_A T lymphocyte activation antigen CD86; IG V, beta strands, immune
system; 2.70A {Homo sapiens} SCOP: b.1.1.1 PDB: 1i85_A
Length = 110
Score = 28.3 bits (63), Expect = 3.0
Identities = 7/37 (18%), Positives = 18/37 (48%)
Query: 178 LYYSGVELKFANSTKFLGLVWDSKLNWSLHINYVKTR 214
Y G E + +K++G +W+L ++ ++ +
Sbjct: 43 EVYLGKEKFDSVHSKYMGRTSFDSDSWTLRLHNLQIK 79
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 27.8 bits (63), Expect = 5.4
Identities = 7/31 (22%), Positives = 9/31 (29%)
Query: 509 NLNFVWCPSHCGITGNELVDIAARNPITNIT 539
+ F H N D AR I +
Sbjct: 116 RVTFHKVKGHSDNPYNSRADELARLAIKENS 146
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 28.1 bits (62), Expect = 6.6
Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 16/44 (36%)
Query: 32 RCPPCSSTLSPYL---SRHTDMLCR------GTRI------WRS 60
CP C P + D++C ++ WR+
Sbjct: 23 TCPECKVY-PPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRT 65
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 0.137 0.426
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: 8,737,496
Number of extensions: 509669
Number of successful extensions: 922
Number of sequences better than 10.0: 1
Number of HSP's gapped: 915
Number of HSP's successfully gapped: 19
Length of query: 586
Length of database: 6,701,793
Length adjustment: 99
Effective length of query: 487
Effective length of database: 3,937,614
Effective search space: 1917618018
Effective search space used: 1917618018
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: 60 (26.8 bits)