RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10247
(315 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 = 50.6 bits (120), Expect = 4e-07
Identities = 39/257 (15%), Positives = 81/257 (31%), Gaps = 80/257 (31%)
Query: 89 ILKCLEYIMSLVIVDN---------FNFRS-VIICSDSRSSLEALRTQFTLNEISFNILC 138
+LK Y L+++ N FN +++ + + + L T + +
Sbjct: 237 LLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSM 296
Query: 139 TVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSIYAQLLKSVVVK------DVIIQS 192
T+ + + + +K+L Q L V+ +I +S
Sbjct: 297 TLTPDEVKSLLLKYLDCR--------------------PQDLPREVLTTNPRRLSIIAES 336
Query: 193 KKTILNEWKTDWLENQLYERNKLRE-IKKDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQ 251
+ L W W +KL I+ + + +R D ++V
Sbjct: 337 IRDGLATWDN-WKH---VNCDKLTTIIESSLNVLEPAEYRKMFDRLSV------------ 380
Query: 252 EYLFKKDAP-PECRTCGVVLTI----------KHILTQCKAYAALRRKWKLESTMEKILQ 300
F A P ++L++ ++ + Y+ + ++ K EST+
Sbjct: 381 ---FPPSAHIPT-----ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPK-ESTIS---- 427
Query: 301 DDHDI--VLRCINNNRY 315
I L+ N Y
Sbjct: 428 -IPSIYLELKVKLENEY 443
Score = 32.1 bits (72), Expect = 0.28
Identities = 22/108 (20%), Positives = 36/108 (33%), Gaps = 11/108 (10%)
Query: 181 KSVVVKDVIIQSKKTILNEWKTDWLE-NQLYERNKLREIKKDIKTWKTVHWRNRRDEIAV 239
K+ V DV + K ++K WL + E+ + + +W +R D +
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN 222
Query: 240 CRLRIGHTKLTQEYLFKKDAPPECRTCGVVL-------TIKHILTQCK 280
+LRI + L K C +VL CK
Sbjct: 223 IKLRIHSIQAELRRLLKSKPYENCL---LVLLNVQNAKAWNAFNLSCK 267
>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 = 42.0 bits (99), Expect = 5e-05
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 143 LKARDINIKFLWIPSHCGIVENERVDQAAKNSI 175
+ F + +H G N+ VD AK+++
Sbjct: 103 MNQYRGIYSFEKVKAHSGNEFNDYVDMKAKSAL 135
>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 = 42.0 bits (98), Expect = 2e-04
Identities = 52/336 (15%), Positives = 95/336 (28%), Gaps = 118/336 (35%)
Query: 8 PWIIASPTIIYLLNENKKSLIPQQARNSFLEFKSQNLDSLFIFTDGTKTATNTGFAYVSG 67
P ++ ++ ++L L+P SF SQ + F T GFA
Sbjct: 8 PLTLSHGSLEHVL------LVPT---ASFF-IASQLQEQ---FNKILPEPT-EGFA---A 50
Query: 68 DLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFN-FRSVIICSDSRSSLEALRTQ 126
D + ++ AE + K L Y+ SLV F V+ L
Sbjct: 51 D-------DEPTTP--AELVG--KFLGYVSSLVEPSKVGQFDQVL-----NLCLTEFENC 94
Query: 127 FTL--NEISFNILCTVHQLKAR-------DINIKFLWIPS--HCGIVENERVD------- 168
+ L N+I H L A+ + I + I+ D
Sbjct: 95 Y-LEGNDI--------HALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSAL 145
Query: 169 -QAA---KNSIYAQL------------LKSV------VVKDVIIQSKKTILNEWKTDWLE 206
+A + A L+ + +V D+I S +T+ +T
Sbjct: 146 FRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDA 205
Query: 207 NQLYERNKLREIKKDIKTWKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPECRTC 266
+++ + +I W L ++YL +
Sbjct: 206 EKVFTQGL------NILEW----------------LENPSNTPDKDYL---------LSI 234
Query: 267 GVVLTIKHI-LTQCKAYAALRRKWKLE-STMEKILQ 300
+ + I + Q Y + + L+
Sbjct: 235 PISCPL--IGVIQLAHYVVTAKLLGFTPGELRSYLK 268
Score = 40.0 bits (93), Expect = 8e-04
