RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5071
(366 letters)
>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 = 57.8 bits (139), Expect = 3e-09
Identities = 85/440 (19%), Positives = 129/440 (29%), Gaps = 181/440 (41%)
Query: 17 KELYHTNINVNDFPPNKPKPLCVRIKDMSDFL-PLITDSEFVP--FTR------------ 61
++LY T + L IK ++ L LI + FT+
Sbjct: 174 RDLYQT------YHVL-VGDL---IKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPS 223
Query: 62 PRPPWSFQVPSIDFSLHLDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDG---SKTVNS 118
P + + SI S P I Q H +VT K +L FT G S +
Sbjct: 224 NTPDKDY-LLSIPISC--------PLIGVIQLAHYVVTAK----LLGFTPGELRSYLKGA 270
Query: 119 TSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFL--------PSTNF--TLISD 168
T + + V A + + +S S +++ + L F+ P+T+ +++ D
Sbjct: 271 TGHSQGL---VTAVAIAETDSW-ESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILED 326
Query: 169 S-------MSALLAISNCK-----------NDH-PL-----VSLVYTTWLEAKDCGKNLN 204
S S +L+ISN N H P +SLV G N
Sbjct: 327 SLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLV---------NGAK-N 376
Query: 205 FVWCPSHCGITGN---------ELVDIAA-------------RNP-ITN----IT----- 232
V ++G L A R +N +
Sbjct: 377 LV-------VSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHS 429
Query: 233 --LKNCTSF---DFRPVISSIIHKQWQI------SWDNV---INNKLKRVKPLI----VD 274
L + D S K QI ++ + +R+ I V
Sbjct: 430 HLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVK 489
Query: 275 WETSNRNSRYEEVVITRLRIGHTRVTH--DHLFKRDPRPTCGCGDTLTVDHIFN---CRT 329
WET+ + TH D F P G G LT + R
Sbjct: 490 WETTT----------------QFKATHILD--F--GPGGASGLGV-LT-HRNKDGTGVRV 527
Query: 330 HLQIRASLPSPPALDNNPAN 349
I A LD NP +
Sbjct: 528 ---IVAG-----TLDINPDD 539
Score = 38.1 bits (88), Expect = 0.005
Identities = 62/430 (14%), Positives = 111/430 (25%), Gaps = 161/430 (37%)
Query: 19 LYHTNINVNDFP-PNKPKPLCVRIKDMSDF---LPLITDSEFVPFTRPRPPWS------- 67
L H ++ P + ++++ F LP T+ F P +
Sbjct: 11 LSHGSLEH-VLLVPTASFFIASQLQE--QFNKILPEPTEG----FAADDEPTTPAELVGK 63
Query: 68 FQVPSIDFSLHLDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGN 127
F + + L F ++ + F + Y GN
Sbjct: 64 F----LGYVSSLVEPSK------VGQFDQVLNL----CLTEFEN----------CYLEGN 99
Query: 128 QVHAF----------KLNKVNSVLSS-----------------------------ELMAI 148
+HA L K ++ + +L+AI
Sbjct: 100 DIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAI 159
Query: 149 L-------LCVKNLIFLPSTNFTLISD---SMSALLAISNCKNDHPLVSLVYT------T 192
+ L L T L+ D + L S V+T
Sbjct: 160 FGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETL--SELIRTTLDAEKVFTQGLNILE 217
Query: 193 WLEAKDCGKNLNF-----VWCPSHCGITGNELVDIAARNPITN--ITLK--NCTSFDFRP 243
WLE + ++ + CP I ++ +A + +T K T + R
Sbjct: 218 WLENPSNTPDKDYLLSIPISCP---LIG---VIQLA------HYVVTAKLLGFTPGELRS 265
Query: 244 VISSII-HKQWQI---------SWDNVINNKLKRVKPLIVDW------ETSNRNSRYEEV 287
+ H Q + SW++ + K + L + E S +
Sbjct: 266 YLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLF--FIGVRCYEAYPNTSLPPSI 323
Query: 288 VITRLRIGHTRVTHDHLFKRDPRP---TCGCGDTLTVDHIFNCRTHL----QIRASLPSP 340
+ L P P D++ +HL Q+ SL
Sbjct: 324 LEDSLENNEGV----------PSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLV-- 371
