RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14468
(108 letters)
>3m66_A Mterf3, mterf domain-containing protein 1, mitochondrial;
mitochondrion, DNA binding protein, transcription
factor, transcription termination; 1.60A {Homo sapiens}
PDB: 3opg_A 3my3_A
Length = 270
Score = 103 bits (259), Expect = 1e-28
Identities = 40/96 (41%), Positives = 63/96 (65%)
Query: 13 FLSLDATELVKTFNYVHSDMKVPHERILEFPNILTSRRFRIENRHSYLKSLGRDQYDPCK 72
L+ + +L +TF++VH+ M +PH I++FP + +R F+++ RH +L LGR QYDP K
Sbjct: 175 MLTANKMKLTETFDFVHNVMSIPHHIIVKFPQVFNTRLFKVKERHLFLTYLGRAQYDPAK 234
Query: 73 ENYVSMKSLVSGTDAEFCANVAKTTPETYNLFLKSL 108
NY+S+ LVS D FC +AK + + + FLK+L
Sbjct: 235 PNYISLDKLVSIPDEIFCEEIAKASVQDFEKFLKTL 270
>3mva_O Transcription termination factor, mitochondrial; all alpha-helix,
protein-DNA, transcription factor, terminat
mitochondria; 2.20A {Homo sapiens} PDB: 3n6s_A* 3mvb_O
3n7q_A*
Length = 343
Score = 58.9 bits (142), Expect = 1e-11
Identities = 14/85 (16%), Positives = 34/85 (40%), Gaps = 8/85 (9%)
Query: 13 FLSLDATELVKTFNYVHSDMKVPHERILEFPNILTSRRFRIENRHSYLKSLGRDQYDPCK 72
+ L + + + + + +I+E P +L S +++R L + G +
Sbjct: 267 VIFLAEKKFNDKIDCLM-EENISISQIIENPRVLDSSISTLKSRIKELVNAG---CNLST 322
Query: 73 ENYVSMKSLVSGTDAEFCANVAKTT 97
N +L+S + + A + K +
Sbjct: 323 LNI----TLLSWSKKRYEAKLKKLS 343
>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 = 32.1 bits (72), Expect = 0.021
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 25 FNYV--HSDMKVPHERILEFPNILTSRRFRIEN--RHS 58
++++ H ER+ F + RF +E RH
Sbjct: 474 YSHIGHHLKNIEHPERMTLFRMVFLDFRF-LEQKIRHD 510
Score = 28.7 bits (63), Expect = 0.37
Identities = 17/98 (17%), Positives = 27/98 (27%), Gaps = 37/98 (37%)
Query: 14 LSLD---ATELVKTFNYVHSDMKVPHERILEFPNILTSRRFRIENRHSYLKSLGRDQYDP 70
L L + FN + +IL LT+R ++ D
Sbjct: 248 LVLLNVQNAKAWNAFN-LSC-------KIL-----LTTRFKQVT-----------DFLSA 283
Query: 71 CKENYVSMKSLVSGTDAEFCANVAKTTPETYNLFLKSL 108
++S+ T E +L LK L
Sbjct: 284 ATTTHISLDHHSMT----L------TPDEVKSLLLKYL 311
Score = 25.2 bits (54), Expect = 6.4
Identities = 14/84 (16%), Positives = 24/84 (28%), Gaps = 18/84 (21%)
Query: 1 MTRSTSTALQAIFLSLDATELVKTFNYVHSDMKVPHERILEFPNILT--SRRFRIE-NRH 57
+T +L +L +L P E + P L+ + R
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDL-------------PREVLTTNPRRLSIIAESIRDGLATW 344
Query: 58 SYLKSLGRDQYDPCKENYVSMKSL 81
K + D+ E S+ L
Sbjct: 345 DNWKHVNCDKLTTIIE--SSLNVL 366
Score = 24.8 bits (53), Expect = 7.6
Identities = 14/76 (18%), Positives = 27/76 (35%), Gaps = 13/76 (17%)
Query: 29 HSDMKVPHERILEFPNILTSRRFRIENRHSYLKSLGRDQYDPCKENYVSMKSLVSGTDAE 88
H D + E ++ +IL + + + +D CK+ KS++S + +
Sbjct: 6 HMDFET-GEHQYQYKDIL----------SVFEDAFVDN-FD-CKDVQDMPKSILSKEEID 52
Query: 89 FCANVAKTTPETYNLF 104
T LF
Sbjct: 53 HIIMSKDAVSGTLRLF 68
>1qop_B Tryptophan synthase beta chain; lyase, carbon-oxygen lyase,
tryptophan biosynthesis, pyridoxal phosphate; HET: IPL
PLP; 1.4A {Salmonella typhimurium} SCOP: c.79.1.1 PDB:
1k7e_B* 1k7f_B* 1kfb_B* 1k3u_B* 1tjp_B* 1wbj_B* 2cli_B*
2clk_B* 2cll_B* 2j9x_B* 3cep_B* 1kfc_B* 1k8x_B* 1kfj_B*
1kfk_B* 2rh9_B* 2rhg_B* 2j9y_B* 1cw2_B* 1a5s_B* ...
