RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8542
(182 letters)
>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 = 90.7 bits (225), Expect = 7e-25
Identities = 33/66 (50%), Positives = 52/66 (78%)
Query: 63 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
+DAQVI+++ +E ++ Y+PR V Q+LEF Y T+IL+D++VYANHA+KKT+D++D++L
Sbjct: 2 KDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRL 61
Query: 123 AITNQL 128
A L
Sbjct: 62 ATEVTL 67
Score = 73.0 bits (179), Expect = 7e-18
Identities = 27/57 (47%), Positives = 43/57 (75%)
Query: 14 PRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVN 70
P+DAQVI+++ +E ++ Y+PR V Q+LEF Y T+IL+D++VYANHAR + ++
Sbjct: 1 PKDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLD 57
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A
{Pyrococcus horikoshii} SCOP: a.22.1.2
Length = 70
Score = 43.5 bits (103), Expect = 1e-06
Identities = 19/59 (32%), Positives = 34/59 (57%)
Query: 68 IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN 126
+ + ++AG + + + + E++ Y I + + +A HA +KTV VEDIKLAI +
Sbjct: 12 VDRLIRKAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIKS 70
>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 = 43.4 bits (102), Expect = 3e-06
Identities = 14/61 (22%), Positives = 26/61 (42%)
Query: 67 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN 126
+I +F + + + Y I D Y+ HA +KTV++ D++L +
Sbjct: 12 LIKQIFSHYVKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRR 71
Query: 127 Q 127
Q
Sbjct: 72 Q 72
Score = 27.3 bits (60), Expect = 1.4
Identities = 8/45 (17%), Positives = 14/45 (31%)
Query: 19 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAR 63
+I +F + + + Y I D Y+ HA
Sbjct: 12 LIKQIFSHYVKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAG 56
>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 = 43.0 bits (101), Expect = 3e-06
Identities = 14/61 (22%), Positives = 27/61 (44%)
Query: 67 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN 126
I + + G+K ++ + + ++ D+ Y HAK+KTV D+ A+
Sbjct: 34 AIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKR 93
Query: 127 Q 127
Q
Sbjct: 94 Q 94
Score = 27.6 bits (61), Expect = 1.1
Identities = 7/45 (15%), Positives = 18/45 (40%)
Query: 19 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAR 63
I + + G+K ++ + + ++ D+ Y HA+
Sbjct: 34 AIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAK 78
>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 = 43.1 bits (101), Expect = 3e-06
Identities = 15/61 (24%), Positives = 30/61 (49%)
Query: 67 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITN 126
I + + G+K +++ + ++ +++ DS Y HAK+KTV D+ A+
Sbjct: 33 AIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKR 92
Query: 127 Q 127
Q
Sbjct: 93 Q 93
Score = 28.5 bits (63), Expect = 0.60
Identities = 8/45 (17%), Positives = 21/45 (46%)
Query: 19 VIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAR 63
I + + G+K +++ + ++ +++ DS Y HA+
Sbjct: 33 AIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAK 77
>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 = 40.8 bits (96), Expect = 9e-06
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 84 CVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAI 124
+ ++LE I ++ A HA +KT+ EDI+LA
Sbjct: 27 ALAKVLE---EMGEEIASEAVKLAKHAGRKTIKAEDIELAR 64
>3v9r_A MHF1, uncharacterized protein YOL086W-A; histone fold, fanconi
anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces
cerevisiae}
Length = 90
Score = 41.5 bits (97), Expect = 1e-05
Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 3/59 (5%)
Query: 67 VIVNMFQEAGIK---NYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
+ Q+ Y PR + +LE + D + +A HA + V+ D+ L
Sbjct: 17 RVEERLQQVLSSEDIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLML 75
>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 = 41.3 bits (97), Expect = 1e-05
Identities = 13/53 (24%), Positives = 24/53 (45%)
Query: 75 AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ 127
G+K ++ + + ++ D+ Y HAK+KTV D+ A+ Q
Sbjct: 23 GGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ 75
>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone
chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl
y-1140}
Length = 103
Score = 41.6 bits (97), Expect = 1e-05
Identities = 14/60 (23%), Positives = 29/60 (48%)
