RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7609
(226 letters)
>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding
motif, ATP- binding, nucleotide-binding, transferase;
HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB:
3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*
Length = 260
Score = 52.6 bits (126), Expect = 1e-08
Identities = 30/150 (20%), Positives = 61/150 (40%), Gaps = 12/150 (8%)
Query: 2 KHEYKLVSINSEPLRDHIKGSWVQVVDKTTKCLNRLLELGFSRRRNYILDQTNVYVSAQK 61
K+ ++ + S+ +R+ + + K RL++ + I+D TN Y S ++
Sbjct: 30 KNNIDVIVLGSDLIRESFPVWKEKYEEFIKKSTYRLIDS-ALKNYWVIVDDTNYYNSMRR 88
Query: 62 RKMRSYFGFQ-RKAIVVVPTNEDYLARLEMHREKEGKDDVPPDNVILEMKANFKLPEVGE 120
+ + AI+ + + D L R + R ++ P+ VI +M F P
Sbjct: 89 DLINIAKKYNKNYAIIYLKASLDVLIRRNIERGEK-----IPNEVIKKMYEKFDEPGKKY 143
Query: 121 LFEEVTYI-----ELQHPEAEKIIDEYNKN 145
++E I ++ E K + E +K
Sbjct: 144 KWDEPFLIIDTTKDIDFNEIAKKLIEKSKE 173
>3zvl_A Bifunctional polynucleotide phosphatase/kinase;
hydrolase-transferase complex, base excision repair,
BER, non-homologous END-joining, NHEJ; 1.65A {Mus
musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B*
3u7h_B* 3u7g_A*
Length = 416
Score = 49.9 bits (118), Expect = 2e-07
Identities = 23/123 (18%), Positives = 44/123 (35%), Gaps = 7/123 (5%)
Query: 31 TKCLNRLLELGFSRRRNYILDQTNVYVSAQKR--KMRSYFGFQRKAIVVVPTNEDYLARL 88
+C++ + + ++D TN V ++ R + G + T E
Sbjct: 296 QRCVSSCQAA-LRQGKRVVIDNTNPDVPSRARYIQCAKDAGVPCRCFNFCATIEQARHNN 354
Query: 89 EMHREKEGKDDVP-PDNVILEMKANFKLPEVGELFEEVTYIELQHPEAEKIIDE--YNKN 145
RE P D V+ + F+ P + E F E+ I + E + Y +
Sbjct: 355 R-FREMTDPSHAPVSDMVMFSYRKQFEPPTLAEGFLEILEIPFRLQEHLDPALQRLYRQF 413
Query: 146 ADG 148
++G
Sbjct: 414 SEG 416
>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A
{Enterobacteria phage T4} SCOP: c.37.1.1
Length = 181
Score = 43.6 bits (103), Expect = 9e-06
Identities = 23/127 (18%), Positives = 40/127 (31%), Gaps = 18/127 (14%)
Query: 25 QVVDKTTKCLNRLLELGFSRRRNYILDQTNVYVSAQKR--KMRSYFGFQRKAIVVVPTNE 82
V +L G S + I+ TN+ + +G++ + V
Sbjct: 59 IVTGMQFDTAKSILYGGDSVK-GVIISDTNLNPERRLAWETFAKEYGWKVEHKVFDVPWT 117
Query: 83 DYLARLEMHREKEGKDDVPPDNVILEMKANFKLPEVGELFEEVTYIELQHPEAEKIIDEY 142
+ + R K VP D V+ M + + ++ P+A I D
Sbjct: 118 ELVKRNSKRGTK----AVPID-VLRSMYKSMREYLGLPVYNG----TPGKPKA-VIFD-- 165
Query: 143 NKNADGT 149
DGT
Sbjct: 166 ---VDGT 169
>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 = 42.0 bits (98), Expect = 9e-05
Identities = 41/265 (15%), Positives = 79/265 (29%), Gaps = 95/265 (35%)
Query: 25 QVVDKTTKCLNRLLELGFSR-RRNYILDQTNVY-------------VSAQKRKMRSYFGF 70
V +++L L + Y L+ +++ + K +++Y
Sbjct: 71 LVEPSKVGQFDQVLNLCLTEFENCY-LEGNDIHALAAKLLQENDTTLVKTKELIKNY--- 126
Query: 71 QRKAIVVVPTNEDYLARLEMHREKEGKDDVPPDNVILE--MKANFKL------------- 115
AR+ R + ++ + + N +L
Sbjct: 127 -------------ITARIMAKRPFDK----KSNSALFRAVGEGNAQLVAIFGGQGNTDDY 169
Query: 116 -PEVGELFEEVTY----IELQHPEAEKIIDEYNKNADGTYNYPQNWNAQNW--------- 161
E+ +L++ TY +L AE + + D + Q N W
Sbjct: 170 FEELRDLYQ--TYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPD 227
Query: 162 QGY-----------G------YSTTGQTG--TTGQTGQSTQGAS----KMISAADFESGG 198
+ Y G Y T + T G+ +GA+ +++A
Sbjct: 228 KDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETD 287
Query: 199 WW--FESKSRYKISLVQLFVRFLGV 221
W F R I++ LF F+GV
