RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8831
(88 letters)
>1gnf_A Transcription factor GATA-1; zinc finger, transcription
regulation; NMR {Mus musculus} SCOP: g.39.1.1 PDB:
1y0j_A 2l6y_A 2l6z_A
Length = 46
Score = 55.9 bits (135), Expect = 9e-13
Identities = 16/31 (51%), Positives = 18/31 (58%)
Query: 16 SGVSCANCSTTCTTLWRRNNNGEPVCNACGL 46
C NC T T LWRR+ G +CNACGL
Sbjct: 3 EARECVNCGATATPLWRRDRTGHYLCNACGL 33
>4gat_A Nitrogen regulatory protein AREA; DNA binding protein,
transcription factor, zinc binding domain, complex
(transcription regulation/DNA); HET: DNA; NMR
{Emericella nidulans} SCOP: g.39.1.1 PDB: 5gat_A*
6gat_A* 7gat_A*
Length = 66
Score = 56.6 bits (136), Expect = 1e-12
Identities = 20/47 (42%), Positives = 27/47 (57%)
Query: 10 QTGNKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDINAP 56
+ G + +C NC T T LWRRN G+P+CNACGL + + P
Sbjct: 2 KNGEQNGPTTCTNCFTQTTPLWRRNPEGQPLCNACGLFLKLHGVVRP 48
>3dfx_A Trans-acting T-cell-specific transcription factor GATA-3;
activator, DNA-binding, metal-binding, nucleus; HET:
DNA; 2.70A {Mus musculus} PDB: 3dfv_D* 2gat_A* 3gat_A*
1gat_A* 1gau_A*
Length = 63
Score = 55.8 bits (134), Expect = 2e-12
Identities = 29/46 (63%), Positives = 34/46 (73%)
Query: 11 TGNKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDINAP 56
+ +R+G SCANC TT TTLWRRN NG+PVCNACGL +IN P
Sbjct: 1 SAARRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINRP 46
>2vut_I AREA, nitrogen regulatory protein AREA; transcription regulation,
protein-protein interactions, metal-binding, nitrate
assimilation; HET: NAD; 2.3A {Emericella nidulans}
SCOP: g.39.1.1 PDB: 2vus_I* 2vuu_I*
Length = 43
Score = 53.2 bits (128), Expect = 1e-11
Identities = 18/28 (64%), Positives = 21/28 (75%)
Query: 19 SCANCSTTCTTLWRRNNNGEPVCNACGL 46
+C NC T T LWRRN G+P+CNACGL
Sbjct: 3 TCTNCFTQTTPLWRRNPEGQPLCNACGL 30
>2kae_A GATA-type transcription factor; zinc finger, GATA-type, DNA; NMR
{Caenorhabditis elegans}
Length = 71
Score = 49.5 bits (118), Expect = 5e-10
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 14 KRSGVSCANCSTTCTTLWRRNNNGEPV-CNACGL 46
+ C+NCS T T WR + E + CNAC +
Sbjct: 5 NKKSFQCSNCSVTETIRWRNIRSKEGIQCNACFI 38
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 44.3 bits (104), Expect = 4e-07
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 3/51 (5%)
Query: 9 EQTGNKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIM--NTVDINAPE 57
+ N ++C C + R + G+ VC CGL++ VD E
Sbjct: 13 RRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTR-SE 62
>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
DNA-binding, DNA- directed RNA polymerase, isopeptide
bond, magnesium; 3.80A {Saccharomyces cerevisiae}
Length = 345
Score = 34.5 bits (78), Expect = 0.002
Identities = 10/42 (23%), Positives = 19/42 (45%)
Query: 8 REQTGNKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMN 49
+ N ++C C + R + G+ VC CGL+++
Sbjct: 12 GRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLS 53
>3cw2_K Translation initiation factor 2 subunit beta; AIF2, intact AIF2,
initiation factor 2 alpha subunit, initiation factor 2
beta subunit; 2.80A {Sulfolobus solfataricus} PDB:
2nxu_A 2qmu_C* 3v11_C*
Length = 139
Score = 28.4 bits (63), Expect = 0.20
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 18 VSCANCSTTCTTLWRRNNNGEPVCNACG 45
V C+ C + T L + + VC ACG
Sbjct: 104 VECSTCKSLDTILKKEKKSWYIVCLACG 131
>3mpx_A FYVE, rhogef and PH domain-containing protein 5; structural
genomics consortium, DH domain, SGC, L binding protein;
2.80A {Homo sapiens}
Length = 434
Score = 27.7 bits (61), Expect = 0.45
Identities = 8/27 (29%), Positives = 11/27 (40%)
