RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5196
(252 letters)
>4f3t_A Protein argonaute-2; hydrolase/gene regulation, RNAI, slicer,
hydrolase-RNA; 2.25A {Homo sapiens} PDB: 4ei1_A 4ei3_A*
1r4k_A 1si2_A 1si3_A
Length = 861
Score = 159 bits (402), Expect = 1e-44
Identities = 68/248 (27%), Positives = 119/248 (47%), Gaps = 15/248 (6%)
Query: 2 TIASSSSSSSISSAASGAGSKGLYQIPRRSNKDGGTLGRRTQVDTNHFAITFKNPNLVIF 61
+ S + + A ++ P R + GT GR ++ N F + P + I+
Sbjct: 2 AMYSGAGPALAPPAPPPPIQGYAFKPPPRPDF--GTSGRTIKLQANFFEMDI--PKIDIY 57
Query: 62 HYDVAIDPDK-PVRYMRPVMQKVAREY----FPNSPCGYDGKKNLFSKGTLPFGTAMNCT 116
HY++ I P+K P R R +++ + + + F + +DG+KNL++ LP G
Sbjct: 58 HYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGR-DKVE 116
Query: 117 VSIFDEERMKDKEYKVEIKKAQEISFASIVEFMR-TGVNRPQIAIQALDVVLREPCSLNA 175
+ + KD+ +KV IK +S ++ + + + P IQALDVV+R S+
Sbjct: 117 LEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSM-- 174
Query: 176 NFVRVGRSYFSPPDPNRLVDLGDGLHLWNGFYQSAGIG-WRPYLNVDVAHKGFPEEKSVI 234
+ VGRS+F+ + LG G +W GF+QS W+ LN+DV+ F + + VI
Sbjct: 175 RYTPVGRSFFTASEGCS-NPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVI 233
Query: 235 KVIDEICR 242
+ + E+
Sbjct: 234 EFVCEVLD 241
>4f1n_A Kpago; argonaute, RNAI, RNAse H, RNA binding protein-RNA complex;
3.19A {Vanderwaltozyma polyspora}
Length = 1046
Score = 117 bits (294), Expect = 3e-30
Identities = 35/299 (11%), Positives = 82/299 (27%), Gaps = 72/299 (24%)
Query: 9 SSSISSAASGAGSKGLYQIPRRSNKDGGTLGRRTQVDTNHFAITFKN------------- 55
S+ + + +Y++ R + GT G + + TNH + N
Sbjct: 1 STEKTVDQPKEDTHAIYKVENRHDY--GTKGTKVDILTNHILLAVGNDVPTEKIDKELVP 58
Query: 56 ------PNLVIFHYDVAIDPDKPV---------------RYMRPVMQKVAREY----FPN 90
IF Y + P + +++ + E
Sbjct: 59 KLDGWWKTAFIFTYHIDFKPQQKGPPRRGKPVPPQELSKPKKYELIEALLDEDEILYKYR 118
Query: 91 SPCGYDGKKNLFSKGTLPFGTAMNCTVSIFDEER-----------------------MKD 127
++G+ ++S L T + + ++++ +++
Sbjct: 119 DRIAFNGEDTIYSHVPLEEFTLFDGCWEVSNKQKKKVVPGMGAPSNKASLQKKIDPELEE 178
Query: 128 KEYKVEIKKAQEISFASIVEFMRT-------GVNRPQIAIQALDVVLREPCSLNAN-FVR 179
++ +K + ++ I T L ++ + S + F
Sbjct: 179 MVSQITLKFSGKVGLKDIYNDTTTQDTEVQESRMSAIDKTCLLSLLGAKFMSTDDLIFQV 238
Query: 180 VGRSYFSPPDPNRLVDLGDGLHLWNGFYQSAGIG-WRPYLNVDVAHKGFPEEKSVIKVI 237
G +F + + + G +L GF S LN F + +
Sbjct: 239 QGNKFFIFNNFAKAIPFQIGGYLLQGFTVSLTHVYGGVALNTVSVPAPFIKHTKYLPGD 297
>3ho1_A Argonaute; argonaute, protein-DNA-RNA complex, nucleic acid binding
Pro RNA complex; 2.60A {Thermus thermophilus} PDB:
3dlb_A* 3dlh_A* 3f73_A* 3hm9_A 3hvr_A 3hxm_A* 3hk2_A
3hjf_A
Length = 685
Score = 81.2 bits (200), Expect = 1e-17
Identities = 32/204 (15%), Positives = 59/204 (28%), Gaps = 27/204 (13%)
Query: 40 RRTQVDTNHFAITF-KNPNLVIFHYDVAIDPDKPVRYMRPVMQKVAREYFPNSPCGYDGK 98
+T+V N FA+ L + +V +DP + P++ +VAR G
Sbjct: 5 GKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARR--------AGGV 56
