RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8832
(144 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 = 67.8 bits (166), Expect = 1e-16
Identities = 30/42 (71%), Positives = 37/42 (88%)
Query: 38 KECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVNRPPVR 79
+ECVNC A +TPLWRRD TGH+LCNACGLY+++NG NRP +R
Sbjct: 5 RECVNCGATATPLWRRDRTGHYLCNACGLYHKMNGQNRPLIR 46
Score = 63.2 bits (154), Expect = 8e-15
Identities = 18/38 (47%), Positives = 22/38 (57%)
Query: 94 SGVSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHNV 131
C NC T T LWRR+ G +CNACGLY K++
Sbjct: 3 EARECVNCGATATPLWRRDRTGHYLCNACGLYHKMNGQ 40
>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 = 64.3 bits (156), Expect = 5e-15
Identities = 31/43 (72%), Positives = 37/43 (86%)
Query: 89 TGNKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHNV 131
+ +R+G SCANC TT TTLWRRN NG+PVCNACGLY+KLHN+
Sbjct: 1 SAARRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNI 43
Score = 57.0 bits (137), Expect = 3e-12
Identities = 24/57 (42%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 38 KECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVNRPPVRTNQKKALQQTGNKRS 94
C NC +T LWRR+ G +CNACGLY +++ +NRP KK QT N++
Sbjct: 8 TSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINRP---LTMKKEGIQTRNRKM 61
>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 = 64.3 bits (156), Expect = 5e-15
Identities = 23/44 (52%), Positives = 29/44 (65%)
Query: 88 QTGNKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHNV 131
+ G + +C NC T T LWRRN G+P+CNACGL+ KLH V
Sbjct: 2 KNGEQNGPTTCTNCFTQTTPLWRRNPEGQPLCNACGLFLKLHGV 45
Score = 56.6 bits (136), Expect = 5e-12
Identities = 25/60 (41%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 38 KECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVNRPPVRTNQKKALQQTGNKRSGVS 97
C NC +TPLWRR+ G LCNACGL+ +++GV RP + K + + N+ S S
Sbjct: 10 TTCTNCFTQTTPLWRRNPEGQPLCNACGLFLKLHGVVRP---LSLKTDVIKKRNRNSANS 66
>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 = 62.1 bits (151), Expect = 2e-14
Identities = 22/35 (62%), Positives = 26/35 (74%)
Query: 97 SCANCSTTCTTLWRRNNNGEPVCNACGLYFKLHNV 131
+C NC T T LWRRN G+P+CNACGL+ KLH V
Sbjct: 3 TCTNCFTQTTPLWRRNPEGQPLCNACGLFLKLHGV 37
Score = 57.9 bits (140), Expect = 8e-13
Identities = 21/39 (53%), Positives = 27/39 (69%)
Query: 38 KECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVNRP 76
C NC +TPLWRR+ G LCNACGL+ +++GV RP
Sbjct: 2 TTCTNCFTQTTPLWRRNPEGQPLCNACGLFLKLHGVVRP 40
>2kae_A GATA-type transcription factor; zinc finger, GATA-type, DNA; NMR
{Caenorhabditis elegans}
Length = 71
Score = 61.4 bits (149), Expect = 8e-14
Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 1/65 (1%)
Query: 34 NMDIKECVNCAANSTPLWRRDGTGHH-LCNACGLYNRINGVNRPPVRTNQKKALQQTGNK 92
N +C NC+ T WR + CNAC +Y R RP N+ + + +
Sbjct: 5 NKKSFQCSNCSVTETIRWRNIRSKEGIQCNACFIYQRKYNKTRPVTAVNKYQKRKLKVQE 64
Query: 93 RSGVS 97
+GV
Sbjct: 65 TNGVD 69
Score = 58.4 bits (141), Expect = 1e-12
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 92 KRSGVSCANCSTTCTTLWRRNNNGEPV-CNACGLYFKLHNV 131
+ C+NCS T T WR + E + CNAC +Y + +N
Sbjct: 5 NKKSFQCSNCSVTETIRWRNIRSKEGIQCNACFIYQRKYNK 45