Query: 68 IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ 127
I + + G+K +++ + + +++ D+ Y HAK+KTV D+ A+ Q
Sbjct: 35 IRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQ 94
Score = 27.3 bits (60), Expect = 1.4
Identities = 8/56 (14%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 8 SSTSKLPRDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAR 63
+ + + A I + + G+K +++ + + +++ D+ Y HA+
Sbjct: 25 DNIQGITKPA--IRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAK 78
>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 = 40.8 bits (95), Expect = 2e-05
Identities = 11/56 (19%), Positives = 23/56 (41%)
Query: 68 IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA 123
+ + + + + E +D ++A HAK+ T++ ED+KL
Sbjct: 36 LCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLL 91
>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 = 41.0 bits (95), Expect = 1e-04
Identities = 26/157 (16%), Positives = 52/157 (33%), Gaps = 40/157 (25%)
Query: 15 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQV------- 67
+D I+++F++A + N+D + VQ M + + + ++ + + +
Sbjct: 19 KD---ILSVFEDAFVDNFDCKDVQDMPKSI--LSKEEIDH--IIMSKDAVSGTLRLFWTL 71
Query: 68 ------IVNMFQEAGI-KNYD-------PRCVQQMLEFV--NNYTTTILEDSRVYANHAK 111
+V F E + NY Q + + D++V+A
Sbjct: 72 LSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFA---- 127
Query: 112 KKTVDVEDIKLAITNQLSGSFAKPPPRES----KGSG 144
K V L + L +P GSG
Sbjct: 128 KYNVSRLQPYLKLRQALLE--LRPAKNVLIDGVLGSG 162
Score = 29.1 bits (64), Expect = 0.93
Identities = 20/156 (12%), Positives = 46/156 (29%), Gaps = 31/156 (19%)
Query: 8 SSTSKLPRDAQVIVNMFQEA------GIKNYDPRCVQQMLEFVNNYTTTILEDSR----- 56
S R ++ M+ E + + V + L+ +LE
Sbjct: 96 SPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSR-LQPYLKLRQALLELRPAKNVL 154
Query: 57 VY-----------ANHARDAQVIVNMFQEA---GIKNYDPRCVQQMLEFVNNYTTTILED 102
+ + +V M + +KN + + +LE + I +
Sbjct: 155 IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCN--SPETVLEMLQKLLYQIDPN 212
Query: 103 SRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPR 138
++H+ + + I+ + L +KP
Sbjct: 213 WTSRSDHSSNIKLRIHSIQAELRRLLK---SKPYEN 245
>3nqj_A Histone H3-like centromeric protein A; alpha helix, histone fold,
centromere, DNA binding protein; 2.10A {Homo sapiens}
Length = 82
Score = 38.1 bits (88), Expect = 1e-04
Identities = 12/56 (21%), Positives = 25/56 (44%)
Query: 68 IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA 123
I F N+ + + + E + + ED+ + HA + T+ +D++LA
Sbjct: 16 ICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLA 71
>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA,
nucleus, DNA binding protein; 2.15A {Gallus gallus}
Length = 107
Score = 38.5 bits (89), Expect = 2e-04
Identities = 13/55 (23%), Positives = 22/55 (40%)
Query: 68 IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
+ E + + V + E D ++A HAK+ T+ ED+KL
Sbjct: 28 LCQDVAEDKGVLFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKL 82
>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 = 38.0 bits (87), Expect = 3e-04
Identities = 12/56 (21%), Positives = 25/56 (44%)
Query: 68 IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA 123
I F N+ + + + E + + ED+ + HA + T+ +D++LA
Sbjct: 74 ICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLA 129
>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding, nucleus,
binding protein; 2.40A {Gallus gallus} PDB: 3vh6_A
Length = 140
Score = 37.8 bits (87), Expect = 4e-04
Identities = 17/101 (16%), Positives = 33/101 (32%), Gaps = 10/101 (9%)
Query: 68 IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL----- 122
+ E + + V + E D ++A HAK+ T+ ED+KL
Sbjct: 28 LAQDVAEDKGVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARRS 87
Query: 123 -----AITNQLSGSFAKPPPRESKGSGQAGAMGSNAHNKAP 158
IT + + ++ K ++ A +
Sbjct: 88 NSLLKYITQKSDELASSNMEQKEKKKKKSSAAKGRKTEENE 128
>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA binding
prote; 1.70A {Xenopus laevis}
Length = 77
Score = 35.6 bits (82), Expect = 9e-04
Identities = 14/45 (31%), Positives = 23/45 (51%)
Query: 79 NYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA 123
+ V + E Y + ED+ + A HAK+ T+ +DI+LA
Sbjct: 25 RFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLA 69
>3r45_A Histone H3-like centromeric protein A; histone fold, centromere,
