RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3267
(105 letters)
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1
Length = 83
Score = 59.2 bits (144), Expect = 2e-13
Identities = 27/37 (72%), Positives = 33/37 (89%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
+YAFFVQ REEHKKKHP+ +V F+EFSKKC+ERWK+
Sbjct: 14 SYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKT 50
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group
protein 2A, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 86
Score = 59.3 bits (144), Expect = 2e-13
Identities = 30/37 (81%), Positives = 33/37 (89%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AYAFFVQ CREEHKKK+PE V FAEFSKKC+ERWK+
Sbjct: 22 AYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKT 58
>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 = 57.8 bits (140), Expect = 6e-13
Identities = 28/37 (75%), Positives = 34/37 (91%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
+YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWK+
Sbjct: 8 SYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKT 44
>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 = 52.3 bits (125), Expect = 6e-10
Identities = 28/37 (75%), Positives = 34/37 (91%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
+YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWK+
Sbjct: 22 SYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKT 58
Score = 39.6 bits (92), Expect = 3e-05
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
A+ F R + K +HP + + +KK E W +
Sbjct: 108 AFFLFCSEYRPKIKGEHPGLS--IGDVAKKLGEMWNN 142
>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 = 50.2 bits (120), Expect = 3e-09
Identities = 9/36 (25%), Positives = 14/36 (38%)
Query: 12 YAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AF V + K + +E SK+ +WK
Sbjct: 10 NAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKM 45
Score = 34.8 bits (80), Expect = 0.002
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
A+ F R + K +HP + + +KK E W +
Sbjct: 95 AFFLFCSEYRPKIKGEHP--GLSIGDVAKKLGEMWNN 129
>2lhj_A High mobility group protein homolog NHP1; structural genomics,
seattle structural genomics center for infectious
disease, ssgcid; NMR {Babesia bovis}
Length = 97
Score = 47.8 bits (114), Expect = 8e-09
Identities = 10/37 (27%), Positives = 15/37 (40%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
+Y FF + R E ++PE A K W +
Sbjct: 29 SYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNA 65
>3tq6_A Transcription factor A, mitochondrial; transcription,
transcription regulation, mitochondrion; HET: DNA BRU
1PE; 2.45A {Homo sapiens}
Length = 214
Score = 45.9 bits (108), Expect = 2e-07
Identities = 8/37 (21%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
+Y F + K ++P+ E ++ A+RW+
Sbjct: 16 SYLRFSKEQLPIFKAQNPDAK--TTELIRRIAQRWRE 50
Score = 32.4 bits (73), Expect = 0.012
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 6/37 (16%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AY +V +E K P+ E K E WK+
Sbjct: 121 AYNVYVAERFQEAKGDSPQ------EKLKTVKENWKN 151
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group,
transcription, LSP1, mitochon transcription-DNA
complex; HET: DNA; 2.50A {Homo sapiens}
Length = 238
Score = 44.8 bits (105), Expect = 5e-07
Identities = 8/37 (21%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
+Y F + K ++P+ E ++ A+RW+
Sbjct: 48 SYLRFSKEQLPIFKAQNPDAK--TTELIRRIAQRWRE 82
Score = 32.5 bits (73), Expect = 0.013
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 6/37 (16%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AY +V +E K P+ E K E WK+
Sbjct: 153 AYNVYVAERFQEAKGDSPQ------EKLKTVKENWKN 183
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 92
Score = 42.8 bits (101), Expect = 7e-07
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
A A FVQ R + ++P+ + + + + E WK+
Sbjct: 14 ASALFVQDHRPQFLIENPKTS--LEDATLQIEELWKT 48
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial
transcription, activator, DNA- binding, mitochondrion,
phosphoprotein; 1.35A {Homo sapiens}
Length = 67
Score = 40.0 bits (94), Expect = 5e-06
