RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13691
(103 letters)
>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 = 83.9 bits (207), Expect = 2e-22
Identities = 35/89 (39%), Positives = 62/89 (69%), Gaps = 4/89 (4%)
Query: 1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
M E ++DLNLP+A+I RLIKEALP+ +VSK+ R A +AAS+F + +T+ + ++A
Sbjct: 1 MVERIEDLNLPNAVIGRLIKEALPES----ASVSKEARAAIARAASVFAIFVTSSSTALA 56
Query: 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEIL 89
+++N KT++ D+++ + ++ FE + L
Sbjct: 57 HKQNHKTITAKDILQTLTELDFESFVPSL 85
>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo
sapiens} SCOP: a.22.1.3
Length = 93
Score = 79.1 bits (195), Expect = 4e-21
Identities = 25/84 (29%), Positives = 48/84 (57%), Gaps = 4/84 (4%)
Query: 6 DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR 65
D+ LP A + R++K A+P+ ++KD + + S FI +T+EA +++ R
Sbjct: 5 QDIYLPIANVARIMKNAIPQTG----KIAKDAKECVQECVSEFISFITSEASERCHQEKR 60
Query: 66 KTLSGVDVIEGVKQIGFEVIIEIL 89
KT++G D++ + +GF+ +E L
Sbjct: 61 KTINGEDILFAMSTLGFDSYVEPL 84
>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 = 77.9 bits (191), Expect = 9e-20
Identities = 28/84 (33%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 6 DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR 65
DDL +P A I ++IKE LP + V+ D R + FI +++EA I N+ +
Sbjct: 12 DDLTIPRAAINKMIKETLPN-----VRVANDARELVVNCCTEFIHLISSEANEICNKSEK 66
Query: 66 KTLSGVDVIEGVKQIGFEVIIEIL 89
KT+S VI+ ++ +GF I +
Sbjct: 67 KTISPEHVIQALESLGFGSYISEV 90
>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo
sapiens} SCOP: a.22.1.3
Length = 97
Score = 46.9 bits (111), Expect = 2e-08
Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 5/79 (6%)
Query: 1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60
+ LP A I++++K E +S + + KAA +FI LT A
Sbjct: 11 TVKDFRVQELPLARIKKIMKLD-----EDVKMISAEAPVLFAKAAQIFITELTLRAWIHT 65
Query: 61 NEKNRKTLSGVDVIEGVKQ 79
+ R+TL D+ + +
Sbjct: 66 EDNKRRTLQRNDIAMAITK 84
>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 = 44.3 bits (104), Expect = 1e-06
Identities = 20/123 (16%), Positives = 44/123 (35%), Gaps = 36/123 (29%)
Query: 1 MAESLDDLNLPSAI---IQR--LIKEALPKDAEGKINVSKDVRLAA---GKAASLF---- 48
+A+ + + S + R ++ A+P+D G+ N + A G+ A+ F
Sbjct: 1773 LADVMS---IESLVEVVFYRGMTMQVAVPRDELGRSNYG----MIAINPGRVAASFSQEA 1825
Query: 49 -------ILHLTTEALSIANEKNRKTLSG--VDVIEGVKQIGFEVIIEILGKSYNAAVSI 99
+ T + I N N + V G + + + +L ++ I
Sbjct: 1826 LQYVVERVGKRTGWLVEIVNY-N---VENQQY-VAAGDLR-ALDTVTNVL--NFIKLQKI 1877
Query: 100 KVV 102
++
Sbjct: 1878 DII 1880
>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 = 42.0 bits (98), Expect = 3e-06
Identities = 12/74 (16%), Positives = 29/74 (39%), Gaps = 6/74 (8%)
Query: 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKN-R 65
+ LP + ++ ++K + ++ +V K LF+ HL A + +
Sbjct: 17 ETFLPLSRVRTIMKSS-----MDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPG 71
Query: 66 KTLSGVDVIEGVKQ 79
+ L + + V +
Sbjct: 72 EALKYEHLSQVVNK 85
>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 = 40.7 bits (95), Expect = 5e-06
Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRK 66
+ P A I+++++ E V+ V + +A LF+ L +A + +N K
Sbjct: 9 NARFPPARIKKIMQTD-----EEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAK 63
Query: 67 TLSGVDVIEGVKQ 79
T++ + + ++
Sbjct: 64 TMTTSHLKQCIEL 76
>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 = 38.4 bits (90), Expect = 2e-05
Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 6/71 (8%)
Query: 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69
LP A I R+IK A + VS D R+A K + +EA+ +A RKT+
Sbjct: 3 LPIAPIGRIIKNAGAE------RVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIK 56
Query: 70 GVDVIEGVKQI 80
D+ K
Sbjct: 57 AEDIELARKMF 67
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A
{Pyrococcus horikoshii} SCOP: a.22.1.2
Length = 70
Score = 38.1 bits (89), Expect = 3e-05
Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 6/69 (8%)
Query: 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69
LP A + RLI++A + VS+ + + + + +A+ A RKT+
Sbjct: 7 LPIAPVDRLIRKAGAE------RVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVK 60
Query: 70 GVDVIEGVK 78
D+ +K
Sbjct: 61 VEDIKLAIK 69
>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 = 35.0 bits (80), Expect = 9e-04
Identities = 12/74 (16%), Positives = 32/74 (43%), Gaps = 6/74 (8%)
Query: 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTL 68
+ S++I+++ K V++D K + + ++++ + + RKT+
Sbjct: 7 EIASSLIKQIFSHY------VKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTV 60
Query: 69 SGVDVIEGVKQIGF 82
DV +++ G
Sbjct: 61 EMADVELLMRRQGL 74
>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 = 31.5 bits (71), Expect = 0.014
Identities = 14/72 (19%), Positives = 32/72 (44%), Gaps = 6/72 (8%)
Query: 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69
+ I+RL + G +S + +F+ ++ +A++ RKT++
Sbjct: 30 ITKPAIRRLARRG------GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVT 83
Query: 70 GVDVIEGVKQIG 81
+DV+ +K+ G
Sbjct: 84 AMDVVYALKRQG 95
>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 = 30.8 bits (69), Expect = 0.027
Identities = 13/72 (18%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69
+ I+RL + G +S + F+ + ++++ RKT++
Sbjct: 29 ITKPAIRRLARRG------GVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVT 82
Query: 70 GVDVIEGVKQIG 81
+DV+ +K+ G
Sbjct: 83 SLDVVYALKRQG 94
>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone
chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl
y-1140}
Length = 103
Score = 30.0 bits (67), Expect = 0.047
Identities = 16/69 (23%), Positives = 32/69 (46%), Gaps = 2/69 (2%)
Query: 15 IQRLIKEALPKDAE--GKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVD 72
IQ + K A+ + A G +S + F+ + +A++ RKT++ +D
Sbjct: 27 IQGITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLD 86
Query: 73 VIEGVKQIG 81
V+ +K+ G
Sbjct: 87 VVYALKRQG 95
>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 = 29.4 bits (66), Expect = 0.060
Identities = 14/67 (20%), Positives = 31/67 (46%), Gaps = 6/67 (8%)
Query: 15 IQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVI 74
I+RL + G +S + +F+ ++ +A++ RKT++ +DV+
Sbjct: 16 IRRLARRG------GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVV 69
Query: 75 EGVKQIG 81
+K+ G
Sbjct: 70 YALKRQG 76
>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 = 29.4 bits (65), Expect = 0.16
Identities = 9/65 (13%), Positives = 23/65 (35%), Gaps = 4/65 (6%)
Query: 6 DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAA--GKAASLFILHLTTEALSIANEK 63
++P+ ++ + + + D +N L K +++ I + E +
Sbjct: 383 PSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELK--VKLE 440
Query: 64 NRKTL 68
N L
Sbjct: 441 NEYAL 445
Score = 28.7 bits (63), Expect = 0.38
Identities = 18/119 (15%), Positives = 35/119 (29%), Gaps = 31/119 (26%)