Query: 99 KNLFSKGTLPFGTAMNCTVSIFDEERMKDKEYKVEIKKAQEISFASIVEFMRTGVNRPQI 158
G + + + Y++ K + + E
Sbjct: 57 TVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGE----------- 105
Query: 159 AIQALDVVLREPCSLNANFVRVGRSYFSPPDPNRLVDL-GDGLHLWNGFYQSAGIG--WR 215
L + R L R+ + R G G + G +
Sbjct: 106 -RSVLSALARR--LLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGA 162
Query: 216 PYLNVDVAHKGFPEEKSVIKVIDE 239
L VD A++ E S+ + +
Sbjct: 163 FLLEVDPAYRILCEM-SLEAWLAQ 185
>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 = 53.9 bits (129), Expect = 2e-08
Identities = 48/305 (15%), Positives = 93/305 (30%), Gaps = 99/305 (32%)
Query: 31 SNKDGGTLGRRTQV---DTNHFAITFKNPNLVIFHYDVA-IDPDKPVRYMRPVMQKVARE 86
S + +G+ QV F + N + H A + + ++ +++ +
Sbjct: 70 SLVEPSKVGQFDQVLNLCLTEFENCYLEGNDI--HALAAKLLQENDTTLVK--TKELIKN 125
Query: 87 YF-----PNSPCGYDGKKNLF---SKGTLPF-------GTAMNCTVSIFDEERMKDKEYK 131
Y P LF +G G + F+E R + Y
Sbjct: 126 YITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDY----FEELRDLYQTYH 181
Query: 132 VEIKKAQEISFASIVEFMRTGVNRPQIAIQALDVV--LREP---------------CSLN 174
V + + S ++ E +RT ++ ++ Q L+++ L P C L
Sbjct: 182 VLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLI 241
Query: 175 -----ANFVRVGRSY-FSPPDPNRLVDLGDGL--HL--------------WNGFYQSAG- 211
A++V + F+P + L G H W F+ S
Sbjct: 242 GVIQLAHYVVTAKLLGFTPGE---LRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRK 298
Query: 212 -------IGWR-----PYLNVD-------VAH-KGFP---------EEKSVIKVIDEICR 242
IG R P ++ + + +G P ++ V +++
Sbjct: 299 AITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNS 358
Query: 243 GLPPE 247
LP
Sbjct: 359 HLPAG 363
Score = 37.0 bits (85), Expect = 0.006
Identities = 45/274 (16%), Positives = 84/274 (30%), Gaps = 90/274 (32%)
Query: 3 IASSSSSSSISSAASGA-------GSKGLYQIPRRS--------NKDGGT------LG-- 39
IA + S S + A G + P S + + L
Sbjct: 283 IAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSIS 342
Query: 40 --RRTQVD-----TN-------HFAITFKN-P-NLVIFHYDVAIDPDKPVRYMRPVMQKV 83
+ QV TN I+ N NLV V+ P + + + ++K
Sbjct: 343 NLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLV-----VSGPP-QSLYGLNLTLRKA 396
Query: 84 AREYFPNSPCGYDGKKNLFSKG-----------TLPFGTA-MNCTVSIFDEERMKDKEYK 131
P G D + FS+ PF + + + +++ +K+
Sbjct: 397 KA------PSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKN---N 447
Query: 132 VEIKKAQEISFASIVEFMRTGVN----RPQIAIQALDVVLREPCSLNANFVRVGRSYFSP 187
V A++I V G + I+ + +D ++R P + +
Sbjct: 448 VSF-NAKDIQIP--VYDTFDGSDLRVLSGSISERIVDCIIRLPV----KWETT-----TQ 495
Query: 188 PDPNRLVDLGDGLHLWNGFYQSAGIGWRPYLNVD 221
++D G G ++G+G + N D
Sbjct: 496 FKATHILDFGPG--------GASGLGVLTHRNKD 521
Score = 30.8 bits (69), Expect = 0.57
Identities = 38/225 (16%), Positives = 63/225 (28%), Gaps = 71/225 (31%)
Query: 45 DTNHFAIT---FKNPNLVIFHYDVAIDPDKPVRYMRPVMQK------VAREYFPNSPCGY 95
DT F+I NP + H+ Y + + + F
