RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15631
(213 letters)
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional
regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus
musculus}
Length = 79
Score = 69.1 bits (170), Expect = 4e-16
Identities = 21/32 (65%), Positives = 26/32 (81%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
+K PFI EA+RLR HM ++PDYKYRPR+K K
Sbjct: 48 DKIPFIQEAERLRLKHMADYPDYKYRPRKKVK 79
>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus
musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B
Length = 80
Score = 69.1 bits (170), Expect = 4e-16
Identities = 31/33 (93%), Positives = 32/33 (96%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
EKRPFIDEAKRLRA+HMKEHPDYKYRPRRK KT
Sbjct: 48 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT 80
>1j46_A SRY, sex-determining region Y protein; MALE sex determining
factor, SRY, sex-reversal mutation; NMR {Homo sapiens}
SCOP: a.21.1.1 PDB: 1j47_A
Length = 85
Score = 69.2 bits (170), Expect = 6e-16
Identities = 20/33 (60%), Positives = 27/33 (81%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
EK PF EA++L+AMH +++P+YKYRPRRK K
Sbjct: 50 EKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKM 82
>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain,
endodermal, activator, DNA- nucleus, transcription
regulation, transcrip complex; HET: DNA; 2.75A {Mus
musculus} PDB: 2yul_A
Length = 83
Score = 67.2 bits (165), Expect = 3e-15
Identities = 21/32 (65%), Positives = 29/32 (90%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
EKRPF++EA+RLR HM++HP+YKYRPRR+ +
Sbjct: 52 EKRPFVEEAERLRVQHMQDHPNYKYRPRRRKQ 83
>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG,
TCR-A, transcription factor; HET: DNA; NMR {Mus
musculus} SCOP: a.21.1.1
Length = 86
Score = 65.7 bits (161), Expect = 1e-14
Identities = 8/34 (23%), Positives = 17/34 (50%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTP 35
E+ + + A++ R +HM+ +P + R K
Sbjct: 48 EQAKYYELARKERQLHMQLYPGWSARDNYGKKKK 81
>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA
recognition, chromatin, DNA binding protein, DNA
sequence specific, testis determining.; NMR {Mus
musculus} SCOP: a.21.1.1
Length = 81
Score = 65.3 bits (160), Expect = 1e-14
Identities = 15/30 (50%), Positives = 23/30 (76%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRK 31
EK+P+ +E RL H++++PDYKY+PR K
Sbjct: 50 EKQPYYEEQARLSKQHLEKYPDYKYKPRPK 79
>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX
domain, structural genomics, NPPSFA, riken structural
genomics/proteomics initiative; NMR {Mus musculus}
Length = 82
Score = 64.2 bits (157), Expect = 4e-14
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRR 30
EK+ + D AK + MK +P Y+ P
Sbjct: 53 EKQKYTDMAKEYKDAFMKANPGYRSGPSS 81
>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain,
activator, DNA-binding, NUC transcription; HET: DNA;
2.77A {Homo sapiens}
Length = 106
Score = 63.9 bits (156), Expect = 9e-14
Identities = 21/30 (70%), Positives = 27/30 (90%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRK 31
EKRPF++EA+RLR H K+HPDYKY+PRR+
Sbjct: 75 EKRPFVEEAERLRVQHKKDHPDYKYQPRRR 104
>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA
complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1
PDB: 1hrz_A*
Length = 76
Score = 59.9 bits (146), Expect = 1e-12
