RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12553
(401 letters)
>3kio_A Ribonuclease H2 subunit A; aicardi-goutieres syndrome, RNAse H2,
protein complex, autoimmune disease, endonuclease,
hydrolase, metal-binding; 2.90A {Mus musculus} PDB:
3p5j_A 3puf_A 3p56_A
Length = 301
Score = 314 bits (806), Expect = e-106
Identities = 136/309 (44%), Positives = 193/309 (62%), Gaps = 23/309 (7%)
Query: 19 SNDNSRNLIISSTIPESCKSQPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGC 78
DN+ +SS +P C +PCVLG+DEAGRGPVLGPMVY YCP +L + L
Sbjct: 7 ERDNTGRCRLSSPVPAVCLKEPCVLGVDEAGRGPVLGPMVYAICYCPLSRLADL-EALKV 65
Query: 79 ADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGL 138
ADSK LTE +R+ + + ++ ++GW ++++SPN+I SML R KY+LN +SHD A GL
Sbjct: 66 ADSKTLTENERERLFAKMEEDGDFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTAAGL 125
Query: 139 IRKVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKAD 198
I+ + VNV +V+VDTVG PE+Y+ +L + FP + +TV +KAD
Sbjct: 126 IQYALDQNVNVTQVFVDTVGMPETYQARLQQHFPGIEVTV---------------KAKAD 170
Query: 199 STYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFG 258
S +PVV AASI AKV+RD A+K+W F E +Q ++ +GSGYP DP TK +L +++DPVFG
Sbjct: 171 SLFPVVSAASIFAKVARDKAVKNWQFVENLQDLDSDYGSGYPNDPKTKAWLRKHVDPVFG 230
Query: 259 FPQLVRFSWSTASKILKEKAVLVEGDEIDDEEEEGENKKTRSIRNFFKPKADENVESPVV 318
FPQ VRFSWSTA IL+++A V ++ + EE+ K I ++F
Sbjct: 231 FPQFVRFSWSTAQAILEKEAEDVIWEDSEAEEDPERPGK---ITSYFSQGPQTCRP---- 283
Query: 319 EERHAFFKE 327
+ H +F+E
Sbjct: 284 QAPHRYFQE 292
>1eke_A Ribonuclease HII; endonuclease, structural genomics, BSGC structure
funded by NIH, protein structure initiative, PSI; HET:
MES; 2.00A {Methanocaldococcus jannaschii} SCOP:
c.55.3.1
Length = 230
Score = 231 bits (591), Expect = 8e-75
Identities = 76/240 (31%), Positives = 109/240 (45%), Gaps = 22/240 (9%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
++GIDEAGRGPVLGPMV K+ EEL K LG DSK LT+ KR + + +
Sbjct: 3 IIGIDEAGRGPVLGPMVVCAFAIEKEREEEL-KKLGVKDSKELTKNKRAYLKKLL-ENLG 60
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAA---GVNVREVYVDTVG 158
+ I+ I M +LN++ +A + + +I + E+Y+D
Sbjct: 61 Y--VEKRILEAEEINQLM---NSINLNDIEINAFSKVAKNLIEKLNIRDDEIEIYIDACS 115
Query: 159 PPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSA 218
KK + F + I + + + ++ KAD+ YPVV AASI AK RD
Sbjct: 116 TNT---KKFEDSFKDKIEDIIKERNLNIKII---AEHKADAKYPVVSAASIIAKAERDEI 169
Query: 219 LKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKEKA 278
+ + G GSGYP DP T KFL + P + R W T +IL +
Sbjct: 170 IDYYKKIYG------DIGSGYPSDPKTIKFLEDYFKKHKKLPDIARTHWKTCKRILDKSK 223
>1uax_A Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid
ribonucleotidohydrolase, hydrolase; 2.00A {Pyrococcus
