RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12829
(181 letters)
>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1
d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C
1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C*
1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C
1y77_C* ...
Length = 318
Score = 152 bits (385), Expect = 5e-46
Identities = 83/176 (47%), Positives = 112/176 (63%), Gaps = 5/176 (2%)
Query: 6 QPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIA 65
P V I + + +NV F + + +L++ANSLRRV IAE PT+AID V++E N+TVL+DEFIA
Sbjct: 5 GPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIA 64
Query: 66 SRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDA 125
R+GLIPL S + ++++ YSRDC C D C +CSV TL + T +V + DL
Sbjct: 65 HRLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVS- 122
Query: 126 RVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
+ RN + + E + +LI KLRKGQEL+L AKKG KEHAKW P A
Sbjct: 123 ---NLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAA 175
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 297
Score = 140 bits (354), Expect = 1e-41
Identities = 70/181 (38%), Positives = 106/181 (58%), Gaps = 11/181 (6%)
Query: 5 NQPSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFI 64
++ + I +++ +V F + +T L+VANSLRRV +AE PT+AID V++ N++V+ DEF+
Sbjct: 3 SETHITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFL 62
Query: 65 ASRIGLIPLTSDEVVDRIL----YSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL 120
A R+G+IPL S + + Y+R+C C +C +CSVE L+ KC + T + DL
Sbjct: 63 AHRLGMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDL 122
Query: 121 KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
+ + ++ LI KLRK QE+ LR AKKG KEHAKW+PT+
Sbjct: 123 VVSSNSSLGHPILADP-------KSRGPLICKLRKEQEISLRCIAKKGIAKEHAKWSPTS 175
Query: 181 G 181
Sbjct: 176 A 176
>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding
motif, platform for RNA polymer assembly, transferase;
1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D
2waq_D 2wb1_D 2y0s_D
Length = 265
Score = 133 bits (335), Expect = 4e-39
Identities = 52/174 (29%), Positives = 87/174 (50%), Gaps = 16/174 (9%)
Query: 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
S+++ D + E L N++RR + P MA+D V N++ L DE +A R
Sbjct: 2 SINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHR 61
Query: 68 IGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
+ LIP S+E +D + +C C + C +C + ++ + ++ R + + D+KS D
Sbjct: 62 LALIPFMSEEALDTYRWPEECIECTENCEKCYTKIYIEAEA-PNEPRMIYSKDIKSEDPS 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
VVP+ + DI IV L Q++ L A + G+GKEHAK+ P +
Sbjct: 121 VVPI--------------SGDIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVS 160
>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 = 42.1 bits (98), Expect = 5e-05
Identities = 23/128 (17%), Positives = 45/128 (35%), Gaps = 24/128 (18%)
Query: 49 WVQLEANSTVLSDEFIASRIGLIPLTSDEVVD---RILYSRD-CTCV----DFCSECSVE 100
Q++ N T SD I L + R+L S+ C+ + + +
Sbjct: 206 LYQIDPNWTSRSDHSSN-----IKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWN 260
Query: 101 FTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYG----ETDDILIVKLR-K 155
++ C + +TT + TD + T+ + D + E +L+ L +
Sbjct: 261 -AFNLSC---KIL-LTTRFKQVTDF-LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR 314
Query: 156 GQELRLRA 163
Q+L
Sbjct: 315 PQDLPREV 322
Score = 33.7 bits (76), Expect = 0.031
Identities = 24/128 (18%), Positives = 37/128 (28%), Gaps = 36/128 (28%)
Query: 72 PLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQT----RHVTTADLKSTDARV 127
+ S E +D I+ S+D + Q + V + +
Sbjct: 44 SILSKEEIDHIIMSKD-------AVSGTLRLFWTLL-SKQEEMVQKFVEEVLRINYKFLM 95
Query: 128 VPVTSRNRDADMN--EYGETDDIL-----------------IVKLRKG-QELR----LRA 163
P+ + R M Y E D L +KLR+ ELR +
Sbjct: 96 SPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI 155
Query: 164 YAKKGFGK 171
G GK
Sbjct: 156 DGVLGSGK 163
Score = 27.5 bits (60), Expect = 2.8
Identities = 11/59 (18%), Positives = 17/59 (28%), Gaps = 24/59 (40%)
Query: 103 LDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRL 161
D K V D + + + + E D I++ K LRL
Sbjct: 33 FDCKDVQDMPKSILSKE------------------------EIDHIIMSKDAVSGTLRL 67
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 37.3 bits (86), Expect = 0.002
Identities = 25/158 (15%), Positives = 43/158 (27%), Gaps = 61/158 (38%)
