RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13847
(91 letters)
>1ozj_A SMAD 3; MAD homology domain 1, DNA recognition, TGF-beta
signaling, zinc-binding module, transcription/DNA
complex; 2.40A {Homo sapiens} SCOP: d.164.1.1 PDB:
1mhd_A*
Length = 144
Score = 101 bits (252), Expect = 2e-29
Identities = 55/84 (65%), Positives = 64/84 (76%), Gaps = 3/84 (3%)
Query: 1 MTSLFPFTPPIVKKLLGWKKGDG---EDKYSEKAVKSLVKKLKKSNGLDELEKAITTQDP 57
M+S+ PFTPPIVK+LLGWKKG+ E+K+ EKAVKSLVKKLKK+ LDELEKAITTQ+
Sbjct: 1 MSSILPFTPPIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNV 60
Query: 58 NTKCVTIPRLQFEDLQQSGVCSSP 81
NTKC+TIPR LQ S P
Sbjct: 61 NTKCITIPRSLDGRLQVSHRKGLP 84
>3kmp_A SMAD1-MH1; protein-DNA complex, SMAD1, SBE DNA, MH1 domain, beta
hairpin, nucleus, transcription; 2.70A {Mus musculus}
Length = 124
Score = 90.4 bits (224), Expect = 2e-25
Identities = 41/76 (53%), Positives = 52/76 (68%), Gaps = 1/76 (1%)
Query: 7 FTPPIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKSNG-LDELEKAITTQDPNTKCVTIP 65
FT P VK+LLGWK+GD E+K++EKAV +LVKKLKK G ++ELEKA++ + CVTIP
Sbjct: 1 FTSPAVKRLLGWKQGDEEEKWAEKAVDALVKKLKKKKGAMEELEKALSCPGQPSNCVTIP 60
Query: 66 RLQFEDLQQSGVCSSP 81
R LQ S P
Sbjct: 61 RSLDGRLQVSHRKGLP 76
>3qsv_A SMAD4, mothers against decapentaplegic homolog 4; MH1,
transcription factor, DNA binding; HET: DNA; 2.71A {Mus
musculus}
Length = 132
Score = 79.6 bits (196), Expect = 4e-21
Identities = 29/74 (39%), Positives = 43/74 (58%), Gaps = 2/74 (2%)
Query: 10 PIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKSNG-LDELEKAITTQDPN-TKCVTIPRL 67
IV L+ ++G + ++++A++SLVKKLK+ LD L AITT + +KCVTI R
Sbjct: 10 SIVHSLMCHRQGGESETFAKRAIESLVKKLKEKKDELDSLITAITTNGAHPSKCVTIQRT 69
Query: 68 QFEDLQQSGVCSSP 81
LQ +G P
Sbjct: 70 LDGRLQVAGRKGFP 83
>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 = 37.5 bits (86), Expect = 2e-04
Identities = 18/74 (24%), Positives = 25/74 (33%), Gaps = 16/74 (21%)
Query: 3 SLFPFTPPIVKKLLG--WKKGDGEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQDPNTK 60
S+FP + I LL W D V L K L +EK P
Sbjct: 379 SVFPPSAHIPTILLSLIWFDVIKSD--VMVVVNKLHKY-----SL--VEK-----QPKES 424
Query: 61 CVTIPRLQFEDLQQ 74
++IP + E +
Sbjct: 425 TISIPSIYLELKVK 438
>3fwm_A Penicillin-binding protein 1B; bacterial cell WALL synthesis,
antibiotics design, transferase, hydrolase; HET: M0E;
2.16A {Escherichia coli} PDB: 3fwl_A* 3vma_A*
Length = 751
Score = 29.2 bits (66), Expect = 0.13
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 26 KYSEKAVKSLVKKLKKSNGLDELEKAITTQDPNT 59
+EKA + LKK L +LE AI D +
Sbjct: 395 DAAEKAAVEGIPALKKQRKLSDLETAIVVVDRFS 428
>3ele_A Amino transferase; RER070207001803, structural genomics, JOI for
structural genomics, JCSG; HET: MSE PLP; 2.10A
{Eubacterium rectale}
Length = 398
Score = 27.1 bits (61), Expect = 0.65
Identities = 7/21 (33%), Positives = 10/21 (47%), Gaps = 3/21 (14%)
Query: 45 LDELEKAITTQDPNTKCVTIP 65
D LE+ I +T+ V I
Sbjct: 162 FDALEERIN---AHTRGVIIN 179
>1hyq_A MIND, cell division inhibitor (MIND-1); MINC, FTSZ, bacterial cell
division, cell cycle; 2.60A {Archaeoglobus fulgidus}
