RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2213
(194 letters)
>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 = 1e-04
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 8/75 (10%)
Query: 4 LPKEKFVIISDSKSTLLALSNPSNTNPI--VSLIHSCWSDLLCCGKQLAFLWCPSHTG-- 59
+K + +DS+ S I + I + L K+L+ + CP H
Sbjct: 78 AEGKKLNVYTDSRYAFATAHVHSEGREIKNKNEILAL-LKALFLPKRLSIIHCPGHQKGN 136
Query: 60 ---IQGNEAVDRAAR 71
+GN D+AAR
Sbjct: 137 SAEARGNRMADQAAR 151
>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 = 36.6 bits (84), Expect = 0.004
Identities = 44/272 (16%), Positives = 84/272 (30%), Gaps = 103/272 (37%)
Query: 3 SLPKEKFVIISDSKSTLLA--LSNPSNTNPIVS-LIHSCWSD----LLCCGKQ------- 48
+L K K +I K+ + A ++ S L + + G Q
Sbjct: 115 TLVKTKELI----KNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYF 170
Query: 49 --LAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDL--WQQSW 104
L L+ H + + + +A +L L + + D + + + ++ W ++
Sbjct: 171 EELRDLYQTYHVLVG--DLIKFSA----ETLSEL-IRTTLDAEKVFTQGL-NILEWLENP 222
Query: 105 SSIPNSNKLKSIK---PIIGPWPSSDRQ-NRYEEVVICR--------MRIGHTRATHGH- 151
S+ P+ + L SI P+IG Q Y VV + +R + + GH
Sbjct: 223 SNTPDKDYLLSIPISCPLIGVI-----QLAHY--VVTAKLLGFTPGELR-SYLKGATGHS 274
Query: 152 ----------------------------LFK---RA---------PPST------CGCGE 165
LF R PPS G
Sbjct: 275 QGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGV 334
Query: 166 ---ILSVQHILTCALHGHIR---ASLPTPPAL 191
+LS+ ++ + ++ + LP +
Sbjct: 335 PSPMLSISNLTQEQVQDYVNKTNSHLPAGKQV 366
Score = 32.3 bits (73), Expect = 0.11
Identities = 27/161 (16%), Positives = 53/161 (32%), Gaps = 64/161 (39%)
Query: 86 EDFKPFIRKLIK------------------------DL--WQQSWSSIPNSNKLKSIK-- 117
+ + + LIK ++ W ++ S+ P+ + L SI
Sbjct: 178 QTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPIS 237
Query: 118 -PIIGPWPSSDRQ-NRYEEVVICRMRIGHTRATHGHLFKRAPPSTCGCGE-ILS------ 168
P+IG Q Y VV + +G T G L +T G + +++
Sbjct: 238 CPLIGVI-----QLAHY--VVTAK-LLGF---TPGELRSYLKGAT-GHSQGLVTAVAIAE 285
Query: 169 ----------VQHILTCA----LHGHIRASLPT-PPALTDD 194
V+ +T + + + PP++ +D
Sbjct: 286 TDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILED 326
Score = 29.2 bits (65), Expect = 1.1
Identities = 6/20 (30%), Positives = 8/20 (40%), Gaps = 3/20 (15%)
Query: 172 ILTCALHGHIRASLPTPPAL 191
L+ HG + L P A
Sbjct: 10 TLS---HGSLEHVLLVPTAS 26
Score = 26.9 bits (59), Expect = 5.8
Identities = 28/146 (19%), Positives = 49/146 (33%), Gaps = 45/146 (30%)
Query: 6 KEKFVIISDSK----STLL----ALSNPSNTNPIVSLIHSCWSDLLCC-GKQLAFLWCPS 56
K K +I +D+ S L AL++ ++ I SL+ +++ G + P
Sbjct: 1748 KSKGLIPADATFAGHS--LGEYAALASLADVMSIESLV-----EVVFYRGMTMQVA-VPR 1799
Query: 57 HTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIRKLIKDL-W-----------QQ-- 102
G A NP S E + + ++ K W QQ
Sbjct: 1800 --DELGRSNYGMIAINPGR---VAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYV 1854
Query: 103 ---------SWSSIPNSNKLKSIKPI 119
+ +++ N KL+ I I
Sbjct: 1855 AAGDLRALDTVTNVLNFIKLQKIDII 1880
>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 = 34.3 bits (79), Expect = 0.008
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 47 KQLAFLWCPSHTGIQGNEAVDRAAR 71
+F +H+G + N+ VD A+
Sbjct: 108 GIYSFEKVKAHSGNEFNDYVDMKAK 132
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 34.1 bits (79), Expect = 0.012
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 41 DLLCCGKQLAFLWCPSHTGIQGNEAVDRAARN 72
+ L G + ++ P H+G GNE DR AR
Sbjct: 116 ERLTQGMDIQWMHVPGHSGFIGNEEADRLARE 147
>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 = 34.4 bits (79), Expect = 0.021
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 11 IISDSKSTL-LALSNPSNT-NPIVSLIHSCWSDLLCCGKQLAFL-WCPSHTGIQGNEAVD 67
I++DS+ L + + P + + +V+ I K+ +L W P+H GI GNE VD
