RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17038
(399 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 = 45.4 bits (108), Expect = 4e-06
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 26 NPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEAL 70
N Q ++ + + I F V +H G N+ D AK AL
Sbjct: 93 NEFTQAYAKLMNQYRGIY--SFEKVKAHSGNEFNDYVDMKAKSAL 135
>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 = 47.2 bits (111), Expect = 8e-06
Identities = 62/419 (14%), Positives = 119/419 (28%), Gaps = 129/419 (30%)
Query: 4 MLQN-----SSKDSLSALQSIQNEFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVG 58
MLQ + + S + + I E+R +L + L V +V
Sbjct: 201 MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL---LVLLNV---- 253
Query: 59 NEESDRLAKEALSSNSPSVNTIPINYFKRFLKSKILSTWNTEWVNLAD----NKLRQIKE 114
+ N F L KIL T T + + D I
Sbjct: 254 --------------QNAKA----WNAFN--LSCKILLT--TRFKQVTDFLSAATTTHISL 291
Query: 115 EKRPWNPSLHESRE-------SNSARLP----QVSLAELKVIQETLGDLERQGDLDLDLC 163
+ + E + LP + L +I E++ D L
Sbjct: 292 DHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRD-------GLATW 344
Query: 164 DSWRN---------LAESQEANDDGDLSSHHVTLDLANRIVQSYTGIQADLKYGVSGIL- 213
D+W++ + S + + L+ + I + ++
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD--RLS--VFPPSAHIPTI----LLSLIW 396
Query: 214 -----SEIMDLVQDVVTSSEAGEDGLELPVARKREYQEARQKCQREV---RRIREEWWNK 265
S++M +V + S + E ++ Y E + K + E R I + +
Sbjct: 397 FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIP 456
Query: 266 KINELQEFA-NKNDTYNL-YRG--MKSA-----VGPIRKP---LNIIEDK---------N 304
K + + D Y + G +K+ + R +E K
Sbjct: 457 KTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNA 516
Query: 305 GNKISNKEERLERWREHFQHVFNQQTTVNLEGIEIDPITDNLPNDERPTENEIMLETLI 363
I N ++L+ ++ + I DN P ER ++ ++
Sbjct: 517 SGSILNTLQQLKFYKPY--------------------ICDNDPKYER------LVNAIL 549
Score = 41.4 bits (96), Expect = 5e-04
Identities = 41/342 (11%), Positives = 88/342 (25%), Gaps = 111/342 (32%)
Query: 143 KVIQETLGDLERQGDLDL-DLCDSWRNLAESQEANDDGDLSSHHVTLDLANRIVQSYTGI 201
++ + D D+ D +++ +E + + + + +
Sbjct: 20 DILSVFEDAFVD--NFDCKDVQDMPKSILSKEEIDH---------IIMSKDAVSGTLRLF 68
Query: 202 QADLKYGVSGI---LSEIMDLVQDVVTSSEAGEDGLELPVARKREYQEARQKCQREVRRI 258
L + + E++ + + S E P R Y E R + + +
Sbjct: 69 WTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQ--RQPSMMTRMYIEQRDRLYNDNQVF 126
Query: 259 ------REEWWNKKINELQEFANKNDTYNLYRGM----KSA------------------- 289
R + + K L E + L G+ K+
Sbjct: 127 AKYNVSRLQPYLKLRQALLEL--RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKI 184
Query: 290 ----VGPIRKPLNIIE---------DKNGNK----ISNKEERLERWREHFQHVFNQQTTV 332
+ P ++E D N SN + R+ + + + +
Sbjct: 185 FWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYE 244
Query: 333 N----LEGIEIDP--------------------ITDNLPNDER-------------PTEN 355
N L ++ + +TD L P E
Sbjct: 245 NCLLVLLNVQ-NAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV 303