Query: 2 PYANQPSVH--ITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVL 59
P+ DL NV F +D + + V+ D L +
Sbjct: 430 HL-LVPASDLINKDLVKNNVSFNAKD--IQIP-----VYDTFD---GSDLRVLSGS---- 474
Query: 60 SDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHV---- 115
I+ RI VD I+ V + + H+
Sbjct: 475 ----ISERI----------VDCII----RLPVKW-----------ETTTQFKATHILDFG 505
Query: 116 ----------TTADLKSTDARVVPVTSRNRDADMNEYG 143
T + T RV+ + + + D ++YG
Sbjct: 506 PGGASGLGVLTHRNKDGTGVRVIVAGTLDINPD-DDYG 542
Score = 31.6 bits (71), Expect = 0.14
Identities = 26/170 (15%), Positives = 56/170 (32%), Gaps = 48/170 (28%)
Query: 21 FQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDE-------FIASRIGLIPL 73
V +A+ L+ F P + + +T E +++S + +
Sbjct: 20 LLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPA--ELVGKFLGYVSSLVEPSKV 77
Query: 74 TS-DEVVDRILYSRDCTCVDFCSEC-------SVEFTLDVKCVDDQTRHVTTAD-LKS-T 123
D+V++ L +F + ++ L ++ T V T + +K+
Sbjct: 78 GQFDQVLNLCL-------TEFENCYLEGNDIHALAAKLL---QENDTTLVKTKELIKNYI 127
Query: 124 DARVV---PVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFG 170
AR++ P ++ A L + +G + A FG
Sbjct: 128 TARIMAKRPFDKKSNSA-----------LFRAVGEGN---AQLVAI--FG 161
>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium,
protein STRU initiative, PSI, structural genomics, DNA
synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum}
SCOP: c.37.1.24 g.39.1.14
Length = 191
Score = 28.3 bits (64), Expect = 1.1
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 12/75 (16%)
Query: 60 SDEFIASRIGL----IPLTS-DEVVDRILYSRDCTCVD---FCSECSVEFTLDVKCVDDQ 111
S E + S +G + + + E++ + +D F + VE V + +
Sbjct: 51 SKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIAIDEVQFFDDEIVEI---VNKIAES 107
Query: 112 TRHVTTADLKSTDAR 126
R V A L D R
Sbjct: 108 GRRVICAGLD-MDFR 121
>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis,
nucleotide-B transferase; HET: MSE; 2.01A
{Staphylococcus aureus}
Length = 219
Score = 26.9 bits (60), Expect = 3.0
Identities = 16/75 (21%), Positives = 26/75 (34%), Gaps = 12/75 (16%)
Query: 60 SDEFIASRIGL----IPLTS-DEVVDRILYSRDCTCVD---FCSECSVEFTLDVKCVDDQ 111
E + S G I ++ E++ L + D +D F + V V+ +
Sbjct: 71 HKEKVVSHNGNAIEAINISKASEIMTHDLTNVDVIGIDEVQFFDDEIVSI---VEKLSAD 127
Query: 112 TRHVTTADLKSTDAR 126
V A L D R
Sbjct: 128 GHRVIVAGLD-MDFR 141
>3mtc_A Type II inositol-1,4,5-trisphosphate 5-phosphatas;
INPP5BA,phosphoinositide 5-phosphatase, inositol
signalling, phosphatase, magnesium; HET: PIF; 2.40A
{Homo sapiens} PDB: 3n9v_A
Length = 313
Score = 27.1 bits (60), Expect = 3.7
Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 11/46 (23%)
Query: 80 DRILY-SRDCTCVDFCSECSV----------EFTLDVKCVDDQTRH 114
DRIL+ ++ T + + S ++ F + V+ V H
Sbjct: 267 DRILWKGKNITQLSYQSHMALKTSDHKPVSSVFDIGVRVVAHHHHH 312
>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding,
deoxyribonucleoside kinase, DNA synthesis, phosphate
accept nucleotide-binding; HET: THM; 2.7A {Bacillus
anthracis} PDB: 2ja1_A*
Length = 214
Score = 26.1 bits (58), Expect = 7.2
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 12/75 (16%)
Query: 60 SDEFIASRIGL----IPLTS-DEVVDRILYSRDCTCVD---FCSECSVEFTLDVKCVDDQ 111
S+E + S GL +P+++ ++ I D +D F VE V+ + ++
Sbjct: 71 SEEDVVSHNGLKVKAVPVSASKDIFKHITEEMDVIAIDEVQFFDGDIVEV---VQVLANR 127
Query: 112 TRHVTTADLKSTDAR 126
V A L D R
Sbjct: 128 GYRVIVAGLD-QDFR 141
>3htn_A Putative DNA binding protein; DUF269 family protein, structural
genomics, joint center for structural genomics, JCSG;
HET: MSE 1PE; 1.50A {Bacteroides thetaiotaomicron
vpi-5482}
Length = 149
Score = 25.7 bits (56), Expect = 7.6
Identities = 8/38 (21%), Positives = 16/38 (42%), Gaps = 3/38 (7%)
Query: 132 SRNRDADMNEYGETDDILIVKLRKGQELR--LRAYAKK 167
++N Y + + IV + E+ L A+ K+
Sbjct: 2 AQNEKNMY-SYKKIGNKYIVSINNHTEIVKALNAFCKE 38
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
0.318 0.132 0.386
Gapped
Lambda K H
0.267 0.0640 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,706,685
Number of extensions: 152984
Number of successful extensions: 297
Number of sequences better than 10.0: 1
Number of HSP's gapped: 288
Number of HSP's successfully gapped: 19
Length of query: 181
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 93
Effective length of database: 4,244,745
Effective search space: 394761285
Effective search space used: 394761285
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: 54 (24.8 bits)