RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13186
(170 letters)
>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 = 133 bits (334), Expect = 3e-40
Identities = 98/161 (60%), Positives = 127/161 (78%)
Query: 10 SNDDDELILPRASINKIIKEILPNIRVANESRELVMNCCMEFIHLISSEANDICNEQQKK 69
S +DD+L +PRA+INK+IKE LPN+RVAN++RELV+NCC EFIHLISSEAN+ICN+ +KK
Sbjct: 8 SGNDDDLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKK 67
Query: 70 TINAEHVLQALDQLGFGDYKSEAEEVMKDCKIVAANRKKQSNRLENLGIPEEELLRQQQE 129
TI+ EHV+QAL+ LGFG Y SE +EV+++CK VA R+K S+RLENLGIPEEELLRQQQE
Sbjct: 68 TISPEHVIQALESLGFGSYISEVKEVLQECKTVALKRRKASSRLENLGIPEEELLRQQQE 127
Query: 130 LFAKAREEQAAADLSQWQHIQEITSQQKQQEESDLESDEES 170
LFAKAR++QA +W +Q+ Q + S S++
Sbjct: 128 LFAKARQQQAELAQQEWLQMQQAAQQAQLAAASASASNQAG 168
>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens}
SCOP: a.22.1.3
Length = 93
Score = 99 bits (249), Expect = 2e-28
Identities = 30/92 (32%), Positives = 57/92 (61%), Gaps = 1/92 (1%)
Query: 10 SNDDDELILPRASINKIIKEILP-NIRVANESRELVMNCCMEFIHLISSEANDICNEQQK 68
S + ++ LP A++ +I+K +P ++A +++E V C EFI I+SEA++ C+++++
Sbjct: 1 SFREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKR 60
Query: 69 KTINAEHVLQALDQLGFGDYKSEAEEVMKDCK 100
KTIN E +L A+ LGF Y + ++ +
Sbjct: 61 KTINGEDILFAMSTLGFDSYVEPLKLYLQKFR 92
>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 = 99.3 bits (247), Expect = 1e-27
Identities = 28/122 (22%), Positives = 55/122 (45%), Gaps = 1/122 (0%)
Query: 9 ISNDDDELILPRASINKIIKEILP-NIRVANESRELVMNCCMEFIHLISSEANDICNEQQ 67
+ ++L LP A I ++IKE LP + V+ E+R + F ++S + + ++Q
Sbjct: 1 MVERIEDLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQN 60
Query: 68 KKTINAEHVLQALDQLGFGDYKSEAEEVMKDCKIVAANRKKQSNRLENLGIPEEELLRQQ 127
KTI A+ +LQ L +L F + + ++ + V +K+ ++ E
Sbjct: 61 HKTITAKDILQTLTELDFESFVPSLTQDLEVYRKVVKEKKESKASKKDSNTAENANASAT 120
Query: 128 QE 129
Sbjct: 121 AT 122
>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 = 48.1 bits (115), Expect = 2e-08
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 18 LPRASINKIIKEILPNIRVANESRELVMNCCMEFIHLISSEANDICNEQQKKTINAEHVL 77
LP A I +IIK RV++++R + E I+SEA + +KTI AE +
Sbjct: 3 LPIAPIGRIIKNAGAE-RVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIE 61
Query: 78 QALDQL 83
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 = 45.8 bits (109), Expect = 1e-07
Identities = 13/63 (20%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 18 LPRASINKIIKEILPNIRVANESRELVMNCCMEFIHLISSEANDICNEQQKKTINAEHVL 77
LP A ++++I++ RV+ ++ +++ E+ I+ +A + +KT+ E +
Sbjct: 7 LPIAPVDRLIRKAGAE-RVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIK 65
Query: 78 QAL 80
A+
Sbjct: 66 LAI 68
>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo
sapiens} SCOP: a.22.1.3
Length = 97
Score = 44.9 bits (106), Expect = 6e-07
Identities = 15/73 (20%), Positives = 29/73 (39%)
Query: 10 SNDDDELILPRASINKIIKEILPNIRVANESRELVMNCCMEFIHLISSEANDICNEQQKK 69
D LP A I KI+K ++ E+ L FI ++ A + +++
Sbjct: 12 VKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRR 71
Query: 70 TINAEHVLQALDQ 82
T+ + A+ +
Sbjct: 72 TLQRNDIAMAITK 84
>3b0c_W CENP-W, centromere protein W; histone fold, DNA binding, DNA
