RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11391
(112 letters)
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A
{Schizosaccharomyces pombe}
Length = 203
Score = 72.0 bits (176), Expect = 4e-17
Identities = 29/89 (32%), Positives = 46/89 (51%), Gaps = 3/89 (3%)
Query: 2 VTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNE--GDKHDLFMDPGDKIKFRVTSEL 59
VT+ FF+DI IP + L P F E+ WVW+ + E + +L+ D ++I+F++ SE
Sbjct: 99 VTISFFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQIESED 158
Query: 60 FTETSPISCPDIHDGAPGSEVDTPKIPYS 88
F + SP G+E PY+
Sbjct: 159 FVDISPKR-NKNATAITGTEALESVSPYT 186
>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide;
multiprotein complex, nucleotidyltransferase, nuclear
protein, hypothetical protein; 3.2A {Saccharomyces
cerevisiae}
Length = 218
Score = 61.3 bits (148), Expect = 6e-13
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 3 TLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELFTE 62
LG F+DI IP L + + +E W+W D ++ L+ D +KI+FR+ E+F +
Sbjct: 101 LLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMD---EETKLYFDVNEKIRFRIEREVFVD 157
Query: 63 TSPIS 67
P S
Sbjct: 158 VKPKS 162
>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase,
transcription; 1.75A {Methanococcus jannaschii} SCOP:
b.40.4.5 d.230.1.1
Length = 187
Score = 56.1 bits (135), Expect = 4e-11
Identities = 8/67 (11%), Positives = 24/67 (35%), Gaps = 6/67 (8%)
Query: 1 MVTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELF 60
V LG + ++ + + +D K + + + + ++ GD ++ R+ +
Sbjct: 98 FVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGK------ETGKVLEIGDYVRARIVAISL 151
Query: 61 TETSPIS 67
Sbjct: 152 KAERKRG 158
>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide;
transferase; 2.30A {Saccharomyces cerevisiae} SCOP:
b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G
1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G*
2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H
3hou_G* 3hov_G* ...
Length = 171
Score = 54.5 bits (131), Expect = 1e-10
Identities = 7/68 (10%), Positives = 22/68 (32%), Gaps = 8/68 (11%)
Query: 1 MVTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELF 60
V +G + + + Q F+ ++ + + +I+ ++ +
Sbjct: 100 EVQVGPM-KVFVTKHLMPQDLTFNAGSNPPSYQ------SSEDVITIKSRIRVKIEGCIS 152
Query: 61 TETSPISC 68
+ S I
Sbjct: 153 -QVSSIHA 159
>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide;
DNA-dependent RNA polymerase, cellular RNA polymerase;
4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5
d.230.1.1
Length = 215
Score = 54.3 bits (130), Expect = 2e-10
Identities = 7/68 (10%), Positives = 22/68 (32%), Gaps = 8/68 (11%)
Query: 1 MVTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELF 60
V +G + + + Q F+ ++ + + +I+ ++ +
Sbjct: 100 EVQVGPM-KVFVTKHLMPQDLTFNAGSNPPSYQ------SSEDVITIKSRIRVKIEGCIS 152
Query: 61 TETSPISC 68
+ S I
Sbjct: 153 -QVSSIHA 159
>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E
4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E
Length = 180
Score = 53.4 bits (128), Expect = 3e-10
Identities = 12/56 (21%), Positives = 22/56 (39%), Gaps = 6/56 (10%)
Query: 2 VTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTS 57
V LG + ++ + ++D + E K + GDK++ RV S
Sbjct: 99 VNLGPMDGLVHISQITDDTLKYDNVRGIIFGE------KSKKVIQKGDKVRARVIS 148
>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide;
transcription, nucleotidyltransferase; 2.70A {Homo
sapiens} SCOP: b.40.4.5 d.230.1.1
Length = 172
Score = 51.8 bits (124), Expect = 1e-09
Identities = 8/68 (11%), Positives = 20/68 (29%), Gaps = 6/68 (8%)
Query: 1 MVTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELF 60
+G I + FD + + D+ + D+I+ ++
Sbjct: 98 FTEIGPM-SCFISRHSIPSEMEFDPNSNPPCY----KTMDEDIVIQQDDEIRLKIVGTRV 152
Query: 61 TETSPISC 68
+ + I
Sbjct: 153 -DKNDIFA 159
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 172
Score = 43.8 bits (103), Expect = 1e-06
