RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16895
(93 letters)
>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA
binding prote; 1.70A {Xenopus laevis}
Length = 77
Score = 124 bits (314), Expect = 1e-39
Identities = 71/76 (93%), Positives = 73/76 (96%)
Query: 18 LLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI 77
LIRKLPFQRLVREIAQDFKTDLRFQS+A+ ALQEASEAYLV LFEDTNLCAIHAKRVTI
Sbjct: 2 ALIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI 61
Query: 78 MPKDIQLARRIRGERA 93
MPKDIQLARRIRGERA
Sbjct: 62 MPKDIQLARRIRGERA 77
>1tzy_C Histone H3; histone-fold, tetramer-dimer-dimer, DNA binding
protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB:
1eqz_C 1hq3_C 2aro_C 2f8n_A 2hio_C 3av1_A 3lel_A 3afa_A
3azi_A 3azj_A 3azk_A 3azl_A 3azm_A 3azn_A 2cv5_A*
1u35_A* 2nqb_A 2io5_B 2pyo_A* 3c9k_C ...
Length = 136
Score = 119 bits (298), Expect = 1e-36
Identities = 90/93 (96%), Positives = 92/93 (98%)
Query: 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVG 60
PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQS+A+ ALQEASEAYLVG
Sbjct: 44 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVG 103
Query: 61 LFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 93
LFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Sbjct: 104 LFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136
>2yfv_A Histone H3-like centromeric protein CSE4; cell cycle, kinetochore,
centromere, histone chaperone, BUDD; 2.32A
{Kluyveromyces lactis nrrl y-1140} PDB: 2yfw_A
Length = 100
Score = 114 bits (285), Expect = 6e-35
Identities = 61/92 (66%), Positives = 74/92 (80%), Gaps = 3/92 (3%)
Query: 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD---LRFQSAAIGALQEASEAY 57
P +AL EIR+YQ+ST+LLI ++PF RLV+E+ F T+ LR+QS AI ALQEASEAY
Sbjct: 9 PTDLALAEIRKYQRSTDLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAY 68
Query: 58 LVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 89
LVGL E TNL A+HAKR+TIM KD+QLARRIR
Sbjct: 69 LVGLLEHTNLLALHAKRITIMRKDMQLARRIR 100
>3nqj_A Histone H3-like centromeric protein A; alpha helix, histone fold,
centromere, DNA binding protein; 2.10A {Homo sapiens}
Length = 82
Score = 107 bits (268), Expect = 2e-32
Identities = 47/77 (61%), Positives = 55/77 (71%), Gaps = 2/77 (2%)
Query: 18 LLIRKLPFQRLVREIAQDFKT--DLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRV 75
LLIRKLPF RL REI F D +Q+ A+ ALQEA+EA+LV LFED L +HA RV
Sbjct: 2 LLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRV 61
Query: 76 TIMPKDIQLARRIRGER 92
T+ PKD+QLARRIRG
Sbjct: 62 TLFPKDVQLARRIRGLE 78
>3nqu_A Histone H3-like centromeric protein A; alpha helix, histone fold,
centromere, DNA binding protein; 2.50A {Homo sapiens}
PDB: 3an2_A
Length = 140
Score = 106 bits (264), Expect = 3e-31
Identities = 55/95 (57%), Positives = 65/95 (68%), Gaps = 2/95 (2%)
Query: 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF--KTDLRFQSAAIGALQEASEAYL 58
L+EIR+ QKST LLIRKLPF RL REI F D +Q+ A+ ALQEA+EA+L
Sbjct: 43 RRQGWLKEIRKLQKSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFL 102
Query: 59 VGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 93
V LFED L +HA RVT+ PKD+QLARRIRG
Sbjct: 103 VHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGLEE 137
>2l5a_A Histone H3-like centromeric protein CSE4, protein histone H4; A
single chain of CSE4+SCM3+H4, fusion protein; NMR
{Saccharomyces cerevisiae}
Length = 235
Score = 107 bits (266), Expect = 1e-30
Identities = 54/88 (61%), Positives = 66/88 (75%), Gaps = 3/88 (3%)
Query: 9 IRRYQKSTELLIRKLPFQRLVREIAQDFKT---DLRFQSAAIGALQEASEAYLVGLFEDT 65
+ + +LLI K+PF RLV+E+ +F T DLR+QS AI ALQEASEAYLVGL E T
Sbjct: 1 MHHHHHHKKLLISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHT 60
Query: 66 NLCAIHAKRVTIMPKDIQLARRIRGERA 93
NL A+HAKR+TIM KD+QLARRIRG+
Sbjct: 61 NLLALHAKRITIMKKDMQLARRIRGQFL 88
Score = 36.5 bits (83), Expect = 3e-04
Identities = 15/89 (16%), Positives = 31/89 (34%), Gaps = 2/89 (2%)
Query: 2 GTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGL 61
A + + ++R + E D R ++ +++L +
Sbjct: 141 TLTANNSTKDKRTKYTSVLRD--IIDISDEEDGDKGGVKRISGLIYEEVRAVLKSFLESV 198
Query: 62 FEDTNLCAIHAKRVTIMPKDIQLARRIRG 90
D+ HAKR T+ D+ A + +G
Sbjct: 199 IRDSVTYTEHAKRKTVTSLDVVYALKRQG 227