binding protein; HET: CIT; 2.20A {Gallus gallus} PDB:
3b0d_W* 3vh5_W 3vh6_W
Length = 76
Score = 40.4 bits (94), Expect = 1e-05
Identities = 21/61 (34%), Positives = 34/61 (55%)
Query: 19 PRASINKIIKEILPNIRVANESRELVMNCCMEFIHLISSEANDICNEQQKKTINAEHVLQ 78
PR ++ KIIK+ P++R+A + LV + F+H ++ EA E + K I EH +
Sbjct: 6 PRGTLRKIIKKHKPHLRLAANTDLLVHLSFLLFLHRLAEEARTNAFENKSKIIKPEHTIA 65
Query: 79 A 79
A
Sbjct: 66 A 66
>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 = 39.1 bits (91), Expect = 6e-05
Identities = 14/75 (18%), Positives = 28/75 (37%)
Query: 8 PISNDDDELILPRASINKIIKEILPNIRVANESRELVMNCCMEFIHLISSEANDICNEQQ 67
P P A I KI++ +VA ++ F+ + +A + +
Sbjct: 2 PSKKKKYNARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRN 61
Query: 68 KKTINAEHVLQALDQ 82
KT+ H+ Q ++
Sbjct: 62 AKTMTTSHLKQCIEL 76
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 37.1 bits (85), Expect = 0.001
Identities = 16/80 (20%), Positives = 38/80 (47%), Gaps = 10/80 (12%)
Query: 90 SEAEEVMKDCKIVAANRKKQSNRLENLGIPEEELLRQQQELFAKAREEQAAADLSQWQHI 149
++A+ + ++ + + R++Q RL+ L + +QE E+A DL +W
Sbjct: 75 AQADRLTQEPESIRKWREEQRKRLQEL---DAASKVMEQEW-----REKAKKDLEEWNQR 126
Query: 150 QEITSQQKQQEESDLESDEE 169
Q Q ++ + ++ +D+
Sbjct: 127 QS--EQVEKNKINNRIADKA 144
>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 = 34.7 bits (79), Expect = 0.005
Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 1/76 (1%)
Query: 8 PISNDDDELILPRASINKIIKEILPNIRVANESRELVMNCCMEFIHLISSEANDICNEQQ 67
E LP + + I+K + + NE L+ C F+ ++ A Q+
Sbjct: 10 VERPPTAETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQR 69
Query: 68 K-KTINAEHVLQALDQ 82
+ + EH+ Q +++
Sbjct: 70 PGEALKYEHLSQVVNK 85
>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 = 31.7 bits (71), Expect = 0.12
Identities = 26/185 (14%), Positives = 54/185 (29%), Gaps = 58/185 (31%)
Query: 7 DPISNDDDELI---LPRASINKIIKEILPNIR------------------VANESRELVM 45
D + ND+ + R +++ L +R + +
Sbjct: 117 DRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKV 176
Query: 46 NCCMEF-IHLISSEANDICNEQQKKTINAEHVLQALDQLGFGDYKSEAEEVMKDCKIVAA 104
C M+F I ++ N CN E VL+ L +L +
Sbjct: 177 QCKMDFKIFWLNL-KN--CNS-------PETVLEMLQKL---------------LYQIDP 211
Query: 105 NRKKQSNRLENLGIPEEELLRQQQELFAKAREEQA---AADLSQWQHIQE--------IT 153
N +S+ N+ + + + + L E ++ + +T
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLT 271
Query: 154 SQQKQ 158
++ KQ
Sbjct: 272 TRFKQ 276
>2nqb_D Histone H2B; nucleosome, NCP, chromatin, structural protein/DNA
complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_D*
Length = 123
Score = 30.4 bits (68), Expect = 0.12
Identities = 8/54 (14%), Positives = 31/54 (57%)
Query: 23 INKIIKEILPNIRVANESRELVMNCCMEFIHLISSEANDICNEQQKKTINAEHV 76
I ++K++ P+ +++++ ++ + + I++EA+ + + ++ TI + +
Sbjct: 39 IYTVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREI 92
>1tzy_B Histone H2B; histone-fold, tetramer-dimer-dimer, DNA binding
protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB:
1eqz_B 1hq3_B 2aro_B 2hio_B 3c9k_B 3azg_D 3a6n_D 3an2_D
3av1_D 3av2_D 3ayw_D 3aze_D 3azf_D 3afa_D 3azh_D 3azi_D
3azj_D 3azk_D 3azl_D 3azm_D ...
