RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6829
(369 letters)
>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 = 43.1 bits (102), Expect = 2e-05
Identities = 12/90 (13%), Positives = 24/90 (26%), Gaps = 7/90 (7%)
Query: 190 NNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN--TSIPLIAHILNT 247
E+ A ++ + V I+ D + A
Sbjct: 45 AATMRNVAGEIAAALYAVKKASQLG-VKIRILHDYAG-IAFWATGEWKAKNEFTQAYAKL 102
Query: 248 WHTLKSCGKKVAFLWCPSHTGISGNEIVDR 277
+ + +F +H+G N+ VD
Sbjct: 103 MNQYR---GIYSFEKVKAHSGNEFNDYVDM 129
>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 = 43.5 bits (102), Expect = 9e-05
Identities = 67/412 (16%), Positives = 118/412 (28%), Gaps = 150/412 (36%)
Query: 19 LLKLYQSY---VSPIIDY-GSSIYSSAKDHIINKLNPVHHNGIRI-----------ATGA 63
L LYQ+Y V +I + ++ + + V G+ I
Sbjct: 173 LRDLYQTYHVLVGDLIKFSAETLSELIRTTL--DAEKVFTQGLNILEWLENPSNTPDKDY 230
Query: 64 LRSSPVQSLYAESNIPPLSVRRDKL--LFNYVV--KLYGCPLNP--MHKILFGNVDSFNI 117
L S P+ S PL + L +YVV KL G P + L G
Sbjct: 231 LLSIPI-SC-------PLIG----VIQLAHYVVTAKLLG--FTPGELRSYLKG------A 270
Query: 118 TPNKPLPLKIRFNCIRE-VSAV-----------LKNT-KVVPYSQGFPPW-----YSDFP 159
T + V+AV + K + F + Y +P
Sbjct: 271 T-----------GHSQGLVTAVAIAETDSWESFFVSVRKAITVL--F--FIGVRCYEAYP 315
Query: 160 VVDLSLYGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLD----------- 208
L +++ ++ S +L +I+++ ++ V +
Sbjct: 316 NTSLP---PSILED---SLENNEGVPSPML-SISNLTQEQVQDYVNKTNSHLPAGKQVEI 368
Query: 209 SVKNRPDVNTLIVC---DSMSALTSI-------ANKNTS-IPLIAHILNTWHTLKSCGKK 257
S+ N L+V S+ L + + S IP +K
Sbjct: 369 SLVNGAK--NLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPF-------------SERK 413
Query: 258 VAFLW------CPSHTGISGNEIVDRATRQLDG-AEFVNLS-SPADL-ISVGKKYIHEKW 308
+ F P H+ ++ A+ ++ N+S + D+ I V Y
Sbjct: 414 LKFSNRFLPVASPFHS-----HLLVPASDLINKDLVKNNVSFNAKDIQIPV---Y-D--- 461
Query: 309 QKSWSDLTNNKLKCVKPTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLF 360
SDL + I + +E + TH F
Sbjct: 462 TFDGSDLRVLS-GSISERIVDCIIRLPVK-WETTT-------QFKATHILDF 504
Score = 38.9 bits (90), Expect = 0.003
Identities = 56/313 (17%), Positives = 90/313 (28%), Gaps = 113/313 (36%)
Query: 72 LYAESNIPPLSVRRDKLLFN----YVVKLYGCPLNPMHKILFGNVDSFNITPNKPLPLKI 127
LY S +D ++N + YG IL +I N P+ L I
Sbjct: 1635 LYKTS-----KAAQD--VWNRADNHFKDTYG------FSIL-------DIVINNPVNLTI 1674
Query: 128 RFNC-----IRE-VSAVLKNTKVVPYSQGFPPWYSDFPVVDLSL-----YGSK-----TI 171
F IRE SA++ T G F ++ K T
Sbjct: 1675 HFGGEKGKRIRENYSAMIFET----IVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSAT- 1729
Query: 172 QNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSM------ 225
Q T A + E A L K++ LI D+
Sbjct: 1730 QFTQPA-----------------LTLMEK-AAFEDL---KSK----GLIPADATFAGHSL 1764
Query: 226 ---SALTSIANKNTSIPL-------------IAHILNTWHTLKSCGKKVAFLWCPSHTGI 269
+AL S+A+ + + + + +S +A P
Sbjct: 1765 GEYAALASLAD---VMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAIN--PGRVAA 1819
Query: 270 SGNE-----IVDRATRQLDG-AEFVNLSSPADLISV-GKKYIHEKWQKSWSDLTN--NKL 320
S ++ +V+R ++ E VN + G ++ +TN N +
Sbjct: 1820 SFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDL-------RALDTVTNVLNFI 1872
Query: 321 KCVKPTIGPWNVS 333
K K I S
Sbjct: 1873 KLQKIDIIELQKS 1885
Score = 32.7 bits (74), Expect = 0.22
Identities = 32/171 (18%), Positives = 52/171 (30%), Gaps = 76/171 (44%)
Query: 13 GLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDH---------------------IINKLN- 50
G+ ++Y P SI + ++ +NK N
Sbjct: 307 GVRCY------EAY--PNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNS 358