Length = 396
Score = 27.1 bits (61), Expect = 1.3
Identities = 12/32 (37%), Positives = 14/32 (43%), Gaps = 13/32 (40%)
Query: 57 HSYLKSLGRDQYDPCKENYVSMKSLVSGTDAE 88
H+YL S+GR Y VS TD E
Sbjct: 312 HAYLNSIGRADY-------------VSITDDE 330
>1v8z_A Tryptophan synthase beta chain 1; beta+alpha, riken structural
genomics/proteomics initiative, structural genomics,
lyase; HET: PLP; 2.21A {Pyrococcus furiosus} SCOP:
c.79.1.1 PDB: 1wdw_B*
Length = 388
Score = 26.4 bits (59), Expect = 1.8
Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 13/32 (40%)
Query: 57 HSYLKSLGRDQYDPCKENYVSMKSLVSGTDAE 88
H+YLK + R +Y V+ TD E
Sbjct: 308 HAYLKKIQRAEY-------------VTVTDEE 326
>1x1q_A Tryptophan synthase beta chain; structural genomics, riken
structural genomics/proteomics initiative, RSGI, NPPSFA;
2.50A {Thermus thermophilus}
Length = 418
Score = 26.4 bits (59), Expect = 1.9
Identities = 8/32 (25%), Positives = 9/32 (28%), Gaps = 13/32 (40%)
Query: 57 HSYLKSLGRDQYDPCKENYVSMKSLVSGTDAE 88
HSY G +Y TD E
Sbjct: 337 HSYYADAGVAEYASV-------------TDEE 355
>2o2e_A Tryptophan synthase beta chain; amino-acid biosynthesis, tryptophan
biosynthesis, structural genomics; 2.20A {Mycobacterium
tuberculosis} PDB: 2o2j_A
Length = 422
Score = 26.4 bits (59), Expect = 2.1
Identities = 10/32 (31%), Positives = 13/32 (40%), Gaps = 13/32 (40%)
Query: 57 HSYLKSLGRDQYDPCKENYVSMKSLVSGTDAE 88
H++LK GR Y P TD+E
Sbjct: 339 HAWLKEAGRVDYRPI-------------TDSE 357
>3eqc_A Dual specificity mitogen-activated protein kinase; MEK1 kinase,
ATP-binding, disease mutation, nucleoti binding,
phosphoprotein; HET: 3BM AGS; 1.80A {Homo sapiens} PDB:
3eqd_A* 3eqf_A* 3eqg_A* 3eqh_A* 3eqi_A* 2y4i_C* 3eqb_A*
2p55_A* 1s9j_A* 3dy7_A* 3e8n_A* 3dv3_A* 3mbl_A* 3pp1_A*
3orn_A* 3os3_A* 3sls_A* 1s9i_A*
Length = 360
Score = 24.4 bits (53), Expect = 9.5
Identities = 9/33 (27%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 18 ATELVKTFNYVHSDMKVPHERILEFPNILTSRR 50
+ ++K Y+ K+ H R ++ NIL + R
Sbjct: 137 SIAVIKGLTYLREKHKIMH-RDVKPSNILVNSR 168
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
0.319 0.131 0.372
Gapped
Lambda K H
0.267 0.0530 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,487,646
Number of extensions: 73058
Number of successful extensions: 130
Number of sequences better than 10.0: 1
Number of HSP's gapped: 130
Number of HSP's successfully gapped: 24
Length of query: 108
Length of database: 6,701,793
Length adjustment: 72
Effective length of query: 36
Effective length of database: 4,691,481
Effective search space: 168893316
Effective search space used: 168893316
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (23.9 bits)