RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1398
(102 letters)
>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA
binding prote; 1.70A {Xenopus laevis}
Length = 77
Score = 112 bits (281), Expect = 2e-34
Identities = 66/68 (97%), Positives = 66/68 (97%)
Query: 18 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI 77
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLV LFEDTNLCAIHAKRVTI
Sbjct: 2 ALIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI 61
Query: 78 MPKDIQLA 85
MPKDIQLA
Sbjct: 62 MPKDIQLA 69
>3nqj_A Histone H3-like centromeric protein A; alpha helix, histone fold,
centromere, DNA binding protein; 2.10A {Homo sapiens}
Length = 82
Score = 97.0 bits (241), Expect = 2e-28
Identities = 45/87 (51%), Positives = 55/87 (63%), Gaps = 10/87 (11%)
Query: 18 LLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRV 75
LLIRKLPF RL REI F D +Q+ A++ALQEA+EA+LV LFED L +HA RV
Sbjct: 2 LLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRV 61
Query: 76 TIMPKDIQLAAESVENARLRIRLISTP 102
T+ PKD+QLA RIR +
Sbjct: 62 TLFPKDVQLA--------RRIRGLEEG 80
>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 = 90.5 bits (223), Expect = 4e-25
Identities = 74/84 (88%), Positives = 76/84 (90%)
Query: 2 NWVARERFQKPMKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGL 61
VA ++ KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGL
Sbjct: 45 GTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGL 104
Query: 62 FEDTNLCAIHAKRVTIMPKDIQLA 85
FEDTNLCAIHAKRVTIMPKDIQLA
Sbjct: 105 FEDTNLCAIHAKRVTIMPKDIQLA 128
>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 = 89.7 bits (221), Expect = 9e-24
Identities = 49/81 (60%), Positives = 59/81 (72%), Gaps = 6/81 (7%)
Query: 8 RFQKPMKSTELLIRKLPFQRLVREIAQDFKT---DLRFQSSAVMALQEASEAYLVGLFED 64
+LLI K+PF RLV+E+ +F T DLR+QS A+MALQEASEAYLVGL E
Sbjct: 3 HHHH---HKKLLISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEH 59
Query: 65 TNLCAIHAKRVTIMPKDIQLA 85
TNL A+HAKR+TIM KD+QLA
Sbjct: 60 TNLLALHAKRITIMKKDMQLA 80
Score = 35.0 bits (79), Expect = 0.002
Identities = 12/61 (19%), Positives = 22/61 (36%)
Query: 25 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL 84
+ E D R ++ +++L + D+ HAKR T+ D+
Sbjct: 162 IIDISDEEDGDKGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVY 221
Query: 85 A 85
A
Sbjct: 222 A 222
>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 = 81.8 bits (201), Expect = 6e-22
Identities = 49/75 (65%), Positives = 61/75 (81%), Gaps = 3/75 (4%)
Query: 14 KSTELLIRKLPFQRLVREIAQDFKTD---LRFQSSAVMALQEASEAYLVGLFEDTNLCAI 70
+ST+LLI ++PF RLV+E+ F T+ LR+QS A+MALQEASEAYLVGL E TNL A+
Sbjct: 22 RSTDLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLAL 81
Query: 71 HAKRVTIMPKDIQLA 85
HAKR+TIM KD+QLA
Sbjct: 82 HAKRITIMRKDMQLA 96
>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 = 77.2 bits (189), Expect = 7e-20
Identities = 48/91 (52%), Positives = 58/91 (63%), Gaps = 10/91 (10%)
Query: 14 KSTELLIRKLPFQRLVREIAQDF--KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIH 71
KST LLIRKLPF RL REI F D +Q+ A++ALQEA+EA+LV LFED L +H
Sbjct: 56 KSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLH 115
Query: 72 AKRVTIMPKDIQLAAESVENARLRIRLISTP 102
A RVT+ PKD+QLA RIR +
Sbjct: 116 AGRVTLFPKDVQLA--------RRIRGLEEG 138
>3r45_A Histone H3-like centromeric protein A; histone fold, centromere,
CENP-A, histone chaperone, hjurp; 2.60A {Homo sapiens}
Length = 156
Score = 76.6 bits (187), Expect = 2e-19
Identities = 48/91 (52%), Positives = 58/91 (63%), Gaps = 10/91 (10%)
Query: 14 KSTELLIRKLPFQRLVREIAQDF--KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIH 71
KST LLIRKLPF RL REI F D +Q+ A++ALQEA+EA+LV LFED L +H