horikoshii} SCOP: c.55.3.1
Length = 220
Score = 227 bits (580), Expect = 3e-73
Identities = 72/237 (30%), Positives = 115/237 (48%), Gaps = 30/237 (12%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
V G+DEAGRGPV+GP+V G A + N E L +++G DSK LT +R+ + +
Sbjct: 3 VAGVDEAGRGPVIGPLVIGVAVIDEKNIERL-RDIGVKDSKQLTPGQREKLFSKLIDIL- 60
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPE 161
+ V +++P I + +S+NE+ + + + + + +++YVD+
Sbjct: 61 -DDYYVLLVTPKEI-----DERHHSMNELEAEK---FVVALNSLRIKPQKIYVDSADVDP 111
Query: 162 SYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALKS 221
L + + TV + KAD+ Y +V AASI AKV+RD ++
Sbjct: 112 KRFASLIKAGLKYEATVIA-------------EHKADAKYEIVSAASIIAKVTRDREIEK 158
Query: 222 WTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKEKA 278
+ G +GSGYP DP TK++L E FP +VR +W TA KI +
Sbjct: 159 LKQKYG------EFGSGYPSDPRTKEWLEEYYKQYGDFPPIVRRTWETARKIEERFR 209
>1i39_A Ribonuclease HII, RNAse HII; mixed beta sheet, helix-loop-helix,
hydrolase; 1.95A {Archaeoglobus fulgidus} SCOP: c.55.3.1
PDB: 1i3a_A 3p83_D*
Length = 225
Score = 222 bits (567), Expect = 3e-71
Identities = 65/242 (26%), Positives = 103/242 (42%), Gaps = 36/242 (14%)
Query: 37 KSQPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSI 96
+ GIDEAG+G V+GP+V C ++ L+ LG DSK L++ +R+++ + I
Sbjct: 17 RGSHMKAGIDEAGKGCVIGPLVVAGVACSDEDR---LRKLGVKDSKKLSQGRREELAEEI 73
Query: 97 CKENAWLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDT 156
K V +SP + M + ++NE+ + +I + + YVD+
Sbjct: 74 RKI---CRTEVLKVSPENLDERMAAK---TINEILKECYAEIILR-----LKPEIAYVDS 122
Query: 157 VGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRD 216
+ E L + KAD YP+V AASI AKV R+
Sbjct: 123 PDVIPERLSRELEEITGLRVVA---------------EHKADEKYPLVAAASIIAKVERE 167
Query: 217 SALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKE 276
++ + G +GSGY DP T++ L E I P VR W T S + ++
Sbjct: 168 REIERLKEKFG------DFGSGYASDPRTREVLKEWIAS-GRIPSCVRMRWKTVSNLRQK 220
Query: 277 KA 278
Sbjct: 221 TL 222
>1io2_A Ribonuclease HII; endonuclease, hydrolase; 2.00A {Thermococcus
kodakarensis} SCOP: c.55.3.1 PDB: 2dfh_A 2dff_A 2dfe_A
1x1p_A
Length = 213
Score = 217 bits (554), Expect = 2e-69
Identities = 73/237 (30%), Positives = 109/237 (45%), Gaps = 32/237 (13%)
Query: 42 VLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENA 101
+ GIDEAGRGPV+GPMV +++ +L + L DSK LT K+R+ + + I
Sbjct: 3 IAGIDEAGRGPVIGPMVIAAVVVDENSLPKL-EELKVRDSKKLTPKRREKLFNEI-LGVL 60
Query: 102 WLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVG-PP 160
+++ + P+VI ++ +LNE + + + + V +Y D
Sbjct: 61 -DDYVILELPPDVI-----GSREGTLNEFEVEN---FAKALNSLKVKPDVIYADAADVDE 111
Query: 161 ESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRDSALK 220
