RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12993
(243 letters)
>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA
binding domain, poly(A polymerase, mitochondria,
transferase; 3.10A {Homo sapiens}
Length = 464
Score = 145 bits (367), Expect = 3e-41
Identities = 49/237 (20%), Positives = 91/237 (38%), Gaps = 32/237 (13%)
Query: 1 MTLSKAVEEYVRFTLRDPAHVRLFVVGSTMTGFGLDSSDVDMCLGIRPYEFDRGQAIRVL 60
+E+ D + GS++ FG D+DM L + I
Sbjct: 156 YLTCSLIEDMAAAYFPD---CIVRPFGSSVNTFGKLGCDLDMFLDLDETRNLSAHKISGN 212
Query: 61 CVLETSDVDMCLEIFKKADLIHAKVPILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQ 120
++E ++ E ++ L
Sbjct: 213 FLMEFQVKNVPSERIATQKILSVLGECLDHFGPGC------------------------- 247
Query: 121 KIFKKADLIHAKVPILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQMDWRIRPLVLLV 180
+++A+ P+++F + + L NN + + ++ LLY Y +D R+R LV V
Sbjct: 248 --VGVQKILNARCPLVRFSHQASGFQCALTTNNRIALTSSELLYIYGALDSRVRALVFSV 305
Query: 181 KLWAQAHNINDA-KNMTISSYSFTLMVIHFLQCGTSPPVLPNLVAQYPTKFSPNSNI 236
+ WA+AH++ + I+++S T+MVI FLQ SPP+LP L + + + +
Sbjct: 306 RCWARAHSLTSSIPGAWITNFSLTMMVIFFLQR-RSPPILPTLDSLKTLADAEDKCV 361
>3hj4_A Minor editosome-associated tutase; nucleotidyltransferase, RNA
UTP-binding, transferase; 1.56A {Trypanosoma brucei}
PDB: 3hiy_A 3hj1_A*
Length = 384
Score = 135 bits (341), Expect = 5e-38
Identities = 40/240 (16%), Positives = 80/240 (33%), Gaps = 51/240 (21%)
Query: 1 MTLSKAVEEYVRFTLRDPAHVRLFVVGSTMTGFGLDSSDVDMCLGIRPYEFDRGQAIRVL 60
L K V + + + + GS ++GF SD D+ L
Sbjct: 29 HELQKRVLDIGMLAVNK---AHVELFGSHVSGFCTPHSDADISL---------------- 69
Query: 61 CVLETSDVDMCLEIFKKADLIHAKVPILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQ 120
+ L+ ++ D + K ++ + +G+ +
Sbjct: 70 ---TYRNFSPWLQGMERVDEQNNK-----------RMTRFGKEASAMGMEDVRY------ 109
Query: 121 KIFKKADLIHAKVPILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQMDWRIR-PLVLL 179
I A++P+++F D + D++ N+ GV N+ +L Q+ + L
Sbjct: 110 --------IRARIPVVQFTDGVTGIHCDVSIGNIGGVENSKILCAIRQVFPDFYGAYIHL 161
Query: 180 VKLWAQAHNINDAKNMTISSYSFTLMVIHFLQCGTSPPVLPNLVAQYPTKFSPNSNIDNI 239
VK W +A + + T +S++ T M + LQ +LP +
Sbjct: 162 VKAWGKAREVIAPERSTFNSFTVTTMALMVLQE---LGLLPVFSKPTGEFGELTVADAEM 218
>2b4v_A RNA editing complex protein MP57; tbret2, TBMP57, terminal uridylyl
transferase, editosome, transferase/RNA binding protein
complex; 1.80A {Trypanosoma brucei} SCOP: a.160.1.4
d.218.1.10 PDB: 2b51_A* 2b56_A*
Length = 468
Score = 124 bits (311), Expect = 3e-33
Identities = 22/113 (19%), Positives = 43/113 (38%), Gaps = 2/113 (1%)
Query: 129 IHAKVPILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQMD-WRIRPLVLLVKLWAQAH 187
V ++F F D++ GV+N++L+ Y R + VK W +A