Sbjct: 72 KSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLH 131
Query: 72 AKRVTIMPKDIQLAAESVENARLRIRLISTP 102
A RVT+ PKD+QLA RIR +
Sbjct: 132 AGRVTLFPKDVQLA--------RRIRGLEEG 154
>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 = 37.3 bits (87), Expect = 5e-05
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 5/67 (7%)
Query: 24 PFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQ 83
P R+++ R A +AL + E + + A HA R TI +DI+
Sbjct: 7 PIGRIIKN-----AGAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIE 61
Query: 84 LAAESVE 90
LA + +
Sbjct: 62 LARKMFK 68
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A
{Pyrococcus horikoshii} SCOP: a.22.1.2
Length = 70
Score = 37.0 bits (86), Expect = 7e-05
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 24 PFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQ 83
P RL+R+ R A L E E Y + + + A HA R T+ +DI+
Sbjct: 11 PVDRLIRK-----AGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIK 65
Query: 84 LAAES 88
LA +S
Sbjct: 66 LAIKS 70
>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 = 34.6 bits (79), Expect = 0.001
Identities = 17/81 (20%), Positives = 28/81 (34%), Gaps = 5/81 (6%)
Query: 5 ARERFQKPMKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFED 64
+R +K ++ I K +RL R R + + +L + D
Sbjct: 15 GAKRHRKVLRDNIQGITKPAIRRLARRGGVK-----RISGLIYEETRGVLKVFLENVIRD 69
Query: 65 TNLCAIHAKRVTIMPKDIQLA 85
HAKR T+ D+ A
Sbjct: 70 AVTYTEHAKRKTVTAMDVVYA 90
>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 = 33.3 bits (76), Expect = 0.002
Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 27 RLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAA 86
+++ I ++ ++ V L E + Y+ + +D + A HA++ TI D++LA
Sbjct: 5 QVIMSILKELNVQ-EYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLAT 63
Query: 87 ESVEN 91
E +
Sbjct: 64 EVTLD 68
>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 = 33.5 bits (76), Expect = 0.003
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 26 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85
L E+A D + +F + A+ E + +D + A HAKR TI +D++L
Sbjct: 34 GCLCEEVALDKEM--QFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLL 91
Query: 86 A 86
A
Sbjct: 92 A 92
>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 = 33.0 bits (75), Expect = 0.005
Identities = 12/58 (20%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 29 VREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAA 86
+++I + A +++ SE Y + D + HA R T+ D++L
Sbjct: 13 IKQIFSHY-VKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLM 69
>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA,
nucleus, DNA binding protein; 2.15A {Gallus gallus}
Length = 107
Score = 32.3 bits (73), Expect = 0.009
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 2/60 (3%)
Query: 27 RLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAA 86
L +++A+D F V A+ E + D + A HAKR TI +D++L A
Sbjct: 27 CLCQDVAEDKGV--LFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKLLA 84
>3v9r_A MHF1, uncharacterized protein YOL086W-A; histone fold, fanconi
anemia, DNA repair, DNA BI protein; 2.40A
{Saccharomyces cerevisiae}
Length = 90
Score = 31.9 bits (72), Expect = 0.010
Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 27 RLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAA 86
++++ D+++ + +L E + L + D A HA R + D+ L
Sbjct: 20 ERLQQVLSSE--DIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYL 77
>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone
chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl
y-1140}
Length = 103
Score = 31.9 bits (72), Expect = 0.010
Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 5/81 (6%)