E + ++L E VA KAD +PVV AASI AKV+RD A++
Sbjct: 112 ERFARELGERLNFEAEVVAKH--------------KADDIFPVVSAASILAKVTRDRAVE 157
Query: 221 SWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRFSWSTASKILKEK 277
+ G GSGYP DP T+ FL FP +VR W T KI ++
Sbjct: 158 KLKEEYG------EIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTLKKIAEKV 208
>2d0b_A RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase; 2.10A
{Geobacillus stearothermophilus} PDB: 2d0a_A 2d0c_A
3asm_A
Length = 310
Score = 175 bits (444), Expect = 7e-52
Identities = 45/256 (17%), Positives = 85/256 (33%), Gaps = 22/256 (8%)
Query: 21 DNSRNLIISSTIPESCKSQPCVLGIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCAD 80
N S + +G DE G G GP+V AY + + + + LG D
Sbjct: 72 SNETADHQPSALAAHQLGSLSAIGSDEVGTGDYFGPIVVAAAYVDRPHIAK-IAALGVKD 130
Query: 81 SKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIR 140
SK L ++ I +I + + + +P + + + H+ + +
Sbjct: 131 SKQLNDEAIKRIAPAIMETVPH--AVTVLDNPQYNRWQRSGMPQTKMKALLHNRTLVKLV 188
Query: 141 KVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADST 200
I A + +D +SY + LS+ + V KA+S
Sbjct: 189 DAI-APAEPEAIIIDEFLKRDSYFRYLSDEDRIIRERVHC-------------LPKAESV 234
Query: 201 YPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFP 260
+ V AASI A+ ++ + G+ + G+G D + +
Sbjct: 235 HVSVAAASIIARYVFLEEMEQLSRAVGLLLP---KGAGAIVDEAAARIIRAR--GEEMLE 289
Query: 261 QLVRFSWSTASKILKE 276
+ ++ K L
Sbjct: 290 TCAKLHFANTKKALAI 305
>2etj_A Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII (EC 3.1.26.4)
(RNAse HII), structur genomics, joint center for
structural genomics; 1.74A {Thermotoga maritima} SCOP:
c.55.3.1 PDB: 3o3g_A* 3o3f_A* 3o3h_A*
Length = 250
Score = 65.7 bits (161), Expect = 2e-12
Identities = 49/175 (28%), Positives = 64/175 (36%), Gaps = 50/175 (28%)
Query: 44 GIDEAGRGPVLGPMVYGTAYCPKDNNEELLKNLGCADSKALTEKKRDDILDSICKENAWL 103
G+DEAGRG + GP+V A + E + DSK L+ KR+ +LD I E A
Sbjct: 28 GVDEAGRGCLAGPVV--AAAVVLEKEIEGIN-----DSKQLSPAKRERLLDEI-MEKAA- 78
Query: 104 GWMVEIISPNVICNSMLRRQKYSLN--EVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPE 161
+ I SP I N + A + R + V V VD G
Sbjct: 79 -VGIGIASPEEID---------LYNIFNATKLA---MNRALENLSVKPSFVLVDGKGIEL 125
Query: 162 SYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASICAKVSRD 216
S +V K D ++GAASI AKV RD
Sbjct: 126 SVPGT--------------------CLV------KGDQKSKLIGAASIVAKVFRD 154
>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 = 53.7 bits (128), Expect = 6e-08
Identities = 65/448 (14%), Positives = 132/448 (29%), Gaps = 122/448 (27%)
Query: 37 KSQPCVLGIDEAGRGPVLGPMVYG-----TAYCPKDNNE-ELLKNLGCADSKALTEKKRD 90
K+ + +D V M + C E+L+ L T R
Sbjct: 163 KT---WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTS--RS 217