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 6/37 (16%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AY +V +E K P+ E K E WK+
Sbjct: 9 AYNVYVAERFQEAKGDSPQ------EKLKTVKENWKN 39
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding
protein; NMR {Drosophila melanogaster}
Length = 73
Score = 39.6 bits (93), Expect = 8e-06
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
A+ ++ RE K+++P + E +KK E WK
Sbjct: 10 AFMLWLNDTRESIKRENP--GIKVTEIAKKGGEMWKE 44
>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 = 39.2 bits (92), Expect = 1e-05
Identities = 11/37 (29%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AYA ++ RE K+++P + E +K+ E W++
Sbjct: 10 AYALWLNSARESIKRENP--GIKVTEVAKRGGELWRA 44
>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 = 39.6 bits (93), Expect = 1e-05
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AY FF R+ + ++P ++ F + KK E+WK+
Sbjct: 27 AYMFFANENRDIVRSENP--DITFGQVGKKLGEKWKA 61
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box
domain, structural genomics, NPPSFA; NMR {Mus musculus}
Length = 102
Score = 38.9 bits (91), Expect = 2e-05
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AYA F + + K ++P N F E SK A W
Sbjct: 24 AYALFFRDTQAAIKGQNP--NATFGEVSKIVASMWDG 58
>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 = 3e-05
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
A+ F R + K +HP + + +KK E W +
Sbjct: 13 AFFLFCSEYRPKIKGEHP--GLSIGDVAKKLGEMWNN 47
>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 = 37.4 bits (87), Expect = 8e-05
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
Y F+ RE+ + +HP ++ F E +K W
Sbjct: 14 GYVRFLNERREQIRTRHP--DLPFPEITKMLGAEWSK 48
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding
protein; NMR {Homo sapiens} SCOP: a.21.1.1
Length = 99
Score = 35.9 bits (83), Expect = 3e-04
Identities = 9/37 (24%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
Y F R ++ K HPE + + +K ++++K
Sbjct: 17 PYFRFFMEKRAKYAKLHPEMS--NLDLTKILSKKYKE 51
>1v63_A Nucleolar transcription factor 1; DNA binding, structural
genomics, riken structural genomics/proteomics
initiative, RSGI, DNA binding protein; NMR {Mus
musculus} SCOP: a.21.1.1
Length = 101
Score = 33.0 bits (75), Expect = 0.004
Identities = 7/37 (18%), Positives = 10/37 (27%), Gaps = 4/37 (10%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
Y F Q + H E + RW+
Sbjct: 15 GYQKFSQELLSNGELNHLP----LKERMVEIGSRWQR 47
>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 = 32.0 bits (73), Expect = 0.008
Identities = 7/37 (18%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
A F + R + +++ P + +E ++ A W
Sbjct: 27 AMFIFSEEKRRQLQEERP--ELSESELTRLLARMWND 61
>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 = 30.7 bits (68), Expect = 0.045
Identities = 8/50 (16%), Positives = 18/50 (36%), Gaps = 22/50 (44%)
Query: 39 KKCAERWKSSRIVNPFVGRKFAPVFLTFLSRMKDSILFCVNPVLAVGSRI 88
K+ ++ ++S + +A DS P LA+ + +
Sbjct: 19 KQALKKLQASL-------KLYAD----------DSA-----PALAIKATM 46
>1v64_A Nucleolar transcription factor 1; DNA binding, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1
Length = 108
Score = 28.8 bits (64), Expect = 0.18
Identities = 6/37 (16%), Positives = 12/37 (32%), Gaps = 6/37 (16%)
Query: 11 AYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
+Y+ + K E C+++WK
Sbjct: 24 SYSLYCAELMANMKDVPS------TERMVLCSQQWKL 54
>3s6b_A Methionine aminopeptidase; malaria, proteolysis, "PITA bread"
fold, structur genomics, structural genomics
consortium, SGC, hydrolase; 1.95A {Plasmodium
falciparum}
Length = 368
Score = 28.1 bits (63), Expect = 0.46
Identities = 12/60 (20%), Positives = 23/60 (38%), Gaps = 1/60 (1%)
Query: 2 QNKLNMQGIAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKSSRIVNPFVGRKFAP 61
+ + G +F Q +E+H K ++++ F + W + FV KF
Sbjct: 3 HHHHHSSGRENLYF-QGEKEDHLKTIVKKHLSPENFDPTNRKYWVYDDHLKNFVNFKFTG 61
>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 = 27.3 bits (60), Expect = 1.2
Identities = 25/108 (23%), Positives = 41/108 (37%), Gaps = 18/108 (16%)
Query: 14 FFVQVCREEHKKKHPEENVVFA---EFSKKCAERWKS-----SRIVNPFVGRKFAPVFLT 65
F +E+ K PE FA E + AE S +V P +F V