Query: 5 ARERFQKPMKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFED 64
+R +K ++ I K +RL R R ++ + +L + D
Sbjct: 15 GAKRHRKILRDNIQGITKPAIRRLARRGGVK-----RISGLIYEEVRNVLKTFLESVIRD 69
Query: 65 TNLCAIHAKRVTIMPKDIQLA 85
HAKR T+ D+ A
Sbjct: 70 AVTYTEHAKRKTVTSLDVVYA 90
>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 = 31.6 bits (71), Expect = 0.012
Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 5/79 (6%)
Query: 7 ERFQKPMKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTN 66
+R +K ++ I K +RL R R ++ +++L + D+
Sbjct: 16 KRHRKILRDNIQGITKPAIRRLARRGGVK-----RISGLIYEEVRAVLKSFLESVIRDSV 70
Query: 67 LCAIHAKRVTIMPKDIQLA 85
HAKR T+ D+ A
Sbjct: 71 TYTEHAKRKTVTSLDVVYA 89
>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding,
nucleus, binding protein; 2.40A {Gallus gallus} PDB:
3vh6_A
Length = 140
Score = 32.1 bits (72), Expect = 0.014
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 26 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85
L +++A+D + F V A+ E + D + A HAKR TI +D++L
Sbjct: 26 GALAQDVAEDK--GVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLL 83
Query: 86 A 86
A
Sbjct: 84 A 84
>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 = 30.9 bits (70), Expect = 0.019
Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 5/75 (6%)
Query: 11 KPMKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAI 70
K ++ I K +RL R R + + +L + D
Sbjct: 2 KVLRDNIQGITKPAIRRLARRGGVK-----RISGLIYEETRGVLKVFLENVIRDAVTYTE 56
Query: 71 HAKRVTIMPKDIQLA 85
HAKR T+ D+ A
Sbjct: 57 HAKRKTVTAMDVVYA 71
>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo
sapiens} SCOP: a.22.1.3
Length = 93
Score = 30.6 bits (69), Expect = 0.032
Identities = 13/70 (18%), Positives = 25/70 (35%)
Query: 21 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 80
LP + R + + A +QE ++ + + + KR TI +
Sbjct: 7 IYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGE 66
Query: 81 DIQLAAESVE 90
DI A ++
Sbjct: 67 DILFAMSTLG 76
>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 = 26.9 bits (59), Expect = 0.85
Identities = 13/70 (18%), Positives = 23/70 (32%)
Query: 21 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 80
LP + R I + A A+ A+ + + + + A TI K
Sbjct: 8 LNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAK 67
Query: 81 DIQLAAESVE 90
DI ++
Sbjct: 68 DILQTLTELD 77
>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 = 26.3 bits (57), Expect = 1.9
Identities = 10/70 (14%), Positives = 30/70 (42%), Gaps = 1/70 (1%)
Query: 21 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 80
+P + + + ++ ++R + A + ++ + + N +++ TI P+
Sbjct: 14 LTIPRAAINK-MIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPE 72
Query: 81 DIQLAAESVE 90
+ A ES+
Sbjct: 73 HVIQALESLG 82
>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A
{Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19
c.37.1.19
Length = 780
Score = 24.5 bits (54), Expect = 8.7
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 6/40 (15%)
Query: 8 RFQKPMKSTELLIRKLPF------QRLVREIAQDFKTDLR 41
+ K E I+ LPF +R +EI D ++
Sbjct: 350 PKKIEGKLAEEFIKSLPFKLTNAQKRAHQEIRNDMISEKP 389
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
0.324 0.133 0.370
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: 1,479,283
Number of extensions: 74432
Number of successful extensions: 216
Number of sequences better than 10.0: 1
Number of HSP's gapped: 211
Number of HSP's successfully gapped: 29
Length of query: 102
Length of database: 6,701,793
Length adjustment: 67
Effective length of query: 35
Effective length of database: 4,831,086
Effective search space: 169088010
Effective search space used: 169088010
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)