Query: 91 DILDSI-CKENAWLGWMVEIISPNVICNSMLRRQKYSLNEVSH----DA-AIG---LI-- 139
D +I + ++ + ++ N +L L V + +A + L+
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLKSKPYENCLL-----VLLNVQNAKAWNAFNLSCKILLTT 272
Query: 140 --RKVIAAGVNVREVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKA 197
++V ++ + + L++ P +
Sbjct: 273 RFKQVTDFLSAATTTHISLDHHSMTLTPDEVK---SLLLKYLDCRPQDLP-------REV 322
Query: 198 DSTYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPV- 256
+T P SI A+ RD L +W + + + + + L ++P
Sbjct: 323 LTTNPR--RLSIIAESIRD-GLATWDNWKHVNCDKL--------TTIIESSL-NVLEPAE 370
Query: 257 -------FG-FPQ--------LVRFSWSTASK-----ILKE--KAVLVEGDEID------ 287
FP L W K ++ + K LVE +
Sbjct: 371 YRKMFDRLSVFPPSAHIPTILLSLI-WFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIP 429
Query: 288 ----DEEEEGENKKT--RSIRNFFKP--KADENVESPVVEERHAFFKESPY-----GGSK 334
+ + + EN+ RSI + + D + P +++ F+ + +
Sbjct: 430 SIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQY-FYSHIGHHLKNIEHPE 488
Query: 335 VFEVLNSTYLNILEMAHFIGKKLNLTSI-------------DLLFYIPLLTRN---LEVK 378
+ +L+ F+ +K+ S L FY P + N E
Sbjct: 489 RMTLFRMVFLDF----RFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERL 544
Query: 379 LKS--KF-FKLGEEL---KHQLIFFLGL 400
+ + F K+ E L K+ + + L
Sbjct: 545 VNAILDFLPKIEENLICSKYTDLLRIAL 572
Score = 41.8 bits (97), Expect = 4e-04
Identities = 49/383 (12%), Positives = 101/383 (26%), Gaps = 129/383 (33%)
Query: 63 YCPKD----NNEELLKNLGCAD-----SKALTEKKRDDILDSICKENA-----WL----- 103
Y KD + + N C D L++++ D I+ S + W
Sbjct: 16 YQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQ 75
Query: 104 ----------------GWMVEIISPNVICNSMLRRQ-KYSLNEVSHDAAIGLIRKVIAAG 146
+++ I SM+ R + + +D + K
Sbjct: 76 EEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV--FAKY---- 129
Query: 147 VNV-REVYVDTVGPPESYKKKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVG 205
NV R + ++ L E+ P + + V+G+ G
Sbjct: 130 -NVSRLQPYLKL------RQALLELRPAKNVLI-------DGVLGS-------------G 162
Query: 206 AASICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDPVTKKFLSENIDPVFGFPQLVRF 265
+ V ++ I W + L P L +
Sbjct: 163 KTWVALDVCLSYKVQC-KMDFKI-----FW--------LN---LKNCNSPETVLEMLQKL 205
Query: 266 SWSTASKILKEKAVLVEGDE-IDDEEEEGENKKTRSIRNFFKPKA----DENVESP-VVE 319
+I + I + + R +++ NV++
Sbjct: 206 L----YQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL-NVQNAKAWN 260
Query: 320 ERHAFFKESPYGGSK---------VFEVLNSTYLNILEMAHFIGKKLNLTSIDLLFYIPL 370
AF K V + L++ + + H + LT ++ L
Sbjct: 261 ---AF-----NLSCKILLTTRFKQVTDFLSAATTTHISLDHH---SMTLTPDEVK---SL 306
Query: 371 LTRNLEVKLKSKFFKLGEELKHQ 393
L + L+ + ++L +
Sbjct: 307 LLKYLDCRP--------QDLPRE 321
>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 = 47.0 bits (111), Expect = 9e-06
