RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8269
(386 letters)
>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens}
SCOP: a.22.1.3
Length = 97
Score = 126 bits (318), Expect = 3e-36
Identities = 70/84 (83%), Positives = 78/84 (92%)
Query: 109 DLKTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTL 168
D + Q LPLARIKKIMKLD+ VKMISAEAP+LF+KAA++FI ELT+RAWIHTEDNKRRTL
Sbjct: 14 DFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTL 73
Query: 169 QRNDIAMAITKYDMFDFLIDIVPR 192
QRNDIAMAITK+D FDFLIDIVPR
Sbjct: 74 QRNDIAMAITKFDQFDFLIDIVPR 97
>2byk_A Chrac-16; nucleosome sliding, histone fold, DNA-binding protein;
2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB:
2bym_A
Length = 140
Score = 126 bits (317), Expect = 1e-35
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 1/83 (1%)
Query: 111 KTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHT-EDNKRRTLQ 169
LPL+R++ IMK +I+ E L +K ELF+ L A+ L+
Sbjct: 16 AETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALK 75
Query: 170 RNDIAMAITKYDMFDFLIDIVPR 192
++ + K +FL+ IVP+
Sbjct: 76 YEHLSQVVNKNKNLEFLLQIVPQ 98
>1jfi_A Transcription regulator NC2 alpha chain; histone, H2A/H2B,
tata-DNA, transcription initiation, NC2, negative
cofactor, structural genomics, PSI; 2.62A {Homo sapiens}
SCOP: a.22.1.3
Length = 98
Score = 114 bits (287), Expect = 1e-31
Identities = 24/93 (25%), Positives = 42/93 (45%), Gaps = 2/93 (2%)
Query: 111 KTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQR 170
P ARIKKIM+ D+ + ++A P++ S+A ELF+ L +A T+ +T+
Sbjct: 8 YNARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTT 67
Query: 171 NDIAMAITKYDMFDFLIDIVPREEVKTATGPHR 203
+ + I D + +E A +
Sbjct: 68 SHLKQCIELEG--DPAANKARKEAELAAATAEQ 98
>2byk_B Chrac-14; nucleosome sliding, histone fold, DNA-binding protein;
2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB:
2bym_B
Length = 128
Score = 90.4 bits (224), Expect = 3e-22
Identities = 25/109 (22%), Positives = 45/109 (41%), Gaps = 10/109 (9%)
Query: 115 LPLARIKKIMK--LDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRND 172
LP A I +++K L + + S EA ++AA +F +T + +T+ D
Sbjct: 10 LPNAVIGRLIKEALPESASV-SKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKD 68
Query: 173 IAMAITKYDMFDFLIDIVP------REEVKTATGPHRRDDATKTALNPD 215
I +T+ D F+ + + R+ VK + TA N +
Sbjct: 69 ILQTLTELD-FESFVPSLTQDLEVYRKVVKEKKESKASKKDSNTAENAN 116
>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens}
SCOP: a.22.1.3
Length = 93
Score = 79.9 bits (197), Expect = 7e-19
Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 2/80 (2%)
Query: 115 LPLARIKKIMKLD-DGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDI 173
LP+A + +IMK I+ +A + FI +T A KR+T+ DI
Sbjct: 9 LPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDI 68
Query: 174 AMAITKYDMFDFLIDIVPRE 193
A++ FD ++ +
Sbjct: 69 LFAMSTLG-FDSYVEPLKLY 87
>2xov_A Rhomboid protease GLPG; membrane protein, hydrolase, intramembrane
protease; HET: BNG; 1.65A {Escherichia coli} PDB:
2ic8_A* 2nrf_A 2xtu_A* 2irv_A* 3b45_A* 2o7l_A* 2xow_A*
3txt_A* 2xtv_A* 3b44_A*
Length = 181
Score = 73.9 bits (182), Expect = 8e-16
Identities = 22/136 (16%), Positives = 45/136 (33%), Gaps = 16/136 (11%)
