RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4528
(87 letters)
>3muj_A Transcription factor COE3; immunoglobulin like fold,
helix-loop-helix, structural genom consortium, SGC, DNA
binding protein; 1.92A {Homo sapiens} PDB: 3mqi_A
Length = 138
Score = 75.4 bits (185), Expect = 2e-19
Identities = 41/49 (83%), Positives = 46/49 (93%)
Query: 1 MSLNEPTIDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYSMP 49
+LNEPTIDYGFQRLQK+IPRHPGDPE+LPKE++LKRAADL EALY MP
Sbjct: 89 TALNEPTIDYGFQRLQKVIPRHPGDPERLPKEVLLKRAADLVEALYGMP 137
>3mlp_A Transcription factor COE1; transcription factor, pseudo-IG-fold,
TIG-domain, IPT-domain loop-helix; HET: DNA CIT; 2.80A
{Mus musculus} PDB: 3n50_A
Length = 402
Score = 68.0 bits (165), Expect = 2e-15
Identities = 50/91 (54%), Positives = 57/91 (62%), Gaps = 14/91 (15%)
Query: 1 MSLNEPTIDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYSMPRNNQ------- 53
+LNEPTIDYGFQRLQK+IPRHPGDPE+LPKE+ILKRAADL EALY MP NNQ
Sbjct: 315 TALNEPTIDYGFQRLQKVIPRHPGDPERLPKEVILKRAADLVEALYGMPHNNQEIILKRA 374
Query: 54 ----LPLPAPPRSPHHFNSYTGQLNVTVQEN 80
L + PR+ N L +
Sbjct: 375 ADIAEALYSVPRNH---NQLAAVLEHHHHHH 402
>1hlo_A Protein (transcription factor MAX); transcriptional regulation,
DNA binding, complex (transcription factor MAX/DNA),
transcription/DNA complex; HET: DNA; 2.80A {Homo
sapiens} SCOP: a.38.1.1
Length = 80
Score = 30.0 bits (68), Expect = 0.028
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 8 IDYGFQRLQKLIPRHPGDPEKLPKEIILKRAAD 40
I F L+ +P G EK + IL +A +
Sbjct: 27 IKDSFHSLRDSVPSLQG--EKASRAQILDKATE 57
>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic
helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB:
2ql2_A*
Length = 76
Score = 29.9 bits (67), Expect = 0.030
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 8 IDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYSMPRNNQLPLPAPPRSPHH 65
I+ F+ L ++ H + K +IL++A + L R L P HH
Sbjct: 20 INEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNLN-PLNHHHHHH 76
>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ,
heterodimer, transcription/DNA complex; 1.80A {Homo
sapiens} SCOP: a.38.1.1
Length = 88
Score = 30.0 bits (68), Expect = 0.030
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 11 GFQRLQKLIPRHPGDPEKLPKEIILKRAAD 40
F L+ IP + EK PK +ILK+A
Sbjct: 24 SFFALRDQIP-ELENNEKAPKVVILKKATA 52
>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 = 30.8 bits (69), Expect = 0.039
Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 12/59 (20%)
Query: 2 SLNEPTIDYGFQRLQKLIPRHPGDPEKLPKEII-----LKRAAD------LAEALYSMP 49
L I + + L +LI R D EK+ + + L+ ++ L S P
Sbjct: 182 VLVGDLIKFSAETLSELI-RTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCP 239
>2ql2_B Neurod1, neurogenic differentiation factor 1;
basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}
Length = 60
Score = 27.6 bits (62), Expect = 0.16
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 6/47 (12%)
Query: 2 SLNEPTIDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYSM 48
LN L+K++P + +KL K L+ A + AL +
Sbjct: 16 GLNA-----ALDNLRKVVPCYSKT-QKLSKIETLRLAKNYIWALSEI 56
>2fiq_A Putative tagatose 6-phosphate kinase 1; structural genomics, PSI,
protein structure initiative, NEW research center for
structural genomics; 2.25A {Escherichia coli} SCOP:
c.1.10.7
Length = 420
Score = 27.7 bits (61), Expect = 0.47
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 23 PGDPEKLPKEIILKRAADLAEALYSMPRNNQLPLP 57
GDP L E + +RAA L A S+ + Q
Sbjct: 130 AGDPIPLAPETVAERAAVLCFAAESVATDCQREQL 164
>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ,
transcription/DNA complex; 2.00A {Homo sapiens} SCOP:
a.38.1.1
Length = 80
Score = 25.9 bits (57), Expect = 0.83
Identities = 7/30 (23%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 11 GFQRLQKLIPRHPGDPEKLPKEIILKRAAD 40
++L+ L+P P D + +L +A
Sbjct: 19 SLEKLKGLVPLGP-DSSRHTTLSLLTKAKL 47
>2hpi_A DNA polymerase III alpha subunit; POL-beta-like
nucleotidyltransferase fold, transferase; HET: DNA;
3.00A {Thermus aquaticus} PDB: 2hpm_A* 3e0d_A*
Length = 1220
Score = 26.5 bits (59), Expect = 1.3
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 3/48 (6%)
Query: 8 IDYGF-QRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYSMPRNNQL 54
I + + L KLIP G P+ L + ++ +L + R Q+
Sbjct: 513 IPHKKAEELAKLIPVQFGKPKPLQE--AIQVVPELRAEMEKDERIRQV 558
>3sho_A Transcriptional regulator, RPIR family; structural genomics,
PSI-biology, midwest center for structu genomics, MCSG;
1.80A {Sphaerobacter thermophilus}
Length = 187
Score = 26.0 bits (58), Expect = 1.5
Identities = 7/20 (35%), Positives = 8/20 (40%)
Query: 56 LPAPPRSPHHFNSYTGQLNV 75
L A R H S G + V
Sbjct: 136 LVAATRGVGHSLSPVGLIAV 155
>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A);
basic-helix-loop- helix-leucine zipper, transcription
factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1
PDB: 1ukl_C
Length = 82
Score = 25.4 bits (56), Expect = 1.5
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 8 IDYGFQRLQKLIPRHPGDPEKLPKEIILKRAAD 40
I+ L+ L+ G KL K +L++A D
Sbjct: 21 INDKIIELKDLVV---GTEAKLNKSAVLRKAID 50
>3txv_A Probable tagatose 6-phosphate kinase; structural genomics,
PSI-biology, NEW YORK structural genomi research
consortium, nysgrc; 2.80A {Sinorhizobium meliloti}
Length = 450
Score = 26.2 bits (57), Expect = 1.6
Identities = 11/35 (31%), Positives = 12/35 (34%)
Query: 23 PGDPEKLPKEIILKRAADLAEALYSMPRNNQLPLP 57
G+P LP RAA LA LP
Sbjct: 137 AGEPTALPDATTAARAARLAAVAEDAVGGRGGVLP 171
>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP
complex, calcium stimulation, RECA, DMC1; HET: DNA ANP;
1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11
PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A*
3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A*
3etl_A* 4dc9_A* 2gdj_A*
Length = 322
Score = 25.7 bits (56), Expect = 2.0
Identities = 4/33 (12%), Positives = 13/33 (39%)
Query: 13 QRLQKLIPRHPGDPEKLPKEIILKRAADLAEAL 45
+R+ ++ D + + + RA + +
Sbjct: 157 ERIMQMAEHAGIDGQTVLDNTFVARAYNSDMQM 189
>2uxw_A VERY-long-chain specific acyl-COA dehydrogenase; fatty acid
metabolism, transit peptide, disease mutation, LI
metabolism, coenzyme A dehydrogenase; HET: FAD TH3;
1.45A {Homo sapiens} PDB: 3b96_A*
Length = 607
Score = 25.4 bits (56), Expect = 2.6
Identities = 10/42 (23%), Positives = 18/42 (42%), Gaps = 9/42 (21%)
Query: 7 TIDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYSM 48
++ + +K I + +L+R AD A LY+M
Sbjct: 498 VVEAKLIKHKKGIVNE---------QFLLQRLADGAIDLYAM 530
>2qxf_A Exodeoxyribonuclease I; alpha-beta domain, DNAQ superfamily,