Identities = 34/214 (15%), Positives = 72/214 (33%), Gaps = 63/214 (29%)
Query: 70 EELLKN-LGCADSKALTEKKRDDILDSICKENAWLGWMVEIISPNVICNSMLRRQKYSLN 128
+++L L ++ L DI +A +++ ++ L + +
Sbjct: 81 DQVLNLCLTEFENCYLEGN---DI-------HALAAKLLQENDTTLVKTKELIKNYITAR 130
Query: 129 EVS-------HDAAIGLIRKVIAAGVNVREVYVDTV----GPPESYKKKLSEIFPELIIT 177
++ ++A L R V G N + + + G + Y ++L +++
Sbjct: 131 IMAKRPFDKKSNSA--LFRAV-GEG-NAQ-LV--AIFGGQGNTDDYFEELRDLY------ 177
Query: 178 VASKADSTY-PVVGAAIASKADSTYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWG 236
TY +VG I +A +++ R + F +G+ I W
Sbjct: 178 ------QTYHVLVGDLIKF----------SAETLSELIRTTLDAEKVFTQGLNIL--EWL 219
Query: 237 SGYPGDPVTKKFLSENIDPVFGFP-----QLVRF 265
P + K +L P+ P QL +
Sbjct: 220 EN-PSNTPDKDYLLSI--PI-SCPLIGVIQLAHY 249
Score = 46.2 bits (109), Expect = 2e-05
Identities = 42/227 (18%), Positives = 72/227 (31%), Gaps = 53/227 (23%)
Query: 197 ADSTYPVV---GAASICAKVSRD-----SALKSWTFQEGI-QIENNAWGSGYPGDPV--T 245
A ST P+ G+ V S L+ F + + + P P
Sbjct: 3 AYSTRPLTLSHGSLEHVLLVPTASFFIASQLQE-QFNKILPEPTEGFAADDEPTTPAELV 61
Query: 246 KKFL---SENIDP--VFGFPQLVRFSWSTASKILKEKAVLVEGDEI-------DDEEEEG 293
KFL S ++P V F Q++ + E L EG++I E +
Sbjct: 62 GKFLGYVSSLVEPSKVGQFDQVLNLCLTEF-----ENCYL-EGNDIHALAAKLLQENDTT 115
Query: 294 ENKKTRSIRNFFKPKADENVESPVVE-ERHAFFKESPYGGSKVFEVL-----NSTYLNIL 347
K I+N+ A + P + A F+ G +++ + Y
Sbjct: 116 LVKTKELIKNYI--TARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFE-- 171
Query: 348 EM-------AHFIGKKLNLTSIDLLFYIPLLTRNLEVKLKSKFFKLG 387
E+ +G + ++ L L+ L+ K F G
Sbjct: 172 ELRDLYQTYHVLVGDLIKFSAETLS---ELIRTTLDA---EKVFTQG 212
Score = 38.5 bits (89), Expect = 0.005
Identities = 57/326 (17%), Positives = 90/326 (27%), Gaps = 146/326 (44%)
Query: 126 SLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVG--PPESYKKKLSEI---FPELI-IT-- 177
L + DA KV G+N+ E +++ P + Y L I P LI +
Sbjct: 197 ELIRTTLDA-----EKVFTQGLNILE-WLENPSNTPDKDY---LLSIPISCP-LIGVIQL 246
Query: 178 ----VASKADSTYP----------------VVGAAIASKADS------------------ 199
V +K P +V A ++ DS
Sbjct: 247 AHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFI 306
Query: 200 ------TYPVVGAASICAKVSRDSALKSWTFQEGIQIENNAWGSGYPGDP------VTKK 247
YP S+ + DS +EN G P P +T++
Sbjct: 307 GVRCYEAYPNT---SLPPSILEDS------------LEN---NEGVPS-PMLSISNLTQE 347
Query: 248 FLSENID------P-----------------VFGFPQ-LVRFSWSTASKILKEKAVLVEG 283
+ + ++ P V G PQ L + + K KA
Sbjct: 348 QVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLN----LTLRKAKA----P 399
Query: 284 DEIDDEEEEGENKKTRSIRNFFKPKADENVESPVVEERHAFFKESPYGGSKVFEVLNSTY 343
+D +K + N F P V SP H S L
Sbjct: 400 SGLDQSRIPFSERKLK-FSNRFLP-----VASPF----H-----SHL--------LVPAS 436
