RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15323
(139 letters)
>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 = 79.3 bits (195), Expect = 5e-21
Identities = 43/72 (59%), Positives = 49/72 (68%), Gaps = 10/72 (13%)
Query: 56 TATRRLGLCCTNCGTRMTTLWRRNNDGEPVCNACGLYYKLHNVNRPLAMRHLAMRPLAMR 115
+A RR G C NC T TTLWRRN +G+PVCNACGLYYKLHN+N RPL M+
Sbjct: 1 SAARRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNIN----------RPLTMK 50
Query: 116 KDGIQTRKRKPK 127
K+GIQTR RK
Sbjct: 51 KEGIQTRNRKMS 62
Score = 58.1 bits (140), Expect = 1e-12
Identities = 23/55 (41%), Positives = 32/55 (58%)
Query: 6 GEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNRPLVKPSKRLTATRR 60
G C NC +T LWRR+ G +CNACGLY+K++ +NRPL + + R
Sbjct: 5 RAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINRPLTMKKEGIQTRNR 59
>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 = 76.3 bits (187), Expect = 9e-20
Identities = 30/72 (41%), Positives = 40/72 (55%), Gaps = 10/72 (13%)
Query: 57 ATRRLGLCCTNCGTRMTTLWRRNNDGEPVCNACGLYYKLHNVNRPLAMRHLAMRPLAMRK 116
+ CTNC T+ T LWRRN +G+P+CNACGL+ KLH V RPL+++
Sbjct: 4 GEQNGPTTCTNCFTQTTPLWRRNPEGQPLCNACGLFLKLHGVV----------RPLSLKT 53
Query: 117 DGIQTRKRKPKK 128
D I+ R R
Sbjct: 54 DVIKKRNRNSAN 65
Score = 56.2 bits (135), Expect = 5e-12
Identities = 23/53 (43%), Positives = 31/53 (58%)
Query: 8 GRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNRPLVKPSKRLTATRR 60
C NC +TPLWRR+ G LCNACGL+ K++G+ RPL + + R
Sbjct: 9 PTTCTNCFTQTTPLWRRNPEGQPLCNACGLFLKLHGVVRPLSLKTDVIKKRNR 61
>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 = 75.1 bits (185), Expect = 1e-19
Identities = 37/45 (82%), Positives = 40/45 (88%)
Query: 6 GEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNRPLVK 50
E RECVNCGA +TPLWRRD TGHYLCNACGLYHKMNG NRPL++
Sbjct: 2 SEARECVNCGATATPLWRRDRTGHYLCNACGLYHKMNGQNRPLIR 46
Score = 68.2 bits (167), Expect = 9e-17
Identities = 22/41 (53%), Positives = 27/41 (65%)
Query: 62 GLCCTNCGTRMTTLWRRNNDGEPVCNACGLYYKLHNVNRPL 102
C NCG T LWRR+ G +CNACGLY+K++ NRPL
Sbjct: 4 ARECVNCGATATPLWRRDRTGHYLCNACGLYHKMNGQNRPL 44
>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 = 71.0 bits (174), Expect = 5e-18
Identities = 26/40 (65%), Positives = 33/40 (82%)
Query: 65 CTNCGTRMTTLWRRNNDGEPVCNACGLYYKLHNVNRPLAM 104
CTNC T+ T LWRRN +G+P+CNACGL+ KLH V RPL++
Sbjct: 4 CTNCFTQTTPLWRRNPEGQPLCNACGLFLKLHGVVRPLSL 43
Score = 61.7 bits (150), Expect = 3e-14
Identities = 22/40 (55%), Positives = 28/40 (70%)
Query: 9 RECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNRPL 48
C NC +TPLWRR+ G LCNACGL+ K++G+ RPL
Sbjct: 2 TTCTNCFTQTTPLWRRNPEGQPLCNACGLFLKLHGVVRPL 41
>2kae_A GATA-type transcription factor; zinc finger, GATA-type, DNA; NMR
{Caenorhabditis elegans}
Length = 71
Score = 66.4 bits (162), Expect = 6e-16
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 12/68 (17%)
Query: 65 CTNCGTRMTTLWRRNNDGEPV-CNACGLYYKLHNVNRPLAMRHLAMRPLAMRKDGIQTRK 123
C+NC T WR E + CNAC +Y + +N RP+ + Q RK
Sbjct: 11 CSNCSVTETIRWRNIRSKEGIQCNACFIYQRKYNKTRPVTA-----------VNKYQKRK 59
Query: 124 RKPKKQGG 131
K ++ G
Sbjct: 60 LKVQETNG 67
Score = 62.2 bits (151), Expect = 3e-14