Sbjct: 288 SWESFFVSVRKAITV--LF--FIGV 308
Score = 32.3 bits (73), Expect = 0.15
Identities = 38/197 (19%), Positives = 54/197 (27%), Gaps = 84/197 (42%)
Query: 1 M-KHEYKLVSINSEPLRDHIKGSWVQVVDKTTKCLNRLLELGFSRRRNYILDQTNVYVSA 59
M YK S+ +D V ++ GFS ILD V
Sbjct: 1631 MGMDLYK----TSKAAQD--------VWNRADNHFKD--TYGFS-----ILD----IVIN 1667
Query: 60 QKRKMRSYFGFQR-KAIVVVPTNEDYLARLEMHREKEGKDDVPPDNVILEMKANFKLPEV 118
+ +FG ++ K I E+Y A M E D L+ + FK
Sbjct: 1668 NPVNLTIHFGGEKGKRI-----RENYSA---MIFET------IVDGK-LKTEKIFK---- 1708
Query: 119 GELFEEVTYIELQHPEAEKIIDEYNKNADGTYNYPQNWNAQNWQGYGYSTTGQTGTTGQT 178
E+ E T + + G T
Sbjct: 1709 -EINEHSTSYTFRSEK--------------------------------------GLLSAT 1729
Query: 179 GQSTQGASKMISAADFE 195
Q TQ A ++ A FE
Sbjct: 1730 -QFTQPALTLMEKAAFE 1745
Score = 28.1 bits (62), Expect = 2.8
Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 7/37 (18%)
Query: 6 KLVSINSEPLRDHIKGSWVQVVDKTTKCLNRLLELGF 42
L N + G+ V+V+ T +N + GF
Sbjct: 514 VLTHRNKD-------GTGVRVIVAGTLDINPDDDYGF 543
>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 = 35.6 bits (81), Expect = 0.012
Identities = 42/229 (18%), Positives = 71/229 (31%), Gaps = 76/229 (33%)
Query: 7 LVSINSEPLRDHIK--GSWVQV-VDKTTKCLNRLLELGFSRRRNYILDQTNVYVSAQKRK 63
+SI +E +RD + +W V DK L ++E + +L+
Sbjct: 329 RLSIIAESIRDGLATWDNWKHVNCDK----LTTIIESSLN-----VLEPAE--------- 370
Query: 64 MRSYFGFQRKAIVVVPTN----EDYLARL--------------EMHR----EKEGKDDVP 101
R F + V P + L+ + ++H+ EK+ K+
Sbjct: 371 YRKMF----DRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTI 426
Query: 102 --PDNVILEMKANFKLPEVGELFEEVTYIELQHPEAEKIIDEYNKNADGTYNYPQN-WNA 158
P + LE+K KL L H I+D YN + +
Sbjct: 427 SIPS-IYLELKV--KLENEYAL----------H---RSIVDHYNIPK----TFDSDDLIP 466
Query: 159 QNWQGYGYSTTGQTGTTGQTGQSTQGASKMISAADFESGGWWFESKSRY 207
Y YS G + + + DF + E K R+
Sbjct: 467 PYLDQYFYSHIGHHLKNIEHPERMTLFRMVF--LDFR----FLEQKIRH 509
Score = 34.1 bits (77), Expect = 0.037
Identities = 39/312 (12%), Positives = 85/312 (27%), Gaps = 103/312 (33%)
Query: 1 MKHEYK-LVSINSEPLR---------------------DHIKGS-----------WVQVV 27
+++YK ++S+ + DHI S W ++
Sbjct: 14 HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWT-LL 72
Query: 28 DKTTKCLNRLLELGFSRRRNYILDQTNVYVSAQKRKMRSYFGFQRKAIVVVPTNEDY-LA 86
K + + + +E +++ R Y + + Y ++
Sbjct: 73 SKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVS 132
Query: 87 RLEMHRE-KEG-KDDVPPDNVILE-MK------------ANFKLPE----------VGEL 121
RL+ + + ++ + P NV+++ + ++K+ +
Sbjct: 133 RLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNC 192
Query: 122 FEEVTYIELQHPEAEKIIDEYNKNADGTYNYPQN-------------------------- 155
T +E+ +I + +D + N
Sbjct: 193 NSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLN 252
Query: 156 -WNAQNWQGYGYS-----TTGQTGTTGQTGQSTQGASKMISAADFESGGWWFESKSRYKI 209
NA+ W + S TT T +T IS E KS
Sbjct: 253 VQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATT---THISLDHHSMTLTPDEVKS---- 305
Query: 210 SLVQLFVRFLGV 221
L +++L
Sbjct: 306 ----LLLKYLDC 313
Score = 32.9 bits (74), Expect = 0.093
Identities = 23/185 (12%), Positives = 49/185 (26%), Gaps = 50/185 (27%)
Query: 1 MKHEYKLVSINSEPLRDHIKGS-------WVQVVDK-----TTKCLNR-LLELGFSRRRN 47
+ + +S+ W V+ K L+E
Sbjct: 371 YRKMFDRLSV----FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTI 426
Query: 48 YILDQTNVYVSAQK---------RKMRSYFGFQRKAI---VVVPTNEDY--------LAR 87