Identities = 40/268 (14%), Positives = 68/268 (25%), Gaps = 114/268 (42%)
Query: 35 SFLEFKSQNLDSLFIFTDGTKTATNTGFAYVSGDLCQ-TYRLNPLSSIFTAES------- 86
SF + + LF G C Y L +S
Sbjct: 291 SFFVSVRKAITVLFF----------IGVR------CYEAYPNTSLPPSILEDSLENNEGV 334
Query: 87 ----LAI----LKCLE----------------YIMSLVIVDNFNFRSVIICSDSRSSLEA 122
L+I + ++ I SLV N ++ S SL
Sbjct: 335 PSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEI-SLV-----NGAKNLVVSGPPQSLYG 388
Query: 123 LRTQF-------TLN--EISFNILCTVHQLKARDINIKFLWI--PSHCGIVENERVDQAA 171
L L+ I F+ + K + + +FL + P H
Sbjct: 389 LNLTLRKAKAPSGLDQSRIPFS------ERKLK-FSNRFLPVASPFHS------------ 429
Query: 172 KNSIYAQLLKSVVVKDVIIQ--SKKTILNEWKTDWLENQLYE----RNKLREIKKDIK-- 223
LL D+I + K + + ++ +Y+ + LR + I
Sbjct: 430 ------HLLVPAS--DLINKDLVKNNV--SFNAKDIQIPVYDTFDGSD-LRVLSGSISER 478
Query: 224 -----TWKTVHWRNRRDEIAVCRLRIGH 246
V W + + H
Sbjct: 479 IVDCIIRLPVKWE------TTTQFKATH 500
Score = 35.8 bits (82), Expect = 0.017
Identities = 15/92 (16%), Positives = 34/92 (36%), Gaps = 15/92 (16%)
Query: 15 TIIYLLNENKKSLIP-------QQARNSFLEFKSQ-----NLDSLFIFTDGTKTATNTGF 62
+I+ ++ N +L ++ R ++ + L + IF + + +T+ F
Sbjct: 1660 SILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTF 1719
Query: 63 AYVSGDLCQTYRLNPLSSIFTAESLAILKCLE 94
G L T P ++ A + L+
Sbjct: 1720 RSEKGLLSATQFTQP--ALTLM-EKAAFEDLK 1748
>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 = 40.2 bits (94), Expect = 2e-04
Identities = 27/151 (17%), Positives = 50/151 (33%), Gaps = 22/151 (14%)
Query: 47 LFIFTDGTKTATN----TGFAYVSGD-LCQTYRLNPLSSIFTAESLAILKCLEYIMSLVI 101
+TDG+ G A + + L +S AE +A+ + L+
Sbjct: 24 YTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEG--- 80
Query: 102 VDNFNFRSVIICSDSRSSLEALRTQFTLNEISFN--ILCTVHQLKARDINIKFLWIPSHC 159
+ + + +DSR + EI IL + L + + P H
Sbjct: 81 ------KKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPK-RLSIIHCPGHQ 133
Query: 160 GIVE-----NERVDQAAKNSIYAQLLKSVVV 185
N DQAA+ + +L++ +
Sbjct: 134 KGNSAEARGNRMADQAAREAAMKAVLETSTL 164
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 37.9 bits (89), Expect = 0.001
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 148 INIKFLWIPSHCGIVENERVDQAAKNSI 175
++I+++ +P H G + NE D+ A+
Sbjct: 122 MDIQWMHVPGHSGFIGNEEADRLAREGA 149
>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 = 37.5 bits (88), Expect = 0.001
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 149 NIKFLWIPSHCGIVENERVDQAAKNSI 175
+ W+P+H GI NE+VD+ I
Sbjct: 119 KVYLAWVPAHKGIGGNEQVDKLVSAGI 145
>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 = 36.7 bits (86), Expect = 0.003
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 149 NIKFLWIPSHCGIVENERVDQAAKNSI 175
IK+ W+ H G ENER D+ A+ +
Sbjct: 115 QIKWEWVKGHAGHPENERADELARAAA 141
>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 = 0.006
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 149 NIKFLWIPSHCGIVENERVDQAAKNSI 175
+ F + H N R D+ A+ +I
Sbjct: 116 RVTFHKVKGHSDNPYNSRADELARLAI 142
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 35.6 bits (83), Expect = 0.007
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 149 NIKFLWIPSHCGIVENERVDQAAKNSI 175