>3r45_A Histone H3-like centromeric protein A; histone fold, centromere,
CENP-A, histone chaperone, hjurp; 2.60A {Homo sapiens}
Length = 156
Score = 101 bits (253), Expect = 2e-29
Identities = 55/95 (57%), Positives = 65/95 (68%), Gaps = 2/95 (2%)
Query: 1 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF--KTDLRFQSAAIGALQEASEAYL 58
L+EIR+ QKST LLIRKLPF RL REI F D +Q+ A+ ALQEA+EA+L
Sbjct: 59 RRQGWLKEIRKLQKSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFL 118
Query: 59 VGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 93
V LFED L +HA RVT+ PKD+QLARRIRG
Sbjct: 119 VHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGLEE 153
>4dra_A Centromere protein S; DNA binding complex, DNA damage repair,
histone-fold, DNA BI protein; 2.41A {Homo sapiens} PDB:
4drb_A
Length = 113
Score = 35.0 bits (80), Expect = 6e-04
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 26 QRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85
L E+A D + +F I A+ E + +D + A HAKR TI +D++L
Sbjct: 34 GCLCEEVALDKEM--QFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLL 91
Query: 86 RR 87
R
Sbjct: 92 AR 93
>3v9r_A MHF1, uncharacterized protein YOL086W-A; histone fold, fanconi
anemia, DNA repair, DNA BI protein; 2.40A
{Saccharomyces cerevisiae}
Length = 90
Score = 33.8 bits (77), Expect = 0.001
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 2/61 (3%)
Query: 27 RLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 86
++++ D+++ I +L E + L + D A HA R + D+ L
Sbjct: 20 ERLQQVLSSE--DIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYL 77
Query: 87 R 87
R
Sbjct: 78 R 78
>3b0c_T CENP-T, centromere protein T; histone fold, DNA binding, DNA
binding protein; HET: CIT; 2.20A {Gallus gallus} PDB:
3b0d_T* 3vh5_T 3vh6_T
Length = 111
Score = 33.8 bits (77), Expect = 0.002
Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 29 VREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA-RR 87
+++I + A +++ SE Y + D + HA R T+ D++L RR
Sbjct: 13 IKQIFSHY-VKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRR 71
Query: 88 IR 89
Sbjct: 72 QG 73
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A
{Pyrococcus horikoshii} SCOP: a.22.1.2
Length = 70
Score = 32.7 bits (75), Expect = 0.002
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 5/64 (7%)
Query: 24 PFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQ 83
P RL+R+ R A L E E Y + + + A HA R T+ +DI+
Sbjct: 11 PVDRLIRK-----AGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIK 65
Query: 84 LARR 87
LA +
Sbjct: 66 LAIK 69
>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA,
nucleus, DNA binding protein; 2.15A {Gallus gallus}
Length = 107
Score = 33.5 bits (76), Expect = 0.002
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 27 RLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 86
L +++A+D F + A+ E + D + A HAKR TI +D++L
Sbjct: 27 CLCQDVAEDKGV--LFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKLLA 84
Query: 87 R 87
R
Sbjct: 85 R 85
>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 = 32.3 bits (74), Expect = 0.003
Identities = 15/45 (33%), Positives = 20/45 (44%)
Query: 41 RFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85
R A AL + E + + A HA R TI +DI+LA
Sbjct: 19 RVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELA 63
>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding,
nucleus, binding protein; 2.40A {Gallus gallus} PDB:
3vh6_A
Length = 140
Score = 33.2 bits (75), Expect = 0.004
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 26 QRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85
L +++A+D + F + A+ E + D + A HAKR TI +D++L
Sbjct: 26 GALAQDVAEDK--GVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLL 83
Query: 86 RR 87
R
Sbjct: 84 AR 85
>1taf_A TFIID TBP associated factor 42; transcription initiation, histone
fold, complex (TWO transcr factors); 2.00A {Drosophila
melanogaster} SCOP: a.22.1.3
Length = 68
Score = 31.4 bits (71), Expect = 0.007
Identities = 13/59 (22%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 27 RLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85
+++ I ++ ++ + L E + Y+ + +D + A HA++ TI D++LA
Sbjct: 5 QVIMSILKELNVQ-EYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLA 62
>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 = 29.9 bits (67), Expect = 0.042
