RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13107
(170 letters)
>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 = 185 bits (472), Expect = 5e-61
Identities = 139/170 (81%), Positives = 159/170 (93%)
Query: 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
MFYHISLEHEILLHPRYFGP L TVKQKL++EVEGTCTGKYGFVIAVTTID+IGAG+IQ
Sbjct: 1 MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ 60
Query: 61 PGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFC 120
PG+GFV+YPVKY+AIVFRPFKGEV+DAVVTQVNKVG+F EIGP+SCFIS HSIP++M+F
Sbjct: 61 PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD 120
Query: 121 PNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL 170
PNSNP CYK++ ++VIQ+DDEIRLKIVGTRVD + IFAIG+LMDDYLGL
Sbjct: 121 PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGL 170
>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 = 178 bits (452), Expect = 4e-58
Identities = 74/172 (43%), Positives = 103/172 (59%), Gaps = 4/172 (2%)
Query: 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTID--SIGAGL 58
MF+ L I LHP +FGP++ + +K KL EVEG+CTGK+G+++ V D I G
Sbjct: 1 MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGR 60
Query: 59 IQPGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQ 118
I P G + VKYRA+VF+PFKGEV+D V ++ G ++GP+ F++ H +P D+
Sbjct: 61 ILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT 120
Query: 119 FCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL 170
F SNP Y+S E VI IR+KI G S I AIG++ +DYLG
Sbjct: 121 FNAGSNPPSYQS--SEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGA 170
>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 = 176 bits (446), Expect = 1e-56
Identities = 74/172 (43%), Positives = 103/172 (59%), Gaps = 4/172 (2%)
Query: 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTID--SIGAGL 58
MF+ L I LHP +FGP++ + +K KL EVEG+CTGK+G+++ V D I G
Sbjct: 1 MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGR 60
Query: 59 IQPGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQ 118
I P G + VKYRA+VF+PFKGEV+D V ++ G ++GP+ F++ H +P D+
Sbjct: 61 ILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT 120
Query: 119 FCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL 170
F SNP Y+S E VI IR+KI G S I AIG++ +DYLG
Sbjct: 121 FNAGSNPPSYQS--SEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGA 170
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 172
Score = 163 bits (415), Expect = 2e-52
Identities = 87/172 (50%), Positives = 120/172 (69%), Gaps = 4/172 (2%)
Query: 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTT--IDSIGAGL 58
F+ L I LHP YFGP++ + +K KL ++VEGTC+G+YG++I V I G
Sbjct: 2 PFFLKELSLTISLHPSYFGPRMQDYLKAKLLADVEGTCSGQYGYIICVLDSNTIDIDKGR 61
Query: 59 IQPGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQ 118
+ PGQGF + VKYRA+++RPF+GEV+DA+VT VNK+G FA IGPL+ F+S H +P DM+
Sbjct: 62 VVPGQGFAEFEVKYRAVLWRPFRGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPPDMK 121
Query: 119 FCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLGL 170
F P +NP Y + VI++ +RLKIVGTR DA+ IFAI T+ +DYLG+
Sbjct: 122 FDPTANPPNYSG--EDQVIEKGSNVRLKIVGTRTDATEIFAIATMKEDYLGV 171
>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 = 162 bits (412), Expect = 6e-52
Identities = 40/172 (23%), Positives = 73/172 (42%), Gaps = 3/172 (1%)
Query: 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
M+ I + + P FG L E +L + + G V+A+ + + G++
Sbjct: 1 MYKLIKARSIVRIPPNEFGKPLNEIALNELRQQYQEKILKDLGLVLAILNVKTSEEGMLV 60
Query: 61 PGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFC 120
G G + V++ I + P EV++ V QV+ G+F +GP+ + I D
Sbjct: 61 FGDGATYHEVEFDMITYVPVVQEVVEGEVLQVDNYGVFVNLGPMDGLVHISQITDDTLKY 120
Query: 121 PNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI-FAIGTLM-DDYLGL 170
N + + + VIQ+ D++R +++ +G I M YLG
Sbjct: 121 DNVRGIIFGE-KSKKVIQKGDKVRARVISVASTVTGRLPRIALTMRQPYLGK 171