Sbjct: 229 YTRDVLDVRFVPEMFMYRWDISFVGY-GVKNSYLIRHYLHNGPVAARHTAMAVKAWGKAT 287
Query: 188 NINDAKNMTISSYSFTLMVIHFLQCGTSPPVLPNLVAQYPTKFSPNSNIDNIQ 240
N+ ++SY+ T+M I++L + +P + +
Sbjct: 288 NVGAGSGAMLTSYAVTVMFIYYLLVTRQVLWVDPWSLPHPAHLPRYPDFSPLY 340
>4e8f_A Poly(A) RNA polymerase protein CID1; beta polymerase-like
nucleotidyl transferase, terminal uridi transferase,
UTP, cytoplasmic; 2.60A {Schizosaccharomyces pombe
972h-} PDB: 4e7x_A* 4e80_A
Length = 405
Score = 120 bits (301), Expect = 4e-32
Identities = 43/141 (30%), Positives = 73/141 (51%), Gaps = 9/141 (6%)
Query: 98 EVDLNCNNVVGVRNTHLLYCYAQKI----FKKADLIHAKVPILKFQDS-----SFKLEVD 148
++DL V++ + + +++ F+ L A++PI+K + D
Sbjct: 101 DMDLCVLMDSRVQSDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSDTKNGFGASFQCD 160
Query: 149 LNCNNVVGVRNTHLLYCYAQMDWRIRPLVLLVKLWAQAHNINDAKNMTISSYSFTLMVIH 208
+ NN + + NT LL Y ++D R++P+VLLVK WA+ IN T+SSY + LMV++
Sbjct: 161 IGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLY 220
Query: 209 FLQCGTSPPVLPNLVAQYPTK 229
+L PPV PNL+ +
Sbjct: 221 YLIHVIKPPVFPNLLLSPLKQ 241
>4ep7_A Poly(A) RNA polymerase protein CID1; poly(U) polymerase, UTP
binding, transferase; HET: UTP; 2.28A
{Schizosaccharomyces pombe}
Length = 340
Score = 115 bits (288), Expect = 1e-30
Identities = 42/141 (29%), Positives = 72/141 (51%), Gaps = 9/141 (6%)
Query: 98 EVDLNCNNVVGVRNTHLLYCYAQKIFKKAD----LIHAKVPILKFQDS-----SFKLEVD 148
++DL V++ + + +++ + L A++PI+K + D
Sbjct: 64 DMDLCVLMDSRVQSDTIALQFYEELIAEGFEGKFLQRARIPIIKLTSDTKNGFGASFQCD 123
Query: 149 LNCNNVVGVRNTHLLYCYAQMDWRIRPLVLLVKLWAQAHNINDAKNMTISSYSFTLMVIH 208
+ NN + + NT LL Y ++D R++P+VLLVK WA+ IN T+SSY + LMV++
Sbjct: 124 IGFNNRLAIHNTLLLSSYTKLDARLKPMVLLVKHWAKRKQINSPYFGTLSSYGYVLMVLY 183
Query: 209 FLQCGTSPPVLPNLVAQYPTK 229
+L PPV PNL+ +
Sbjct: 184 YLIHVIKPPVFPNLLLSPLKQ 204
>2ikf_A RNA uridylyl transferase; tutase, nucleotidyltransferase,
UTP-binding, RNA editing; HET: UTP; 2.00A {Trypanosoma
brucei} PDB: 2nom_A* 2q0c_A* 2q0d_A* 2q0e_A* 2q0f_A*
2q0g_A*
Length = 353
Score = 114 bits (287), Expect = 2e-30
Identities = 39/225 (17%), Positives = 82/225 (36%), Gaps = 41/225 (18%)
Query: 21 VRLFVVGSTMT-GFGLDSSDVDMCLGIRPYEFDRGQAIRVLCVLETSDVDMCLEIFKKAD 79
+RL+ GST+ G SDVD + + D V + D+ ++ +
Sbjct: 67 MRLYTFGSTVVYGVHEKGSDVDFVVLNKTDVEDGKGGDAATQVAKGLQADILAKLAR--- 123
Query: 80 LIHAKVPILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQKIFKKADLIHAKVPILKFQ 139
+++ + S+ +E + +VP+++ +
Sbjct: 124 -------VIRQKHLSWNVEE----------------------------VRRTRVPVVRVK 148
Query: 140 DSSFKLEVDLNCNNVVGVRNTHLLYCYAQMDWRIRPLVLLVKLWAQAHNINDA-KNMTIS 198
++ D+ GVRN+ LL Y + + R L + +K W++ +N + +I+
