RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 045123
(219 letters)
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase
subunit A', DNA-directed...; transcription, fusion
protein, chimera protein, multiprotein; 3.30A
{Pyrococcus furiosus}
Length = 436
Score = 209 bits (535), Expect = 2e-66
Identities = 65/203 (32%), Positives = 96/203 (47%), Gaps = 24/203 (11%)
Query: 14 KVRMVQFSILSPDEIRKMSVTEIDHGKT-TERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
+ ++F ILSP EIRKMS E+ T + G P+ GG+ D R+G ID +CETC
Sbjct: 68 VIGSIEFGILSPQEIRKMSAVEVTVPDTYDDDGYPIEGGVMDKRMGVIDPGLRCETCGGR 127
Query: 73 MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKF--KLALKIRHP 130
GECPGHFGH+ELA+P+ H+GF KT+ I+ C C +I +E+ + K R+
Sbjct: 128 AGECPGHFGHIELARPVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKKIELARNR 187
Query: 131 KSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTIDGMNMIA 190
+S +I+ K K R CGA Q + + +
Sbjct: 188 RSEFNEIIKEIHKKAKE--------------------RMVCPHCGAPQYPIKFEKPTIYW 227
Query: 191 EYKAQRKKNDDQGQL-PEPVERK 212
E + + N+ + +L P V
Sbjct: 228 EIRKDEQGNEYRHRLMPTEVRDW 250
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 219 bits (558), Expect = 5e-66
Identities = 84/202 (41%), Positives = 117/202 (57%), Gaps = 4/202 (1%)
Query: 5 FTFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTE--RGMPMAGGLSDLRLGTIDK 62
F+ S + +V VQF ILSP+EIR MSV +I+ +T + P GGL D RLGTID+
Sbjct: 6 FSPSSVPLRRVEEVQFGILSPEEIRSMSVAKIEFPETMDESGQRPRVGGLLDPRLGTIDR 65
Query: 63 RFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK 122
+FKC+TC M +CPGHFGH+ELAKP+FHIGF+ + I+ CVC+NC K+ D + KF
Sbjct: 66 QFKCQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFN 125
Query: 123 LALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLT 182
+ R PK+RL + CKTK C+ G + GCGA QPT+
Sbjct: 126 DTQRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDN--FDLSNPSANMGHGGCGAAQPTIR 183
Query: 183 IDGMNMIAEYKAQRKKNDDQGQ 204
DG+ + +K + ++D +
Sbjct: 184 KDGLRLWGSWKRGKDESDLPEK 205
>1twf_A B220, DNA-directed RNA polymerase II largest subunit;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB:
1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A
1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A*
1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 212 bits (541), Expect = 1e-63
Identities = 76/216 (35%), Positives = 113/216 (52%), Gaps = 16/216 (7%)
Query: 6 TFSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKT--TERGMPMAGGLSDLRLGTIDKR 63
+S + V+ VQF + SP+E+R +SV +I +T + GGL+D RLG+ID+
Sbjct: 5 QYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRN 64
Query: 64 FKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKL 123
KC+TC M ECPGHFGH++LAKP+FH+GF+ + + CVC +C K+L DE ++ +
Sbjct: 65 LKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQ 124
Query: 124 ALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTI 183
AL I+ K R I CKTK CE + + + GCG QPT+
Sbjct: 125 ALAIKDSKKRFAAIWTLCKTKMVCETDVP--------SEDDPTQLVSRGGCGNTQPTIRK 176
Query: 184 DGMNMIAEYKAQRKKNDDQGQLPEPVERKQTLTAER 219
DG+ ++ +K R D + L+ E
Sbjct: 177 DGLKLVGSWKKDRATGDADE------PELRVLSTEE 206
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A
2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A
Length = 880
Score = 169 bits (429), Expect = 1e-48
Identities = 52/186 (27%), Positives = 82/186 (44%), Gaps = 18/186 (9%)
Query: 14 KVRMVQFSILSPDEIRKMSVTEIDHGKT-TERGMPMAGGLSDLRLGTIDKRFKCETCSSN 72
