RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11392
(169 letters)
>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 = 75.5 bits (185), Expect = 1e-17
Identities = 34/92 (36%), Positives = 53/92 (57%)
Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEG 82
K+ PNVGLC+ +YD+ +E+ + PGDG+S+ V FR VVF+PF+ EI+ G I C+ EG
Sbjct: 37 KIIPNVGLCITIYDLLTVEEGQLKPGDGSSYINVTFRAVVFKPFLGEIVTGWISKCTAEG 96
Query: 83 VHDSQSSNQPEQPISDSTVKDILKYFAEKDKP 114
+ S + I + + + Y E+
Sbjct: 97 IKVSLLGIFDDIFIPQNMLFEGCYYTPEESAW 128
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription;
2.19A {Schizosaccharomyces pombe}
Length = 203
Score = 69.7 bits (170), Expect = 2e-15
Identities = 30/62 (48%), Positives = 45/62 (72%)
Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEG 82
KV N+GL + +YD KI + +I GDG+S+ V FR ++FRPF E+++GKI+SCS+EG
Sbjct: 37 KVIQNIGLAICVYDFLKIGEGIIKYGDGSSYMNVVFRLIIFRPFRGEVMLGKIKSCSEEG 96
Query: 83 VH 84
+
Sbjct: 97 IR 98
>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 = 60.3 bits (146), Expect = 4e-12
Identities = 15/64 (23%), Positives = 34/64 (53%)
Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEG 82
++ +VG + + D+ I + ++ GDG+++ V F +V+ P + E+I G++ + G
Sbjct: 37 RLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPEMYELIEGEVVDVVEFG 96
Query: 83 VHDS 86
Sbjct: 97 SFVR 100
>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 = 59.9 bits (145), Expect = 5e-12
Identities = 17/62 (27%), Positives = 28/62 (45%)
Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEG 82
G + + I I VI PG G V+++ +VFRPF E++ + +K G
Sbjct: 37 TCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVG 96
Query: 83 VH 84
+
Sbjct: 97 LF 98
>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 = 58.8 bits (142), Expect = 1e-11
Identities = 17/64 (26%), Positives = 38/64 (59%)
Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEG 82
K+ ++GL + + ++ E+ +++ GDGA++ +VEF + + P V E++ G++ G
Sbjct: 37 KILKDLGLVLAILNVKTSEEGMLVFGDGATYHEVEFDMITYVPVVQEVVEGEVLQVDNYG 96
Query: 83 VHDS 86
V +
Sbjct: 97 VFVN 100
>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 = 55.5 bits (133), Expect = 4e-10
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 23 KVFPNVG--LCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSK 80
G LC++ YD I+ I+P DG++ V++R VVF+PF E++ G + SCS+
Sbjct: 37 SCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQ 96
Query: 81 EGVH 84
G
Sbjct: 97 HGFE 100
>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 = 54.2 bits (130), Expect = 7e-10
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 23 KVFPNVG--LCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSK 80
G LC++ YD I+ I+P DG++ V++R VVF+PF E++ G + SCS+
Sbjct: 37 SCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQ 96
Query: 81 EGVH 84
G
Sbjct: 97 HGFE 100
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 172
Score = 51.5 bits (123), Expect = 5e-09
Identities = 17/101 (16%), Positives = 40/101 (39%), Gaps = 17/101 (16%)
Query: 1 MLYDITKIEDSVIIP----GDGASHT-----------KVFPNVGLCMMLYD--ITKIEDS 43
M + + ++ ++ + G G + + D I+
Sbjct: 1 MPFFLKELSLTISLHPSYFGPRMQDYLKAKLLADVEGTCSGQYGYIICVLDSNTIDIDKG 60
Query: 44 VIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVH 84
++PG G + +V++R V++RPF E++ + + +K G
Sbjct: 61 RVVPGQGFAEFEVKYRAVLWRPFRGEVVDAIVTTVNKMGFF 101
>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 = 38.9 bits (90), Expect = 3e-04
Identities = 9/40 (22%), Positives = 15/40 (37%)
Query: 45 IIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVH 84
I P T V++P V +++ G I S +
Sbjct: 107 ITPDTPFGFTWCHVNLYVWQPQVGDVLEGYIFIQSASHIG 146
>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 = 33.5 bits (76), Expect = 0.031
Identities = 18/90 (20%), Positives = 30/90 (33%), Gaps = 16/90 (17%)
Query: 48 GDGASHTKV-EFR--YVVFRPFVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVKDI 104
G G + E R Y + V ++I + S+ + Q + +I
Sbjct: 162 GQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGL------NI 215
Query: 105 LKYFAEKD-KPDPVRDFLMGAIAPALRSLP 133
L++ PD D+L P S P
Sbjct: 216 LEWLENPSNTPDK--DYL--LSIPI--SCP 239