CENP-A, histone chaperone, hjurp; 2.60A {Homo sapiens}
Length = 156
Score = 36.1 bits (82), Expect = 0.002
Identities = 14/61 (22%), Positives = 28/61 (45%)
Query: 63 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
R A+ I F N+ + + + E + + ED+ + HA + T+ +D++L
Sbjct: 85 RLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQL 144
Query: 123 A 123
A
Sbjct: 145 A 145
>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 = 34.4 bits (78), Expect = 0.004
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 95 YTTTILEDSRVYANHAKKKTVDVEDIKLA 123
Y +LE + + A HAK+ T+ +D++LA
Sbjct: 68 YLVGLLEHTNLLALHAKRITIMRKDMQLA 96
>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 = 35.0 bits (79), Expect = 0.007
Identities = 14/55 (25%), Positives = 28/55 (50%)
Query: 73 QEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ 127
+ G+K +++ + ++ +++ DS Y HAK+KTV D+ A+ Q
Sbjct: 172 DKGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ 226
Score = 28.4 bits (62), Expect = 1.1
Identities = 12/46 (26%), Positives = 23/46 (50%)
Query: 79 NYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAI 124
+ + + E Y +LE + + A HAK+ T+ +D++LA
Sbjct: 36 RWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMKKDMQLAR 81
>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 = 34.0 bits (77), Expect = 0.010
Identities = 16/58 (27%), Positives = 28/58 (48%)
Query: 71 MFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQL 128
+ + AGI+ V + + T + E + YA+ +KTV ED++ AIT +
Sbjct: 91 ILKRAGIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYSM 148
>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 = 31.0 bits (70), Expect = 0.037
Identities = 12/56 (21%), Positives = 30/56 (53%)
Query: 68 IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA 123
+ + + G+ + +++ E V+ I++D+ + NHAK++ + V DI ++
Sbjct: 12 MKVIAESIGVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMS 67
>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 = 31.9 bits (71), Expect = 0.046
Identities = 14/45 (31%), Positives = 23/45 (51%)
Query: 79 NYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA 123
+ V + E Y + ED+ + A HAK+ T+ +DI+LA
Sbjct: 84 RFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 128
>2olt_A Hypothetical protein; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2, unknown function; HET: MSE; 2.00A {Shewanella
oneidensis} PDB: 2iiu_A*
Length = 227
Score = 30.0 bits (67), Expect = 0.33
Identities = 9/56 (16%), Positives = 15/56 (26%)
Query: 84 CVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAKPPPRE 139
C ++ F T +D+ + +K I L P R
Sbjct: 29 CASLLVPFFEATITGNWDDAVQIRKQISLAEKQGDSLKREIRLTLPSGLFMPVERT 84
>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 = 28.2 bits (63), Expect = 0.43
Identities = 9/44 (20%), Positives = 25/44 (56%)
Query: 81 DPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAI 124
D + +L+ +++ +++ + A H K T++V+D++L +
Sbjct: 25 DEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHL 68
>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics
consortium, SGC, GDP, membrane, nucleotide-binding,
nucleotide binding protein; HET: GDP; 1.82A {Homo
sapiens}
Length = 195
Score = 29.1 bits (66), Expect = 0.53
Identities = 5/37 (13%), Positives = 15/37 (40%), Gaps = 9/37 (24%)
Query: 90 EFVNNYTTTILEDSRVYANHAKKKTVDV--EDIKLAI 124
+ + + ED+ ++ + V E++ L +
Sbjct: 47 QGDSAHEPENPEDT-------YERRIMVDKEEVTLVV 76
>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 = 28.1 bits (62), Expect = 1.9
Identities = 20/120 (16%), Positives = 34/120 (28%), Gaps = 57/120 (47%)
Query: 71 MFQEAGIKNYDPRCVQQMLEFVNNYTTTIL-EDSRVYANHAKKKTVDVEDIKLAITNQ-- 127
M I N VQ + N++ L +V +++ N
Sbjct: 338 ML---SISNLTQEQVQDYVNKTNSH----LPAGKQVE---------------ISLVNGAK 375
Query: 128 ---LSGSFAKPPP----------RESK---GSGQAGAMGSNAHNKAPLTKGAMKTVPQAR 171
+SG PP R++K G Q ++ P ++ K R
Sbjct: 376 NLVVSG-----PPQSLYGLNLTLRKAKAPSGLDQ---------SRIPFSE--RKLKFSNR 419
Score = 26.6 bits (58), Expect = 5.7
Identities = 10/50 (20%), Positives = 15/50 (30%), Gaps = 12/50 (24%)
Query: 23 MFQEAGIKNYDPRCVQQMLEFVNNYTTTIL-EDSRVYA---NHARDAQVI 68
M I N VQ + N++ L +V N V+
Sbjct: 338 ML---SISNLTQEQVQDYVNKTNSH----LPAGKQVEISLVN-GAKNLVV 379
>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 = 26.8 bits (59), Expect = 1.9