Query: 225 STFSHQSPLHIFANMFVLHSFMPSSVED-LGKEQFVGFYLTAGVVASLLSYVHKILVRKP 283
H S +HI N+ + VE LG + + L + +++ +
Sbjct: 51 HALMHFSLMHILFNLLWWWYLGGA-VEKRLGSGKLIVITLISALLSGYVQQKF-----SG 104
Query: 284 GLSIGASGAIMAVLAHTCITHPD--TELGILFVPYVRFSAEHAIQGIMLLDFLGVLFRWR 341
G SG + A++ + + L + F+ + G L + +
Sbjct: 105 PWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSM----- 159
Query: 342 LFDHAAHLGGALFGIL 357
+ AH+ G G+
Sbjct: 160 --ANGAHIAGLAVGLA 173
>2nr9_A Protein GLPG homolog; intramembrane peptidase, rhomboid protease,
membrane protein; HET: PA6 PQE; 2.20A {Haemophilus
influenzae} SCOP: f.51.1.1 PDB: 3odj_A
Length = 196
Score = 71.2 bits (175), Expect = 1e-14
Identities = 30/137 (21%), Positives = 50/137 (36%), Gaps = 14/137 (10%)
Query: 225 STFSHQSPLHIFANMFVLHSFMPSSVED-LGKEQFVGFYLTAGVVASLLSYVHKILVRKP 283
T H S LHI N+ F +E G + + Y+ A + +
Sbjct: 56 HTLVHLSNLHILFNLSWFFIFGG-MIERTFGSVKLLMLYVVASAITGYVQNYV-----SG 109
Query: 284 GLSIGASGAIMAVLAHTCITHP-DTELGILFVPYVRFSAEHAIQGIMLLDFLGVLFRWRL 342
G SG + AVL + I + L L + + L F+ LF +
Sbjct: 110 PAFFGLSGVVYAVLGYVFIRDKLNHHLFDLPEGFFTMLL-----VGIALGFISPLFGVEM 164
Query: 343 FDHAAHLGGALFGILYS 359
+AAH+ G + G+++
Sbjct: 165 -GNAAHISGLIVGLIWG 180
>1jfi_B DR1 protein, transcription regulator NC2 beta chain; histone,
H2A/H2B, tata-DNA, transcription initiation, NC2,
negative cofactor, structural genomics, PSI; 2.62A {Homo
sapiens} SCOP: a.22.1.3
Length = 179
Score = 64.4 bits (156), Expect = 2e-12
Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 1/76 (1%)
Query: 115 LPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIA 174
+P A I K++K ++ +A L FIH ++ A ++++T+ +
Sbjct: 16 IPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVI 75
Query: 175 MAITKYDMFDFLIDIV 190
A+ F I V
Sbjct: 76 QALESLG-FGSYISEV 90
>1b67_A Protein (histone HMFA); DNA binding protein; 1.48A {Methanothermus
fervidus} SCOP: a.22.1.2 PDB: 1hta_A 1a7w_A 1b6w_A
1bfm_A
Length = 68
Score = 58.5 bits (142), Expect = 1e-11
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 115 LPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIA 174
LP+A I +I+K + G + +S +A + +K E E+ A + R+T++ DI
Sbjct: 3 LPIAPIGRIIK-NAGAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIE 61
Query: 175 MAITKY 180
+A +
Sbjct: 62 LARKMF 67
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A
{Pyrococcus horikoshii} SCOP: a.22.1.2
Length = 70
Score = 57.0 bits (138), Expect = 5e-11
Identities = 15/63 (23%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 115 LPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIA 174
LP+A + ++++ G + +S +A + ++ E + E+ +A R+T++ DI
Sbjct: 7 LPIAPVDRLIR-KAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIK 65
Query: 175 MAI 177
+AI
Sbjct: 66 LAI 68
>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 = 49.3 bits (117), Expect = 2e-06
Identities = 53/311 (17%), Positives = 93/311 (29%), Gaps = 86/311 (27%)
Query: 29 WNALHPGDRVYVPILFLNGVVFLAWFYPR--LHPVLYKYFASN----PQSM----GITL- 77
W + R + +LF GV YP L P + + N P M +T
Sbjct: 289 WESFFVSVRKAITVLFFIGVRCYEA-YPNTSLPPSILEDSLENNEGVPSPMLSISNLTQE 347
Query: 78 RLHAVSPEFDSRLGRSFFGSVLEVQGALSM------LDLKTQALPLARIKKIMKLDDGVK 131