Query: 341 PALDNNPANI 350
N N+
Sbjct: 372 ----NGAKNL 377
Score = 29.2 bits (65), Expect = 2.7
Identities = 44/255 (17%), Positives = 80/255 (31%), Gaps = 84/255 (32%)
Query: 75 FSLHLD-NKDNIPPIVFQQHF-----HDLVTNKYSDSVLCF---TDGS-------KTVNS 118
FS+ LD +N P+ HF + N YS + F DG K +N
Sbjct: 1659 FSI-LDIVINN--PVNLTIHFGGEKGKRIREN-YSA--MIFETIVDGKLKTEKIFKEINE 1712
Query: 119 TSCAYSIGNQVHAFKLNK-VNS----VLSSELMAILLCVKNLIFLPSTNFTLISDSM--- 170
S +Y+ ++ L+ + L A +K+ +P+ D+
Sbjct: 1713 HSTSYTFRSE--KGLLSATQFTQPALTLME--KAAFEDLKSKGLIPA-------DATFAG 1761
Query: 171 ------SALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAA 224
+AL ++++ + LV +V+ G + P G + A
Sbjct: 1762 HSLGEYAALASLADVMSIESLVEVVFYR-------GMTMQVA-VPR--DELGRSNYGMIA 1811
Query: 225 RNPITNITLKNCTSFDFRPVISSIIHKQ-WQISWDNVINNKLKRVKPLIVDWETSNRNSR 283
NP + + + V+ + + W + IV N N
Sbjct: 1812 INP--GRVAASFSQEALQYVVERVGKRTGWLVE---------------IV-----NYNVE 1849
Query: 284 YEEVVITRLRIGHTR 298
++ V G R
Sbjct: 1850 NQQYVAA----GDLR 1860
>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 = 48.7 bits (116), Expect = 3e-07
Identities = 29/143 (20%), Positives = 48/143 (33%), Gaps = 16/143 (11%)
Query: 109 FTDGSKTVNS--TSCAYSIG---NQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNF 163
+TDGS + ++ + A L S +EL+A+ + L
Sbjct: 27 YTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALT---QALKMAEGKKL 83
Query: 164 TLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCG-----ITG 216
+ +DS A + + + L+A K L+ + CP H G
Sbjct: 84 NVYTDSRYAFATAHVHSEGREIKNKNEI-LALLKALFLPKRLSIIHCPGHQKGNSAEARG 142
Query: 217 NELVDIAARNPITNITLKNCTSF 239
N + D AAR L+ T
Sbjct: 143 NRMADQAAREAAMKAVLETSTLL 165
>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 = 42.9 bits (100), Expect = 2e-04
Identities = 47/306 (15%), Positives = 92/306 (30%), Gaps = 93/306 (30%)
Query: 73 IDFS---LHLDNKDNIPPIVFQQHF-HDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQ 128
+DF KD + VF+ F + D K++ S I
Sbjct: 7 MDFETGEHQYQYKDILS--VFEDAFVDNFDCKDVQDMP-------KSILSKEEIDHI--- 54
Query: 129 VHAFKLNKVNSVLSSELMAILLCVKN----LIFLPS---TNFTLISDSMSALLAISNCKN 181
+ ++V + + L K F+ N+ + + +
Sbjct: 55 -----IMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKT-------EQ 102
Query: 182 DHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITLKNCTSFDF 241
P S++ ++E +D N N V+ + ++ + L+ +
Sbjct: 103 RQP--SMMTRMYIEQRDRLYNDNQVFAKYN--VSRLQPYL----------KLRQALL-EL 147
Query: 242 RPVISSIIH------KQW-----------------QISWDNVINNK-----LKRVKPLIV 273
RP + +I K W +I W N+ N L+ ++ L+
Sbjct: 148 RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLY 207
Query: 274 DWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTCGCGDTLTVDHI--------- 324
+ N SR + +LRI + L K P C L + ++
Sbjct: 208 QID-PNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC----LLVLLNVQNAKAWNAF 262
Query: 325 -FNCRT 329
+C+
Sbjct: 263 NLSCKI 268
Score = 40.6 bits (94), Expect = 8e-04
Identities = 46/291 (15%), Positives = 88/291 (30%), Gaps = 69/291 (23%)
Query: 74 DFSLHLDNKDNIPPIV--FQQHFHDLVTNK-YSDSVLCFTDGSKTVNSTSCAYSIGNQVH 130
+++ D+ NI + Q L+ +K Y + +L + V + +
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLN----VQNAKA-------WN 260