Query: 18 VSCANCSTTCTTLWRRNNNGEPVCNAC 44
+ C NCS L + VC+ C
Sbjct: 400 IVCRNCSRNKYPLKYLKDRMAKVCDGC 426
>2d74_B Translation initiation factor 2 beta subunit; protein complex;
2.80A {Pyrococcus furiosus} PDB: 2dcu_B*
Length = 148
Score = 26.5 bits (58), Expect = 0.88
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 18 VSCANCSTTCTTLWRRNNNGEPVCNACG 45
V C C + T + +R+ C ACG
Sbjct: 105 VICPVCGSPDTKIIKRDRFHFLKCEACG 132
>1nee_A EIF-2-beta, probable translation initiation factor 2 beta subunit;
two domain protein, mixed alpha-beta structure; NMR
{Methanothermobacterthermautotrophicus} SCOP: d.241.1.1
g.59.1.1
Length = 138
Score = 26.1 bits (57), Expect = 1.4
Identities = 9/28 (32%), Positives = 11/28 (39%)
Query: 18 VSCANCSTTCTTLWRRNNNGEPVCNACG 45
V C C+ T + R C ACG
Sbjct: 103 VICHECNRPDTRIIREGRISLLKCEACG 130
>1m2k_A Silent information regulator 2; protein-ligand complex, gene
regulation; HET: APR; 1.47A {Archaeoglobus fulgidus}
SCOP: c.31.1.5 PDB: 1m2g_A* 1m2h_A* 1m2j_A* 1m2n_A*
1ici_A*
Length = 249
Score = 26.0 bits (58), Expect = 1.5
Identities = 12/68 (17%), Positives = 23/68 (33%), Gaps = 8/68 (11%)
Query: 18 VSCANCSTTCTTLWRRNNNGEPVCNACGLIMNTVDI-----NAPEKIMPPIESMISRNGD 72
V C +C+ + P C+ CG ++ + P ++ + D
Sbjct: 122 VRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRP-GVVWAGEMLPPDVLDRAMREV-ERAD 179
Query: 73 ALSVI-TS 79
+ V TS
Sbjct: 180 VIIVAGTS 187
>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics,
structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB:
2yqm_A
Length = 82
Score = 24.7 bits (54), Expect = 3.1
Identities = 7/28 (25%), Positives = 11/28 (39%), Gaps = 5/28 (17%)
Query: 20 CANCSTTCTTLWRRNNNGEPVCNACGLI 47
C C + R+++ C CG I
Sbjct: 22 CRQCEKEFSISRRKHH-----CRNCGHI 44
>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation;
NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A
Length = 58
Score = 24.1 bits (52), Expect = 3.6
Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 2/41 (4%)
Query: 9 EQTGNKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLIMN 49
+ V+C N L G+ +C CGL++
Sbjct: 3 TSRLDALPRVTCPNHP--DAILVEDYRAGDMICPECGLVVG 41
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation
factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1
Length = 50
Score = 23.6 bits (51), Expect = 3.7
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 2/30 (6%)
Query: 20 CANCSTTCTTLWRRNNNGEPVCNACGLIMN 49
C C + L GE VC CG ++
Sbjct: 8 CPACESA--ELIYDPERGEIVCAKCGYVIE 35
>3ono_A Ribose/galactose isomerase; structural genomics, PSI-2, protein
structure initiative, MI center for structural genomics,
MCSG; HET: MSE; 1.75A {Vibrio parahaemolyticus}
Length = 214
Score = 24.9 bits (54), Expect = 4.2
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 11 TGNKRSGVSCANCSTTCTT-LWRRNNNG 37
+ N GV C C L+ + NNG
Sbjct: 83 SCNLHPGVVCGYCLEPSDAFLFNQINNG 110
>2ppw_A Conserved domain protein; the putative RPIB, PSI-2, protein
initiative, MCSG, structural genomics, midwest center
for S genomics; HET: MSE; 2.01A {Streptococcus
pneumoniae}
Length = 216
Score = 24.8 bits (54), Expect = 4.5
Identities = 7/28 (25%), Positives = 9/28 (32%), Gaps = 1/28 (3%)
Query: 11 TGNKRSGVSCANCSTTCTT-LWRRNNNG 37
N GV C L+ + N G
Sbjct: 84 ALNSFPGVVCGLAVDPTDAYLYSQINGG 111
>1vf5_C Cytochrome F; photosynthesis, membrane protein complex, electron
transfer complex; HET: HEM TDS PL9 OPC CLA BCR; 3.00A
{Mastigocladus laminosus} SCOP: b.2.6.1 b.84.2.2
f.23.23.1 PDB: 2d2c_C* 2e74_C* 2e75_C* 2e76_C* 2zt9_C*
Length = 289
Score = 24.6 bits (53), Expect = 4.6
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 33 RNNNGEPVCNACGLIMNTVDINAPEKIMP 61