++ ++F ILSPDEIRKMSVT I E G P+ G + D RLG I+ KC TC +
Sbjct: 5 NIKGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCGNT 64
Query: 73 MGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLALKIRHPKS 132
+G CPGHFGH+EL +P+ H+GF+K + ++ C C ++ E++ + + K
Sbjct: 65 LGNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKR 124
Query: 133 RLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTIDGMNMIAEY 192
+ K + CG Q + ++ E
Sbjct: 125 WPSAARRLTEYVKKTAMK-----------------AQVCPHCGEKQFKIKLEKPYNFYEE 167
Query: 193 KAQRKK 198
+ +
Sbjct: 168 RKEGVA 173
>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 = 41.2 bits (96), Expect = 2e-04
Identities = 36/215 (16%), Positives = 67/215 (31%), Gaps = 62/215 (28%)
Query: 15 VRMVQFSI------LSPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTIDKRFKCET 68
+++ + + +P E+R H + G+ A ++ + F
Sbjct: 244 IQLAHYVVTAKLLGFTPGELRSYLKGATGHSQ----GLVTAVAIA---ETDSWESF--FV 294
Query: 69 CSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRC-----VCFNCSKILADEEDDKFKL 123
+ + +F IG RC IL D ++ +
Sbjct: 295 SVRKA---------ITV---LFFIGV--------RCYEAYPNTSLPPSILEDSLENNEGV 334
Query: 124 A---LKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRK---SGCGAL 177
L I + EQ+ N + +SL +G + SG
Sbjct: 335 PSPMLSISNL--TQEQVQDYVNKTNSHLPAGKQVEISL--VNG-----AKNLVVSG---- 381
Query: 178 QPTLTIDGMNMIAEYKAQRKKNDDQGQLPEPVERK 212
P ++ G+N+ KA+ DQ ++P ERK
Sbjct: 382 -PPQSLYGLNLTLR-KAKAPSGLDQSRIPFS-ERK 413
>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 = 40.6 bits (94), Expect = 3e-04
Identities = 25/115 (21%), Positives = 39/115 (33%), Gaps = 18/115 (15%)
Query: 82 HLELAKPMFHI------GFMKTLLTIMRCVCFNCSKILADEEDDKFKLAL-KIRHPKSRL 134
L +P ++ G KT + + VC + K+ + F L L P++ L
Sbjct: 143 ALLELRPAKNVLIDGVLGSGKTWVALD--VCLS-YKVQCKMDFKIFWLNLKNCNSPETVL 199
Query: 135 EQI--LCACKTKNKCEGGDEIDVLSLLGHDGEEPLR---KRKSGCGALQPTLTID 184
E + L N D + L H + LR K K L L +
Sbjct: 200 EMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL---LVLL 251
Score = 40.2 bits (93), Expect = 4e-04
Identities = 33/219 (15%), Positives = 64/219 (29%), Gaps = 59/219 (26%)
Query: 11 KVAKVRMVQFSILSPDEIRKM----SVTEID------------HGKTTERGMPMAGGLSD 54
K+ + ++L P E RKM SV M + L
Sbjct: 354 KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHK 413
Query: 55 LRLGTIDKRFKCETCSSNMGECPGHFGHLELAKPMFHIGFM-KTLLT---IMRCVCFNCS 110
L ++K+ K T S +LEL + + + ++++ I + +
Sbjct: 414 YSL--VEKQPKESTISI-------PSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD-- 462
Query: 111 KILADEEDDKF--KLALKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLR 168
++ D F + H K E + + + ++ D R
Sbjct: 463 DLIPPYLDQYFYSHIG---HHLK--------------NIEHPERMTLFRMVFLD----FR 501
Query: 169 ----K-RKSGCGALQPTLTIDGMNMIAEYKAQRKKNDDQ 202
K R ++ + + YK ND +
Sbjct: 502 FLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPK 540
Score = 39.5 bits (91), Expect = 7e-04
Identities = 28/158 (17%), Positives = 47/158 (29%), Gaps = 36/158 (22%)
Query: 79 HFGHLELAKPMFHIGFMKTLLTIMRCVC--FNCS-------KILADEEDDKFKLALKIRH 129
H H++ + L F+C IL+ EE D + +
Sbjct: 3 HHHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHI---IMSKD 59
Query: 130 PKSRLEQILCACKTKNK------CEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTI 183
S ++ +K + E I+ L+ P++ QP++
Sbjct: 60 AVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLM-----SPIKTE-----QRQPSMMT 109
Query: 184 DGMNMIAEYKAQRKK--NDDQGQLPEPVERKQTLTAER 219