Query: 131 AFKLN-KV-----NSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCK-NDH 183
AF L+ K+ ++ L A +L T T + S LL +C+ D
Sbjct: 261 AFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMT-LTP-DEVKSLLLKYLDCRPQDL 318
Query: 184 PLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAAR---------NPITNI--- 231
P E P I + D A + +T I
Sbjct: 319 PR---------EVLTTN--------PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIES 361
Query: 232 TLKNCTSFDFR---------PVISSIIHKQWQISWDNV-------INNKLKRVKPLIVDW 275
+L ++R P + I + W +V + NKL + L+
Sbjct: 362 SLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHK-YSLVEKQ 420
Query: 276 ETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTCGCGDTLTVDHIFN 326
+ S + ++++ + H + P D L ++
Sbjct: 421 PKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471
Score = 31.0 bits (69), Expect = 0.81
Identities = 51/308 (16%), Positives = 93/308 (30%), Gaps = 78/308 (25%)
Query: 22 TNINVNDFPPNKPK--PLCV-----RIKDM---SDFLPLITDSEFVPFTRPRPPWSFQVP 71
+ D P P + I+D D + + T
Sbjct: 311 LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKL---TT---------- 357
Query: 72 SIDFSLHLDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHA 131
I+ SL + + P +++ F L F + I +
Sbjct: 358 IIESSL-----NVLEPAEYRKMFDRLSV---------FPPSAH----------IPTIL-- 391
Query: 132 FKLNKV-NSVLSSELMAIL--LCVKNLIFLPSTNFTL-ISD-SMSALLAISNCKNDHPLV 186
L+ + V+ S++M ++ L +L+ T+ I + + + N H
Sbjct: 392 --LSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR-- 447
Query: 187 SLV--YTTW--LEAKDCGKNLNFVWCPSHCG--ITGNELVDIAARNPITNITLKNCTSFD 240
S+V Y ++ D + SH G + E + +TL D
Sbjct: 448 SIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPE--------RMTLFRMVFLD 499
Query: 241 FRPVISSIIHKQWQISWDNVINN---KLKRVKPLIVDWETSNRNSRYEEVVITRL-RIGH 296
FR + I H + I N +LK KP I D + R ++ L +I
Sbjct: 500 FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICD--NDPKYERLVNAILDFLPKIEE 557
Query: 297 TRVTHDHL 304
+ +
Sbjct: 558 NLICSKYT 565
>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 = 38.9 bits (91), Expect = 6e-04
Identities = 22/133 (16%), Positives = 40/133 (30%), Gaps = 14/133 (10%)
Query: 103 SDSVLCFTDGSKTVNSTSCAYSI---GNQVHAFKL------NKVNSVLSSELMAILLCVK 153
+TDGS + AY+ G + ++ E+ A L VK
Sbjct: 4 RTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVK 63
Query: 154 NLIFLPSTNFTLISDSMSALLAISNC-KNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHC 212
L ++ D + K + + + +F +H
Sbjct: 64 KASQLGV-KIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQYR---GIYSFEKVKAHS 119
Query: 213 GITGNELVDIAAR 225
G N+ VD+ A+
Sbjct: 120 GNEFNDYVDMKAK 132
>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 = 37.0 bits (86), Expect = 0.008
Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 10/81 (12%)
Query: 143 SELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDCG 200
+EL AI L +++ +++DS AL I K++ LV+ + L K+
Sbjct: 479 TELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI-IEQLIKKE-- 531
Query: 201 KNLNFVWCPSHCGITGNELVD 221
+ 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 = 33.2 bits (76), Expect = 0.12