Query: 356 EIMLETLI------FPKSPIKMNFPFLVLCLLAEEHGKMNNR 391
+ +L + P+ + N P L ++AE
Sbjct: 304 KSLLLKYLDCRPQDLPREVLTTN-P-RRLSIIAESIRDGLAT 343
Score = 38.3 bits (88), Expect = 0.005
Identities = 65/428 (15%), Positives = 132/428 (30%), Gaps = 143/428 (33%)
Query: 30 QEIRNILVKNKH--ILSLHFTWVPSHVGIVGNEESDRLAKEALSSNSPSVNTIPINYFKR 87
++R L++ + + + G++G+ ++ +A + S +
Sbjct: 138 LKLRQALLELRPAKNVLID--------GVLGSGKT-WVALDVCLSYK----------VQC 178
Query: 88 FLKSKILSTWNTEWVNLA-----DNKLRQIKEEKRPWNPSLHESRESNSARLPQVSLAEL 142
+ KI W+NL + L +++ +P+ SR +S+ + +
Sbjct: 179 KMDFKIF------WLNLKNCNSPETVLEMLQKLLYQIDPNWT-SRSDHSSNIKL----RI 227
Query: 143 KVIQETLGDLERQGD-------LDLDLCDSW-----------------RNLAESQEANDD 178
IQ L L + L ++ ++ + + + A
Sbjct: 228 HSIQAELRRLLKSKPYENCLLVLL-NVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATT 286
Query: 179 GDLSSHHV----TLDLANRIVQSYTGIQA-DLKYGVSGI----LSEIMDLVQD------- 222
+S H T D ++ Y + DL V LS I + ++D
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDN 346
Query: 223 --------VVTSSEAGEDGLELPVARKREYQEARQKC---QREVRRIREE-----WWNKK 266
+ T E+ + LE P EY++ + I W++
Sbjct: 347 WKHVNCDKLTTIIESSLNVLE-PA----EYRKMFDRLSVFPPSAH-IPTILLSLIWFDVI 400
Query: 267 INELQEFANKNDTYNLYRGMKSAVGPIRKPLNIIEDKNGNKIS-------NKEERLERWR 319
+++ NK Y+L + + + IS K + +
Sbjct: 401 KSDVMVVVNKLHKYSL----------------VEKQPKESTISIPSIYLELKVKLENEYA 444
Query: 320 EHFQHV--FNQQTTVNLEGIEIDPITDN---------LPNDERPTENEIMLETLIFPKSP 368
H V +N T + + + I P D L N E E +F
Sbjct: 445 LHRSIVDHYNIPKTFDSDDL-IPPYLDQYFYSHIGHHLKNIEH-PE-----RMTLFRM-- 495
Query: 369 IKMNFPFL 376
+ ++F FL
Sbjct: 496 VFLDFRFL 503
Score = 29.4 bits (65), Expect = 2.5
Identities = 27/186 (14%), Positives = 60/186 (32%), Gaps = 47/186 (25%)
Query: 3 TMLQNSSKDSLSALQSIQNEFS-SNPIAQEIRNILV---------KNKHILSLH-----F 47
++++ K+S ++ SI E + +V + ++ + +
Sbjct: 415 SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFY 474
Query: 48 TWVPSHVGIVGNEESDRLAKEALSSNSPSVNTIPINYFKRFLKSKILSTWNTEWVNLAD- 106
+ + H+ + + E L + +++ RFL+ KI +T W
Sbjct: 475 SHIGHHLKNIEHPERMTLFRMVF-----------LDF--RFLEQKIRHD-STAWNASGSI 520
Query: 107 -NKLRQIKEEKR---PWNPSLHE----------SRESNSARLPQVSLAELKVIQET---L 149
N L+Q+K K +P E N L + ++ E
Sbjct: 521 LNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIF 580
Query: 150 GDLERQ 155
+ +Q
Sbjct: 581 EEAHKQ 586
>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 = 43.2 bits (102), Expect = 1e-04
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 7 NSSKDSLSALQSIQN--EFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDR 64
N DS AL IQ + S + + +I L+K + + + WVP+H GI GNE+ D+
Sbjct: 496 NIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKV---YLAWVPAHKGIGGNEQVDK 552
Query: 65 L 65
L
Sbjct: 553 L 553
>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 = 43.1 bits (101), Expect = 2e-04
Identities = 61/472 (12%), Positives = 120/472 (25%), Gaps = 172/472 (36%)