Identities = 10/67 (14%), Positives = 23/67 (34%), Gaps = 6/67 (8%)
Query: 82 PRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ---LSGSFAKPPPR 138
P + + LE + ++L+ + KT+ +K I + + K
Sbjct: 35 PVIISRALEL---FLESLLKKACQVTQSRNAKTMTTSHLKQCIELEGDPAANKARKEAEL 91
Query: 139 ESKGSGQ 145
+ + Q
Sbjct: 92 AAATAEQ 98
>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein;
HET: GNP; 1.76A {Mus musculus}
Length = 169
Score = 27.1 bits (61), Expect = 2.2
Identities = 6/35 (17%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 90 EFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAI 124
+ + + ED+ ++ VD E++ L +
Sbjct: 26 QGDHAHEMENSEDTYE-----RRIMVDKEEVTLIV 55
>3t66_A Nickel ABC transporter (nickel-binding protein); structural
genomics, PSI-biology, NEW YORK structural genomi
research consortium, nysgrc; 2.80A {Bacillus halodurans}
Length = 496
Score = 26.9 bits (60), Expect = 4.9
Identities = 11/56 (19%), Positives = 20/56 (35%), Gaps = 5/56 (8%)
Query: 23 MFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIK 78
+EAG + + + T+L A AQV + ++ GI+
Sbjct: 310 YLEEAGYTLENGQMQKDGEPL----HFTVLTYGS-RAELPLIAQVFQSNAKQIGIE 360
>1uqw_A Putative binding protein YLIB; Zn binding protein, transport,
lipoprotein, bacterial targets at IGS-CNRS, france,
BIGS, structural genomics; 2.72A {Escherichia coli}
SCOP: c.94.1.1
Length = 509
Score = 26.5 bits (59), Expect = 5.5
Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 32 YDPRCVQQMLE---FVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIK 78
YDP +++L+ + N ++TT+ ++ + Q + GIK
Sbjct: 326 YDPVKARELLKEAGYPNGFSTTLWSSHN-HSTAQKVLQFTQQQLAQVGIK 374
>1vr5_A Oligopeptide ABC transporter, periplasmic oligope binding protein;
TM1223, periplasmic oligopepti binding, structural
genomics; HET: EPE; 1.73A {Thermotoga maritima} SCOP:
c.94.1.1
Length = 547
Score = 26.6 bits (59), Expect = 5.9
Identities = 9/56 (16%), Positives = 18/56 (32%), Gaps = 2/56 (3%)
Query: 23 MFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIK 78
+ E G K+ + ++ + TI + + Q I + GI
Sbjct: 344 ILDELGFKDVNKDGFREDPN-GKPFKLTIECPYG-WTDWMVSIQSIAEDLVKVGIN 397
>2jss_A Chimera of histone H2B.1 and histone H2A.Z; histone/chaperone
complex, intrinsically unfolded protein,
chaperone/structural protein complex; NMR {Saccharomyces
cerevisiae} SCOP: a.22.1.1 a.22.1.1
Length = 192
Score = 25.9 bits (55), Expect = 6.5
Identities = 14/53 (26%), Positives = 25/53 (47%)
Query: 82 PRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAK 134
+ + + FVN+ I ++ A + KK T+ +I+ A+ L G AK
Sbjct: 24 QKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAK 76
>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding
mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli}
SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*
Length = 758
Score = 26.4 bits (59), Expect = 6.5
Identities = 12/85 (14%), Positives = 24/85 (28%), Gaps = 22/85 (25%)
Query: 99 ILEDSRVYANHAKKKTVDVEDIKLAI----------------------TNQLSGSFAKPP 136
+L+ + + + + V ++ +AI N +S K
Sbjct: 87 VLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHGTRKDE 146
Query: 137 PRESKGSGQAGAMGSNAHNKAPLTK 161
P +S G A + L
Sbjct: 147 PTQSSDPGSQPNSEEQAGGEERLEN 171
>3ijm_A Uncharacterized restriction endonuclease-like FOL superfamily
protein; DUF820, cyanobacteria, PD(D/E)XK superfamily,
structural GEN PSI-2; 1.70A {Spirosoma linguale}
Length = 151
Score = 25.9 bits (56), Expect = 6.9
Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 10/63 (15%)
Query: 44 VNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNYDPRCVQQMLE---------FVNN 94
+ ++ + D +Y + +A+VI+ + Q +G+K+ D + +++E FV N
Sbjct: 59 LTEGYSSPVPDVLLYDHQTEEAKVIIEVCQNSGLKH-DTSKIVKLIEDNAYGILEGFVFN 117
Query: 95 YTT 97
Y T
Sbjct: 118 YKT 120
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
0.313 0.126 0.347
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: 2,522,583
Number of extensions: 140036
Number of successful extensions: 305
Number of sequences better than 10.0: 1
Number of HSP's gapped: 304
Number of HSP's successfully gapped: 52
Length of query: 182
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 94
Effective length of database: 4,244,745
Effective search space: 399006030
Effective search space used: 399006030
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 (21.9 bits)
S2: 54 (25.0 bits)