Score = 30.8 bits (69), Expect = 0.21
Identities = 24/168 (14%), Positives = 42/168 (25%), Gaps = 53/168 (31%)
Query: 8 IEDSVIIPGDGASHTKV----F------PNVGLCMMLYDITKIE---------DSVIIPG 48
+E +++P F P G T E S++ P
Sbjct: 16 LEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPS 75
Query: 49 DGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVKDILK-Y 107
+V + F + + G +H + E + K+++K Y
Sbjct: 76 KVGQFDQV--LNLCLTEFENCYLEGN-------DIHALAAKLLQENDTTLVKTKELIKNY 126
Query: 108 FAEKDKPDPVRDFLMGAIAPALRSLPRH----LFLKAKKE------IF 145
A A R + LF + IF
Sbjct: 127 IT--------------ARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF 160
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 31.8 bits (71), Expect = 0.059
Identities = 12/47 (25%), Positives = 16/47 (34%), Gaps = 23/47 (48%)
Query: 100 TVKDI---LKYFAEKDKPDPVRDFLMGAIAPALRSLPRHLFLKAKKE 143
+K + LK +A D APAL +KA E
Sbjct: 21 ALKKLQASLKLYA----DDS---------APALA-------IKATME 47
>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 = 29.1 bits (64), Expect = 0.77
Identities = 18/111 (16%), Positives = 32/111 (28%), Gaps = 36/111 (32%)
Query: 85 DSQSSNQPEQPISDSTVKDILKYFAEKDKPD----PVRDFLMGAI----------APALR 130
D ++ KDIL F + + V+D + +
Sbjct: 8 DFETGEH------QYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAV 61
Query: 131 SLPRHLF--LKAK-----KEIFEAVHK--YEMIAE-------EQSGDQYEY 165
S LF L +K ++ E V + Y+ + + S Y
Sbjct: 62 SGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMY 112
>3umv_A Deoxyribodipyrimidine photo-lyase; CPD cyclobutane pyrimidine
dimers, UV damaged DNA, DNA repai flavoprotein; HET:
FAD; 1.71A {Oryza sativa japonica group}
Length = 506
Score = 27.4 bits (61), Expect = 2.6
Identities = 22/112 (19%), Positives = 38/112 (33%), Gaps = 9/112 (8%)
Query: 41 EDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDST 100
+ ++P AS K+E+ FR VS+++ + + QPE D+
Sbjct: 167 DAHNVVPVWTAS-AKMEYSAKTFRGKVSKVMDEYLVEFPELPAVVPWDREQPEGVDWDAL 225
Query: 101 VKDILKYFAEKDKPDPVRDFLMGAIAPALRSLPRHLFLKAKKEIFEAVHKYE 152
+ + + D AI L S FL + + YE
Sbjct: 226 IARVCSEAENVPEIDWCEPGEEAAIEALLGSKDG--FLT------KRIKSYE 269
>1o7x_A Citrate synthase; lyase, tricarboxylic acid cycle; 2.7A {Sulfolobus
solfataricus} SCOP: a.103.1.1
Length = 377
Score = 26.7 bits (60), Expect = 4.6
Identities = 6/24 (25%), Positives = 9/24 (37%), Gaps = 2/24 (8%)
Query: 100 TVKDILKYFAEKDKPDPVRDFLMG 123
+ +F +K R LMG
Sbjct: 234 DPNRVQNWFNDKVVNQKNR--LMG 255
>2ifc_A Citrate synthase; oxaloacetate, EC 2.3.3.1, transferase; 1.70A
{Thermoplasma acidophilum} PDB: 2r9e_A* 2r26_A*
Length = 385
Score = 26.0 bits (58), Expect = 6.9
Identities = 6/24 (25%), Positives = 9/24 (37%), Gaps = 2/24 (8%)
Query: 100 TVKDILKYFAEKDKPDPVRDFLMG 123
+ K+F + R LMG
Sbjct: 239 DPAMVEKWFNDNIINGKKR--LMG 260
>3ot1_A 4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis
enzyme; csgid, structural genomics; HET: MSE CSX; 1.16A
{Vibrio cholerae o1 biovar el tor}
Length = 208
Score = 25.7 bits (57), Expect = 7.5
Identities = 7/47 (14%), Positives = 17/47 (36%), Gaps = 10/47 (21%)
Query: 98 DSTVKDILKYFAEKDKPDPVRDFLMGAI--APALRSLPRHLFLKAKK 142
+ + ++ F+++ K + AI PAL + +
Sbjct: 90 STALLALIDAFSQQGKL-------VAAICATPAL-VFAKQQKFVGAR 128
>2xzm_L 40S ribosomal protein S12; ribosome, translation; 3.93A
{Tetrahymena thermophila} PDB: 2xzn_L 3j0o_L 3j0l_L
3j0p_L 3j0q_L 3iz6_L 3jyv_L* 1s1h_L*
Length = 142
Score = 25.4 bits (55), Expect = 7.6
Identities = 5/21 (23%), Positives = 8/21 (38%)
Query: 46 IPGDGASHTKVEFRYVVFRPF 66
+P DG + E V+
Sbjct: 86 VPMDGCLNFLAENDEVLVAGL 106
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 0.137 0.395
Gapped
Lambda K H
0.267 0.0827 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,609,487
Number of extensions: 151717
Number of successful extensions: 424
Number of sequences better than 10.0: 1
Number of HSP's gapped: 420
Number of HSP's successfully gapped: 36
Length of query: 169
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 82
Effective length of database: 4,272,666
Effective search space: 350358612
Effective search space used: 350358612
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: 54 (24.4 bits)