Query: 2 ATMLQNSSKDSLSALQ---SIQNEFSSNP---------IAQEIRNILVKN-KHILSL--- 45
A+ LQ L + +E ++ ++ + V +L+L
Sbjct: 30 ASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLT 89
Query: 46 HFTWVPSHVGIVGNEESDRLAKE---ALSSNSPSVNTIPINYFKRFLKSKILSTWNTEWV 102
F E+ L AL++ N + K +K+ I
Sbjct: 90 EF-------------ENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYIT-------- 128
Query: 103 NLADNKLRQIKEEKRPWNPSLHESRESNSARL---------PQVSLAELKVIQET----L 149
A + + + N +L + +A+L EL+ + +T +
Sbjct: 129 --ARIMAK--RPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLV 184
Query: 150 GDL-ERQGDLDLDL--------------CD--SWRNLAESQEANDDGDLSSHHVTL---- 188
GDL + + +L + W L D L S ++
Sbjct: 185 GDLIKFSAETLSELIRTTLDAEKVFTQGLNILEW--LENPSNTPDKDYLLSIPISCPLIG 242
Query: 189 --DLAN-RIVQSYTGIQ-ADLKYGVSGILSEIMDLVQDVVTSSEAGEDGLELPVARKREY 244
LA+ + G +L+ + G LV V + + +
Sbjct: 243 VIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESF---------F 293
Query: 245 QEARQ----------KCQREVRRIREEWWNKKINELQEFANKND---TYNLYRGMKSAVG 291
R+ +C + L++ N+ + M S
Sbjct: 294 VSVRKAITVLFFIGVRCYEAYPNTSLP-----PSILEDSLENNEGVPSP-----MLSISN 343
Query: 292 PIRKPLNIIEDKNGNKISNKEERLERWREHF---QHV----FN--QQTTV---------- 332
++ + ++ + + H + V N + V
Sbjct: 344 LTQEQV--------------QDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGL 389
Query: 333 --NLEGIEIDPITD--NLPNDERPTENEIMLETLIFPKSPIKMNF-----PF 375
L + D +P ER K F PF
Sbjct: 390 NLTLRKAKAPSGLDQSRIPFSER--------------KLKFSNRFLPVASPF 427
Score = 40.0 bits (93), Expect = 0.001
Identities = 61/337 (18%), Positives = 96/337 (28%), Gaps = 135/337 (40%)
Query: 18 SIQNEFSSNPIAQEIRNILVKNKHILSLH--FTWVPSHVGIVGNEESDRLAKEALSS--- 72
SI + +NP+ I K K I + + G + E+ + E +S
Sbjct: 1660 SILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTF 1719
Query: 73 NSPSVNTIPINYFKRFLKSKILSTWNTEWVNLADNKLRQIKEEKRPWNPSLHESRESNSA 132
S K + +T T Q P+L +
Sbjct: 1720 RSE--------------KGLLSATQFT-----------Q---------PAL-------TL 1738
Query: 133 RLPQVSLAELKVIQETLGDLERQGDLDLDLCDSWRNLAESQEANDDGDLSSHHVTLDLAN 192
+ A + ++ +G + D A G H
Sbjct: 1739 ----MEKAAFEDLKS-------KGLIPADAT-----FA--------G----H-------- 1762
Query: 193 RIVQS---YTGIQADLKYGVSGILS--EIMDLV-------QDVVTSSEAGEDGLEL---- 236
S Y A L ++ ++S ++++V Q V E G +
Sbjct: 1763 ----SLGEYA---A-L-ASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAIN 1813
Query: 237 P--VARKREYQEARQKCQREVRRIREEWWNKKINELQEFANKNDTYNL----Y--RGMKS 288
P VA QEA Q V R+ + L E N YN+ Y G
Sbjct: 1814 PGRVAASFS-QEALQYV---VERVGKR-----TGWLVEIVN----YNVENQQYVAAGDLR 1860
Query: 289 AVGPIRKPLNIIEDKNGNKISNKE----ERLERWREH 321
A+ + LN I+ + KI E LE H
Sbjct: 1861 ALDTVTNVLNFIKLQ---KIDIIELQKSLSLEEVEGH 1894
Score = 29.6 bits (66), Expect = 2.6
Identities = 25/154 (16%), Positives = 49/154 (31%), Gaps = 60/154 (38%)
Query: 12 SL---SALQSIQNEFSSNPIAQEIRNILVK------------------NKHILSLHFTWV 50
SL +AL S+ + S I + +V N +++++
Sbjct: 1763 SLGEYAALASLADVMS---IESLVE--VVFYRGMTMQVAVPRDELGRSNYGMIAIN---- 1813
