RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15118
(132 letters)
>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 = 124 bits (310), Expect = 1e-37
Identities = 117/117 (100%), Positives = 117/117 (100%)
Query: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE 60
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
Sbjct: 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE 60
Query: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 117
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR
Sbjct: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 117
>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 = 103 bits (258), Expect = 4e-30
Identities = 51/86 (59%), Positives = 66/86 (76%), Gaps = 3/86 (3%)
Query: 37 KKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD---LRFQSSAVMAL 93
+ RY+P +AL EIR+YQ+ST+LLI ++PF RLV+E+ F T+ LR+QS A+MAL
Sbjct: 2 ARGTRYKPTDLALAEIRKYQRSTDLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMAL 61
Query: 94 QEASEAYLVGLFEDTNLCAIHAKRMI 119
QEASEAYLVGL E TNL A+HAKR+
Sbjct: 62 QEASEAYLVGLLEHTNLLALHAKRIT 87
>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 = 100 bits (250), Expect = 2e-28
Identities = 52/118 (44%), Positives = 68/118 (57%), Gaps = 7/118 (5%)
Query: 8 ARKSTGGKAPRKQ----LATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLI 63
R+S +APR++ T + P+ G H R L+EIR+ QKST LLI
Sbjct: 4 RRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQH-SRRRQGWLKEIRKLQKSTHLLI 62
Query: 64 RKLPFQRLVREIAQDF--KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMI 119
RKLPF RL REI F D +Q+ A++ALQEA+EA+LV LFED L +HA R+
Sbjct: 63 RKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVT 120
>3r45_A Histone H3-like centromeric protein A; histone fold, centromere,
CENP-A, histone chaperone, hjurp; 2.60A {Homo sapiens}
Length = 156
Score = 97.0 bits (240), Expect = 7e-27
Identities = 52/125 (41%), Positives = 69/125 (55%), Gaps = 7/125 (5%)
Query: 1 MARTKQTARKSTGGKAPRKQ----LATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQ 56
+ R+S +APR++ T + P+ G H R L+EIR+ Q
Sbjct: 13 DPNSMGPRRRSRKPEAPRRRSPSPTPTPGPSRRGPSLGASSHQHS-RRRQGWLKEIRKLQ 71
Query: 57 KSTELLIRKLPFQRLVREIAQDF--KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIH 114
KST LLIRKLPF RL REI F D +Q+ A++ALQEA+EA+LV LFED L +H
Sbjct: 72 KSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLH 131
Query: 115 AKRMI 119
A R+
Sbjct: 132 AGRVT 136
>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA binding
prote; 1.70A {Xenopus laevis}
Length = 77
Score = 91.9 bits (228), Expect = 7e-26
Identities = 55/57 (96%), Positives = 55/57 (96%)
Query: 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 117
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLV LFEDTNLCAIHAKR
Sbjct: 2 ALIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKR 58
>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 = 82.8 bits (203), Expect = 1e-20
Identities = 41/71 (57%), Positives = 52/71 (73%), Gaps = 3/71 (4%)
Query: 52 IRRYQKSTELLIRKLPFQRLVREIAQDFKT---DLRFQSSAVMALQEASEAYLVGLFEDT 108
+ + +LLI K+PF RLV+E+ +F T DLR+QS A+MALQEASEAYLVGL E T
Sbjct: 1 MHHHHHHKKLLISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHT 60
Query: 109 NLCAIHAKRMI 119
NL A+HAKR+
Sbjct: 61 NLLALHAKRIT 71
>3nqj_A Histone H3-like centromeric protein A; alpha helix, histone fold,
centromere, DNA binding protein; 2.10A {Homo sapiens}
Length = 82
Score = 77.7 bits (191), Expect = 3e-20
Identities = 34/59 (57%), Positives = 41/59 (69%), Gaps = 2/59 (3%)
Query: 61 LLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 117
LLIRKLPF RL REI F D +Q+ A++ALQEA+EA+LV LFED L +HA R
Sbjct: 2 LLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGR 60
>2x4w_B Histone H3.2; transcription, metal-binding, zinc-finger,
chromatin regulator, transcription regulation; HET:
M3L; 1.50A {Homo sapiens} PDB: 2x4x_B* 2x4y_B*
Length = 26
Score = 41.1 bits (95), Expect = 2e-06
Identities = 20/21 (95%), Positives = 20/21 (95%)
Query: 23 TKAARKSAPATGGVKKPHRYR 43