>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 = 158 bits (401), Expect = 4e-50
Identities = 47/174 (27%), Positives = 77/174 (44%), Gaps = 6/174 (3%)
Query: 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
M+ + + + + P FG L ETVK+ L + EG GFV+++ + IG G +
Sbjct: 1 MYKILEIADVVKVPPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVV 60
Query: 61 PGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTD-MQF 119
G G +PV + +V+ P E+++ V V + G F +GPL I I D + +
Sbjct: 61 HGDGSAYHPVVFETLVYIPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSY 120
Query: 120 CPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI---FAIGTLMDDYLGL 170
P + K V++ D +R +IV + A T+ YLG
Sbjct: 121 DPKREAIIGK--ETGKVLEIGDYVRARIVAISLKAERKRGSKIALTMRQPYLGK 172
>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 = 157 bits (399), Expect = 2e-49
Identities = 27/154 (17%), Positives = 62/154 (40%), Gaps = 3/154 (1%)
Query: 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
MF + + + P F + +L ++ G I + + ++ G ++
Sbjct: 1 MFILSKIADLVRIPPDQFHRDTISAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLK 60
Query: 61 PGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPL--SCFISHHSIPTDMQ 118
PG G V +RA+VF+PF GE++ +++ G+ + + FI + +
Sbjct: 61 PGDGSSYINVTFRAVVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCY 120
Query: 119 FCPNSNPVCYKS-VHGEVVIQEDDEIRLKIVGTR 151
+ P + + ++ +++IR +I
Sbjct: 121 YTPEESAWIWPMDEETKLYFDVNEKIRFRIEREV 154
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A
{Schizosaccharomyces pombe}
Length = 203
Score = 145 bits (366), Expect = 1e-44
Identities = 40/158 (25%), Positives = 63/158 (39%), Gaps = 7/158 (4%)
Query: 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
MF I +HP F E + ++++ + G I V IG G+I+
Sbjct: 1 MFLLSRFSDIISIHPSNFWKPTKEALAEEIHKKYANKVIQNIGLAICVYDFLKIGEGIIK 60
Query: 61 PGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSC-FISHHSIPTDMQF 119
G G V +R I+FRPF+GEV+ + ++ G+ I FI + F
Sbjct: 61 YGDGSSYMNVVFRLIIFRPFRGEVMLGKIKSCSEEGIRVTISFFDDIFIPKDMLFDPCVF 120
Query: 120 CPNSNPVCYK------SVHGEVVIQEDDEIRLKIVGTR 151
P+ +K S E+ D+EIR +I
Sbjct: 121 RPDERAWVWKIEGEDGSEGTELYFDIDEEIRFQIESED 158
>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 = 84.0 bits (207), Expect = 1e-20
Identities = 31/177 (17%), Positives = 52/177 (29%), Gaps = 15/177 (8%)
Query: 2 FYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIA------------VT 49
+ + + L P Y L +KQ L V G V+
Sbjct: 38 IVRVPIALYVSLAPMYLENPLQGVMKQHLNPLVMKYNNKVGGVVLGYEGLKILDADPLSK 97
Query: 50 TIDSIGAGLIQPGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNK--VGMFAEIGPLSCF 107
S I P F V++P G+VL+ + + +G+ +
Sbjct: 98 EDTSEKLIKITPDTPFGFTWCHVNLYVWQPQVGDVLEGYIFIQSASHIGLLI-HDAFNAS 156
Query: 108 ISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLM 164
I ++IP D F N D ++R + + GTL+
Sbjct: 157 IKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTGRVVSVDGTLI 213
>3hh7_A Muscarinic toxin-like protein 3 homolog; haditoxin, three finger
toxin, snake venom, neurotoxin, nicotinic acetylcholine
receptors; 1.55A {Ophiophagus hannah}
Length = 65
Score = 27.6 bits (61), Expect = 0.50
Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 3/36 (8%)
Query: 106 CFISHHSIPTDMQFCPNSNPVCYK---SVHGEVVIQ 138
C+ + P + CP+S CYK E I+
Sbjct: 3 CYNHQSTTPETTEICPDSGYFCYKSSWIDGREGRIE 38
>3neq_A Muscarinic M1-toxin1, muscarinic toxin 1; chimeric muscarinic
toxin, HM1-muscarinic receptor, snake to green mamba;
1.25A {Dendroaspis angusticeps} PDB: 2vlw_A* 3fev_A
Length = 66
Score = 26.4 bits (58), Expect = 1.5
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 104 LSCFISHHSIPTDMQFCPNSNPVCYK 129
L+C S+ + CP+ +C+K
Sbjct: 1 LTCVKSNSIWFPTSEDCPDGQNLCFK 26
>2c1o_A IGK-C protein; FAB fragment, enantioselective, finrozole, immune
system, antibody, ENA11His antibody, immunoglobulin
domain; 2.75A {Mus musculus}
Length = 254
Score = 27.8 bits (62), Expect = 1.7