I +Y+ + R + ++ + ++ P + Y L
Sbjct: 427 SIPS---IYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKN 483
Query: 88 LEMHREKEGKDDVPPDNVILEMK------ANFKLPEVGELFEEV----TYIELQHPEAEK 137
+E V D LE K A + +++ YI P+ E+
Sbjct: 484 IEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYER 543
Query: 138 IIDEY 142
+++
Sbjct: 544 LVNAI 548
>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop,
transferase; HET: ADP; 2.33A {Enterobacteria phage T4}
SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A*
2ia5_A
Length = 301
Score = 31.6 bits (71), Expect = 0.18
Identities = 14/81 (17%), Positives = 25/81 (30%), Gaps = 7/81 (8%)
Query: 25 QVVDKTTKCLNRLLELGFSRRRNYILDQTNVYVSAQK--RKMRSYFGFQRKAIVVVPTNE 82
V +L G S + I+ TN+ + +G++ + V
Sbjct: 59 IVTGMQFDTAKSILYGGDSVK-GVIISDTNLNPERRLAWETFAKEYGWKVEHKVFDVPWT 117
Query: 83 DYLARLEMHREKEGKDDVPPD 103
+ + R K VP D
Sbjct: 118 ELVKRNSKRGTK----AVPID 134
>3dva_I Dihydrolipoyllysine-residue acetyltransferase component of pyruvate
dehydrogenase...; oxidoreductase, multienzyme complex;
HET: TPW; 2.35A {Bacillus stearothermophilus} PDB:
3dv0_I* 3duf_I* 1b5s_A 1lab_A 1lac_A 1w3d_A
Length = 428
Score = 27.6 bits (62), Expect = 3.4
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 109 MKANFKLPEVGELFEEVTYIE 129
M FKLP++GE E ++
Sbjct: 1 MAFEFKLPDIGEGIHEGEIVK 21
>2sas_A Sarcoplasmic calcium-binding protein; 2.40A {Branchiostoma
lanceolatum} SCOP: a.39.1.5
Length = 185
Score = 27.2 bits (60), Expect = 3.4
Identities = 12/79 (15%), Positives = 22/79 (27%), Gaps = 8/79 (10%)
Query: 82 EDYLARLEMHREKEGKDDVPPDNVILEMKANFKLP--------EVGELFEEVTYIELQHP 133
E+YLA E P + FK ++ E +LQ
Sbjct: 80 EEYLAMWEKTIATCKSVADLPAWCQNRIPFLFKGMDVSGDGIVDLEEFQNYCKNFQLQCA 139
Query: 134 EAEKIIDEYNKNADGTYNY 152
+ + + T++
Sbjct: 140 DVPAVYNVITDGGKVTFDL 158
>3akb_A Putative calcium binding protein; EF-hand, metal binding protein;
1.50A {Streptomyces coelicolor} PDB: 3aka_A
Length = 166
Score = 26.2 bits (58), Expect = 7.0
Identities = 8/71 (11%), Positives = 18/71 (25%), Gaps = 8/71 (11%)
Query: 90 MHREKEGKDDVPPDNVILEMKANFKLP--------EVGELFEEVTYIELQHPEAEKIIDE 141
+ K D + + A + V + +T + A +
Sbjct: 81 AVKRLRDKPDRFAEMARPFLHAALGVADTDGDGAVTVADTARALTAFGVPEDLARQAAAA 140
Query: 142 YNKNADGTYNY 152
+ + DG
Sbjct: 141 LDTDGDGKVGE 151
>3k21_A PFCDPK3, calcium-dependent protein kinase 3; calcium kinase
structural genomics malaria, structural genom
consortium, SGC, ATP-binding; 1.15A {Plasmodium
falciparum} PDB: 3o4y_A
Length = 191
Score = 26.1 bits (58), Expect = 8.8
Identities = 5/34 (14%), Positives = 15/34 (44%)
Query: 119 GELFEEVTYIELQHPEAEKIIDEYNKNADGTYNY 152
++ + +++I + +KN DG ++
Sbjct: 149 YNGNKKGNITQRDVNRVKRMIRDVDKNNDGKIDF 182
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
0.316 0.133 0.395
Gapped
Lambda K H
0.267 0.0457 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,551,099
Number of extensions: 208787
Number of successful extensions: 624
Number of sequences better than 10.0: 1
Number of HSP's gapped: 623
Number of HSP's successfully gapped: 24
Length of query: 226
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 136
Effective length of database: 4,188,903
Effective search space: 569690808
Effective search space used: 569690808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.6 bits)