Identities = 16/27 (59%), Positives = 23/27 (85%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRP 28
EK PF EA++L+AMH +++P+YKYRP
Sbjct: 50 EKWPFFQEAQKLQAMHREKYPNYKYRP 76
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens}
Length = 71
Score = 53.4 bits (129), Expect = 3e-10
Identities = 16/24 (66%), Positives = 22/24 (91%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYK 25
EKRPF++EA+RLR HM++HP+YK
Sbjct: 48 EKRPFVEEAERLRVQHMQDHPNYK 71
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX,
amphoterin, DNA/structural protein complex; NMR {Homo
sapiens} SCOP: a.21.1.1 a.21.1.1
Length = 159
Score = 54.1 bits (130), Expect = 1e-09
Identities = 6/26 (23%), Positives = 16/26 (61%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYR 27
+K+P+ +A +L+ + K+ Y+ +
Sbjct: 134 DKQPYEKKAAKLKEKYEKDIAAYRAK 159
Score = 40.6 bits (95), Expect = 7e-05
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 11/61 (18%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPS 61
EK PF EA++L+AMH +++P+YKYR K AP +AF
Sbjct: 50 EKWPFFQEAQKLQAMHREKYPNYKYRKGETKKKFKDP-----------NAPKRPPSAFFL 98
Query: 62 F 62
F
Sbjct: 99 F 99
>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box
transcription factor 1, high mobility group box
transcription factor 1, structural genomics; NMR {Homo
sapiens}
Length = 87
Score = 46.6 bits (111), Expect = 1e-07
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPD 23
E+R + EAK L + +PD
Sbjct: 63 ERRMYTLEAKALAEEQKRLNPD 84
>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of
chromatin subfamily...; structural DNA-binding protein
BRAF35, DNA-bending; NMR {Mus musculus}
Length = 92
Score = 42.0 bits (99), Expect = 8e-06
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTP 35
EK+ ++DEA++ + ++KE Y+ K T
Sbjct: 53 EKQRYLDEAEKEKQQYLKELWAYQQSEAYKVCTE 86
>1wgf_A Upstream binding factor 1; transcription factor, DNA binding,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus
musculus} SCOP: a.21.1.1
Length = 90
Score = 40.8 bits (96), Expect = 2e-05
Identities = 3/24 (12%), Positives = 8/24 (33%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYK 25
+K + L+A ++
Sbjct: 66 KKAKYKAREAALKAQSERKSGPSS 89
>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A
1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A
Length = 77
Score = 38.4 bits (90), Expect = 1e-04
Identities = 6/26 (23%), Positives = 16/26 (61%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYR 27
+K+P+ +A +L+ + K+ Y+ +
Sbjct: 52 DKQPYEKKAAKLKEKYEKDIAAYRAK 77
>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 = 40.4 bits (94), Expect = 3e-04
Identities = 42/288 (14%), Positives = 75/288 (26%), Gaps = 121/288 (42%)
Query: 6 FIDEAKRLRAMHMKEHPDYK-YRPRRKP--KTPGQSIPNNKSPNQGAPAPTSASNAFPSF 62
+ +E LR + Y+ Y K +++ ++ A F
Sbjct: 169 YFEE---LRDL-------YQTYHVLVGDLIKFSAETL------SELIRTTLDAEKVFT-- 210
Query: 63 PLPPYFANHG--------GGSHPHPLDSLSAAYPPMNMP--------HYF------G-SP 99
G S+ D L + P++ P HY G +P
Sbjct: 211 --------QGLNILEWLENPSNTPDKDYLLSI--PISCPLIGVIQLAHYVVTAKLLGFTP 260
Query: 100 FDAMNFSKLVQGQT------------SQADTKSS---NAAAAVVSSFY-----------S 133
++G T ++ D+ S + A+ F+ +
Sbjct: 261 G---ELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNT 317
Query: 134 SLYPSV---------------------TSAQTKTF------STPPPSHLS-ALFQHPTAA 165
SL PS+ T Q + + P + +L
Sbjct: 318 SLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNL 377