Identities = 8/37 (21%), Positives = 15/37 (40%)
Query: 55 GAGLIQPGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQ 91
GA L++PG + + + + V+TQ
Sbjct: 7 GAELVRPGTSVKLSCKASGYSFTNYWMNWLRELVMTQ 43
>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 = 28.1 bits (62), Expect = 1.9
Identities = 20/101 (19%), Positives = 32/101 (31%), Gaps = 36/101 (35%)
Query: 4 HISLEHEIL----LHPRYFGPQLYETVKQKLYSEVEGTC-----------TGKY-GFVIA 47
H SLEH +L QL E + L EG GK+ G+V
Sbjct: 13 HGSLEHVLLVPTASFFIAS--QLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYV-- 68
Query: 48 VTTIDSIGAGLIQPGQGFVVYPVKYRAI---VFRPFKGEVL 85
+ L++P + ++ + F+ L
Sbjct: 69 --------SSLVEPSK-----VGQFDQVLNLCLTEFENCYL 96
>2qtx_A Uncharacterized protein MJ1435; HFQ, SM, RNA-binding protein, sRNA,
translational regulation, RNA binding protein; 2.50A
{Methanocaldococcus jannaschii}
Length = 71
Score = 25.8 bits (56), Expect = 2.7
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 82 GEVLDAVVTQVNKVGMFAEIGPLSCFISHHSI 113
GEVLDA VT V+ + ++G + + H+I
Sbjct: 35 GEVLDAEVTGVSNYEIMVKVGDRNLLVFKHAI 66
>3era_A Erabutoxin A; snake neurotoxin, venom, postsynaptic neurotoxin;
1.70A {Laticauda semifasciata} SCOP: g.7.1.1 PDB: 2era_A
Length = 62
Score = 25.6 bits (56), Expect = 3.1
Identities = 7/24 (29%), Positives = 8/24 (33%)
Query: 106 CFISHHSIPTDMQFCPNSNPVCYK 129
CF S P + C CY
Sbjct: 3 CFNHQTSQPQTTKTCSPGESSCYN 26
>1ff4_A Muscarinic toxin/acetylcholine receptor binding P; three fingers
motif; 1.50A {Dendroaspis angusticeps} SCOP: g.7.1.1
Length = 65
Score = 25.2 bits (55), Expect = 3.6
Identities = 7/27 (25%), Positives = 11/27 (40%)
Query: 104 LSCFISHHSIPTDMQFCPNSNPVCYKS 130
L+C + + CP VC+K
Sbjct: 1 LTCVTTKSIGGVTTEDCPAGQNVCFKR 27
>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2,
structure initiative, northeast structural genomics
consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP:
b.40.4.5 b.40.4.16 PDB: 2r7f_A
Length = 469
Score = 26.1 bits (58), Expect = 6.7
Identities = 6/25 (24%), Positives = 6/25 (24%)
Query: 77 FRPFKGEVLDAVVTQVNKVGMFAEI 101
V DAVV I
Sbjct: 399 IAAQPERVWDAVVVDRRGAQATLLI 423
>1zcz_A Bifunctional purine biosynthesis protein PURH; TM1249; HET: PG4;
1.88A {Thermotoga maritima} SCOP: c.24.1.3 c.97.1.4
Length = 464
Score = 25.9 bits (58), Expect = 7.7
Identities = 5/34 (14%), Positives = 10/34 (29%), Gaps = 2/34 (5%)
Query: 120 CPNSNPVCYKSVHGEVVIQEDDEIR--LKIVGTR 151
+ K G +V+ E ++V
Sbjct: 312 PGDYASWAGKMAFGSLVLSERKYPEGNFELVVGE 345
>2hti_A BH0577 protein; structural genomics, joint center for structural
genomics, J protein structure initiative, PSI-2,
FMN-binding protein; HET: FAD; 2.50A {Bacillus
halodurans} SCOP: b.45.1.1
Length = 185
Score = 25.3 bits (55), Expect = 9.1
Identities = 10/48 (20%), Positives = 14/48 (29%), Gaps = 2/48 (4%)
Query: 102 GPLSCFISHHSIPTDMQFCPNSNPVCYKSV--HGEVVIQEDDEIRLKI 147
P CF + T + P Y SV G + E +
Sbjct: 69 NPEVCFTICEDLGTIVSPVPAHTDTAYMSVIIFGTIEPVSAIEEGTEA 116
>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger,
structural genomics, PSI-2, protein structure
initiative; NMR {Methanocaldococcus jannaschii}
Length = 80
Score = 24.2 bits (53), Expect = 9.7
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 82 GEVLDAVVTQVNKVGMFAEIGP 103
G+ VVT++ K G F +
Sbjct: 6 GKFYKGVVTRIEKYGAFINLNE 27
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
0.324 0.143 0.434
Gapped
Lambda K H
0.267 0.0598 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,737,812
Number of extensions: 159438
Number of successful extensions: 361
Number of sequences better than 10.0: 1
Number of HSP's gapped: 348
Number of HSP's successfully gapped: 23
Length of query: 170
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 83
Effective length of database: 4,272,666
Effective search space: 354631278
Effective search space used: 354631278
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (24.9 bits)