>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 = 42.7 bits (100), Expect = 8e-06
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 73 VNRPPVRTNQKKALQQTGNKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGL 124
+ R + K+A ++ N ++C C + R + G+ VC CGL
Sbjct: 2 MTRESID---KRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGL 50
Score = 33.1 bits (75), Expect = 0.019
Identities = 10/34 (29%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 34 NMDIK-ECVNCAANSTPLWRRDGTGHHLCNACGL 66
N++I C C + R G +C CGL
Sbjct: 17 NLNIVLTCPECKVYPPKIVERFSEGDVVCALCGL 50
>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 = 34.9 bits (79), Expect = 0.005
Identities = 12/42 (28%), Positives = 20/42 (47%)
Query: 83 KKALQQTGNKRSGVSCANCSTTCTTLWRRNNNGEPVCNACGL 124
K+A ++ N ++C C + R + G+ VC CGL
Sbjct: 9 KRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGL 50
Score = 26.8 bits (58), Expect = 3.2
Identities = 8/31 (25%), Positives = 11/31 (35%)
Query: 36 DIKECVNCAANSTPLWRRDGTGHHLCNACGL 66
+ C C + R G +C CGL
Sbjct: 20 IVLTCPECKVYPPKIVERFSEGDVVCALCGL 50
>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 = 33.4 bits (76), Expect = 0.015
Identities = 21/112 (18%), Positives = 37/112 (33%), Gaps = 34/112 (30%)
Query: 11 HHVTDGPFQAYLTVIDWPQNMMLNMDIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRI 70
HH + + +++ + P ++ + C+NC + + RR H C+ACG
Sbjct: 349 HHSVEIRERLGVSLGERPPTLVPVTHVMMCMNCGCDFSLTLRR-----HHCHACGK---- 399
Query: 71 NGVNRPPVRTNQKKALQQTGNKRSGVSCANCSTTCTTLWRRNNNGEPVCNAC 122
+ C NCS L + VC+ C
Sbjct: 400 -------------------------IVCRNCSRNKYPLKYLKDRMAKVCDGC 426
>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 = 28.0 bits (62), Expect = 0.73
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 96 VSCANCSTTCTTLWRRNNNGEPVCNACG 123
V C+ C + T L + + VC ACG
Sbjct: 104 VECSTCKSLDTILKKEKKSWYIVCLACG 131
Score = 25.7 bits (56), Expect = 4.6
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 40 CVNCAANSTPLWRRDGTGHHLCNACG 65
C C + T L + + + +C ACG
Sbjct: 106 CSTCKSLDTILKKEKKSWYIVCLACG 131
>2d74_B Translation initiation factor 2 beta subunit; protein complex;
2.80A {Pyrococcus furiosus} PDB: 2dcu_B*
Length = 148
Score = 26.1 bits (57), Expect = 3.5
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 96 VSCANCSTTCTTLWRRNNNGEPVCNACG 123
V C C + T + +R+ C ACG
Sbjct: 105 VICPVCGSPDTKIIKRDRFHFLKCEACG 132
Score = 26.1 bits (57), Expect = 3.6
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 40 CVNCAANSTPLWRRDGTGHHLCNACG 65
C C + T + +RD C ACG
Sbjct: 107 CPVCGSPDTKIIKRDRFHFLKCEACG 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 = 4.0
Identities = 9/28 (32%), Positives = 11/28 (39%)
Query: 96 VSCANCSTTCTTLWRRNNNGEPVCNACG 123
V C C+ T + R C ACG
Sbjct: 103 VICHECNRPDTRIIREGRISLLKCEACG 130
Score = 25.7 bits (56), Expect = 4.1
Identities = 8/26 (30%), Positives = 9/26 (34%)
Query: 40 CVNCAANSTPLWRRDGTGHHLCNACG 65
C C T + R C ACG
Sbjct: 105 CHECNRPDTRIIREGRISLLKCEACG 130
>2zjr_Z 50S ribosomal protein L32; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: g.41.8.5 PDB: 1j5a_M* 1jzy_M*
1jzz_M* 1k01_M* 1nkw_Z 1ond_Z* 1sm1_Z* 1yl3_5 2b66_5
2b9n_5 2b9p_5 2zjp_Y* 2zjq_Z 1jzx_M 3cf5_Y* 3dll_Y*
3pio_Z* 3pip_Z* 1nwy_Z* 1nwx_Z* ...