TKAARKSAPATGGV KPHRYR
Sbjct: 1 TKAARKSAPATGGVXKPHRYR 21
>3avr_B Histone H3; cupin superfamily, TRI/dimethyllysine demethylase,
oxidoredu structural protein complex; HET: M3L OGA EDO;
1.80A {Homo sapiens}
Length = 26
Score = 36.0 bits (82), Expect = 1e-04
Identities = 21/22 (95%), Positives = 21/22 (95%)
Query: 18 RKQLATKAARKSAPATGGVKKP 39
RKQLATKAAR SAPATGGVKKP
Sbjct: 1 RKQLATKAARXSAPATGGVKKP 22
>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 = 28.4 bits (62), Expect = 0.49
Identities = 9/31 (29%), Positives = 10/31 (32%), Gaps = 13/31 (41%)
Query: 5 KQTARKSTGG-K--APRKQLATKAARKSAPA 32
KQ +K K A SAPA
Sbjct: 19 KQALKKLQASLKLYAD----------DSAPA 39
>3a1b_A DNA (cytosine-5)-methyltransferase 3A, histone H3; zinc-finger,
histone binding, chromosomal protein, DNA damag repair,
DNA-binding, methylation; HET: DNA; 2.29A {Homo
sapiens} PDB: 3a1a_A*
Length = 159
Score = 28.2 bits (62), Expect = 0.54
Identities = 20/27 (74%), Positives = 22/27 (81%)
Query: 2 ARTKQTARKSTGGKAPRKQLATKAARK 28
ARTKQTARKSTGGKAPRKQL + +
Sbjct: 1 ARTKQTARKSTGGKAPRKQLRERLVYE 27
>3qnm_A Haloacid dehalogenase-like hydrolase; structural genomics, PSI-2,
protein structure initiative; 1.70A {Bacteroides
thetaiotaomicron}
Length = 240
Score = 26.2 bits (58), Expect = 3.0
Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 6/87 (6%)
Query: 40 HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSS----AVMALQE 95
Y G V E+ R + L + + L ++DF + +S A L+
Sbjct: 59 LEYGEGKVTKEELNRQRFFYPLQAVGVEDEALAERFSEDFFAIIPTKSGLMPHAKEVLEY 118
Query: 96 ASEAYLVGLFEDTNLCAIHAKRMIASL 122
+ Y + + +N R + S
Sbjct: 119 LAPQYNLYIL--SNGFRELQSRKMRSA 143
>1vi6_A 30S ribosomal protein S2P; structural genomics, ribosome; 1.95A
{Archaeoglobus fulgidus} SCOP: c.23.15.1 PDB: 1vi5_A
Length = 208
Score = 25.0 bits (55), Expect = 7.2
Identities = 9/40 (22%), Positives = 17/40 (42%)
Query: 18 RKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQK 57
+Q A K + + G R+ PGT+ + Y++
Sbjct: 76 ARQYAHKPVQMFSKVVGSDYIVGRFIPGTLTNPMLSEYRE 115
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A
{Pyrococcus horikoshii} SCOP: a.22.1.2
Length = 70
Score = 23.9 bits (52), Expect = 7.6
Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 5/51 (9%)
Query: 67 PFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 117
P RL+R+ R A L E E Y + + + A HA R
Sbjct: 11 PVDRLIRK-----AGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGR 56
>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 = 23.8 bits (52), Expect = 8.4
Identities = 9/34 (26%), Positives = 13/34 (38%)
Query: 84 RFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 117
R A +AL + E + + A HA R
Sbjct: 19 RVSDDARIALAKVLEEMGEEIASEAVKLAKHAGR 52
>3u5c_A 40S ribosomal protein S0-A; translation, ribosome, ribosomal,
ribosomal R ribosomal protein, eukaryotic ribosome,
RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB:
3izb_A 3o30_A 3o2z_A 3u5g_A 3jyv_B* 1s1h_B
Length = 252
Score = 24.9 bits (54), Expect = 9.9
Identities = 8/29 (27%), Positives = 12/29 (41%)
Query: 18 RKQLATKAARKSAPATGGVKKPHRYRPGT 46
+ +A K A TG R+ PG+
Sbjct: 78 SRTFGQRAVLKFAAHTGATPIAGRFTPGS 106
>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 = 24.3 bits (52), Expect = 10.0
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 69 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 117
L E+A D + +F + A+ E + +D + A HAKR
Sbjct: 34 GCLCEEVALDKEM--QFSKQTIAAISELTFRQCENFAKDLEMFARHAKR 80
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
0.319 0.130 0.352
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: 1,868,208
Number of extensions: 102971
Number of successful extensions: 231
Number of sequences better than 10.0: 1
Number of HSP's gapped: 219
Number of HSP's successfully gapped: 25
Length of query: 132
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 49
Effective length of database: 4,384,350
Effective search space: 214833150
Effective search space used: 214833150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.3 bits)