Length = 126
Score = 29.4 bits (65), Expect = 0.30
Identities = 8/54 (14%), Positives = 31/54 (57%)
Query: 23 INKIIKEILPNIRVANESRELVMNCCMEFIHLISSEANDICNEQQKKTINAEHV 76
+ K++K++ P+ +++++ ++ + + I+ EA+ + + ++ TI + +
Sbjct: 42 VYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 95
>1h3o_B Transcription initiation factor TFIID 20/15 kDa subunits;
transcription/TBP-associated factors, TBP-associated
factors; 2.3A {Homo sapiens} SCOP: a.22.1.3
Length = 76
Score = 26.7 bits (59), Expect = 1.2
Identities = 11/66 (16%), Positives = 34/66 (51%)
Query: 17 ILPRASINKIIKEILPNIRVANESRELVMNCCMEFIHLISSEANDICNEQQKKTINAEHV 76
+L + + +++E+ PN ++ + E+++ +FI + + A + ++ T+ + V
Sbjct: 5 VLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDV 64
Query: 77 LQALDQ 82
L++
Sbjct: 65 QLHLER 70
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 28.7 bits (64), Expect = 1.3
Identities = 8/69 (11%), Positives = 28/69 (40%), Gaps = 12/69 (17%)
Query: 71 INAEHVLQALDQLGFGDYKSEAEEVMKDCKIVAANRKKQSNRLENLGIPEEELLRQQQE- 129
++ +++ A+ + + +Y ++ R+K + + + G+ +L ++
Sbjct: 1457 VHPDYLYGAITEDRYNEYVAKVSA-----------REKSAYKFFHNGMIYNKLFVSKEHA 1505
Query: 130 LFAKAREEQ 138
+ EE
Sbjct: 1506 PYTDELEED 1514
>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 = 27.5 bits (60), Expect = 1.6
Identities = 18/77 (23%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 18 LPRASINKIIKEILPNIRVANESRELVMNCCMEFIHLISSEANDICNEQQKKTINAEHVL 77
LP+A+I +I ++ + R++ ++++ + + +++ A + + KKT+ EH+
Sbjct: 5 LPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLK 64
Query: 78 QALDQL---GFGDYKSE 91
D L G DY E
Sbjct: 65 ALADVLMVEGVEDYDGE 81
Score = 25.1 bits (54), Expect = 9.9
Identities = 17/80 (21%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 1 MSDVGLDPISNDDDELILPRASINKIIKEILPNIRVANESRELVMNCCMEFIHLISSEAN 60
++DV + D D + RA++ +I+K R ++++ +L + +A
Sbjct: 66 LADVLMVEGVEDYDGELFGRATVRRILKRAGIE-RASSDAVDLYNKLICRATEELGEKAA 124
Query: 61 DICNEQQKKTINAEHVLQAL 80
+ +E +KT+ E V +A+
Sbjct: 125 EYADEDGRKTVQGEDVEKAI 144
>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding,
nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A
{Thermococcus onnurineus}
Length = 604
Score = 27.4 bits (61), Expect = 3.2
Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 5/73 (6%)
Query: 9 ISNDDDELILPRASINKIIKEILPNIRVANESRELVMNCCMEFIHLISSEANDICNEQQK 68
+ D + ++ +I++E + A L + + + I A DI ++ K
Sbjct: 306 VKRDGKIPHFTKEAVEEIVREA---QKRAGRKGHLTLR--LRDLGGIVRAAGDIAVKKGK 360
Query: 69 KTINAEHVLQALD 81
K + E V++A+
Sbjct: 361 KYVEREDVIEAVK 373
>2odp_A Complement C2; C3/C5 convertase, complement serin protease, human
complement system, glycoprotein, SP, VWFA,; HET: NAG;
1.90A {Homo sapiens} PDB: 2odq_A* 2i6q_A* 2i6s_A*
Length = 509
Score = 26.9 bits (59), Expect = 4.2
Identities = 14/146 (9%), Positives = 48/146 (32%), Gaps = 31/146 (21%)
Query: 56 SSEANDICNEQQKKTINAEHVLQALDQLGFGDYK-----------SEAEEVMKDCKIVAA 104
+SE + + + + V+ +L+ + D++ + +M + +
Sbjct: 56 ASEPKVLMSVLNDNSRDMTEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLG 115
Query: 105 NRKKQSNRLE-----------NLGIPEEELLRQQQELFAKAREEQAAADLSQ-------- 145
+ N+G + + +E+ ++ D+
Sbjct: 116 METMAWQEIRHAIILLTDGKSNMGGSPKTAVDHIREILNINQKRNDYLDIYAIGVGKLDV 175
Query: 146 -WQHIQEITSQQKQQEESDLESDEES 170
W+ + E+ S++ + + + D ++
Sbjct: 176 DWRELNELGSKKDGERHAFILQDTKA 201
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 27.0 bits (60), Expect = 4.5
Identities = 15/80 (18%), Positives = 26/80 (32%), Gaps = 11/80 (13%)
Query: 89 KSEAEEVMKDCKIVAANRKKQSNRLENLGIPEEELLRQQQELFAKAREEQAAADLSQWQH 148
K EA V + KK LEN +L R+ E + + + + +
Sbjct: 910 KIEARSVERY--------KKLHIGLENK---IMQLQRKIDEQNKEYKSLLEKMNNLEITY 958
Query: 149 IQEITSQQKQQEESDLESDE 168
E + E + +E
Sbjct: 959 STETEKLRSDVERLRMSEEE 978
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
0.310 0.127 0.342
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,467,791
Number of extensions: 137137
Number of successful extensions: 392
Number of sequences better than 10.0: 1
Number of HSP's gapped: 372
Number of HSP's successfully gapped: 46
Length of query: 170
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 83
Effective length of database: 4,272,666
Effective search space: 354631278
Effective search space used: 354631278
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 (21.8 bits)
S2: 54 (25.3 bits)