Sbjct: 1655 DTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEI--NE 1712
Query: 96 DGKKNLFS--KGTLPFGT-----AMNCTVS--IFDEERMKDKEYKVEIKKAQEISFA--S 144
F KG L T A+ + F E +K K +FA S
Sbjct: 1713 HSTSYTFRSEKGLL-SATQFTQPAL-TLMEKAAF--EDLKSKGLIPADA-----TFAGHS 1763
Query: 145 IVEF----MRTGVNRPQIAIQ-ALDVVLREPCSLNANFVRVGR--SYFSPPDPNRLVDLG 197
+ E+ V ++I+ ++VV F R G P D
Sbjct: 1764 LGEYAALASLADV----MSIESLVEVV----------FYR-GMTMQVAVPRDE------- 1801
Query: 198 DGLHLWNGFYQSAGIGWRPYLNVDVAHKGFPEEKSVIKVIDEICR 242
G I +N F +E ++ V++ + +
Sbjct: 1802 ------LGRSNYGMIA----INPGRVAASFSQE-ALQYVVERVGK 1835
>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 = 37.5 bits (86), Expect = 0.003
Identities = 31/232 (13%), Positives = 72/232 (31%), Gaps = 37/232 (15%)
Query: 40 RRTQVDTNHFAITFKNPNLVIFHYDVAIDPDKPVRYMRPVMQ--KVAREYFPNSPCGYDG 97
R+ + T + I ++ + D + V ++P ++ + E P DG
Sbjct: 103 RQPSMMTRMY-IEQRDR----LYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDG 157
Query: 98 KKNLFSKGTLPFGTAMNCTVSIFDEERMKDKEYKVE-IKKAQEISFASIVEFMRTGVNR- 155
K + C + ++K+ + S +++E ++ + +
Sbjct: 158 VLG-SGKTWV---ALDVCL----SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI 209
Query: 156 PQIAIQALDVVLREPCSLNANFVRVGRSYFSPPDPNRLVDLGD--GLHLWNGF------- 206
D +++ + R S P N L+ L + WN F
Sbjct: 210 DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKIL 269
Query: 207 --------YQSAGIGWRPYLNVDVAHKGFPEEKS---VIKVIDEICRGLPPE 247
++++D ++ ++K +D + LP E
Sbjct: 270 LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPRE 321
Score = 27.9 bits (61), Expect = 4.7
Identities = 17/92 (18%), Positives = 29/92 (31%), Gaps = 19/92 (20%)
Query: 125 MKDKEYKVEIKKAQEISFASIVEFMRTGVNR----PQIAIQALDVVLREPCSLNANFVRV 180
+ ++ E+ + I E +R G+ + L ++ SLN
Sbjct: 313 CRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIES--SLNVLEPAE 370
Query: 181 GRSYFS-----PPD---PNRLVDLGDGLHLWN 204
R F PP P L+ L +W
Sbjct: 371 YRKMFDRLSVFPPSAHIPTILLSL-----IWF 397
>1u04_A Argonaute, hypothetical protein PF0537; RNAI, silencing, PIWI, PAZ,
RISC, slicer, RNAse H hydrolase-gene regulation complex;
2.25A {Pyrococcus furiosus} SCOP: b.34.14.1 c.55.3.10
PDB: 1z25_A 1z26_A
Length = 771
Score = 31.0 bits (69), Expect = 0.47
Identities = 26/188 (13%), Positives = 54/188 (28%), Gaps = 44/188 (23%)
Query: 41 RTQVDTNHFAITFKNPNLVIFHYDVAIDPDKPVRYMRPVMQKVAREYFPNSPCGYDGKKN 100
+ V N I K I+ Y + DP++ ++ + ++A E
Sbjct: 3 KAIVVINLVKINKKIIPDKIYVYRLFNDPEEELQKEGYSIYRLAYEN--VGIVIDPENLI 60
Query: 101 LFSKGTLPFGTAMNCTVSIFDEERMKDKEYKVEIKKAQEISFASIVEFMRTGVNRPQIAI 160
+ + K+ EY+ E EISF+ +
Sbjct: 61 IATT---------------------KELEYEGEFIPEGEISFSELR---------NDYQS 90
Query: 161 QALDVVLREPCSLNANFVRVGRSYFSPPDPNRLVDLGDGLHLWNGFYQSAGIGW---RPY 217
+ + +L+E ++ R + P + S + Y
Sbjct: 91 KLVLRLLKENGIGEYELSKLLRKFRKPKTFGDY-------KVIPSVEMS--VIKHDEDFY 141
Query: 218 LNVDVAHK 225
L + + H+