Query: 51 ------PVH---HNGIR--IATGALRSSPVQSLYA---------------ESNIPPLSVR 84
V NG + + +G P QSLY +S I P S R
Sbjct: 359 HLPAGKQVEISLVNGAKNLVVSG-----PPQSLYGLNLTLRKAKAPSGLDQSRI-PFSER 412
Query: 85 RDKLLFNYV---VKLYGCP-----LNPMHKILFGNVDSFNITPNKPLPLKI 127
KL F+ V P L P ++ ++ N++ N ++I
Sbjct: 413 --KLKFSNRFLPV---ASPFHSHLLVPASDLINKDLVKNNVSFNAK-DIQI 457
>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 = 41.0 bits (96), Expect = 1e-04
Identities = 22/91 (24%), Positives = 38/91 (41%), Gaps = 11/91 (12%)
Query: 198 AELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKK 257
AEL+AL L + +N + DS A + A+ ++ I + LK+
Sbjct: 66 AELIALTQALKMAE-GKKLN--VYTDSRYAF-ATAHVHSEGREIKNKNEILALLKALFLP 121
Query: 258 --VAFLWCPSHTG-----ISGNEIVDRATRQ 281
++ + CP H GN + D+A R+
Sbjct: 122 KRLSIIHCPGHQKGNSAEARGNRMADQAARE 152
>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 = 41.3 bits (97), Expect = 4e-04
Identities = 29/84 (34%), Positives = 40/84 (47%), Gaps = 14/84 (16%)
Query: 198 AELLALVFCL-DSVKNRPDVNTLIVCDSMSALTSIANK--NTSIPLIAHILNTWHTLKSC 254
EL A+ L DS +VN IV DS AL I + + L+ I+ +
Sbjct: 479 TELQAIYLALQDS---GLEVN--IVTDSQYALGIIQAQPDKSESELVNQIIE-----QLI 528
Query: 255 GKKVAFL-WCPSHTGISGNEIVDR 277
K+ +L W P+H GI GNE VD+
Sbjct: 529 KKEKVYLAWVPAHKGIGGNEQVDK 552
>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 = 41.4 bits (96), Expect = 5e-04
Identities = 52/308 (16%), Positives = 100/308 (32%), Gaps = 99/308 (32%)
Query: 4 LKIVSNKNYGLHRQTLLKLYQSYVSPIIDYGSSIYSSAKDHI----------INKLNPVH 53
LK + + L R+ L +P S I S +D + +KL +
Sbjct: 308 LKYLDCRPQDLPREVLT------TNPRRL--SIIAESIRDGLATWDNWKHVNCDKLTTI- 358
Query: 54 HNGIRIATGALRSSPVQSLYAE-------SNIPP--LSV-----------------RRDK 87
I + L + + ++ ++IP LS+ +
Sbjct: 359 ---IESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYS 415
Query: 88 LL----FNYVVKLYGCPLN---------PMHKILFGNVDSFNIT----PNKPLPLKIR-- 128
L+ + + L +H+ + VD +NI + +P +
Sbjct: 416 LVEKQPKESTISIPSIYLELKVKLENEYALHRSI---VDHYNIPKTFDSDDLIPPYLDQY 472
Query: 129 -FNCIREVSAVLKNTKVVPYSQGFPPWYSDFPVVDLSLYGSKTIQNTSCAVYAGGSA--- 184
++ I LKN + F + DF ++ + I++ S A A GS
Sbjct: 473 FYSHI---GHHLKNIEHPERMTLFRMVFLDFRFLE------QKIRHDSTAWNASGSILNT 523
Query: 185 -------KSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIA--NKN 235
K YI +N + + A+ + P + ++C + L IA ++
Sbjct: 524 LQQLKFYKPYICDNDP-KYERLVNAI------LDFLPKIEENLICSKYTDLLRIALMAED 576
Query: 236 TSIPLIAH 243
+I AH
Sbjct: 577 EAIFEEAH 584
Score = 38.7 bits (89), Expect = 0.003
Identities = 66/398 (16%), Positives = 124/398 (31%), Gaps = 126/398 (31%)
Query: 30 IIDYGSSIYSSAK-DHIINKLNPVHHNGIRIATGALRSSPVQSLYA------ESNIP--- 79
+ D SI S + DHII + V +G L S + + N
Sbjct: 38 VQDMPKSILSKEEIDHIIMSKDAV--SGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLM 95
Query: 80 -PLSVR-RDKLLFNYVVKLYGCPLNPMHKILFGNVDSF---NITPNKPLPLKIRFNCIRE 134
P+ R + + ++Y + L+ + F N++ +P LK+R + E
Sbjct: 96 SPIKTEQRQPSM---MTRMYIEQRDR----LYNDNQVFAKYNVSRLQPY-LKLR-QALLE 146
Query: 135 --------------------VSAVLKNTKVVPYSQGFPPWYSDFPV--VDLSLYGS---- 168
V + KV F + ++L S
Sbjct: 147 LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQ---CKMD-----FKIFWLNLKNCNSPETV 198
Query: 169 -KTIQNT----SCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCD 223
+ +Q + S I I+SI AEL L+ K++P N L+V
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSI-QAELRRLL------KSKPYENCLLVLL 251
Query: 224 SMSALTSIANKNTSIPLIAHILNTWHTLK----SC-------GKKVA-FLWCPSHTGISG 271
++ N SC K+V FL + T IS