Query: 51 PSHVGIVGNEESDRLAKEALSSNSPSVNTIPINYFKRFLKSKILSTWNTE---------- 100
P V ++E+ + E + + + I +NY N E
Sbjct: 1814 PGRVAASFSQEALQYVVERVGKRTGWLVEI-VNY-------------NVENQQYVAAGDL 1859
Query: 101 -----WVNLAD-NKLRQIKEEKRPWNPSLHESRE 128
N+ + KL++I + + SL E
Sbjct: 1860 RALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEG 1893
>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 = 39.1 bits (92), Expect = 6e-04
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 39 NKHILSLHFTWVPSHVGIVGNEESDRLAKEA 69
K + L WVP+H GI GNE+ D+L
Sbjct: 116 KKEKVYLA--WVPAHKGIGGNEQVDKLVSAG 144
>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 = 40.9 bits (96), Expect = 7e-04
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 11 DSLSALQSIQN--EFSSNPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRL 65
DS + + + S + I +I ++K + I + WVP+H GI GN+E D L
Sbjct: 497 DSQYVMGIVASQPTESESKIVNQIIEEMIKKEAI---YVAWVPAHKGIGGNQEVDHL 550
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 38.3 bits (90), Expect = 0.001
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 10/43 (23%)
Query: 37 VKNK----------HILSLHFTWVPSHVGIVGNEESDRLAKEA 69
V NK + + + VP H G +GNEE+DRLA+E
Sbjct: 106 VINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAREG 148
>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 = 0.008
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 10/48 (20%)
Query: 37 VKNK-------HILSLH---FTWVPSHVGIVGNEESDRLAKEALSSNS 74
V+N + +LH F V H N +D LA+ A+ NS
Sbjct: 99 VENIDLWQEILKLTTLHRVTFHKVKGHSDNPYNSRADELARLAIKENS 146
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 35.9 bits (82), Expect = 0.009
Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 20/80 (25%)
Query: 240 RK-REYQEAR-QKCQREVRRIREEWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPL 297
RK RE Q R Q+ + + +EW K +L+E+
Sbjct: 88 RKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEW------NQRQSEQVE--------- 132
Query: 298 NIIEDKNGNKISNKEERLER 317
++K N+I++K +
Sbjct: 133 ---KNKINNRIADKAFYQQP 149
Score = 30.5 bits (68), Expect = 0.69
Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 13/70 (18%)
Query: 107 NKLRQIKEEKRPWNPSLHESRESNSARLPQVSLAELKVIQETLGDLERQGDLDLDLCDSW 166
++L Q E R W RE RL ++ A + QE + DL+ +
Sbjct: 78 DRLTQEPESIRKW-------REEQRKRLQELDAASKVMEQE----WREKAKKDLE--EWN 124
Query: 167 RNLAESQEAN 176
+ +E E N
Sbjct: 125 QRQSEQVEKN 134
>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 = 35.2 bits (81), Expect = 0.013
Identities = 14/69 (20%), Positives = 23/69 (33%), Gaps = 9/69 (13%)
Query: 19 IQNEFSSNPIAQEIRNIL--VKNKHILSLHFTWVPSHVG-----IVGNEESDRLAKEALS 71
+ +E EI +L + L P H GN +D+ A+EA
Sbjct: 98 VHSEGREIKNKNEILALLKALFLPK--RLSIIHCPGHQKGNSAEARGNRMADQAAREAAM 155
Query: 72 SNSPSVNTI 80
+T+
Sbjct: 156 KAVLETSTL 164
>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 = 34.4 bits (80), Expect = 0.021
Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 10/48 (20%)