Identities = 5/57 (8%), Positives = 18/57 (31%), Gaps = 7/57 (12%)
Query: 1 MVTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTS 57
+G ++ + + +FD + D ++ G ++ ++
Sbjct: 101 FANIGPL-NVFVSSHLVPPDMKFDPTANPPNYS------GEDQVIEKGSNVRLKIVG 150
>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 = 28.7 bits (63), Expect = 0.44
Identities = 16/113 (14%), Positives = 34/113 (30%), Gaps = 23/113 (20%)
Query: 4 LGFF-EDILIPPEGLQ---QPSRFDEKEQVWVWEFDN----EGDK-------HDLFMDPG 48
L F IP L + V V + E ++++
Sbjct: 378 LSVFPPSAHIPTILLSLIWFDVIKSDVMVV-VNKLHKYSLVEKQPKESTISIPSIYLE-- 434
Query: 49 DKIKFRVTSELFTETSPISCPDIHDGAPGSEVDTPKI-PYSYGY--YSLAVLR 98
+K ++ +E S + +I ++ P + Y Y + + L +
Sbjct: 435 --LKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIE 485
>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA,
DNA-binding, phosphorylation, POL I, POLI, rpoli,
nuclear protein; 3.10A {Saccharomyces cerevisiae}
Length = 214
Score = 26.6 bits (58), Expect = 1.8
Identities = 6/57 (10%), Positives = 17/57 (29%), Gaps = 5/57 (8%)
Query: 1 MVTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTS 57
++ F + I + F + + + + K++F V +
Sbjct: 147 LLIHDAF-NASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPI----DGKLRFTVRN 198
>2fb5_A Hypothetical membrane spanning protein; structural genomics,
membrane protein, PSI, protein structur initiative;
1.99A {Bacillus cereus} SCOP: d.320.1.1
Length = 205
Score = 25.7 bits (56), Expect = 3.3
Identities = 8/34 (23%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 42 DLFMDPGDKIKFRVTSELFTETSPISCPDIHDGA 75
+ + G + +T+ L P +HDGA
Sbjct: 105 EALIQTGTTLNAHLTAPLLESIFYPGNP-LHDGA 137
>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 = 25.8 bits (56), Expect = 4.4
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 57 SELFTETSPISCPDI 71
+ + + PISCP I
Sbjct: 227 DKDYLLSIPISCPLI 241
>3g9v_A Interleukin 22 receptor, alpha 2; cytokine, cytokine receptor,
receptor, glycoprotein, polymorphism, secreted,
cytokine/cytokine receptor complex; 2.76A {Homo sapiens}
Length = 211
Score = 25.1 bits (54), Expect = 5.8
Identities = 13/67 (19%), Positives = 22/67 (32%)
Query: 42 DLFMDPGDKIKFRVTSELFTETSPISCPDIHDGAPGSEVDTPKIPYSYGYYSLAVLRTQL 101
D + RV + S S +++D P + + SL V+
Sbjct: 70 SETSDIQEPYYGRVRAASAGSYSEWSMTPRFTPWWETKIDPPVMNITQVNGSLLVILHAP 129
Query: 102 LSPVRFQ 108
P R+Q
Sbjct: 130 NLPYRYQ 136
>2eja_A URO-D, UPD, uroporphyrinogen decarboxylase; dimer, X-RAY
diffraction, structural genomics, NPPSFA; 1.90A
{Aquifex aeolicus}
Length = 338
Score = 24.8 bits (55), Expect = 7.9
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 6 FFEDILIPPEGLQQPSRFDEKE 27
F DIL+P E L F E E
Sbjct: 72 IFSDILVPLEPLGVKVEFVEGE 93
>4exq_A UPD, URO-D, uroporphyrinogen decarboxylase; ssgcid, NIH, SBRI, heme
biosynthesis, structural GENO niaid; 1.65A {Burkholderia
thailandensis}
Length = 368
Score = 24.8 bits (55), Expect = 8.2
Identities = 7/21 (33%), Positives = 9/21 (42%)
Query: 7 FEDILIPPEGLQQPSRFDEKE 27
F DIL P+ + F E
Sbjct: 80 FSDILTIPDAMGLGLDFAAGE 100
>1lml_A Leishmanolysin; metalloprotease, glycoprotein; 1.86A {Leishmania
major} SCOP: d.92.1.3
Length = 478
Score = 24.7 bits (52), Expect = 9.2
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 47 PGDKIKFRVTSELFTETSPISCPDIHD 73
PG +++ S F I+CP +
Sbjct: 438 PGLRVELSTVSNAFEGGGYITCPPYVE 464
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 0.140 0.438
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,803,388
Number of extensions: 94706
Number of successful extensions: 233
Number of sequences better than 10.0: 1
Number of HSP's gapped: 225
Number of HSP's successfully gapped: 27
Length of query: 112
Length of database: 6,701,793
Length adjustment: 76
Effective length of query: 36
Effective length of database: 4,579,797
Effective search space: 164872692
Effective search space used: 164872692
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 (21.7 bits)
S2: 51 (23.3 bits)