SCOP: c.37.1.10
Length = 263
Score = 26.8 bits (60), Expect = 0.95
Identities = 5/31 (16%), Positives = 12/31 (38%)
Query: 11 IVKKLLGWKKGDGEDKYSEKAVKSLVKKLKK 41
+ + G K + EK + + K+ +
Sbjct: 228 LANYIAGGAKKKVPAEVKEKKKEGALAKMLR 258
>2x65_A Mannose-1-phosphate guanylyltransferase; nucleotidyltransferase;
HET: M1P; 2.10A {Thermotoga maritima} PDB: 2x5z_A*
2x60_A* 2x5s_A*
Length = 336
Score = 26.3 bits (59), Expect = 1.6
Identities = 5/19 (26%), Positives = 12/19 (63%)
Query: 25 DKYSEKAVKSLVKKLKKSN 43
+ + V+ +VKKL +++
Sbjct: 318 KEEYAQKVREVVKKLFRTS 336
>3if2_A Aminotransferase; YP_265399.1, structura genomics, joint center for
structural genomics, JCSG, prote structure initiative,
PSI-2; HET: PLP; 2.50A {Psychrobacter arcticus 273-4}
Length = 444
Score = 25.4 bits (56), Expect = 2.6
Identities = 3/22 (13%), Positives = 7/22 (31%)
Query: 45 LDELEKAITTQDPNTKCVTIPR 66
+ LE ++ + R
Sbjct: 193 FEALENLPALKEGRIGAICCSR 214
>3r8s_C 50S ribosomal protein L2; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
3fik_C 2wwq_C 3oat_C* 3oas_C* 3ofd_C 3ofc_C 3ofr_C*
3ofz_C* 3og0_C 3ofq_C 3r8t_C 3i1n_C 1vs8_C 1vs6_C
2aw4_C 2awb_C 2vhm_C 2vhn_C 3bbx_C 3df2_C ...
Length = 271
Score = 24.4 bits (54), Expect = 6.1
Identities = 6/23 (26%), Positives = 10/23 (43%)
Query: 22 DGEDKYSEKAVKSLVKKLKKSNG 44
+ + K L++K KS G
Sbjct: 19 VNPELHKGKPFAPLLEKNSKSGG 41
>2i5b_A Phosphomethylpyrimidine kinase; ADP complex, PDXK, THID,
ribokinase superfamily, transferase; HET: ADP; 2.80A
{Bacillus subtilis}
Length = 271
Score = 24.3 bits (54), Expect = 6.3
Identities = 4/13 (30%), Positives = 4/13 (30%)
Query: 51 AITTQDPNTKCVT 63
I DPN
Sbjct: 40 VIVAMDPNNSWNH 52
>1zvd_A SMAD ubiquitination regulatory factor 2; ubiquitin ligasecatalytic
mechanism,X-RAY ligase; 2.10A {Homo sapiens}
Length = 380
Score = 24.5 bits (54), Expect = 6.8
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 6 PFTPPIVKKLLGWKKG--DGEDKYSEKAVKSLVKKLKKSNGLDELE 49
FT P K+LLG D E + SL + +++ L+
Sbjct: 135 GFTLPFYKQLLGKSITLDDMELVDPDLH-NSL-VWILENDITGVLD 178
>3v2d_D 50S ribosomal protein L2; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus}
PDB: 1vsp_B 2hgj_D 2hgq_D 2hgu_D 1vsa_B 2j03_D 2jl6_D
2jl8_D 2v47_D 2v49_D 2wdi_D 2wdj_D 2wdl_D 2wdn_D 2wh2_D
2wh4_D 2wrj_D 2wrl_D 2wro_D 2wrr_D ...
Length = 276
Score = 24.0 bits (53), Expect = 9.4
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 22 DGEDKYSEKAVKSLVKKLKKSNG 44
D + + KSLVK LKK+ G
Sbjct: 20 DFSEITKTEPEKSLVKPLKKTGG 42
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
0.313 0.131 0.389
Gapped
Lambda K H
0.267 0.0834 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,354,907
Number of extensions: 65038
Number of successful extensions: 192
Number of sequences better than 10.0: 1
Number of HSP's gapped: 188
Number of HSP's successfully gapped: 21
Length of query: 91
Length of database: 6,701,793
Length adjustment: 58
Effective length of query: 33
Effective length of database: 5,082,375
Effective search space: 167718375
Effective search space used: 167718375
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 (23.2 bits)