Query: 166 --SSHPSQFLYGLKSEQLSPSSSPGESQSQSNNQSALELDQLRRPVPV 211
S P LYGL + G QS+ + + R+
Sbjct: 378 VVSGPPQS-LYGLNLTLRKAKAPSGLDQSR------IPFSE-RKLKFS 417
Score = 34.6 bits (79), Expect = 0.023
Identities = 30/193 (15%), Positives = 49/193 (25%), Gaps = 74/193 (38%)
Query: 61 SFPLPPYFANHGGGS---------HPHPLDSLSAAYPPMNMPHYFGSPFDAMNF--SKLV 109
+P A+ S P P + +A P G F + + S +
Sbjct: 19 VLLVPT--ASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGK-F--LGYVSSLVE 73
Query: 110 QGQTSQADTKSSNAAAAVVSSF---Y----------SSLYPSVTSAQTKTFS-------- 148
+ Q D ++ F Y + L + KT
Sbjct: 74 PSKVGQFD----QVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITA 129
Query: 149 ------TPPPSHLSALFQHPTAASSHPSQF--LYGLKSEQLSPSSSPGESQSQSNNQSAL 200
SALF+ A +Q ++G G Q N
Sbjct: 130 RIMAKRPFDKKSNSALFR---AVGEGNAQLVAIFG------------G----QGNTDDY- 169
Query: 201 ELDQLRRPVPVIY 213
++LR +Y
Sbjct: 170 -FEELRD----LY 177
Score = 32.7 bits (74), Expect = 0.082
Identities = 36/177 (20%), Positives = 51/177 (28%), Gaps = 55/177 (31%)
Query: 58 AFPSFPLPP----YFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQT 113
A+P+ LPP + G P P+ S+S + + V
Sbjct: 313 AYPNTSLPPSILEDSLENNEGV-PSPMLSIS------------NLTQEQVQ--DYVNKTN 357
Query: 114 SQADTKSS------NAA-AAVVSSFYSSLYPSVTSA----------QTKT-FSTPPPSHL 155
S N A VVS SLY + Q++ FS
Sbjct: 358 SHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLK-- 415
Query: 156 SALFQH---PTAASSHPSQFLYGLKSEQLSPSSSPGESQSQSNNQSALELDQLRRPV 209
F + P A+ H S L P+S NN S ++ PV
Sbjct: 416 ---FSNRFLPVASPFH---------SHLLVPASDLINKDLVKNNVS-FNAKDIQIPV 459
Score = 28.9 bits (64), Expect = 1.6
Identities = 30/157 (19%), Positives = 44/157 (28%), Gaps = 66/157 (42%)
Query: 11 KRLR----AMHMKEHPDYKYRPRRKPKTPGQSIPNN--KSPN---------QGAPAPTSA 55
KR+R AM + D K + + K + + +S Q PA T
Sbjct: 1682 KRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQ--PALTLM 1739
Query: 56 SNAF-------PSFPLPPYFANHGGGSHPHPLDSL---SA----AYPPMNMPHYFGSPFD 101
A P FA H SL +A A D
Sbjct: 1740 EKAAFEDLKSKGLIPADATFAGH----------SLGEYAALASLA--------------D 1775
Query: 102 AMNFS---KLVQ--GQTSQ------ADTKSSNAAAAV 127
M+ ++V G T Q +S+ A+
Sbjct: 1776 VMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAI 1812
>2lhj_A High mobility group protein homolog NHP1; structural genomics,
seattle structural genomics center for infectious
disease, ssgcid; NMR {Babesia bovis}
Length = 97
Score = 37.4 bits (87), Expect = 4e-04
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYR 27
EK+P+ + R + +E +Y R
Sbjct: 70 EKKPYERMSDEDRVRYEREKAEYAQR 95
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 37.4 bits (86), Expect = 0.002
Identities = 33/163 (20%), Positives = 50/163 (30%), Gaps = 4/163 (2%)
Query: 32 PKTPGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPY--FANHGGGSHPHPLDSLSAAYPP 89
TP + + + S S GG+ S AY
Sbjct: 1469 GVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGE 1528
Query: 90 MNMPHYFGSPFDAMNFSKLVQGQTSQADTKSSNAAAAVVSSFYSSLYPSVTSAQTKTFST 149
FG + + TS A + +S + + S YS PS + T
Sbjct: 1529 APTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPT-SPSYSPTSPSYSPTSPSYSPT 1587
Query: 150 PPPSHLSALFQHPTAASSHPSQFLYGLKSEQLSPSSSPGESQS 192
P ++ PT+ S P+ Y S SP +SP S +
Sbjct: 1588 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP-TSPSYSPT 1629
Score = 37.0 bits (85), Expect = 0.004
Identities = 40/182 (21%), Positives = 67/182 (36%), Gaps = 15/182 (8%)