Sbjct: 149 GGG-AVDFDITAYRRNGVRNSALLRAYFEQNPPCRWLSMSIKRWSKQTGLNASVIGGSIT 207
Query: 199 SYSFTLMVIHFLQCGTSPPVLPNLVAQYPTKFSPNSNIDNIQEGK 243
SY F LMV+++L +P ++ +
Sbjct: 208 SYGFNLMVVYYLLQRNHLQFVPPSTIDVSRVEPLPPHLPLEEPAD 252
>3nyb_A Poly(A) RNA polymerase protein 2; polya RNA polymerase, zinc
knuckle protein, RNA surveillance binds to TRF4P/AIR2P
heterodimer; 2.70A {Saccharomyces cerevisiae}
Length = 323
Score = 110 bits (277), Expect = 4e-29
Identities = 36/202 (17%), Positives = 66/202 (32%), Gaps = 54/202 (26%)
Query: 20 HVRLFVVGSTMTGFGLDSSDVDMCLGIRPYEFDRGQAIRVLCVLETSDVDMCLEIFKKAD 79
L V GS T L SD+D + + + L
Sbjct: 59 DADLHVFGSYSTDLYLPGSDIDCVVTSELGGKESRNNLYSLA------------------ 100
Query: 80 LIHAKVPILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQKIFKKADLIHAKVPILKFQ 139
LK ++ + ++EV + A+VPI+KF
Sbjct: 101 ------SHLKKKNLATEVEV----------------------------VAKARVPIIKFV 126
Query: 140 DSSFKLEVDLNCNNVVGVRNTHLLYCYAQMDWRIRPLVLLVKLWAQAHNINDAKNMTISS 199
+ + + ++ G+ L+ + +R LVL+VK + A +N+ +
Sbjct: 127 EPHSGIHIAVSFERTNGIEAAKLIREWLDDTPGLRELVLIVKQFLHARRLNNVHTGGLGG 186
Query: 200 YSFTLMVIHFLQCGTSPPVLPN 221
+S +V FL P ++ N
Sbjct: 187 FSIICLVFSFLHM--HPRIITN 206
>2hhp_A Poly(A) polymerase; template-independent RNA polymerase,
transferase; HET: FLC; 1.80A {Saccharomyces cerevisiae}
SCOP: a.160.1.1 d.218.1.3 d.58.16.1 PDB: 1fa0_A* 3c66_A*
2o1p_A 2q66_A*
Length = 530
Score = 69.9 bits (170), Expect = 4e-14
Identities = 33/213 (15%), Positives = 68/213 (31%), Gaps = 27/213 (12%)
Query: 6 AVEEYVRFTLRDPAHVRLFVVGSTMTGFGLDSSDVDMCLGIRPYEFDRGQAIRVLCVLET 65
+ ++ + + A ++F GS G SD+D + + P R V L
Sbjct: 67 SKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLV-VVPKHVTREDFFTVFDSLLR 125
Query: 66 SDVDMCLEIFKKADLIHAKVPILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQKIFKK 125
E+ + A + A VPI+K + S +++ I +
Sbjct: 126 ERK----ELDEIAPVPDAFVPIIKIKFSGISIDL----------------------ICAR 159
Query: 126 ADLIHAKVPILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQMDWRIRPLVLLVKLWAQ 185
D + + + + + + + G R T + R + +KLWAQ
Sbjct: 160 LDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQ 219
Query: 186 AHNINDAKNMTISSYSFTLMVIHFLQCGTSPPV 218
+ ++ ++V Q +
Sbjct: 220 RRAVYANIFGFPGGVAWAMLVARICQLYPNACS 252
>1q79_A Poly(A) polymerase alpha; mRNA processing, nucleotidyl transferase,
transferase; HET: 3AT; 2.15A {Bos taurus} SCOP:
a.160.1.1 d.218.1.3 d.58.16.1 PDB: 1q78_A* 1f5a_A*
Length = 514
Score = 62.2 bits (150), Expect = 2e-11
Identities = 31/197 (15%), Positives = 60/197 (30%), Gaps = 27/197 (13%)
Query: 15 LRDPAHVRLFVVGSTMTGFGLDSSDVDMCLGIRPYEFDRGQAIRVLCVLETSDVDMCLEI 74
+ + ++F GS G +D+D + P DR ++
Sbjct: 89 VIENVGGKIFTFGSYRLGVHTKGADIDALC-VAPRHVDRSDFFTSFYDKLKLQ--EEVKD 145