++ + +S L + V GA ++ L L L + K LD
Sbjct: 348 QVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLD---- 403
Query: 132 MISAEAPMLFSKAAELFIHE-LTIRAWIHT-----------EDNKRRTLQRNDIAMAITK 179
+ P FS+ F + L + + H+ +D + + N + I
Sbjct: 404 --QSRIP--FSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPV 459
Query: 180 YDMFDFLIDIVPREEVKTATGPHRRDDATKTALNPDQYLSVPMLLSTFSHQSPLHIFANM 239
YD T G R +++ V ++ P+
Sbjct: 460 YD---------------TFDGSDLRV--LSGSISER---IVDCIIR-----LPVK----W 490
Query: 240 FVLHSFMPSSVEDLGKEQFVGFYLTAGVVASLLSYVHKILVRKPGLSIGASGAIMAVLAH 299
F + + D G G + L H+ G+ + ++A
Sbjct: 491 ETTTQFKATHILDFG----------PGGASGLGVLTHRNKDGT-GVRV--------IVAG 531
Query: 300 TCITHPDTELG 310
T +PD + G
Sbjct: 532 TLDINPDDDYG 542
Score = 46.6 bits (110), Expect = 1e-05
Identities = 71/411 (17%), Positives = 120/411 (29%), Gaps = 162/411 (39%)
Query: 23 KDLRKRWNALHP-----------------GDRVYVPILFLNGVVFLAWF-YPRLHPVLYK 64
++LR + H + +F G+ L W P P
Sbjct: 171 EELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKD- 229
Query: 65 YFASNPQSM-GITL----------RLHAVSP-EFDSRL---------------------G 91
Y S P S I + +L +P E S L
Sbjct: 230 YLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSW 289
Query: 92 RSFFGSVLEVQGALSMLDLKTQ------ALPLARIKKIMKLDDGVKMISAEAPMLFSKAA 145
SFF SV + L + ++ +LP + ++ ++ ++GV +PML S
Sbjct: 290 ESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGV-----PSPML-S--- 340
Query: 146 ELFIHELT---IRAWIHTEDNKRRTLQRND---IAMAITKYDMFDFLIDIVPREEVKTAT 199
I LT ++ ++ + N L I++ +V +
Sbjct: 341 ---ISNLTQEQVQDYV-NKTNSH--LPAGKQVEISLVNG-AKNL-----VV--------S 380
Query: 200 GP---------HRRDDATKTALNPDQYLSVPMLLSTFSHQSPLHIFANMFVLHSFMPSSV 250
GP R + L DQ +P FS + F + F+P +
Sbjct: 381 GPPQSLYGLNLTLRKAKAPSGL--DQS-RIP-----FSERKL------KFS-NRFLPVAS 425
Query: 251 EDLGKEQFVGF---YLTAGVVASLLSYV--HKILVRKPGLSI-------GA-----SGAI 293
F L + + + + + I G+ SG+I
Sbjct: 426 P---------FHSHLL-VPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSI 475
Query: 294 MAVLAHTCITHPDTELGILFVPYVRFSAEHAIQGIMLLDF-------LGVL 337
+ I P + + +F A H +LDF LGVL
Sbjct: 476 SERIVDCIIRLP-----VKWETTTQFKATH------ILDFGPGGASGLGVL 515
Score = 42.3 bits (99), Expect = 3e-04
Identities = 27/118 (22%), Positives = 46/118 (38%), Gaps = 20/118 (16%)
Query: 40 VPILFLNGVVFLAWFYPRLHPVLYKY--FASNPQSMGITLRLHAVSPEFDSRLGRSFFGS 97
V ++F G+ + PR Y A NP + + A+ R+G+ G
Sbjct: 1783 VEVVFYRGM-TMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQ-YVVERVGKRT-GW 1839
Query: 98 VLEV--------Q----GALSMLDLKTQALPLARIKKI--MKLDDGVKMISAEAPMLF 141
++E+ Q G L LD T L +++KI ++L + + E LF
Sbjct: 1840 LVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEG-HLF 1896
Score = 33.5 bits (76), Expect = 0.14
Identities = 35/227 (15%), Positives = 63/227 (27%), Gaps = 67/227 (29%)
Query: 158 IHT------EDNKRRTLQRNDIAMAITKYDMFDFLIDIVPREEVKTATGPHRRDDATKTA 211
IH ++N ++ ++ I Y + ++ +A + +
Sbjct: 101 IHALAAKLLQENDTTLVKTKEL---IKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLV 157
Query: 212 L------NPDQYL-------------------SVPMLLSTFSHQSP--LHIFANMFVLHS 244
N D Y LS + +F +
Sbjct: 158 AIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILE 217
Query: 245 FM--PSSVEDLGKEQFVGFYL-TAGV------VASLLSY--VHKILVRKPG----LSIGA 289