SH3-like domain, produc structure, DNA damage, DNA
repair, exonuclease; HET: TMP; 1.50A {Escherichia coli}
SCOP: c.55.3.5 PDB: 1fxx_A* 3c94_A 3c95_A 3hl8_A*
3hp9_A*
Length = 482
Score = 25.4 bits (54), Expect = 3.3
Identities = 9/43 (20%), Positives = 17/43 (39%), Gaps = 3/43 (6%)
Query: 3 LNEPTIDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEAL 45
+ LQ L+ ++ D EK+ +LK A+ +
Sbjct: 435 FTPEFLQGYADELQMLVQQYADDKEKV---ALLKALWQYADEI 474
>1dgf_A Catalase; heme, NADPH, hydrogen peroxide, oxidoreductase; HET: HEM
NDP; 1.50A {Homo sapiens} SCOP: e.5.1.1 PDB: 1dgg_A*
1f4j_A* 1qqw_A* 1dgh_A* 1dgb_A* 3rgp_A* 3re8_A* 3rgs_A*
3nwl_A* 4blc_A* 1th2_A* 1th3_A* 1th4_A* 1tgu_A* 7cat_A*
8cat_A*
Length = 497
Score = 24.8 bits (55), Expect = 4.0
Identities = 5/31 (16%), Positives = 11/31 (35%)
Query: 52 NQLPLPAPPRSPHHFNSYTGQLNVTVQENGN 82
+P+ P R+ G + + + G
Sbjct: 367 LHIPVNCPYRARVANYQRDGPMCMQDNQGGA 397
>2k0m_A Uncharacterized protein; structural genomics, unknown function,
PSI-2, protein structure initiative; NMR
{Rhodospirillum rubrum atcc 11170}
Length = 104
Score = 24.1 bits (52), Expect = 5.1
Identities = 5/33 (15%), Positives = 10/33 (30%)
Query: 1 MSLNEPTIDYGFQRLQKLIPRHPGDPEKLPKEI 33
+ L + + RHP K+ +
Sbjct: 31 YRPGDIVSTVDGAFLVEALKRHPDATSKIGPGV 63
>2zy9_A Mg2+ transporter MGTE; membrane protien, metal transport; 2.94A
{Thermus thermophilus} PDB: 2yvx_A
Length = 473
Score = 24.5 bits (54), Expect = 5.8
Identities = 7/44 (15%), Positives = 15/44 (34%), Gaps = 2/44 (4%)
Query: 13 QRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYSMPRNNQLPL 56
LQ+ + GD L + + DL + ++ +
Sbjct: 30 VSLQEAL--QEGDTRALREVLEEIHPQDLLALWDELKGEHRYVV 71
>2iyf_A OLED, oleandomycin glycosyltransferase; antibiotic resistance,
glycosylation, enzyme, macrolide, carbohydrate; HET: ERY
UDP; 1.7A {Streptomyces antibioticus}
Length = 430
Score = 24.4 bits (53), Expect = 6.5
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 10/61 (16%)
Query: 3 LNEPTIDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYSMPRNNQLPLPAPPRS 62
+++P + +R+Q + + G +RAADL EA Q P+ P
Sbjct: 365 VDDPEVARRLRRIQAEMAQEGG----------TRRAADLIEAELPARHERQEPVGDRPNV 414
Query: 63 P 63
Sbjct: 415 G 415
>1fit_A FragIle histidine protein; FHIT, fragIle histidine triad protein,
putative human tumor suppressor, advanced photon source,
APS; HET: FRU; 1.85A {Homo sapiens} SCOP: d.13.1.1 PDB:
1fhi_A* 2fit_A* 3fit_A* 4fit_A 5fit_A* 6fit_A* 2fhi_A*
Length = 147
Score = 23.8 bits (52), Expect = 7.4
Identities = 7/36 (19%), Positives = 14/36 (38%), Gaps = 1/36 (2%)
Query: 18 LIPRHPGDPEKLPKEIILKRAADLAEALYSMPRNNQ 53
++PR GD + I + E + R+ +
Sbjct: 99 VLPRKAGDFHRNDS-IYEELQKHDKEDFPASWRSEE 133
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 0.135 0.417
Gapped
Lambda K H
0.267 0.0649 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,461,048
Number of extensions: 74955
Number of successful extensions: 171
Number of sequences better than 10.0: 1
Number of HSP's gapped: 169
Number of HSP's successfully gapped: 28
Length of query: 87
Length of database: 6,701,793
Length adjustment: 55
Effective length of query: 32
Effective length of database: 5,166,138
Effective search space: 165316416
Effective search space used: 165316416
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: 51 (23.6 bits)