Query: 75 FKKADLIHAKVPILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQKIFKKADLIHAKVP 134
+ + A VP++K ++++ + + L
Sbjct: 146 LRAVE--EAFVPVIKLCFDGIEIDILFARLALQTIPEDLDL------------------- 184
Query: 135 ILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQMDWRIRPLVLLVKLWAQAHNINDAKN 194
DS K ++ G R T + R + +KLWA+ HNI
Sbjct: 185 ---RDDSLLKNLDIRAIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNIL 241
Query: 195 MTISSYSFTLMVIHFLQ 211
+ S+ ++V Q
Sbjct: 242 GFLGGVSWAMLVARTCQ 258
>1r89_A TRNA nucleotidyltransferase; CCA adding enzyme, incoming
nucleotide, nucleotidyltransfera superfamily; HET: CTP;
1.80A {Archaeoglobus fulgidus} SCOP: a.160.1.3 d.218.1.7
d.58.16.2 PDB: 1r8a_A 1r8b_A* 1r8c_A* 1sz1_A* 1tfw_A*
1tfy_A* 1uet_A 1ueu_A* 1uev_A* 2dr5_A 2dr7_A 2dr8_A*
2dr9_A 2dra_A* 2drb_A 2dvi_A* 2zh1_A 2zh2_A 2zh3_A
2zh4_A ...
Length = 437
Score = 33.1 bits (75), Expect = 0.083
Identities = 13/101 (12%), Positives = 38/101 (37%), Gaps = 11/101 (10%)
Query: 119 AQKIFKKADLIHAKVPILKFQDSSFKLEVD--LNCNNVVGVRNT------HLLYCYAQMD 170
+ + ++ +A+ P + +++V +++ H + ++
Sbjct: 83 GKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIK 142
Query: 171 WRIRPLVLLVKLWAQAHNINDAKNMT--ISSYSFTLMVIHF 209
V L+K + +A+ I A+ S Y L+++ +
Sbjct: 143 -GKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFY 182
>2zds_A Putative DNA-binding protein; TIM-barrel fold, structural genomics,
NPPSFA; 2.30A {Streptomyces coelicolor}
Length = 340
Score = 31.6 bits (71), Expect = 0.20
Identities = 15/124 (12%), Positives = 37/124 (29%), Gaps = 23/124 (18%)
Query: 58 RVLCVLETSDVDMCLEIFKKADLIHAKVPILKFQDS-----SFKLEVDLNCNNVVGVRNT 112
+L V + V E+ +++ + + ++ +F L D + +
Sbjct: 164 PILDVFDAEGVRFAHEVHP-SEIAYDYWTTHRALEAVGHRPAFGLNFDPSHFVWQDLDPV 222
Query: 113 HLLYCYAQKIFKKADLIHAKVPILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQMDWR 172
L+ + +I+ + K E + G +HL + + W
Sbjct: 223 GFLWDFRDRIY----HVDCK-------------EARKRLDGRNGRLGSHLPWGDPRRGWD 265
Query: 173 IRPL 176
Sbjct: 266 FVSA 269
>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 = 30.2 bits (67), Expect = 0.68
Identities = 30/264 (11%), Positives = 64/264 (24%), Gaps = 83/264 (31%)
Query: 16 RDPAHVRLFVVGSTM---TGFGLDSSDVDMCLGIRPYEFDRGQAIRVLCVLETSDVDMCL 72
++ F + + T D L E
Sbjct: 254 QNAKAWNAFNLSCKILLTTR---FKQVTDFLSAATTTHISLDHHSMTLTPDEV------K 304
Query: 73 EIF-KKADLIHAKVPILKFQDSSFKLEVDLNCNNVVG--VRNTHLLYCYAQKIF--KKAD 127
+ K D +P + +L +++ +R+ + + + K
Sbjct: 305 SLLLKYLDCRPQDLPREVLTTNPRRL-------SIIAESIRDGLATWDNWKHVNCDKLTT 357
Query: 128 LIHAKVPILKFQDSSFKLEVDLNCNNVVGVRNTHLLYCYAQM-----DWRIRPLVLLVKL 182
+I + + +L+ + R + ++ I P +LL +