I + W+ H G ENER DQ A+ +
Sbjct: 117 QIDWRWVKGHAGHAENERCDQLARAAA 143
>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 = 0.007
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 149 NIKFLWIPSHCGIVENERVDQAAKNSI 175
++F ++ H G ENERVD+ A+
Sbjct: 120 RVRFHFVKGHTGHPENERVDREARRQA 146
>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 = 31.1 bits (69), Expect = 0.25
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 9/31 (29%)
Query: 271 TIKHILTQCKAYA-----ALRRKWKLESTME 296
+K + K YA AL +++TME
Sbjct: 21 ALKKLQASLKLYADDSAPAL----AIKATME 47
>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 = 2.7
Identities = 10/65 (15%), Positives = 24/65 (36%), Gaps = 23/65 (35%)
Query: 106 NFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENE 165
N V+ C + + + +F+ ++ +C + CG+V ++
Sbjct: 17 NLNIVLTCPECKVYPPKIVERFSEGDV----VC------------------ALCGLVLSD 54
Query: 166 R-VDQ 169
+ VD
Sbjct: 55 KLVDT 59
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 28.7 bits (64), Expect = 2.9
Identities = 8/24 (33%), Positives = 15/24 (62%), Gaps = 3/24 (12%)
Query: 120 LEAL--RTQFTLNEISFNILCTVH 141
+E + RT F+ E++FN+L +
Sbjct: 689 IEKMGVRT-FSQKEMAFNLLGLLT 711
>3sbg_A PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain, JAB1/MPN domain;
3.28A {Saccharomyces cerevisiae}
Length = 565
Score = 27.8 bits (61), Expect = 5.0
Identities = 15/74 (20%), Positives = 25/74 (33%), Gaps = 2/74 (2%)
Query: 168 DQAAKNSIYAQLLKSVVVKDVIIQSKKTILN--EWKTDWLENQLYERNKLREIKKDIKTW 225
+ K ++ L +KD+I+ + K LE E+ E
Sbjct: 230 EYGRKYNVNISALTQTEIKDIILGQNIKAPSVKRQKMAELEAARSEKQNDEEAAGASTVM 289
Query: 226 KTVHWRNRRDEIAV 239
KT + +EI V
Sbjct: 290 KTKTINAQGEEIVV 303
>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 = 27.4 bits (61), Expect = 6.7
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 6/62 (9%)
Query: 110 VIICSDSRSSLEALRTQ--FTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVENERV 167
V I +DS+ +L ++ Q + +E+ I + QL ++ + W+P+H GI NE+V
Sbjct: 495 VNIVTDSQYALGIIQAQPDKSESELVNQI---IEQLIKKE-KVYLAWVPAHKGIGGNEQV 550
Query: 168 DQ 169
D+
Sbjct: 551 DK 552
>2kkp_A Phage integrase; SAM-like domain, alpha-helical bundle, structural
genomics, PSI-2, protein structure initiative; NMR
{Moorella thermoacetica atcc 39073}
Length = 117
Score = 26.1 bits (58), Expect = 7.3
Identities = 8/29 (27%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 189 IIQSKKTILNEWKTDWLENQLYERNKLRE 217
+I+ K + +W WL + Y + LR+
Sbjct: 1 MIEPSKITVEQWLNRWLTD--YAKPHLRQ 27
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
0.322 0.135 0.408
Gapped
Lambda K H
0.267 0.0569 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,660,106
Number of extensions: 258454
Number of successful extensions: 453
Number of sequences better than 10.0: 1
Number of HSP's gapped: 451
Number of HSP's successfully gapped: 22
Length of query: 315
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 222
Effective length of database: 4,105,140
Effective search space: 911341080
Effective search space used: 911341080
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 (22.0 bits)
S2: 57 (26.1 bits)