Sbjct: 252 -------------------NVQNAKA-WNAFNLSCKILLTTRFKQVTDFLSAATTTHISL 291
Query: 272 NEIVDRAT-RQLDG--AEFVNLSSPADL-----------ISVGKKYIHE---KWQKSWSD 314
+ T ++ ++++ P DL +S+ + I + W W
Sbjct: 292 DHHSMTLTPDEVKSLLLKYLDC-RPQDLPREVLTTNPRRLSIIAESIRDGLATWDN-WKH 349
Query: 315 LTNNKL-KCVKPTIGPWNVSDCNNRYEEVVLTR--VRI 349
+ +KL ++ ++ ++ ++ + + I
Sbjct: 350 VNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI 387
>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 = 39.7 bits (93), Expect = 0.001
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 14/84 (16%)
Query: 198 AELLALVFCL-DSVKNRPDVNTLIVCDSMSALTSIANK--NTSIPLIAHILNTWHTLKSC 254
AEL A L DS P VN I+ DS + +A++ + ++ I+ +
Sbjct: 476 AELEAFAMALTDS---GPKVN--IIVDSQYVMGIVASQPTESESKIVNQIIE-----EMI 525
Query: 255 GKKVAFL-WCPSHTGISGNEIVDR 277
K+ ++ W P+H GI GN+ VD
Sbjct: 526 KKEAIYVAWVPAHKGIGGNQEVDH 549
>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 = 31.4 bits (72), Expect = 0.19
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 257 KVAFLWCPSHTGISGNEIVDRATRQ 281
KV W P+H GI GNE VD+
Sbjct: 119 KVYLAWVPAHKGIGGNEQVDKLVSA 143
>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 = 31.5 bits (70), Expect = 0.24
Identities = 8/39 (20%), Positives = 16/39 (41%), Gaps = 17/39 (43%)
Query: 46 INKLNPVHHNGIRIATGALRSSPVQSLYAESNIPPLSVR 84
+ KL +L+ LYA+ + P L+++
Sbjct: 22 LKKL-----------QASLK------LYADDSAPALAIK 43
Score = 28.4 bits (62), Expect = 2.2
Identities = 7/22 (31%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 169 KTIQNTSCAVYAGGSAKSYILN 190
K +Q S +YA SA + +
Sbjct: 23 KKLQA-SLKLYADDSAPALAIK 43
Score = 28.0 bits (61), Expect = 3.3
Identities = 7/28 (25%), Positives = 13/28 (46%), Gaps = 6/28 (21%)
Query: 16 RQTL------LKLYQSYVSPIIDYGSSI 37
+Q L LKLY +P + +++
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKATM 46
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 29.8 bits (68), Expect = 0.66
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 257 KVAFLWCPSHTGISGNEIVDRATRQLDGAE 286
+ ++ P H+G GNE DR R+ GA+
Sbjct: 123 DIQWMHVPGHSGFIGNEEADRLARE--GAK 150
>2yuh_A Tubulin-specific chaperone C; microtubule, beta-tubulin folding,
beta-roll, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 179
Score = 27.4 bits (60), Expect = 5.7
Identities = 10/41 (24%), Positives = 17/41 (41%)
Query: 325 PTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDP 365
P + DC++ V ++RI T+ T +L S
Sbjct: 66 PVSTSVFLEDCSDCVLAVACQQLRIHSTKDTRIFLQVTSRA 106
>3bh7_B Protein XRP2; protein-protein complex, GTPase activating protein
and GTPase, retinitis pigmentosa, GTP-binding,
lipoprotein, myristate; HET: GDP; 1.90A {Homo sapiens}
PDB: 3bh6_B* 2bx6_A
Length = 352
Score = 27.9 bits (61), Expect = 5.9
Identities = 7/41 (17%), Positives = 14/41 (34%)
Query: 325 PTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDP 365
P G +C + + + R+ R +L + P
Sbjct: 97 PVKGSVFFRNCRDCKCTLACQQFRVRDCRKLEVFLCCATQP 137
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
0.319 0.135 0.413
Gapped
Lambda K H
0.267 0.0472 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,498,214
Number of extensions: 311990
Number of successful extensions: 614
Number of sequences better than 10.0: 1
Number of HSP's gapped: 610
Number of HSP's successfully gapped: 19
Length of query: 369
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 274
Effective length of database: 4,049,298
Effective search space: 1109507652
Effective search space used: 1109507652
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 (26.7 bits)