Query: 28 PRRKPKTPGQS-IPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAA 86
P P +P S + SP + +PTS S + S P ++ S + S +
Sbjct: 1547 PTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS--PTSPS 1604
Query: 87 YPPMNMPHYFGSPF-----DAMNFSKLVQGQTSQADTKSSNAAAAVVSSFYSSLYPSVTS 141
Y P + + SP + + + TS + + +S + + S YS P+ +
Sbjct: 1605 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT-SPSYSPTSPAYSP 1663
Query: 142 AQTKTFSTPPPSHLSALFQHPTAASSHPSQFLYGLKSEQLSPSS------SPGESQSQSN 195
T P ++ PT+ S P+ Y S SP+S SP S Q
Sbjct: 1664 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDE 1723
Query: 196 NQ 197
+
Sbjct: 1724 QK 1725
Score = 28.1 bits (62), Expect = 2.7
Identities = 31/168 (18%), Positives = 51/168 (30%), Gaps = 12/168 (7%)
Query: 32 PKTPGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMN 91
APTS S P + S P S ++
Sbjct: 1510 AYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTS---PAYSPTSPSYSPT 1566
Query: 92 MPHYFGSPFDAMNFSKLVQGQTSQADTKSSNAAAAVVSSFYSSLYPSVTSAQTKTFSTPP 151
P Y SP ++S + ++ + + S YS PS + T P
Sbjct: 1567 SPSY--SPTS-PSYS------PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1617
Query: 152 PSHLSALFQHPTAASSHPSQFLYGLKSEQLSPSSSPGESQSQSNNQSA 199
++ PT+ S P+ Y S SP+S S + + ++
Sbjct: 1618 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTS 1665
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding
protein; NMR {Drosophila melanogaster}
Length = 73
Score = 34.2 bits (79), Expect = 0.003
Identities = 6/24 (25%), Positives = 12/24 (50%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYK 25
+K + D A + + + E +YK
Sbjct: 47 DKSKWEDAAAKDKQRYHDEMRNYK 70
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 92
Score = 34.7 bits (80), Expect = 0.003
Identities = 6/38 (15%), Positives = 14/38 (36%), Gaps = 1/38 (2%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKP-KTPGQS 38
EK + ++A + + + + + K G S
Sbjct: 53 EKLKYEEKATKDLERYNSQMKRAIEQESQMSLKDSGPS 90
>3nm9_A HMG-D, high mobility group protein D; DNA bending,
non-sequence-specific, HMG chromosomal protein; HET:
DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A*
1hma_A 1qrv_A*
Length = 73
Score = 33.0 bits (76), Expect = 0.010
Identities = 2/24 (8%), Positives = 12/24 (50%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYK 25
+K + +A + + + + +++
Sbjct: 47 DKSEWEAKAAKAKDDYDRAVKEFE 70
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box
domain, structural genomics, NPPSFA; NMR {Mus musculus}
Length = 102
Score = 33.5 bits (77), Expect = 0.011
Identities = 5/37 (13%), Positives = 15/37 (40%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQS 38
+K+ + + + + ++K+ Y+ K T
Sbjct: 63 QKQVYKKKTEAAKKEYLKQLAAYRASLVSKSYTDSGP 99
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 35.1 bits (80), Expect = 0.015
Identities = 34/173 (19%), Positives = 62/173 (35%), Gaps = 9/173 (5%)
Query: 34 TPGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHP-LDSLSAAYPPMNM 92
+ SP G +P+ + ++ P Y + S P S +Y P +
Sbjct: 1538 GYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSP 1597
Query: 93 PHYFGSPFDAMNFSKLVQGQTSQADTKSSNA------AAAVVSSFYSSLYPSVTSAQTKT 146
+ SP + + + TS + + +S + + + S YS PS +
Sbjct: 1598 SYSPTSP--SYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1655
Query: 147 FSTPPPSHLSALFQHPTAASSHPSQFLYGLKSEQLSPSSSPGESQSQSNNQSA 199
T P ++ PT+ S P+ Y S SP+S S S + ++