Query: 37 VKNK-------HILSLH---FTWVPSHVGIVGNEESDRLAKEALSSNS 74
VKN L H + WV H G NE +D LA+ A + +
Sbjct: 98 VKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPT 145
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 34.4 bits (80), Expect = 0.021
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 10/47 (21%)
Query: 37 VKNK-------HILSLH---FTWVPSHVGIVGNEESDRLAKEALSSN 73
VKN LH + WV H G NE D+LA+ A +N
Sbjct: 100 VKNVDLWKRLDKAAQLHQIDWRWVKGHAGHAENERCDQLARAAAEAN 146
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 34.1 bits (79), Expect = 0.036
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 10/48 (20%)
Query: 37 VKNK-------HILSLH---FTWVPSHVGIVGNEESDRLAKEALSSNS 74
VKN+ ++ H F +V H G NE DR A+ S +
Sbjct: 103 VKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQA 150
>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain,
fusion protein, maltose binding protein, HYDR; HET: MLR
TAR; 2.25A {Mycobacterium tuberculosis}
Length = 141
Score = 31.9 bits (73), Expect = 0.17
Identities = 9/46 (19%), Positives = 20/46 (43%), Gaps = 7/46 (15%)
Query: 27 PIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALSS 72
+ + + + +++ WVP N +DRLA +A+ +
Sbjct: 95 KLYVQAQALA---SQFRRINYEWVPRA----RNTYADRLANDAMDA 133
>3um7_A Potassium channel subfamily K member 4; potassium ION channel,
metal transport; 3.31A {Homo sapiens}
Length = 309
Score = 32.1 bits (72), Expect = 0.26
Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 2/58 (3%)
Query: 234 LELP--VARKREYQEARQKCQREVRRIREEWWNKKINELQEFANKNDTYNLYRGMKSA 289
LE P +RE E R+K R + ++ I E+ + +S+
Sbjct: 53 LEQPHEQQAQRELGEVREKFLRAHPCVSDQELGLLIKEVADALGGGADPETQSTSQSS 110
>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of
RNA/DNA hybrid; 1.40A {Uncultured organism}
Length = 140
Score = 30.6 bits (70), Expect = 0.38
Identities = 9/45 (20%), Positives = 13/45 (28%), Gaps = 11/45 (24%)
Query: 37 VKNKHILSLH-----------FTWVPSHVGIVGNEESDRLAKEAL 70
VK + V H+ N +D L EA+
Sbjct: 91 VKEPTLKEKFAKIAHIKMERVPNLVFVHIPREKNARADELVNEAI 135
>3trt_A Vimentin; cytoskeleton, intermediate filament, alpha-helix,
structural protein; 2.30A {Homo sapiens} PDB: 3klt_A*
Length = 77
Score = 27.5 bits (62), Expect = 1.7
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 4/37 (10%)
Query: 241 KREYQEARQKCQREVRRIREEWWNKKINELQEFANKN 277
+++Y+ K +E EEW+ K +L E AN+N
Sbjct: 15 RQQYESVAAKNLQEA----EEWYKSKFADLSEAANRN 47
>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded
RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus
tokodaii} PDB: 3aly_A
Length = 149
Score = 28.5 bits (64), Expect = 2.4
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 26 NPIAQEIRNILVKNKHILSLHFTWVPSHVGIVGNEESDRLAKEALS 71
P+ ++ + K L+ WVP N+E+DRL++ A
Sbjct: 96 IPLYEKAIELKKK----LNATLIWVPRE----ENKEADRLSRVAYE 133
>1wu7_A Histidyl-tRNA synthetase; ligase, structural genomics, dimer; 2.40A