Sbjct: 28 FIASQLQEQFNKILPEPTEGFAADDEPTTP-AELVGKFLGYVSSLVEPSKVGQFDQVLNL 86
Query: 66 FLSRMKDSILFCVNPVLAVGSRILEKFDECLD--------YFGLRALA 105
L+ ++ L N + A+ +++L++ D L Y R +A
Sbjct: 87 CLTEFENCYL-EGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMA 133
Score = 25.8 bits (56), Expect = 3.9
Identities = 21/142 (14%), Positives = 41/142 (28%), Gaps = 54/142 (38%)
Query: 10 IAYAFFVQVCREEHKKKHPEENVVFA-----EFS-------------------------K 39
+ A F + + + + FA E++ +
Sbjct: 1739 MEKAAF-EDLKSKGLIP---ADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQ 1794
Query: 40 KCAERWKSSRI------VNP-FVGRKFAPVFLTFL----SRMKDSILFCVN---P----V 81
R + R +NP V F+ L ++ + ++ VN V
Sbjct: 1795 VAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYV 1854
Query: 82 LAVGS-RILEKFDECLDYFGLR 102
A G R L+ L++ L+
Sbjct: 1855 AA-GDLRALDTVTNVLNFIKLQ 1875
>2j1d_G DAAM1, disheveled-associated activator of morphogenesis; actin
assembly, protein binding; 2.55A {Homo sapiens} PDB:
2z6e_A
Length = 483
Score = 26.0 bits (57), Expect = 2.8
Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 39 KKCAERWKSSRIVNPFVGRKFAPVFLTFLSRMKDSILFCVNPVLAVGSRILEKFDECLDY 98
K + + P G KF V F++ S + V + + + F + + +
Sbjct: 309 KAVETELEYQKSQPPQPGDKFVSVVSQFITVASFSF----SDVEDLLAEAKDLFTKAVKH 364
Query: 99 FG 100
FG
Sbjct: 365 FG 366
>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 = 25.6 bits (55), Expect = 4.5
Identities = 7/33 (21%), Positives = 12/33 (36%)
Query: 20 REEHKKKHPEENVVFAEFSKKCAERWKSSRIVN 52
E +P + AE + W + + VN
Sbjct: 319 PREVLTTNPRRLSIIAESIRDGLATWDNWKHVN 351
>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 = 24.5 bits (54), Expect = 4.9
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 4/37 (10%)
Query: 13 AF--FVQVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AF + + R + ++P +E SK+ +WK
Sbjct: 11 AFIVWSRDQRRKMALENPRMRN--SEISKQLGYQWKM 45
>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 = 24.5 bits (54), Expect = 4.9
Identities = 8/38 (21%), Positives = 14/38 (36%), Gaps = 6/38 (15%)
Query: 13 AFFVQVCREEHKK---KHPEENVVFAEFSKKCAERWKS 47
AF + C+ +HP + +K A+ W
Sbjct: 14 AFLL-FCKRHRSLVRQEHPRLDN--RGATKILADWWAV 48
>3mos_A Transketolase, TK; thiamin diphosphate TPP THDP enzyme catalysis
sugar metaboli transferase; HET: TPP; 1.75A {Homo
sapiens} PDB: 3ooy_A*
Length = 616
Score = 25.2 bits (56), Expect = 5.6
Identities = 7/22 (31%), Positives = 8/22 (36%), Gaps = 5/22 (22%)
Query: 53 PFVGRKFAPVFLTFLSRMKDSI 74
PF F F +R D I
Sbjct: 382 PFCST-----FAAFFTRAFDQI 398
>3obv_E Protein diaphanous homolog 1; autoinhibition, actin, nucleation,
cytoskeleton, structural; HET: SUC; 2.75A {Mus musculus}
PDB: 3o4x_E 2bap_D
Length = 457
Score = 24.8 bits (54), Expect = 7.8
Identities = 9/43 (20%), Positives = 17/43 (39%), Gaps = 4/43 (9%)
Query: 58 KFAPVFLTFLSRMKDSILFCVNPVLAVGSRILEKFDECLDYFG 100
KF +F+ ++ N + + S + + E DYF
Sbjct: 316 KFVEKMTSFVKDAQEQY----NKLRMMHSNMETLYKELGDYFV 354
>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 = 23.7 bits (52), Expect = 7.9
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 4/37 (10%)
Query: 13 AFFV--QVCREEHKKKHPEENVVFAEFSKKCAERWKS 47
AF V + R+ +++P+ + AE SK + WK+
Sbjct: 13 AFMVWAKDERKRLAQQNPDLHN--AELSKMLGKSWKA 47
>1v9d_A Diaphanous protein homolog 1; helix bundle, protein binding; 2.60A
{Mus musculus} SCOP: a.207.1.1
Length = 340
Score = 24.3 bits (53), Expect = 9.8
Identities = 9/43 (20%), Positives = 17/43 (39%), Gaps = 4/43 (9%)
Query: 58 KFAPVFLTFLSRMKDSILFCVNPVLAVGSRILEKFDECLDYFG 100
KF +F+ ++ N + + S + + E DYF
Sbjct: 245 KFVEKMTSFVKDAQEQY----NKLRMMHSNMETLYKELGDYFV 283
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
0.328 0.140 0.431
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: 1,632,471
Number of extensions: 82808
Number of successful extensions: 306
Number of sequences better than 10.0: 1
Number of HSP's gapped: 293
Number of HSP's successfully gapped: 45
Length of query: 105
Length of database: 6,701,793
Length adjustment: 70
Effective length of query: 35
Effective length of database: 4,747,323
Effective search space: 166156305
Effective search space used: 166156305
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (23.5 bits)