Sbjct: 497 IVTDSQYALGIIQAQPDKSESELVNQIIE-----QLIKKEKVYLAWVPAHKGIGGNEQVD 551
Query: 68 R 68
+
Sbjct: 552 K 552
>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 = 32.9 bits (76), Expect = 0.028
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 41 DLLCCGKQLAFLWCPSHTGIQGNEAVDRAARN 72
+ L +++ W P+H GI GNE VD+
Sbjct: 112 EQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA 143
>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 = 33.7 bits (76), Expect = 0.032
Identities = 25/142 (17%), Positives = 49/142 (34%), Gaps = 40/142 (28%)
Query: 8 KFVIISDSKSTLLALSNPSNTNPIVSLIHSCWS-------DLLCCGKQLAFLWCPSHTGI 60
K ++ + K LS + T+ +SL H + LL L +L C
Sbjct: 267 KILLTTRFKQVTDFLSAATTTH--ISLDHHSMTLTPDEVKSLL-----LKYLDCRPQ--- 316
Query: 61 QGNEAVDRAARNPSASLPP-LKLCSPEDFKPFIRKLIKD---LWQQSWSSIPNSNKLKS- 115
LP + +P I + I+D W W + N +KL +
Sbjct: 317 ---------------DLPREVLTTNPRRLS-IIAESIRDGLATWDN-WKHV-NCDKLTTI 358
Query: 116 IKPIIGPWPSSDRQNRYEEVVI 137
I+ + ++ + ++ + +
Sbjct: 359 IESSLNVLEPAEYRKMFDRLSV 380
>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 = 31.6 bits (72), Expect = 0.13
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 8/61 (13%)
Query: 11 IISDSKSTL-LALSNPSNT-NPIVSLIHSCWSDLLCCGKQLAFL-WCPSHTGIQGNEAVD 67
II DS+ + + S P+ + + IV+ I K+ ++ W P+H GI GN+ VD
Sbjct: 494 IIVDSQYVMGIVASQPTESESKIVNQIIE-----EMIKKEAIYVAWVPAHKGIGGNQEVD 548
Query: 68 R 68
Sbjct: 549 H 549
>2zs0_C Extracellular giant hemoglobin major globin subun; annelida,
magnesium, cooperativity, heme, iron, binding, oxygen
transport, secreted; HET: HEM; 1.60A {Oligobrachia
mashikoi} PDB: 2d2n_C* 2d2m_C* 2zfo_C* 2zs1_C*
Length = 147
Score = 27.7 bits (61), Expect = 1.7
Identities = 8/32 (25%), Positives = 14/32 (43%), Gaps = 5/32 (15%)
Query: 83 CSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLK 114
CS ED R + W +WS+ + ++
Sbjct: 4 CSSED-----RANVMHNWDAAWSAAYSDRRVA 30
>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 = 27.5 bits (62), Expect = 1.9
Identities = 10/32 (31%), Positives = 12/32 (37%)
Query: 41 DLLCCGKQLAFLWCPSHTGIQGNEAVDRAARN 72
D Q+ + W H G NE D AR
Sbjct: 108 DAALGQHQIKWEWVKGHAGHPENERADELARA 139
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 27.6 bits (62), Expect = 2.0
Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 2/52 (3%)
Query: 41 DLLCCGKQLAFLWCPSHTGIQGNEAVDRAARN--PSASLPPLKLCSPEDFKP 90
L ++ F + HTG NE VDR AR S + P +P F
Sbjct: 113 LLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQAKTPCPPRAPTLFHE 164
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 27.1 bits (61), Expect = 2.3
Identities = 7/31 (22%), Positives = 10/31 (32%)
Query: 41 DLLCCGKQLAFLWCPSHTGIQGNEAVDRAAR 71
L ++ F H+ N D AR
Sbjct: 109 LKLTTLHRVTFHKVKGHSDNPYNSRADELAR 139
>2zs0_A Extracellular giant hemoglobin major globin subun; annelida,
magnesium, cooperativity, heme, iron, binding, oxygen
transport, secreted; HET: HEM; 1.60A {Oligobrachia
mashikoi} PDB: 2d2n_A* 2d2m_A* 2zfo_A* 2zs1_A*
Length = 140
Score = 27.3 bits (60), Expect = 2.4
Identities = 7/32 (21%), Positives = 13/32 (40%), Gaps = 5/32 (15%)
Query: 82 LCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKL 113
+C+ + + L+K W QS+ N
Sbjct: 1 VCNRLE-----QILVKTQWAQSYGEAENRAAF 27
>1ei6_A Phosphonoacetate hydrolase; zinc,; HET: TLA; 2.10A {Pseudomonas
fluorescens} SCOP: c.76.1.4
Length = 406
Score = 27.5 bits (60), Expect = 2.7
Identities = 21/111 (18%), Positives = 34/111 (30%), Gaps = 17/111 (15%)
Query: 25 PSNTNPI-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLC 83
PS TNP +S++ PS GI GN D+ + L
Sbjct: 60 PSFTNPNNLSIVTGAP---------------PSVHGICGNFFFDQETQEEVLMNDAKYLR 104
Query: 84 SPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEE 134