Sbjct: 142 LVIHIIHQ 149
>2k48_A Nucleoprotein; viral protein; NMR {Andes virus}
Length = 107
Score = 28.6 bits (63), Expect = 0.74
Identities = 18/97 (18%), Positives = 41/97 (42%), Gaps = 5/97 (5%)
Query: 89 PNSPCGYDGKKNLFSKGTLPFGTAMNCTVSIFDEERMKDKE---YKVEIKKAQEISFASI 145
PN G D +NL+ +G PF M+ + + +++ + ++K A++
Sbjct: 12 PNPLLGLDSTENLYFQGIDPF--TMSTLQELQENITAHEQQLVTARQKLKDAEKAVEVDP 69
Query: 146 VEFMRTGVNRPQIAIQALDVVLREPCSLNANFVRVGR 182
+ ++ + + A+ L+ L E A+ V +
Sbjct: 70 DDVNKSTLQNRRAAVSTLETKLGELKRQLADLVAAQK 106
>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 = 29.1 bits (64), Expect = 0.87
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 6/32 (18%)
Query: 131 KVEIKKAQEISFASIVEFMRTGVNRPQIAIQA 162
K +KK Q AS+ + P +AI+A
Sbjct: 19 KQALKKLQ----ASLKLYADDSA--PALAIKA 44
>2cbn_A Ribonuclease Z; phosphodiesterase beta lactamase tRNAse Z,
hydrolase, metal- binding, endonuclease, tRNA
processing, zinc; 2.9A {Escherichia coli} SCOP:
d.157.1.7
Length = 306
Score = 27.8 bits (62), Expect = 3.7
Identities = 10/45 (22%), Positives = 13/45 (28%), Gaps = 11/45 (24%)
Query: 57 NLVIFHYDVAIDPDKPVRYMRPVMQKV---AREYFPNSPCGYDGK 98
L+I H RY Q + R FP + D
Sbjct: 266 KLIITHVSS--------RYDDKGCQHLLRECRSIFPATELANDFT 302
>1csn_A Casein kinase-1; phosphotransferase; HET: ATP; 2.00A
{Schizosaccharomyces pombe} SCOP: d.144.1.7 PDB: 1eh4_A*
2csn_A*
Length = 298
Score = 27.3 bits (61), Expect = 5.5
Identities = 8/23 (34%), Positives = 11/23 (47%), Gaps = 1/23 (4%)
Query: 229 EEKSVIKVIDEICRGLPPELSDY 251
E+K + E+C G P E Y
Sbjct: 235 EKKQSTP-LRELCAGFPEEFYKY 256
>3uzp_A CKI-delta, CKID, casein kinase I isoform delta; CK1D, inhibitor,
PF670462, transferase-transferase I complex; HET: 0CK;
1.94A {Homo sapiens} PDB: 3uys_A* 3uyt_A* 1cki_A 1ckj_A
Length = 296
Score = 26.9 bits (60), Expect = 5.9
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 237 IDEICRGLPPELSDY 251
I+ +C+G P E + Y
Sbjct: 239 IEVLCKGYPSEFATY 253
>3sv0_A Casein kinase I-like; typical kinase domain fold, cytosol,
transferase; 2.00A {Oryza sativa japonica group}
Length = 483
Score = 26.9 bits (59), Expect = 6.7
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 237 IDEICRGLPPELSDY 251
I+ +CRG P E + Y
Sbjct: 237 IEALCRGYPTEFASY 251
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 0.136 0.410
Gapped
Lambda K H
0.267 0.0499 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,076,789
Number of extensions: 251514
Number of successful extensions: 559
Number of sequences better than 10.0: 1
Number of HSP's gapped: 542
Number of HSP's successfully gapped: 16
Length of query: 252
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 161
Effective length of database: 4,160,982
Effective search space: 669918102
Effective search space used: 669918102
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: 56 (25.9 bits)