{Thermoplasma acidophilum} SCOP: c.51.1.1 d.104.1.1
Length = 434
Score = 28.3 bits (64), Expect = 5.3
Identities = 5/53 (9%), Positives = 14/53 (26%), Gaps = 5/53 (9%)
Query: 294 RKPLNIIEDKNGNKISNKE-----ERLERWREHFQHVFNQQTTVNLEGIEIDP 341
+++I D E + V + + ++ + D
Sbjct: 209 EDGVSMIADLCSGTRGIDEMARITGKSSEEIARMAAVEDLLASYGVKNVRYDF 261
>2dla_A 397AA long hypothetical protein; helix bundle, twisted beta-sheet,
replication; 2.90A {Pyrococcus horikoshii}
Length = 222
Score = 27.7 bits (61), Expect = 5.7
Identities = 24/125 (19%), Positives = 51/125 (40%), Gaps = 17/125 (13%)
Query: 233 GLELPVARKREYQEARQKCQREVRRIREEWWNKKINELQEFANKNDTY--NLYRGMKSAV 290
G+EL + +K ++ +R+ + I+ E + ++ EF ++ +Y +
Sbjct: 79 GIELELVKKANLIIYSERLKRK-KEIKPEEISIDVSTAIEFPTEDVRKIERVYGKIPEYT 137
Query: 291 GPIRKPLNIIED--------KNGNKISNKEERLERWREHFQHVFNQQTTVNLEGIEIDPI 342
I L+++ D G +E+ + W + F+ N + VN+ + I
Sbjct: 138 MKISDFLDLVPDEKLANYYIYEGRVYLKREDLIRIWSKAFER--NVERGVNM----LYEI 191
Query: 343 TDNLP 347
D LP
Sbjct: 192 RDELP 196
>1w2q_A Conglutin, ARA H 6; allergen, allergene; NMR {Arachis hypogaea}
Length = 127
Score = 27.2 bits (59), Expect = 6.2
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 237 PVARKREYQEARQKCQREVRRIR----EEWWNKKINELQEFANKNDTYN 281
P+ R+R Q C+R+V R+ E+ ++I QE + D +
Sbjct: 2 PMRRERGRQGDSSSCERQVDRVNLKPCEQHIMQRIMGEQEQYDSYDIRS 50
>3cmm_A Ubiquitin-activating enzyme E1 1; UBA1, protein turnover, ligase,
conformationa thioester, adenylation,
transthioesterification, ATP-bindin nucleotide-binding;
2.70A {Saccharomyces cerevisiae}
Length = 1015
Score = 27.5 bits (60), Expect = 9.2
Identities = 16/91 (17%), Positives = 28/91 (30%)
Query: 255 VRRIREEWWNKKINELQEFANKNDTYNLYRGMKSAVGPIRKPLNIIEDKNGNKISNKEER 314
+ + + + + N G ++ L I D +K N E+
Sbjct: 604 IAWAKSLFQGYFTDSAENVNMYLTQPNFVEQTLKQSGDVKGVLESISDSLSSKPHNFEDC 663
Query: 315 LERWREHFQHVFNQQTTVNLEGIEIDPITDN 345
++ R F+ FN L D T N
Sbjct: 664 IKWARLEFEKKFNHDIKQLLFNFPKDAKTSN 694
>2cb5_A Protein (bleomycin hydrolase); aminopeptidase, cysteine protease,
SELF- compartmentalizing, cylinase; 1.85A {Homo
sapiens} SCOP: d.3.1.1 PDB: 1cb5_A
Length = 453
Score = 27.4 bits (60), Expect = 9.3
Identities = 3/28 (10%), Positives = 13/28 (46%)
Query: 12 SLSALQSIQNEFSSNPIAQEIRNILVKN 39
+ + ++ + +S+P +N+ +
Sbjct: 6 NSEKVAALIQKLNSDPQFVLAQNVGTTH 33
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
0.313 0.131 0.377
Gapped
Lambda K H
0.267 0.0481 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,936,253
Number of extensions: 351380
Number of successful extensions: 652
Number of sequences better than 10.0: 1
Number of HSP's gapped: 643
Number of HSP's successfully gapped: 42
Length of query: 399
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 303
Effective length of database: 4,021,377
Effective search space: 1218477231
Effective search space used: 1218477231
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.7 bits)