Sbjct: 1656 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1708
Score = 33.9 bits (77), Expect = 0.032
Identities = 34/167 (20%), Positives = 49/167 (29%), Gaps = 10/167 (5%)
Query: 24 YKYRPRRKPKTPGQSIPNNKSPNQGAPAPTSA--SNAFPSFPLPPYFANHGGGSHPHPLD 81
Y+ P G SP + + PY G
Sbjct: 1486 YERSPMVDSGFVGSPDAAAFSPLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSS 1545
Query: 82 SLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQTSQADTKSSNAAAAVVSSFYS--SLYPSV 139
++S Y + + SP + S + S + + S YS S S
Sbjct: 1546 AMSPGYGLTSPSYSPSSPGYST--SPAYMPSSPSYSPTSPSYSPT--SPSYSPTSPSYSP 1601
Query: 140 TSAQTKTFSTPPPSHLSALFQHPTAASSHPSQFLYGLKSEQLSPSSS 186
TS S P S S + PT+ S P+ Y S SP+S
Sbjct: 1602 TSPSYSATS-PSYSPTSPSY-SPTSPSYSPTSPSYSPTSPSYSPTSP 1646
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding
protein; NMR {Homo sapiens} SCOP: a.21.1.1
Length = 99
Score = 31.2 bits (71), Expect = 0.067
Identities = 6/39 (15%), Positives = 14/39 (35%), Gaps = 7/39 (17%)
Query: 2 EKRPFIDEAKRLRAMHMKE-------HPDYKYRPRRKPK 33
+K +I + +R + + HPD ++
Sbjct: 56 KKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKKLEH 94
>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA
recognition, chromatin, DNA binding protein; NMR
{Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A
1lwm_A
Length = 93
Score = 28.8 bits (65), Expect = 0.40
Identities = 6/24 (25%), Positives = 12/24 (50%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYK 25
EK+P+ +A+ + + E Y
Sbjct: 66 EKQPYEAKAQADKKRYESEKELYN 89
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 30.2 bits (67), Expect = 0.62
Identities = 20/147 (13%), Positives = 38/147 (25%), Gaps = 1/147 (0%)
Query: 47 QGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFS 106
Q + P+ +PP G S+ A P M + + ++
Sbjct: 13 QLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLH-Q 71
Query: 107 KLVQGQTSQADTKSSNAAAAVVSSFYSSLYPSVTSAQTKTFSTPPPSHLSALFQHPTAAS 166
++ Q TS D N +++ P + P + +
Sbjct: 72 QIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQN 131
Query: 167 SHPSQFLYGLKSEQLSPSSSPGESQSQ 193
P LY + P +
Sbjct: 132 MRPMNQLYPIDLLTELPPPITDLTLPP 158
Score = 27.5 bits (60), Expect = 3.8
Identities = 14/155 (9%), Positives = 28/155 (18%), Gaps = 3/155 (1%)
Query: 45 PNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMN 104
+ P + P + PP G
Sbjct: 5 KKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQ---QF 61
Query: 105 FSKLVQGQTSQADTKSSNAAAAVVSSFYSSLYPSVTSAQTKTFSTPPPSHLSALFQHPTA 164
+ + Q D +++ + + + Q P P
Sbjct: 62 LTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAY 121
Query: 165 ASSHPSQFLYGLKSEQLSPSSSPGESQSQSNNQSA 199
+ QL P E + +
Sbjct: 122 GQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTL 156
Score = 27.5 bits (60), Expect = 4.1
Identities = 16/127 (12%), Positives = 27/127 (21%), Gaps = 6/127 (4%)
Query: 35 PGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPH 94
P ++P+ PA + P AY +P
Sbjct: 49 PQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDP-----NAYMQPQVPV 103
Query: 95 YFGSPFDAMNFSKLVQGQTSQADTKSSNAAAAVVSSFYSSLYPSVTSAQTKTFSTPPPSH 154
G+P + Q + + L + T PPP
Sbjct: 104 QMGTPLQQQQQP-MAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLV 162
Query: 155 LSALFQH 161
+
Sbjct: 163 IPPERML 169
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding,
helix-turn-helix motif, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 173