Y QR + ND+Q V R Q R
Sbjct: 110 R------MYIEQRDRLYNDNQVFAKYNVSRLQPYLKLR 141
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_D*
Length = 1407
Score = 35.7 bits (83), Expect = 0.011
Identities = 32/108 (29%), Positives = 43/108 (39%), Gaps = 34/108 (31%)
Query: 18 VQFSILSPDEIRKMSVTEIDHGKTTE-RGM-PMAGGLSDLRL-GTID---------KRFK 65
++ ++ SPD IR S E+ +T R P GL R+ G + KR K
Sbjct: 20 IKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLK 79
Query: 66 -----CETCS----------SNMGECPGHFGHLELAKPMFHIGFMKTL 98
CE C MG H+ELA P HI F+K+L
Sbjct: 80 HRGVICEKCGVEVTQTKVRRERMG-------HIELASPTAHIWFLKSL 120
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D-
structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB:
1i6v_D* 2gho_D
Length = 1265
Score = 34.6 bits (80), Expect = 0.023
Identities = 31/101 (30%), Positives = 46/101 (45%), Gaps = 20/101 (19%)
Query: 18 VQFSILSPDEIRKMSVTEIDHGKTTE-RGM-PMAGGLSDLRL-GTID---------KRFK 65
V+ ++ SP++IR S E++ +T R + P GL D R+ G I KR +
Sbjct: 8 VRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQR 67
Query: 66 -----CETCSSNMGECP---GHFGHLELAKPMFHIGFMKTL 98
CE C + GH+ELA P HI F+K +
Sbjct: 68 FEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDV 108
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2
PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D*
2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D*
3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Length = 1524
Score = 32.8 bits (75), Expect = 0.077
Identities = 31/101 (30%), Positives = 47/101 (46%), Gaps = 20/101 (19%)
Query: 18 VQFSILSPDEIRKMSVTEIDHGKTTE-RGM-PMAGGLSDLRL-GTID---------KRFK 65
V+ ++ SP++IR S E++ +T R + P GL D R+ G I KR +
Sbjct: 8 VRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQR 67
Query: 66 -----CETCSSNMGECP---GHFGHLELAKPMFHIGFMKTL 98
CE C + + GH+ELA P HI F+K +
Sbjct: 68 FEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDV 108
>1kk1_A EIF2gamma; initiation of translation; HET: GNP; 1.80A {Pyrococcus
abyssi} SCOP: b.43.3.1 b.44.1.1 c.37.1.8 PDB: 1kjz_A*
1kk2_A* 1kk3_A* 1kk0_A* 2d74_A 2dcu_A*
Length = 410
Score = 29.5 bits (67), Expect = 0.91
Identities = 21/99 (21%), Positives = 32/99 (32%), Gaps = 42/99 (42%)
Query: 36 IDHGKTT-----------------ERGMPMAGGLSDLRLGTID-KRFKCETC--SSNMGE 75
+DHGKTT RG+ +++G D + +C C S
Sbjct: 19 VDHGKTTLTKALTGVWTDTHSEELRRGI-------TIKIGFADAEIRRCPNCGRYSTSPV 71
Query: 76 CPGHFGHLELAKPMFHIGF---------MKTLLT---IM 102
CP E + + F M T+L +M
Sbjct: 72 CPYCGHETEFVR---RVSFIDAPGHEALMTTMLAGASLM 107
>1s0u_A EIF-2-gamma, translation initiation factor 2 gamma subunit; GTPase,
EF-1A, tRNA; 2.40A {Methanocaldococcus jannaschii} SCOP:
b.43.3.1 b.44.1.1 c.37.1.8
Length = 408
Score = 29.2 bits (66), Expect = 0.97
Identities = 19/91 (20%), Positives = 30/91 (32%), Gaps = 33/91 (36%)
Query: 36 IDHGKTT-----------------ERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGECPG 78
+DHGKT+ RG+ + G +D I K +C + CP
Sbjct: 17 VDHGKTSLTKALTGVWTDRHSEELRRGISIRLGYAD---CEIRKCPQCG-TYTTKPRCPN 72
Query: 79 HFGHLELAKPMFHIGF---------MKTLLT 100
E + + F M T+L+
Sbjct: 73 CLAETEFLR---RVSFVDSPGHETLMATMLS 100
>1n0u_A EF-2, elongation factor 2; G-protein, CIS-proline, translation;
HET: SO1; 2.12A {Saccharomyces cerevisiae} SCOP:
b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1 PDB:
1n0v_C 1s1h_T 2e1r_A* 2npf_A* 2p8w_T* 3dny_T 3b82_A*
1zm2_A* 1zm3_A* 1zm4_A* 1zm9_A* 2p8x_T* 2p8y_T* 2p8z_T*