Query: 5 LDDLNLPSAI----IQ---------RLIKEALPKDAEGKINVSKDVR-LAAGKAASLFIL 50
L ++ A + + + + L I++ L + SL +
Sbjct: 250 LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLK 309
Query: 51 HLTTE--------------ALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95
+L LSI E R G+ + K + + + I+ S N
Sbjct: 310 YLDCRPQDLPREVLTTNPRRLSIIAESIRD---GLATWDNWKHVNCDKLTTIIESSLNV 365
>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 = 26.5 bits (57), Expect = 1.9
Identities = 12/70 (17%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 14 IIQRLIKEALPKDAE--GKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGV 71
+++ +I + +D + G +S + F+ + ++++ RKT++ +
Sbjct: 158 VLRDIIDISDEEDGDKGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSL 217
Query: 72 DVIEGVKQIG 81
DV+ +K+ G
Sbjct: 218 DVVYALKRQG 227
>1gkp_A Hydantoinase; hydrolase, dihydropyrimidinase, cyclic amidase; HET:
KCX EPE; 1.29A {Thermus SP} SCOP: b.92.1.3 c.1.9.6 PDB:
1gkq_A*
Length = 458
Score = 26.0 bits (58), Expect = 2.6
Identities = 13/89 (14%), Positives = 28/89 (31%), Gaps = 28/89 (31%)
Query: 13 AIIQRLIKEAL--------------PKDAEGKINVSKDVRLAAGKAASLFILHLTTEALS 58
++ RL ++ L P+ E ++ A+ +++HL+ +
Sbjct: 187 ELVGRLQQKLLSEGKTGPEWHEPSRPEAVEA-EGTARFATFLETTGATGYVVHLSCK--- 242
Query: 59 IANEKNRKTLSGVDVIEGVKQIGFEVIIE 87
+D K G + IE
Sbjct: 243 ----------PALDAAMAAKARGVPIYIE 261
>1bh9_B TAFII28; histone fold, tata binding protein, transcription
regulation complex; HET: PMB; 2.60A {Homo sapiens}
SCOP: a.22.1.3 PDB: 1bh8_B*
Length = 89
Score = 24.3 bits (53), Expect = 4.8
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKN 64
P A I+RLI+ +VS++V +A + +F+ + EAL + +
Sbjct: 16 AFPKAAIKRLIQSITGT------SVSQNVVIAMSGISKVFVGEVVEEALDVCEKWG 65
>2fty_A Dihydropyrimidinase; alpha/beta barrel, beta-sandwich, hydrolase;
HET: KCX; 2.40A {Lachancea kluyveri} SCOP: b.92.1.3
c.1.9.6 PDB: 2fvk_A* 2fvm_A*
Length = 559
Score = 25.1 bits (55), Expect = 5.9
Identities = 12/89 (13%), Positives = 29/89 (32%), Gaps = 28/89 (31%)
Query: 13 AIIQRLIKEAL--------------PKDAEGKINVSKDVRLAAGKAASLFILHLTTEALS 58
+++ +I+ P EG ++ + LA + +H+++
Sbjct: 203 DMVKWMIEALEEQGLTDAYYHGVSRPSIVEG-EATNRAITLATTMDTPILFVHVSSP--- 258
Query: 59 IANEKNRKTLSGVDVIEGVKQIGFEVIIE 87
+VI+ + G +V E
Sbjct: 259 ----------QAAEVIKQAQTKGLKVYAE 277
>3e74_A Allantoinase; (beta/alpha)8-barrel domain, small beta-sheet domain,
hydrolase, metal-binding, purine metabolism, zinc; HET:
KCX; 2.10A {Escherichia coli}
Length = 473
Score = 24.5 bits (54), Expect = 9.0
Identities = 11/64 (17%), Positives = 23/64 (35%), Gaps = 14/64 (21%)
Query: 24 PKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE 83
P E + + + LA L + H+++ GV+ + +Q G +
Sbjct: 236 PVFTEV-EAIRRVLYLAKVAGCRLHVCHVSSPE-------------GVEEVTRARQEGQD 281
Query: 84 VIIE 87
+ E
Sbjct: 282 ITCE 285
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
0.314 0.132 0.338
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: 1,508,248
Number of extensions: 83914
Number of successful extensions: 152
Number of sequences better than 10.0: 1
Number of HSP's gapped: 146
Number of HSP's successfully gapped: 29
Length of query: 103
Length of database: 6,701,793
Length adjustment: 68
Effective length of query: 35
Effective length of database: 4,803,165
Effective search space: 168110775
Effective search space used: 168110775
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (23.9 bits)