R G VC C L ++ P+ ++P
Sbjct: 14 REPTGRIVCANCHLAAKPAEVEVPQSVLP 42
>2d8y_A Eplin protein; LIM domain, epithelial protein LOST in neoplasm,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
g.39.1.3 g.39.1.3
Length = 91
Score = 24.0 bits (52), Expect = 5.3
Identities = 4/25 (16%), Positives = 9/25 (36%)
Query: 20 CANCSTTCTTLWRRNNNGEPVCNAC 44
C+ C+ + + +G C
Sbjct: 45 CSYCNNKLSLGTYASLHGRIYCKPH 69
>1g63_A Epidermin modifying enzyme EPID; alpha, beta protein, rossmann like
fold, oxidoreductase; HET: FMN; 2.50A {Staphylococcus
epidermidis} SCOP: c.34.1.1 PDB: 1g5q_A*
Length = 181
Score = 24.5 bits (54), Expect = 5.6
Identities = 5/38 (13%), Positives = 14/38 (36%)
Query: 35 NNGEPVCNACGLIMNTVDINAPEKIMPPIESMISRNGD 72
+ + + G N + + E ++ + + R D
Sbjct: 144 DMNKSFEISSGRYKNNITMPNIENVLNFVLNNEKRPLD 181
>1q90_A Apocytochrome F; membrane protein complex, photosynthesis,
electron transfer, oxydoreductase, chlorophyll; HET:
HEM CL1 BCR TDS SQD LFA LMG; 3.10A {Chlamydomonas
reinhardtii} SCOP: b.2.6.1 b.84.2.2 f.23.23.1
Length = 292
Score = 24.2 bits (52), Expect = 6.9
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 33 RNNNGEPVCNACGLIMNTVDINAPEKIMP 61
R NG VC C L V+I P+ ++P
Sbjct: 13 REANGRIVCANCHLAQKAVEIEVPQAVLP 41
>3c5y_A Ribose/galactose isomerase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2; HET: MSE; 1.81A {Novosphingobium aromaticivorans}
Length = 231
Score = 24.0 bits (52), Expect = 8.0
Identities = 7/26 (26%), Positives = 10/26 (38%), Gaps = 1/26 (3%)
Query: 13 NKRSGVSCANCSTTCTT-LWRRNNNG 37
N GV C L+ + N+G
Sbjct: 102 NAMPGVFCGLVIDPTDAFLFGQINDG 127
>1l8r_A Dachshund; winged-helix, transcription; 1.65A {Homo sapiens}
SCOP: a.6.1.4
Length = 101
Score = 23.5 bits (50), Expect = 8.5
Identities = 9/34 (26%), Positives = 14/34 (41%)
Query: 14 KRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLI 47
KR ++ C+ + R +P N C LI
Sbjct: 53 KRLEITPVVCNVEQVRILRGLGAIQPGVNRCKLI 86
>1ci3_M Protein (cytochrome F); electron transfer protein, complex
subunit, electron transpo; HET: HEM; 1.90A {Phormidium
laminosum} SCOP: b.2.6.1 b.84.2.2 PDB: 1tu2_B*
Length = 249
Score = 23.8 bits (51), Expect = 8.9
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 33 RNNNGEPVCNACGLIMNTVDINAPEKIMP 61
R G VC C L +I P+ ++P
Sbjct: 13 REATGRIVCANCHLAAKPAEIEVPQAVLP 41
>3ec1_A YQEH GTPase; atnos1, atnoa1, trap, PVHL, hydrolase, signaling
protein; HET: GDP; 2.36A {Geobacillus
stearothermophilus}
Length = 369
Score = 23.8 bits (51), Expect = 9.2
Identities = 3/21 (14%), Positives = 6/21 (28%)
Query: 36 NGEPVCNACGLIMNTVDINAP 56
+ C CG + +
Sbjct: 2 EPQLRCIGCGAAIQFENPKNA 22
>1sbx_A SKI oncogene, C-SKI; winged helix, forkhead, oncoprotein; 1.65A
{Homo sapiens} SCOP: a.6.1.4
Length = 106
Score = 23.5 bits (50), Expect = 9.8
Identities = 6/34 (17%), Positives = 12/34 (35%)
Query: 14 KRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLI 47
+ C+ C+ + + +CGLI
Sbjct: 58 DELHIYCSRCTADQLEILKVMGILPFSAPSCGLI 91
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
0.317 0.131 0.407
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: 1,311,571
Number of extensions: 62059
Number of successful extensions: 244
Number of sequences better than 10.0: 1
Number of HSP's gapped: 242
Number of HSP's successfully gapped: 43
Length of query: 88
Length of database: 6,701,793
Length adjustment: 56
Effective length of query: 32
Effective length of database: 5,138,217
Effective search space: 164422944
Effective search space used: 164422944
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: 41 (21.7 bits)
S2: 51 (23.9 bits)