Query: 344 LNILEMAHFIGKKLNLTSIDLLFYIP 369
I + + ++ + D+ IP
Sbjct: 437 DLINK--DLVKNNVSFNAKDIQ--IP 458
>3fv5_A DNA topoisomerase 4 subunit B; topoisomerase IV B subunit complex,
antibiotic resistance, ATP-binding, nucleotide-binding;
HET: DNA 1EU; 1.80A {Escherichia coli} PDB: 1s14_A*
Length = 201
Score = 31.7 bits (73), Expect = 0.29
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 6/36 (16%)
Query: 263 VRFSWSTASKILKEKAVLVEG------DEIDDEEEE 292
RFS S + +LK KAVL G DEI++ E+
Sbjct: 163 PRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQR 198
>2uv8_A Fatty acid synthase subunit alpha (FAS2); fatty acid biosynthesis,
malonyl/palmitoyl transferase, phosphopantetheine,
transferase; HET: GVL FMN; 3.10A {Saccharomyces
cerevisiae} PDB: 2vkz_A* 3hmj_A*
Length = 1887
Score = 31.5 bits (71), Expect = 0.63
Identities = 23/105 (21%), Positives = 40/105 (38%), Gaps = 7/105 (6%)
Query: 105 WMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYK 164
+VEI + R K S+DAA+ L R+++ + +E+Y + K
Sbjct: 43 RVVEIGPSPTLAGMAQRTLK--NKYESYDAALSLHREILCYSKDAKEIYYTPDPSELAAK 100
Query: 165 KKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASI 209
++ P A ++ P AA + + P AA I
Sbjct: 101 EE-----PAKEEAPAPTPAASAPAPAAAAPAPVAAAAPAAAAAEI 140
>1s16_A Topoisomerase IV subunit B; two-domain protein complexed with
ADPNP; HET: ANP; 2.10A {Escherichia coli} SCOP: d.14.1.3
d.122.1.2
Length = 390
Score = 29.7 bits (68), Expect = 1.9
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 6/36 (16%)
Query: 263 VRFSWSTASKILKEKAVLVEG------DEIDDEEEE 292
RFS S + +LK KAVL G DEI++ E+
Sbjct: 177 PRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQR 212
>3lnu_A Topoisomerase IV subunit B; PARE, ATP-binding, nucleotide-BI
topoisomerase; 2.20A {Xanthomonas oryzae PV} PDB:
3lps_A*
Length = 408
Score = 29.4 bits (67), Expect = 2.4
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 6/36 (16%)
Query: 263 VRFSWSTASKILKEKAVLVEG------DEIDDEEEE 292
+F+ +L+ KAVL G DE E++
Sbjct: 196 PKFNVRALRHLLRAKAVLCPGLTVKLHDEATGEQDS 231
>2uv9_A Fatty acid synthase alpha subunits; fungal, dehydratase, enoyl
reductase, ketoacyl synthase, ketoacyl reductase; 3.1A
{Thermomyces lanuginosus} PDB: 2uvb_A*
Length = 1878
Score = 29.1 bits (65), Expect = 3.6
Identities = 18/105 (17%), Positives = 38/105 (36%), Gaps = 7/105 (6%)
Query: 105 WMVEIISPNVICNSMLRRQKYSLNEVSHDAAIGLIRKVIAAGVNVREVYVDTVGPPESYK 164
+VEI + + R + ++DAA + R+++ + +E+Y D +
Sbjct: 43 RIVEIGPSDTLGGMARRTLQ--SKYEAYDAATSVQRQILCYCKDAKEIYYDVEPIEDE-- 98
Query: 165 KKLSEIFPELIITVASKADSTYPVVGAAIASKADSTYPVVGAASI 209
E P + + + A A+ A + AA +
Sbjct: 99 ---PEPTPAAASSADAAPAAAPAAPAAPAAAPAPAPASAGPAAPV 140