++ PS+ D YL + + V L Y K+L PG GA
Sbjct: 218 WLENPSNTPDKD-------YLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGA 270
Query: 290 SGAIMAVLAHTCITHPDTELGILFVPYVRFSAEHAIQGIMLLDFLGV 336
+G ++ I D+ F + I +L F+GV
Sbjct: 271 TGHSQGLVTAVAIAETDSW--------ESF-FVSVRKAITVLFFIGV 308
Score = 31.2 bits (70), Expect = 0.78
Identities = 38/207 (18%), Positives = 52/207 (25%), Gaps = 83/207 (40%)
Query: 190 VPREEVKTATGPHRRDDATKTALNP-------DQYLSVPMLLSTFSHQSPLHIFANMFVL 242
VP A+ ++ K P D+ + L+ F L +V
Sbjct: 22 VPTASFFIAS--QLQEQFNKILPEPTEGFAADDEPTTPAELVGKF-----LG-----YVS 69
Query: 243 HSFMPSSV---EDLGKEQFVGF---YLTAG----VVASLLSYVHKILVRKPGLSIGASGA 292
PS V + + F YL + A LL LV+ L
Sbjct: 70 SLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKEL------- 122
Query: 293 IMA-VLAHTCITHPDTELGILFVPYVRFSAEHAIQGIMLLDFLGVLFRWRLFDHAAHLGG 351
I + A P + SA LFR A G
Sbjct: 123 IKNYITARIMAKRPFDK--------KSNSA---------------LFR------AVGEGN 153
Query: 352 ----ALFG-------------ILYSKY 361
A+FG LY Y
Sbjct: 154 AQLVAIFGGQGNTDDYFEELRDLYQTY 180
>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 = 40.2 bits (93), Expect = 0.001
Identities = 59/363 (16%), Positives = 106/363 (29%), Gaps = 105/363 (28%)
Query: 57 RLHPVLYKYFASNP-QSMGITLRLHAVSPEFDSRL--GRSFFGSVL---EVQGA--LSML 108
+L + + S S I LR+H++ E RL + + +L VQ A +
Sbjct: 204 KLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL-RRLLKSKPYENCLLVLLNVQNAKAWNAF 262
Query: 109 DLKTQALPLARIKKIM-----------KLDDGVKMIS-AEAPMLFSKAAELFIHEL---- 152
+L + L R K++ LD ++ E L K + +L
Sbjct: 263 NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREV 322
Query: 153 -------------TIRAWIHTEDNKRRTLQRNDIAMAITK-------------YDMF--- 183
+IR + T DN + + + + I +D
Sbjct: 323 LTTNPRRLSIIAESIRDGLATWDNWKH-VNCDKLTTIIESSLNVLEPAEYRKMFDRLSVF 381
Query: 184 --DFLI----------DIVPREEVKTATGPHRRDDATKTALN-----PDQYLSVPMLLST 226
I D++ + + H+ K P YL L
Sbjct: 382 PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLE---LKVK 438
Query: 227 FSHQSPLHIFANMFVLHSFMPSSV--EDLGKE-------QFVGFYLTAGVVASLLSYVHK 277
++ LH V H +P + +DL +G +L ++
Sbjct: 439 LENEYALH---RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRM 495
Query: 278 IL---------VRKPGLSIGASGAIMAVLA-------HTCITHPDTELGILFVPYVRFSA 321
+ +R + ASG+I+ L + C P E L + F
Sbjct: 496 VFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYER--LVNAILDFLP 553
Query: 322 EHA 324
+
Sbjct: 554 KIE 556
Score = 36.4 bits (83), Expect = 0.015
Identities = 40/280 (14%), Positives = 81/280 (28%), Gaps = 59/280 (21%)
Query: 20 KWRKD-LRKRWNALHPGDRVYVP---ILFLNGVVFLAWFYPRLHPVLYKYFASNPQSMGI 75
K+ ++ R+Y+ L+ + VF + RL P L
Sbjct: 92 KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYL------------- 138
Query: 76 TLR--LHAVSPEFDSRL-GRSFFG-SVLEVQGALSML-DLKTQALPLARI-----KKIMK 125
LR L + P + + G G + + AL + K Q +I K
Sbjct: 139 KLRQALLELRPAKNVLIDGVLGSGKTWV----ALDVCLSYKVQCKMDFKIFWLNLKNCNS 194
Query: 126 LDDGVKMISAEAPMLFSKAAELFIHELTIRAWIH-TEDNKRRTLQRNDIAMAI------- 177
+ ++M+ + H I+ IH + RR L+ +
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ 254
Query: 178 --TKYDMFDFLIDIVPREEVKTATGPHRRDDATKTALNPDQYLSVPM--LLSTFSHQSPL 233
++ F+ I+ + T R L+ + + T +