Length = 60
Score = 24.5 bits (54), Expect = 4.7
Identities = 9/30 (30%), Positives = 11/30 (36%), Gaps = 8/30 (26%)
Query: 39 ECVNCAANSTPLWRRDGTGHHLCNACGLYN 68
EC C HH+C CG Y+
Sbjct: 32 ECPQCHGKKLS--------HHICPNCGYYD 53
>3v2d_5 50S ribosomal protein L32; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus}
PDB: 2hgq_4 2hgj_4 2hgu_4 2j03_5 2jl6_5 2jl8_5 2v47_5
2v49_5 2wdi_5 2wdj_5 2wdl_5 2wdn_5 2wh2_5 2wh4_5 2wrj_5
2wrl_5 2wro_5 2wrr_5 2x9s_5 2x9u_5 ...
Length = 60
Score = 24.1 bits (53), Expect = 5.9
Identities = 9/30 (30%), Positives = 10/30 (33%), Gaps = 8/30 (26%)
Query: 39 ECVNCAANSTPLWRRDGTGHHLCNACGLYN 68
C C A P H +C CG Y
Sbjct: 32 PCPECKAMKPP--------HTVCPECGYYA 53
>3eh1_A Protein transport protein SEC24B; copii coat protein, vesicle
transport, transport signal sequence, cytoplasm,
endoplasmic reticulum; 1.80A {Homo sapiens} PDB: 2nut_B
2nup_B 3egd_B 3egx_B
Length = 751
Score = 25.7 bits (55), Expect = 7.0
Identities = 9/69 (13%), Positives = 17/69 (24%)
Query: 28 PQNMMLNMDIKECVNCAANSTPLWRRDGTGHHLCNACGLYNRINGVNRPPVRTNQKKALQ 87
++ + I C +C P CN C N + T
Sbjct: 76 QLPVITSNTIVRCRSCRTYINPFVSFIDQRRWKCNLCYRVNDVPEEFMYNPLTRSYGEPH 135
Query: 88 QTGNKRSGV 96
+ ++
Sbjct: 136 KRPEVQNST 144
>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 = 7.8
Identities = 7/29 (24%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 60 LCNACGLYNRINGVNRPPVRTNQKKALQQ 88
L N ++ + N V+R ++AL +
Sbjct: 119 LYNDNQVFAKYN-VSRLQPYLKLRQALLE 146
>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 = 25.2 bits (55), Expect = 8.8
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 89 TGNKRSGVSCANCSTTCTT-LWRRNNNG 115
+ 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 = 25.2 bits (55), Expect = 9.6
Identities = 7/28 (25%), Positives = 9/28 (32%), Gaps = 1/28 (3%)
Query: 89 TGNKRSGVSCANCSTTCTT-LWRRNNNG 115
N GV C L+ + N G
Sbjct: 84 ALNSFPGVVCGLAVDPTDAYLYSQINGG 111
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
0.325 0.137 0.466
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: 2,228,783
Number of extensions: 114076
Number of successful extensions: 426
Number of sequences better than 10.0: 1
Number of HSP's gapped: 423
Number of HSP's successfully gapped: 56
Length of query: 144
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 59
Effective length of database: 4,328,508
Effective search space: 255381972
Effective search space used: 255381972
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.3 bits)