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.8 bits (61), Expect = 4.7
Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 15/74 (20%)
Query: 260 PQLVRFSWSTASKILKE--KAVLVEGDEIDDE-EEEGENKKTRSIRNFFKPKADENVESP 316
P+ +R W +E + L E D E+E K + + + + + E VE
Sbjct: 84 PESIR-KW-------REEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQ-RQSEQVEKN 134
Query: 317 VVEERHA---FFKE 327
+ R A F+++
Sbjct: 135 KINNRIADKAFYQQ 148
>3va4_A Mediator of DNA damage checkpoint protein 1; cell cycle, FHA
domain, DNA-damage, CHK2 and MDC1 dimerizati; HET: TPO;
1.54A {Mus musculus} PDB: 3va1_A* 3umz_A 3unm_A 3unn_A*
3uot_A* 3un0_B
Length = 132
Score = 27.1 bits (60), Expect = 6.1
Identities = 10/62 (16%), Positives = 22/62 (35%), Gaps = 3/62 (4%)
Query: 307 PKADENVESPVVEERHAFFKESPYGGSKVFEVLNS---TYLNILEMAHFIGKKLNLTSID 363
P + P + ++HA + S + + + + S T + G L +
Sbjct: 53 PDCSVALPFPSISKQHAVIEISAWNKAPILQDCGSLNGTQIVKPPRVLPPGVSHRLRDQE 112
Query: 364 LL 365
L+
Sbjct: 113 LI 114
>3ay3_A NAD-dependent epimerase/dehydratase; glucuronic acid dehydrogeanse,
oxidoreductase; 2.10A {Chromohalobacter salexigens}
Length = 267
Score = 27.3 bits (61), Expect = 7.9
Identities = 10/34 (29%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 311 ENVESPVVEERHAFFKESPYGGSKVF-EVLNSTY 343
+ ++ +S YG SK F E L S Y
Sbjct: 116 YYPRTTRIDTEVPRRPDSLYGLSKCFGEDLASLY 149
>2r5i_A L1 protein; HPV18, pentamer, structure, type specific epitope,
capsid, capsid protein, virion; 3.40A {Human
papillomavirus type 18} PDB: 3ofl_A*
Length = 428
Score = 27.4 bits (61), Expect = 8.9
Identities = 10/26 (38%), Positives = 12/26 (46%), Gaps = 3/26 (11%)
Query: 76 LGCADSKALTEKKRD---DILDSICK 98
G D L + K + DI SICK
Sbjct: 186 YGAMDFSTLQDTKCEVPLDICQSICK 211
>3oae_A Late major capsid protein L1; jelly roll, receptor HSPG, virus
capsid, VIR protein; HET: JHM IDS; 2.80A {Human
papillomavirus} PDB: 2r5h_A 2r5j_A 2r5k_A
Length = 428
Score = 27.4 bits (61), Expect = 9.6
Identities = 10/26 (38%), Positives = 11/26 (42%), Gaps = 3/26 (11%)
Query: 76 LGCADSKALTEKKRD---DILDSICK 98
G D L K + DI SICK
Sbjct: 188 FGAMDFTTLQANKSEVPLDICTSICK 213
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
0.316 0.134 0.388
Gapped
Lambda K H
0.267 0.0610 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,092,389
Number of extensions: 371875
Number of successful extensions: 844
Number of sequences better than 10.0: 1
Number of HSP's gapped: 804
Number of HSP's successfully gapped: 30
Length of query: 401
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 305
Effective length of database: 4,021,377
Effective search space: 1226519985
Effective search space used: 1226519985
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.4 bits)