Sbjct: 255 NAKAWNAFNLSCKIL----LTT------RFKQVTDFLSAATTTHISLDHHSMTLTPDEVK 304
Query: 234 HIFANMFVLHSFMPSSVEDLGKEQFVGFYLTAGVVASLLS 273
+ ++ +DL +E ++A +
Sbjct: 305 SLLLK------YLDCRPQDLPREVLTTNPRRLSIIAESIR 338
Score = 29.8 bits (66), Expect = 2.0
Identities = 27/224 (12%), Positives = 61/224 (27%), Gaps = 70/224 (31%)
Query: 180 YDMFDFLIDIVPREEVKTATG-PHRR------------------DDATKTALNPD----- 215
D+ D I+ +EE+ + L +
Sbjct: 36 KDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLM 95
Query: 216 -----QYLSVPMLLSTFSHQ-SPLH----IFANMFV----LHSFMPSSVEDLGKEQFVGF 261
+ M+ + Q L+ +FA V + + ++ +L + V
Sbjct: 96 SPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI 155
Query: 262 Y---------LTAGVVASLLSYVHKILVRKPG----LSIG---ASGAIMAVLAHTC--IT 303
+ V S +K+ + L++ + ++ +L I
Sbjct: 156 DGVLGSGKTWVALDVCLS-----YKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQID 210
Query: 304 HPDTELG-ILFVPYVRFSAEHAIQGIMLLDFLGVLFRWRLFDHA 346
T +R H+IQ L L + + +++
Sbjct: 211 PNWTSRSDHSSNIKLRI---HSIQ-----AELRRLLKSKPYENC 246
>2hue_C Histone H4; mini beta sheet, elongated beta sandwhich, DNA binding
prote; 1.70A {Xenopus laevis} SCOP: a.22.1.1 PDB: 3nqj_B
1aoi_B 3kwq_B* 1hio_D 2yfv_B
Length = 84
Score = 34.0 bits (78), Expect = 0.009
Identities = 14/49 (28%), Positives = 23/49 (46%)
Query: 129 GVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIAMAI 177
GVK IS ++F+ + A +TE KR+T+ D+ A+
Sbjct: 24 GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYAL 72
>1f1e_A Histone fold protein; archaeal histone protein, DNA binding
protein; HET: MSE; 1.37A {Methanopyrus kandleri} SCOP:
a.22.1.2
Length = 154
Score = 34.4 bits (78), Expect = 0.027
Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 4/84 (4%)
Query: 95 FGSVLEVQGALSMLDLKTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTI 154
VL V+G + D + A +++I+K G++ S++A L++K EL
Sbjct: 66 LADVLMVEG---VEDYDGELFGRATVRRILK-RAGIERASSDAVDLYNKLICRATEELGE 121
Query: 155 RAWIHTEDNKRRTLQRNDIAMAIT 178
+A + +++ R+T+Q D+ AIT
Sbjct: 122 KAAEYADEDGRKTVQGEDVEKAIT 145
>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 = 33.8 bits (76), Expect = 0.039
Identities = 8/26 (30%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 121 KKIMKLDDGVKMISAE-APMLFSKAA 145
+ + KL +K+ + + AP L KA
Sbjct: 20 QALKKLQASLKLYADDSAPALAIKAT 45
>1id3_B Histone H4; nucleosome core particle, chromatin, protein/DNA
interaction, nucleoprotein, supercoiled DNA; 3.10A
{Saccharomyces cerevisiae} SCOP: a.22.1.1
Length = 102
Score = 31.9 bits (72), Expect = 0.082
Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 4/90 (4%)
Query: 91 GRSFFGSVLEVQGA---LSMLDLKTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAEL 147
GR G L GA +L Q + I+++ + GVK IS +
Sbjct: 2 GRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLAR-RGGVKRISGLIYEEVRAVLKS 60
Query: 148 FIHELTIRAWIHTEDNKRRTLQRNDIAMAI 177
F+ + + +TE KR+T+ D+ A+
Sbjct: 61 FLESVIRDSVTYTEHAKRKTVTSLDVVYAL 90
>1tzy_D Histone H4-VI; histone-fold, tetramer-dimer-dimer, DNA binding
protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB:
1f66_B 1eqz_D 1hq3_D 1u35_B 2aro_D 2cv5_B* 2f8n_B 3nqu_B
3r45_B 3azg_B 3a6n_B 3an2_B 3av1_B 3av2_B 3ayw_B 3aze_B
3azf_B 3afa_B 3azh_B 3azk_B ...