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 1/55 (1%)
Query: 7 EGRECVNCGAISTPLWRRDGTG-HYLCNACGLYHKMNGMNRPLVKPSKRLTATRR 60
+ +C NC T WR + CNAC +Y + RP+ +K +
Sbjct: 7 KSFQCSNCSVTETIRWRNIRSKEGIQCNACFIYQRKYNKTRPVTAVNKYQKRKLK 61
>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 = 42.3 bits (99), Expect = 1e-05
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 44 MNRP-LVKPSKRLTATRRLGLCCTNCGTRMTTLWRRNNDGEPVCNACGL 91
M R + K + R + L C C + R ++G+ VC CGL
Sbjct: 2 MTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGL 50
Score = 35.4 bits (81), Expect = 0.003
Identities = 8/27 (29%), Positives = 10/27 (37%)
Query: 11 CVNCGAISTPLWRRDGTGHYLCNACGL 37
C C + R G +C CGL
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGL 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 = 37.2 bits (85), Expect = 8e-04
Identities = 12/45 (26%), Positives = 19/45 (42%)
Query: 47 PLVKPSKRLTATRRLGLCCTNCGTRMTTLWRRNNDGEPVCNACGL 91
+ K + R + L C C + R ++G+ VC CGL
Sbjct: 6 SIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGL 50
Score = 30.3 bits (67), Expect = 0.18
Identities = 8/29 (27%), Positives = 10/29 (34%)
Query: 9 RECVNCGAISTPLWRRDGTGHYLCNACGL 37
C C + R G +C CGL
Sbjct: 22 LTCPECKVYPPKIVERFSEGDVVCALCGL 50
>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 = 29.8 bits (66), Expect = 0.27
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 9/50 (18%)
Query: 94 KLHNVNRPLAMRHLAMRPLAMRKDGIQT--RKRKPKK----QGGGGGGGS 137
+L+N N+ A +++ R K ++ + +P K G G G +
Sbjct: 118 RLYNDNQVFAKYNVS-RLQPYLK--LRQALLELRPAKNVLIDGVLGSGKT 164
>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 = 29.2 bits (65), Expect = 0.39
Identities = 17/85 (20%), Positives = 24/85 (28%), Gaps = 30/85 (35%)
Query: 5 FGEGRECVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNRPLVKPSKRLTATRRLGLC 64
C+NCG + RR + C+ACG +
Sbjct: 372 VTHVMMCMNCGCDFSLTLRR-----HHCHACGK-------------------------IV 401
Query: 65 CTNCGTRMTTLWRRNNDGEPVCNAC 89
C NC L + VC+ C
Sbjct: 402 CRNCSRNKYPLKYLKDRMAKVCDGC 426
>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 = 28.4 bits (63), Expect = 0.46
Identities = 8/36 (22%), Positives = 12/36 (33%)
Query: 1 MDFQFGEGRECVNCGAISTPLWRRDGTGHYLCNACG 36
++ + C C T + R C ACG
Sbjct: 95 IEDYVNKFVICHECNRPDTRIIREGRISLLKCEACG 130
Score = 24.9 bits (54), Expect = 9.1
Identities = 8/28 (28%), Positives = 10/28 (35%)
Query: 63 LCCTNCGTRMTTLWRRNNDGEPVCNACG 90
+ 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 = 28.7 bits (65), Expect = 0.48
Identities = 7/26 (26%), Positives = 9/26 (34%)
Query: 65 CTNCGTRMTTLWRRNNDGEPVCNACG 90
CT+C P C+ CG
Sbjct: 124 CTSCNNSFEVESAPKIPPLPKCDKCG 149
>2d74_B Translation initiation factor 2 beta subunit; protein complex;
2.80A {Pyrococcus furiosus} PDB: 2dcu_B*
Length = 148
Score = 28.4 bits (63), Expect = 0.57
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 1 MDFQFGEGRECVNCGAISTPLWRRDGTGHYLCNACG 36
+ E C CG+ T + +RD C ACG
Sbjct: 97 LKKYIKEYVICPVCGSPDTKIIKRDRFHFLKCEACG 132
Score = 25.3 bits (55), Expect = 7.1
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 63 LCCTNCGTRMTTLWRRNNDGEPVCNACG 90
+ C CG+ T + +R+ C ACG
Sbjct: 105 VICPVCGSPDTKIIKRDRFHFLKCEACG 132