Identities = 17/81 (20%), Positives = 28/81 (34%), Gaps = 5/81 (6%)
Query: 10 RRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCA 69
R+ + I K +RL R R + + +L + D
Sbjct: 20 RKVLRDNIQGITKPAIRRLARRGGVK-----RISGLIYEETRGVLKVFLENVIRDAVTYT 74
Query: 70 IHAKRVTIMPKDIQLARRIRG 90
HAKR T+ D+ A + +G
Sbjct: 75 EHAKRKTVTAMDVVYALKRQG 95
>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo
sapiens} SCOP: a.22.1.3
Length = 93
Score = 28.6 bits (64), Expect = 0.11
Identities = 13/65 (20%), Positives = 23/65 (35%)
Query: 21 RKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 80
LP + R + + A +QE ++ + + + KR TI +
Sbjct: 7 IYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGE 66
Query: 81 DIQLA 85
DI A
Sbjct: 67 DILFA 71
>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 = 27.8 bits (62), Expect = 0.19
Identities = 11/50 (22%), Positives = 19/50 (38%)
Query: 41 RFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 90
R + + +L + D HAKR T+ D+ A + +G
Sbjct: 27 RISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG 76
>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone
chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl
y-1140}
Length = 103
Score = 27.7 bits (61), Expect = 0.26
Identities = 18/89 (20%), Positives = 31/89 (34%), Gaps = 5/89 (5%)
Query: 2 GTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGL 61
G + R+ + I K +RL R R ++ + +L +
Sbjct: 12 GKGGAKRHRKILRDNIQGITKPAIRRLARRGGVK-----RISGLIYEEVRNVLKTFLESV 66
Query: 62 FEDTNLCAIHAKRVTIMPKDIQLARRIRG 90
D HAKR T+ D+ A + +G
Sbjct: 67 IRDAVTYTEHAKRKTVTSLDVVYALKRQG 95
>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 = 28.3 bits (62), Expect = 0.31
Identities = 3/77 (3%), Positives = 18/77 (23%), Gaps = 14/77 (18%)
Query: 12 YQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIH 71
+ E + ++ ++ F + + + + +
Sbjct: 5 HHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDV---------QDMPKSILSKEEI---- 51
Query: 72 AKRVTIMPKDIQLARRI 88
+ + + R+
Sbjct: 52 -DHIIMSKDAVSGTLRL 67
>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 = 26.9 bits (59), Expect = 0.61
Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 2/81 (2%)
Query: 10 RRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCA 69
+R++K I+ + + +R +A+ R ++ +++L + D+
Sbjct: 16 KRHRKILRDNIQGIT-KPAIRRLARRGGVK-RISGLIYEEVRAVLKSFLESVIRDSVTYT 73
Query: 70 IHAKRVTIMPKDIQLARRIRG 90
HAKR T+ D+ A + +G
Sbjct: 74 EHAKRKTVTSLDVVYALKRQG 94
>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 = 25.7 bits (56), Expect = 1.8
Identities = 13/65 (20%), Positives = 21/65 (32%)
Query: 21 RKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 80
LP + R I + A A+ A+ + + + + A TI K
Sbjct: 8 LNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAK 67
Query: 81 DIQLA 85
DI
Sbjct: 68 DILQT 72
>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 = 25.2 bits (54), Expect = 3.2
Identities = 8/65 (12%), Positives = 27/65 (41%), Gaps = 1/65 (1%)
Query: 21 RKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 80
+P + + + ++ ++R + A + ++ + + N +++ TI P+
Sbjct: 14 LTIPRAAINK-MIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPE 72
Query: 81 DIQLA 85
+ A
Sbjct: 73 HVIQA 77
>1taf_B TFIID TBP associated factor 62; transcription initiation, histone
fold, complex (TWO transcr factors); 2.00A {Drosophila
melanogaster} SCOP: a.22.1.3
Length = 70
Score = 23.6 bits (51), Expect = 6.5
Identities = 11/43 (25%), Positives = 19/43 (44%)
Query: 46 AIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 88
A L E L + +D HAKR + +DI ++ ++
Sbjct: 28 AAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLKV 70
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 0.138 0.381
Gapped
Lambda K H
0.267 0.0535 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,443,067
Number of extensions: 75195
Number of successful extensions: 226
Number of sequences better than 10.0: 1
Number of HSP's gapped: 221
Number of HSP's successfully gapped: 28
Length of query: 93
Length of database: 6,701,793
Length adjustment: 60
Effective length of query: 33
Effective length of database: 5,026,533
Effective search space: 165875589
Effective search space used: 165875589
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: 51 (23.9 bits)