Length = 103
Score = 31.9 bits (72), Expect = 0.083
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 107 MLDLKTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRR 166
+L Q + I+++ + GVK IS ++F+ + A +TE KR+
Sbjct: 22 VLRDNIQGITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK 80
Query: 167 TLQRNDIAMAI 177
T+ D+ A+
Sbjct: 81 TVTAMDVVYAL 91
>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone
chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl
y-1140}
Length = 103
Score = 30.4 bits (68), Expect = 0.25
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 1/71 (1%)
Query: 107 MLDLKTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRR 166
+L Q + I+++ + GVK IS + F+ + A +TE KR+
Sbjct: 22 ILRDNIQGITKPAIRRLARRG-GVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRK 80
Query: 167 TLQRNDIAMAI 177
T+ D+ A+
Sbjct: 81 TVTSLDVVYAL 91
>3v9r_B MHF2, uncharacterized protein YDL160C-A; histone fold, fanconi
anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces
cerevisiae}
Length = 88
Score = 28.0 bits (62), Expect = 1.3
Identities = 11/62 (17%), Positives = 27/62 (43%), Gaps = 1/62 (1%)
Query: 117 LARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIAMA 176
L +I + + +K I+ E + K ++FI E +R+ +D ++ + ++
Sbjct: 7 LIKILSQNEGGNDMK-IADEVVPMIQKYLDIFIDEAVLRSLQSHKDINGERGDKSPLELS 65
Query: 177 IT 178
Sbjct: 66 HQ 67
>3ffm_A Growth arrest and DNA-damage-inducible protein GADD45 gamma;
beta-turn-helix, cell cycle; 2.30A {Homo sapiens}
Length = 167
Score = 28.1 bits (62), Expect = 3.0
Identities = 22/86 (25%), Positives = 28/86 (32%), Gaps = 1/86 (1%)
Query: 285 LSIGASGAIMAVLAHTCITHPDTELGILFVPYVRFSAEHAIQGIMLLDFLGVLFRWRLFD 344
L++ VLA D L I F F E+ I I+ + + L
Sbjct: 58 LNVDPDNVTFCVLAAGEEDEGDIALQIHFTLIQAFCCENDID-IVRVGDVQRLAAIVGAG 116
Query: 345 HAAHLGGALFGILYSKYGEQTWAHRA 370
A G L IL S E W A
Sbjct: 117 EEAGAPGDLHCILISNPNEDAWKDPA 142
>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA binding
prote; 1.70A {Xenopus laevis}
Length = 77
Score = 26.8 bits (59), Expect = 3.1
Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 1/63 (1%)
Query: 115 LPLAR-IKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDI 173
LP R +++I + + A M +A+E ++ L + KR T+ DI
Sbjct: 7 LPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDI 66
Query: 174 AMA 176
+A
Sbjct: 67 QLA 69
>2pia_A Phthalate dioxygenase reductase; HET: FMN; 2.00A {Burkholderia
cepacia} SCOP: b.43.4.2 c.25.1.2 d.15.4.2
Length = 321
Score = 28.3 bits (64), Expect = 4.3
Identities = 18/92 (19%), Positives = 32/92 (34%), Gaps = 16/92 (17%)
Query: 22 RKDLRKRWNALHPGDRVYV--PILFLNGVVFLA--WFYPRLHPVLYKYFASNPQSMGITL 77
D + P VY P ++ V + W +H ++ F + +
Sbjct: 180 AFDFWSVFEKSKPAQHVYCCGPQALMDTVRDMTGHWPSGTVH---FESFGATNTN----- 231
Query: 78 RLHAVSPEFDSRLGRSFFGSVLEVQGALSMLD 109
+ F RL RS G+ E+ S+L+
Sbjct: 232 --ARENTPFTVRLSRS--GTSFEIPANRSILE 259