>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 = 0.62
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 11 CVNCGAISTPLWRRDGTGHYLCNACG 36
C C ++ T L + + + +C ACG
Sbjct: 106 CSTCKSLDTILKKEKKSWYIVCLACG 131
Score = 24.9 bits (54), Expect = 8.9
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 65 CTNCGTRMTTLWRRNNDGEPVCNACG 90
C+ C + T L + VC ACG
Sbjct: 106 CSTCKSLDTILKKEKKSWYIVCLACG 131
>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 = 26.4 bits (58), Expect = 0.95
Identities = 8/29 (27%), Positives = 11/29 (37%), Gaps = 2/29 (6%)
Query: 63 LCCTNCGTRMTTLWRRNNDGEPVCNACGL 91
+ C N L G+ +C CGL
Sbjct: 12 VTCPNHPDA--ILVEDYRAGDMICPECGL 38
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B
2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
Length = 1131
Score = 27.9 bits (62), Expect = 1.4
Identities = 15/58 (25%), Positives = 19/58 (32%), Gaps = 6/58 (10%)
Query: 65 CTNCGTRMTTLWRRNNDGEPVCNACGLYYKLHNVNRPLAMRHLAMRPLAMRKDGIQTR 122
C CG W N + VC G L V A + L ++M I R
Sbjct: 1064 CDQCGY---IGWYDKNKNKYVCPIHGDKSNLFPVTVSYAFKLLIQELMSM---IISPR 1115
>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein
structure initiative, midwest center for structural
genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP:
e.59.1.1
Length = 309
Score = 27.5 bits (60), Expect = 1.5
Identities = 19/87 (21%), Positives = 30/87 (34%), Gaps = 27/87 (31%)
Query: 31 LCNACGLYHKMNGMNRPLVKPSKRLTATRRL--GLC----------CTNCG-TRMTTLWR 77
LC ACG +++ + T R L LC C++C ++
Sbjct: 184 LCPACGSPPMAG-----MIRQGGKETGLRYLSCSLCACEWHYVRIKCSHCEESKHLAYLS 238
Query: 78 RNNDGEP---------VCNACGLYYKL 95
+DG+P C +C Y K
Sbjct: 239 LEHDGQPAEKAVLRAETCPSCQGYLKQ 265
>3k6g_A Telomeric repeat-binding factor 2-interacting Pro; helix,
chromosomal protein, nucleus, phosphoprotein, telomer
cycle, DNA-binding, protein binding; 1.95A {Homo
sapiens}
Length = 111
Score = 26.6 bits (58), Expect = 2.0
Identities = 11/24 (45%), Positives = 12/24 (50%)
Query: 116 KDGIQTRKRKPKKQGGGGGGGSGG 139
+ R KK G GG GGSGG
Sbjct: 86 AQNVARRIEFRKKGGSGGSGGSGG 109
>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 = 27.2 bits (59), Expect = 2.4
Identities = 6/27 (22%), Positives = 8/27 (29%)
Query: 11 CVNCGAISTPLWRRDGTGHYLCNACGL 37
C +C P + CN C
Sbjct: 88 CRSCRTYINPFVSFIDQRRWKCNLCYR 114
Score = 26.4 bits (57), Expect = 4.5
Identities = 6/32 (18%), Positives = 10/32 (31%)
Query: 64 CCTNCGTRMTTLWRRNNDGEPVCNACGLYYKL 95
C +C T + + CN C +
Sbjct: 87 RCRSCRTYINPFVSFIDQRRWKCNLCYRVNDV 118
>2odx_A Cytochrome C oxidase polypeptide IV; all beta-protein,
metallo-protein, oxidoreductase; NMR {Saccharomyces
cerevisiae}
Length = 80
Score = 25.5 bits (56), Expect = 2.8
Identities = 19/65 (29%), Positives = 25/65 (38%), Gaps = 6/65 (9%)
Query: 44 MNRPLVKPSKRLTATRRLGLCCTNC-GTRMTTLWRRNNDGEPV-CNACGLYYKLHNVNRP 101
M P++ S R +G CT T +W + E C CG YKL+ V P
Sbjct: 19 MKDPIIIES--YDDYRYVG--CTGSPAGSHTIMWLKPTVNEVARCWECGSVYKLNPVGVP 74
Query: 102 LAMRH 106
H
Sbjct: 75 NDDHH 79
>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation
factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1
Length = 50
Score = 24.7 bits (54), Expect = 3.1
Identities = 9/29 (31%), Positives = 10/29 (34%), Gaps = 2/29 (6%)