2zit_A* 1u2r_A* 3b78_A* 3b8h_A*
Length = 842
Score = 29.2 bits (65), Expect = 1.2
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 8/34 (23%)
Query: 17 MVQFSI-------LSPDEIRKMSVT-EIDHGKTT 42
MV F++ +R MSV +DHGK+T
Sbjct: 1 MVAFTVDQMRSLMDKVTNVRNMSVIAHVDHGKST 34
>1np3_A Ketol-acid reductoisomerase; A DEEP figure-OF-eight knot,
C-terminal alpha-helical domain oxidoreductase; 2.00A
{Pseudomonas aeruginosa} SCOP: a.100.1.2 c.2.1.6
Length = 338
Score = 26.9 bits (60), Expect = 5.0
Identities = 12/37 (32%), Positives = 16/37 (43%)
Query: 39 GKTTERGMPMAGGLSDLRLGTIDKRFKCETCSSNMGE 75
G + A G+ R G I+ FK ET + GE
Sbjct: 158 GNAKNVALSYACGVGGGRTGIIETTFKDETETDLFGE 194
>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein,
mostly mixed alpha-beta structures, one domain is
entirely helical; HET: DNA; 2.20A {Thermus aquaticus}
SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A*
1fw6_A* 1ewr_A*
Length = 765
Score = 26.7 bits (60), Expect = 7.3
Identities = 5/17 (29%), Positives = 9/17 (52%), Gaps = 1/17 (5%)
Query: 204 QLPEPVERKQTLT-AER 219
++P+ QTL +R
Sbjct: 459 RVPKEYRPVQTLKDRQR 475
>2r78_A Sensor protein; sensory box sensor histidine kinase/response
regulator, structural genomics, PSI, MCSG; 1.60A
{Geobacter sulfurreducens pca}
Length = 117
Score = 25.6 bits (57), Expect = 7.9
Identities = 3/43 (6%), Positives = 10/43 (23%)
Query: 24 SPDEIRKMSVTEIDHGKTTERGMPMAGGLSDLRLGTIDKRFKC 66
+ DE + + G + + ++
Sbjct: 47 TRDEFLALDWGVLSRGVDSGWAAASLARIVGGEPLREERTVWT 89
>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA
binding, DNA repair, mismatch recognition; HET: DNA ADP;
2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12
c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A*
1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*
Length = 800
Score = 26.7 bits (60), Expect = 8.2
Identities = 8/17 (47%), Positives = 9/17 (52%), Gaps = 1/17 (5%)
Query: 204 QLPEPVERKQTLT-AER 219
P R+QTL AER
Sbjct: 484 LAPINYMRRQTLKNAER 500
>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch
recognition, mismatched unpaired DNA binding protein-DNA
complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A*
2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*
Length = 934
Score = 26.5 bits (59), Expect = 9.4
Identities = 1/25 (4%), Positives = 5/25 (20%), Gaps = 1/25 (4%)
Query: 196 RKKNDDQGQLPEPVERKQTLT-AER 219
K + + + +
Sbjct: 526 TCKEEKVLRNNKNFSTVDIQKNGVK 550
>3bwl_A Sensor protein; structural genomics, APC87707.1, PAS domain,
HTR-like protei protein structure initiative; HET: MSE
I3A; 1.73A {Haloarcula marismortui atcc 43049}
Length = 126
Score = 25.2 bits (56), Expect = 9.7
Identities = 5/21 (23%), Positives = 7/21 (33%)
Query: 24 SPDEIRKMSVTEIDHGKTTER 44
E+ S+ E D E
Sbjct: 53 DESEVLGRSIWEFDLMFDAED 73
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
0.321 0.137 0.414
Gapped
Lambda K H
0.267 0.0623 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,342,663
Number of extensions: 195066
Number of successful extensions: 382
Number of sequences better than 10.0: 1
Number of HSP's gapped: 371
Number of HSP's successfully gapped: 28
Length of query: 219
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 129
Effective length of database: 4,188,903
Effective search space: 540368487
Effective search space used: 540368487
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: 55 (25.2 bits)