>3cg6_A Growth arrest and DNA-damage-inducible 45 gamma; alpha/beta, cell
cycle; 1.70A {Mus musculus} PDB: 2wal_A
Length = 146
Score = 27.7 bits (61), Expect = 4.6
Identities = 23/86 (26%), Positives = 29/86 (33%), Gaps = 1/86 (1%)
Query: 285 LSIGASGAIMAVLAHTCITHPDTELGILFVPYVRFSAEHAIQGIMLLDFLGVLFRWRLFD 344
L++ VLA D L I F F E+ I I+ + + L D
Sbjct: 37 LNVDPDNVTFCVLAADEEDEGDIALQIHFTLIQAFCCENDID-IVRVGDVQRLAAIVGSD 95
Query: 345 HAAHLGGALFGILYSKYGEQTWAHRA 370
G L IL S E TW A
Sbjct: 96 EEGGAPGDLHCILISNPNEDTWKDPA 121
>2axo_A Hypothetical protein ATU2684; alpha beta protein., structural
genomics, PSI, protein struc initiative; 1.80A
{Agrobacterium tumefaciens str} SCOP: c.47.1.19
Length = 270
Score = 27.8 bits (61), Expect = 6.6
Identities = 11/65 (16%), Positives = 19/65 (29%)
Query: 27 KRWNALHPGDRVYVPILFLNGVVFLAWFYPRLHPVLYKYFASNPQSMGITLRLHAVSPEF 86
+ + VY P LNG + R F Q + + + E
Sbjct: 102 YGYMRALGRNGVYTPQAILNGRDHVKGADVRGIYDRLDAFKREGQGLNVPVSSKFAGDEV 161
Query: 87 DSRLG 91
+ +G
Sbjct: 162 EIDIG 166
>3nqj_A Histone H3-like centromeric protein A; alpha helix, histone fold,
centromere, DNA binding protein; 2.10A {Homo sapiens}
Length = 82
Score = 25.7 bits (56), Expect = 8.0
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 3/65 (4%)
Query: 115 LPLAR-IKKIMK--LDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRN 171
LP +R ++I A+A + +AAE F+ L A++ T R TL
Sbjct: 7 LPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPK 66
Query: 172 DIAMA 176
D+ +A
Sbjct: 67 DVQLA 71
>1r8e_A Multidrug-efflux transporter regulator; protein-DNA complex,
MERR-family transcription activator, MU binding protein;
HET: P4P; 2.40A {Bacillus subtilis} SCOP: a.6.1.3
d.60.1.1 PDB: 1exi_A* 1exj_A* 3iao_A 3q5p_A* 3d71_A*
3q3d_A* 3q1m_A* 3q2y_A* 3q5r_A* 3q5s_A* 3d70_A 3d6z_A*
3d6y_A* 1bow_A 2bow_A*
Length = 278
Score = 27.4 bits (61), Expect = 8.0
Identities = 15/89 (16%), Positives = 25/89 (28%), Gaps = 12/89 (13%)
Query: 108 LDLKTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRT 167
LK PL +KK L+ A E IR + +T
Sbjct: 57 KSLKYIGTPLEEMKKAQDLEM------------EELFAFYTEQERQIREKLDFLSALEQT 104
Query: 168 LQRNDIAMAITKYDMFDFLIDIVPREEVK 196
+ M + ++ EE++
Sbjct: 105 ISLVKKRMKRQMEYPALGEVFVLDEEEIR 133
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
0.325 0.139 0.429
Gapped
Lambda K H
0.267 0.0568 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,108,371
Number of extensions: 374271
Number of successful extensions: 915
Number of sequences better than 10.0: 1
Number of HSP's gapped: 900
Number of HSP's successfully gapped: 34
Length of query: 386
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 291
Effective length of database: 4,049,298
Effective search space: 1178345718
Effective search space used: 1178345718
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.5 bits)