Query: 63 LCCTNCGTRMTTLWRRNNDGEPVCNACGL 91
C C + L GE VC CG
Sbjct: 6 KVCPACES--AELIYDPERGEIVCAKCGY 32
>1k81_A EIF-2-beta, probable translation initiation factor 2 beta
subunit; zinc ribbon; NMR {Methanocaldococcus
jannaschii} SCOP: g.59.1.1
Length = 36
Score = 23.6 bits (51), Expect = 5.7
Identities = 8/26 (30%), Positives = 10/26 (38%)
Query: 11 CVNCGAISTPLWRRDGTGHYLCNACG 36
C CG T + + C ACG
Sbjct: 3 CRECGKPDTKIIKEGRVHLLKCMACG 28
>2xqy_A GH, envelope glycoprotein H; immune system-viral protein complex,
envelope protein; HET: NAG; 2.05A {Suid herpesvirus}
Length = 572
Score = 25.6 bits (55), Expect = 7.1
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 128 KQGGGGGGGSGG 139
++GGG GGGSGG
Sbjct: 551 EKGGGSGGGSGG 562
>2f9y_B Acetyl-coenzyme A carboxylase carboxyl transferas beta; zinc
ribbon, crotonase superfamily, spiral domain, ligase;
3.20A {Escherichia coli} SCOP: c.14.1.4
Length = 304
Score = 25.3 bits (56), Expect = 8.0
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 4/37 (10%)
Query: 11 CVNCGAISTPLWRRD-GTGHYLCNACGLYHKMNGMNR 46
C +CG + L+R + +C C + +M NR
Sbjct: 27 CDSCGQV---LYRAELERNLEVCPKCDHHMRMTARNR 60
>1nc5_A Hypothetical protein YTER; structural genomics, helix barrel, PSI,
protein structure initiative, midwest center for
structural genomics, MCSG; 1.60A {Bacillus subtilis}
SCOP: a.102.1.6 PDB: 2d8l_A* 2gh4_A*
Length = 373
Score = 25.5 bits (55), Expect = 8.9
Identities = 9/37 (24%), Positives = 14/37 (37%)
Query: 11 CVNCGAISTPLWRRDGTGHYLCNACGLYHKMNGMNRP 47
+ G I PL+ + Y+ A L +NR
Sbjct: 89 AIQAGLILFPLYEQTKDERYVKAAKRLRSLYGTLNRT 125
>1e07_A Carcinoembryonic antigen; glycoprotein, CEA, tumour marker,
immunoglobulin-fold; NMR {Homo sapiens} PDB: 2dks_A
Length = 642
Score = 25.3 bits (55), Expect = 9.0
Identities = 20/107 (18%), Positives = 29/107 (27%), Gaps = 35/107 (32%)
Query: 13 NCGAISTPL----WRRDGT------------------GHYLC---NACGLYHKMNGMN-- 45
+C A S P W +GT G Y C N+ ++
Sbjct: 224 SCHAASNPPAQYSWFVNGTFQQSTQELFIPNITVNNSGSYTCQAHNSDTGLNRTTVTTIT 283
Query: 46 ------RPLVKPSKRLTATR--RLGLCCTNCGTRMTTLWRRNNDGEP 84
+P + + + L C T LW NN P
Sbjct: 284 VYAEPPKPFITSNNSNPVEDEDAVALTCEPEIQNTTYLWWVNNQSLP 330
>2f9i_B Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta;
zinc ribbon, crotonase superfamily, spiral domain;
1.98A {Staphylococcus aureus}
Length = 285
Score = 24.8 bits (55), Expect = 9.8
Identities = 6/37 (16%), Positives = 13/37 (35%), Gaps = 4/37 (10%)
Query: 11 CVNCGAISTPLWRRD-GTGHYLCNACGLYHKMNGMNR 46
C C I ++ ++ +C C + + R
Sbjct: 33 CPKCKKI---MYTKELAENLNVCFNCDHHIALTAYKR 66
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
0.323 0.140 0.475
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: 2,225,248
Number of extensions: 119832
Number of successful extensions: 481
Number of sequences better than 10.0: 1
Number of HSP's gapped: 470
Number of HSP's successfully gapped: 75
Length of query: 139
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 55
Effective length of database: 4,356,429
Effective search space: 239603595
Effective search space used: 239603595
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.3 bits)