Identities = 17/81 (20%), Positives = 37/81 (45%), Gaps = 10/81 (12%)
Query: 143 SELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDCG 200
+EL A + + + +I DS + +++ +++ +V+ + + K+
Sbjct: 476 AELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQPTESESKIVNQI-IEEMIKKE-- 528
Query: 201 KNLNFVWCPSHCGITGNELVD 221
+ 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 = 31.8 bits (73), Expect = 0.18
Identities = 11/30 (36%), Positives = 14/30 (46%)
Query: 202 NLNFVWCPSHCGITGNELVDIAARNPITNI 231
+ 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 = 30.2 bits (69), Expect = 0.62
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 202 NLNFVWCPSHCGITGNELVDIAARN 226
++ ++ 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 = 29.8 bits (68), Expect = 0.83
Identities = 11/34 (32%), Positives = 15/34 (44%)
Query: 202 NLNFVWCPSHCGITGNELVDIAARNPITNITLKN 235
+ + W H G NE D AR N TL++
Sbjct: 115 QIKWEWVKGHAGHPENERADELARAAAMNPTLED 148
>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 = 29.1 bits (64), Expect = 1.3
Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 6/25 (24%)
Query: 332 QIRASL----P-SPPALDNNPANID 351
+++ASL S PAL A ++
Sbjct: 24 KLQASLKLYADDSAPALAIK-ATME 47
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 27.5 bits (62), Expect = 4.6
Identities = 7/31 (22%), Positives = 9/31 (29%)
Query: 202 NLNFVWCPSHCGITGNELVDIAARNPITNIT 232
+ F H N D AR I +
Sbjct: 116 RVTFHKVKGHSDNPYNSRADELARLAIKENS 146
>1u58_A MHC-I homolog M144; MCMV, MHC-I homolog, immune system; 1.90A
{Murid herpesvirus 1} SCOP: b.1.1.2 d.19.1.1 PDB: 1pqz_A
Length = 253
Score = 27.5 bits (61), Expect = 5.8
Identities = 5/41 (12%), Positives = 12/41 (29%), Gaps = 1/41 (2%)
Query: 275 WETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTCGC 315
+ + + Y ++V+ V R+ C
Sbjct: 126 RDCQKKLTEYRKLVLASAVSPQLEVER-RSSGREGGMRLRC 165
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 26.8 bits (60), Expect = 8.0
Identities = 10/36 (27%), Positives = 13/36 (36%)
Query: 202 NLNFVWCPSHCGITGNELVDIAARNPITNITLKNCT 237
+ F + H G NE VD AR + C
Sbjct: 120 RVRFHFVKGHTGHPENERVDREARRQAQSQAKTPCP 155
>3mwp_A Nucleoprotein; structural genomics, scottish structural PROT
facility, SSPF, nuclear protein; 1.79A {Lassa virus
josiah} PDB: 3mwt_A 3mx2_A* 3mx5_A* 3r3l_A 3t5q_A 3t5n_A
Length = 577
Score = 27.2 bits (60), Expect = 9.0
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 7/40 (17%)
Query: 225 RNPITNITLKNCTSFDFRPVISSIIHKQWQI---SWDNVI 261
RNP NI K C S D P I+S + I +W+N +
Sbjct: 308 RNPYENILYKICLSGDGWPYIAS----RTSITGRAWENTV 343
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 0.136 0.432
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: 5,577,111
Number of extensions: 318022
Number of successful extensions: 573
Number of sequences better than 10.0: 1
Number of HSP's gapped: 571
Number of HSP's successfully gapped: 26
Length of query: 366
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 271
Effective length of database: 4,049,298
Effective search space: 1097359758
Effective search space used: 1097359758
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 (21.9 bits)
S2: 58 (26.0 bits)