Sbjct: 358 IIESSLNVLEPAE----------------YRK-----MFDRLSVFPPSAHI-PTILLSLI 395
Query: 183 WAQA------------HN---IN-DAKNMTISSYSFTLMVIHFLQCGTSPPVLP------ 220
W H + K TIS I + +
Sbjct: 396 WFDVIKSDVMVVVNKLHKYSLVEKQPKESTIS--------IPSIYLELKVKLENEYALHR 447
Query: 221 NLVAQY--PTKFSPNSNIDNIQEG 242
++V Y P F + I +
Sbjct: 448 SIVDHYNIPKTFDSDDLIPPYLDQ 471
>3fuy_A HFX_CASS1, putative integron gene cassette protein; integron
cassette protein, mobIle metagenome, structural
genomics, PSI-2; 2.00A {Uncultured bacterium}
Length = 179
Score = 28.5 bits (63), Expect = 1.7
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 17/69 (24%)
Query: 14 TLRDPAHVRLFVVGSTMTGFGLDSSDVDMCL----GIR--------PYEFD-RGQAIRVL 60
T+RD + + V+ TGF D D+D+CL G+R EF +G IR+
Sbjct: 36 TIRDFDNGQFAVLRIGRTGFPADKGDIDLCLDKMKGVRDAQQSIGDDTEFGFKGPHIRIR 95
Query: 61 CVLETSDVD 69
CV D+D
Sbjct: 96 CV----DID 100
>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 = 27.2 bits (59), Expect = 3.7
Identities = 6/30 (20%), Positives = 12/30 (40%), Gaps = 7/30 (23%)
Query: 35 LDSSDVDMCLGIRPYEFDRGQAIRVLCVLE 64
L +S ++ Y D A+ + +E
Sbjct: 25 LQAS-------LKLYADDSAPALAIKATME 47
>2rff_A Putative nucleotidyltransferase; NP_343093.1,
nucleotidyltransferase domain, structural genomics;
HET: MSE; 1.40A {Sulfolobus solfataricus P2}
Length = 111
Score = 26.5 bits (58), Expect = 4.7
Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 1 MTLSKAVEEYVRFTLRDPAHV-RLFVVGSTMTGFGLDSSDVDMCL 44
+ + K +E V ++ +++ GS G LD+SD+D+
Sbjct: 13 IRMLKLAKEIVEEVASSFPNLEEVYIFGSRARGDYLDTSDIDILF 57
>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 = 27.7 bits (61), Expect = 4.9
Identities = 18/101 (17%), Positives = 32/101 (31%), Gaps = 33/101 (32%)
Query: 169 MD-WRIRPLVL---------LV--KLWAQAHNIND--AKNMTISSYSFTL---------M 205
MD + RPL L LV + A + + K + + F +
Sbjct: 1 MDAYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAEL 60
Query: 206 VIHFL----------QCGTSPPVLPNLVAQYPTKFSPNSNI 236
V FL + G VL + ++ + ++I
Sbjct: 61 VGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDI 101
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
0.325 0.139 0.422
Gapped
Lambda K H
0.267 0.0504 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,614,775
Number of extensions: 200449
Number of successful extensions: 516
Number of sequences better than 10.0: 1
Number of HSP's gapped: 492
Number of HSP's successfully gapped: 29
Length of query: 243
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 152
Effective length of database: 4,160,982
Effective search space: 632469264
Effective search space used: 632469264
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: 40 (21.6 bits)
S2: 56 (25.9 bits)