Score = 28.8 bits (64), Expect = 0.92
Identities = 6/26 (23%), Positives = 16/26 (61%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYR 27
+K+P+ +A +L+ + K+ Y+ +
Sbjct: 147 DKQPYEKKAAKLKEKYEKDIAAYRAK 172
>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT
DNA, protein-drug-DNA compl regulation-DNA complex;
HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1
PDB: 1j3x_A
Length = 71
Score = 27.0 bits (60), Expect = 1.1
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDY 24
EK F D AK +A + +E Y
Sbjct: 49 EKGKFEDMAKADKARYEREMKTY 71
>3pgb_A Putative uncharacterized protein; oxidoreductase, copper amine
oxidase, CAO, topaquinone, TPQ; HET: TPQ NAG BMA MAN;
2.45A {Emericella nidulans}
Length = 797
Score = 28.4 bits (62), Expect = 2.0
Identities = 8/60 (13%), Positives = 14/60 (23%), Gaps = 4/60 (6%)
Query: 27 RPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAA 86
RK + + + P + A P PP + L+
Sbjct: 19 SRGRKNQMRS-LVGRSNQHITHQSRPYTNEYASPCQITPPQEIKA---PKENVWYGLTDD 74
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1
Length = 83
Score = 26.1 bits (58), Expect = 3.2
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYK 25
EK F D AK +A + +E Y
Sbjct: 55 EKGKFEDMAKADKARYEREMKTYI 78
>3myr_B Nickel-dependent hydrogenase large subunit; [NIFE] hydrogenase,
photosynthetic P sulfur bacterium, iron-sulfur cluster,
NI-A state; HET: SF4; 2.10A {Allochromatium vinosum}
Length = 561
Score = 27.5 bits (60), Expect = 3.9
Identities = 13/101 (12%), Positives = 23/101 (22%), Gaps = 4/101 (3%)
Query: 13 LRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKS----PNQGAPAPTSASNAFPSFPLPPYF 68
+ + D+ P + +S P +F
Sbjct: 105 VMHFYHLHALDWVDVVSALSADPRATSELAQSISAWPKSSPGYFADTQKRIKTFVESGQL 164
Query: 69 ANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLV 109
G HP L M + HY + + +K
Sbjct: 165 GIFANGYWGHPAYRLPPEANLMAVAHYLEALAWQRDTAKFH 205
>1b8x_A Protein (AML-1B); nuclear matrix targeting signal protein, signal
protein; 2.70A {Escherichia coli} SCOP: a.45.1.1
c.47.1.5
Length = 280
Score = 27.2 bits (60), Expect = 4.2
Identities = 15/84 (17%), Positives = 28/84 (33%), Gaps = 2/84 (2%)
Query: 55 ASNAFPSFPLPPYFANHGGGSHPHPLDSLSAAYPPMNMPHYFGSPFDAMNFSKLVQGQTS 114
S+ + ++PL + A GGG HP D + ++ P +
Sbjct: 193 KSSKYIAWPLQGWQATFGGGDHPPKSDLVPRGSRRASVGSRMHYP--GAFTYSPTPVTSG 250
Query: 115 QADTKSSNAAAAVVSSFYSSLYPS 138
S+ +A ++ YP
Sbjct: 251 IGIGMSAMGSATRYHTYLPPPYPG 274
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 26.6 bits (58), Expect = 6.4
Identities = 10/70 (14%), Positives = 17/70 (24%)
Query: 27 RPRRKPKTPGQSIPNNKSPNQGAPAPTSASNAFPSFPLPPYFANHGGGSHPHPLDSLSAA 86
+ + + QS + G P +S + F G P +
Sbjct: 154 QFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGG 213
Query: 87 YPPMNMPHYF 96
PP
Sbjct: 214 PPPPFPAGQT 223
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
0.311 0.125 0.369
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,105,569
Number of extensions: 161767
Number of successful extensions: 382
Number of sequences better than 10.0: 1
Number of HSP's gapped: 362
Number of HSP's successfully gapped: 63
Length of query: 213
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 123
Effective length of database: 4,188,903
Effective search space: 515235069
Effective search space used: 515235069
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 (21.8 bits)
S2: 55 (25.0 bits)