+P K + + + + +K I +D+ N E
Sbjct: 105 APTILAEM-AKAGQLVAVVTAKDKLRNLLGHQLKGICFSAEKADQVNLEEH 154
>1x9f_B Erythrocruorin, globin II, extracellular, globin AIII, globin B;
crystal, dodecamer, allosteric, oxygen storage/transport
complex; HET: HEM; 2.60A {Lumbricus terrestris} SCOP:
a.1.1.2 PDB: 2gtl_B*
Length = 145
Score = 26.9 bits (59), Expect = 2.9
Identities = 5/33 (15%), Positives = 11/33 (33%), Gaps = 5/33 (15%)
Query: 81 KLCSPEDFKPFIRKLIKDLWQQSWSSIPNSNKL 113
K C + +K W +++ S +
Sbjct: 2 KQCGVLE-----GLKVKSEWGRAYGSGHDREAF 29
>3bbo_F Ribosomal protein L3; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 259
Score = 27.2 bits (61), Expect = 3.2
Identities = 5/18 (27%), Positives = 6/18 (33%)
Query: 146 RATHGHLFKRAPPSTCGC 163
+ THG R S
Sbjct: 175 QMTHGSKSHRQLGSIGAG 192
>1lr0_A TOLA protein; domain-swapping, TONB, protein transport; 1.91A
{Pseudomonas aeruginosa} SCOP: d.212.1.1
Length = 129
Score = 26.5 bits (58), Expect = 3.5
Identities = 6/38 (15%), Positives = 13/38 (34%), Gaps = 3/38 (7%)
Query: 62 GNEAVDRAARN---PSASLPPLKLCSPEDFKPFIRKLI 96
G++ D +A +P ++ F R+
Sbjct: 76 GDKPFDSSAVAAVRNVGRIPEMQQLPRATFDSLYRQRR 113
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 26.3 bits (59), Expect = 4.2
Identities = 10/32 (31%), Positives = 13/32 (40%)
Query: 41 DLLCCGKQLAFLWCPSHTGIQGNEAVDRAARN 72
D Q+ + W H G NE D+ AR
Sbjct: 110 DKAAQLHQIDWRWVKGHAGHAENERCDQLARA 141
>2zs0_B Extracellular giant hemoglobin major globin subun; annelida,
magnesium, cooperativity, heme, iron, binding, oxygen
transport, secreted; HET: HEM; 1.60A {Oligobrachia
mashikoi} PDB: 2d2n_B* 2d2m_B* 2zfo_B* 2zs1_B*
Length = 142
Score = 25.8 bits (56), Expect = 6.4
Identities = 7/31 (22%), Positives = 13/31 (41%), Gaps = 5/31 (16%)
Query: 83 CSPEDFKPFIRKLIKDLWQQSWSSIPNSNKL 113
C+ + R L+K W +++ N L
Sbjct: 2 CTSLN-----RLLVKRQWAEAYGEGTNRELL 27
>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA
polymer binding protein, RNA binding protein; 2.10A
{Saccharomyces cerevisiae}
Length = 157
Score = 25.9 bits (56), Expect = 6.7
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 83 CSPEDFKPFIRKLIKDLWQQSWSSIPNSNKLKSIK 117
S +D K IR L+ D+W + S + + L +I+
Sbjct: 111 KSNQDHKEKIRMLL-DIWDR--SGLFQKSYLNAIR 142
>3szr_A Interferon-induced GTP-binding protein MX1; interferon-induced
antiviral GTPase, membrane associated, PR binding; 3.50A
{Homo sapiens} PDB: 3zys_B
Length = 608
Score = 26.6 bits (58), Expect = 7.4
Identities = 9/41 (21%), Positives = 12/41 (29%), Gaps = 3/41 (7%)
Query: 147 ATHGHLFKRAPPSTCGCGEILSVQHILTCALHGHIRASLPT 187
H + + + LT L HI SLP
Sbjct: 279 ENHPYFRDLLEEGKAT---VPCLAEKLTSELITHICKSLPL 316
>2iz2_A FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuclear protein,
phosphorylation, PAIR-RULE protein; 2.8A {Drosophila
melanogaster} PDB: 2xhs_A
Length = 243
Score = 25.9 bits (57), Expect = 8.1
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 4/31 (12%)
Query: 32 VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQG 62
+ L+ WSD+L L L H G+
Sbjct: 81 MKLLQHSWSDMLV----LDHLHHRIHNGLPD 107
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 0.134 0.438
Gapped
Lambda K H
0.267 0.0535 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,993,932
Number of extensions: 163214
Number of successful extensions: 338
Number of sequences better than 10.0: 1
Number of HSP's gapped: 337
Number of HSP's successfully gapped: 29
Length of query: 194
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 106
Effective length of database: 4,244,745
Effective search space: 449942970
Effective search space used: 449942970
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: 55 (25.4 bits)