BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy10116
(298 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2NN6|H Chain H, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 308
Score = 280 bits (715), Expect = 9e-76, Method: Compositional matrix adjust.
Identities = 134/263 (50%), Positives = 190/263 (72%), Gaps = 3/263 (1%)
Query: 32 ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYXXXXXXXXX 91
++ PG+T+ G+M GHGT+ +E++ ASV G VE+VN+L+ V+A+ +RY
Sbjct: 41 LVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKALKTRYIGEVGDIVV 100
Query: 92 XRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
R+T +Q ++W V+TNS L+S L L+S+NLPGGE RRRS +DE MR FL+EGDLISAE+
Sbjct: 101 GRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEV 160
Query: 152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWV 211
+ ++G+++LHTRSLKYGKLGQG+L+ V PSL++R K+HF +L CGA VILG NG++W+
Sbjct: 161 QAVFSDGAVSLHTRSLKYGKLGQGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWI 220
Query: 212 SAIDENK---SGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLK 268
E+K +GGFI N+E V L+DRE I+RL N I +L ++ML+DTSI Y YE SL
Sbjct: 221 YPTPEHKEEEAGGFIANLEPVSLADREVISRLRNCIISLVTQRMMLYDTSILYCYEASLP 280
Query: 269 YSTYDLLKPESKLDLVLCTAQKL 291
+ D+LKPE ++V+ T Q+L
Sbjct: 281 HQIKDILKPEIMEEIVMETRQRL 303
>pdb|4IFD|H Chain H, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 361
Score = 169 bits (429), Expect = 1e-42, Method: Compositional matrix adjust.
Identities = 110/305 (36%), Positives = 156/305 (51%), Gaps = 41/305 (13%)
Query: 32 ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYXXXXXXXXX 91
I+TPGE V +M GHGT+ D +SV G V +VN+L+SV + RY
Sbjct: 56 IVTPGELVTDDPIWMRGHGTYFLDNMTYSSVAGTVSRVNRLLSVIPLKGRYAPETGDHVV 115
Query: 92 XRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
R+ + +++W VD + L L SVNLPGG RR+S DE MR FLKEGDL++AE+
Sbjct: 116 GRIAEVGNKRWKVDIGGKQHAVLMLGSVNLPGGILRRKSESDELQMRSFLKEGDLLNAEV 175
Query: 152 HQISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWV 211
+ +GS +LHTRSLKYGKL G+ VP SLI R+K+H NL V+LG NGY+W+
Sbjct: 176 QSLFQDGSASLHTRSLKYGKLRNGMFCQVPSSLIVRAKNHTHNLPGNITVVLGVNGYIWL 235
Query: 212 ------------------SAIDENKSGGFIQ-NMEVVKLSD------------------- 233
S+I G + N + +L +
Sbjct: 236 RKTSQMDLARDTPSANNSSSIKSTGPTGAVSLNPSITRLEEESSWQIYSDENDPSISNNI 295
Query: 234 RETITRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLV---LCTAQK 290
R+ I R NVIKALA ++ + I AYE S+ YS L ++ ++ + + TA+K
Sbjct: 296 RQAICRYANVIKALAFCEIGITQQRIVSAYEASMVYSNVGELIEKNVMESIGSDILTAEK 355
Query: 291 LQTLG 295
++ G
Sbjct: 356 MRGNG 360
>pdb|3L7Z|C Chain C, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|F Chain F, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|I Chain I, Crystal Structure Of The S. Solfataricus Archaeal Exosome
Length = 249
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/157 (24%), Positives = 67/157 (42%), Gaps = 15/157 (9%)
Query: 102 WVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT 161
WVVD + ++ +L + NL G RS+ E +R +L GD + A I
Sbjct: 88 WVVDIKAPYKA--YLPASNLLG-----RSINVGEDLRRYLDVGDYVIARIENFDRSIDPV 140
Query: 162 LHTRSLKYGKLGQGILLTV----PPSLIRRSKSHFCNLA--CGAQVILGCNGYVWVSAID 215
L + G++ GI++ + P +I ++KS + L G + + NG +W +
Sbjct: 141 LSVKGKDLGRVSNGIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPS 200
Query: 216 ENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKV 252
I+ + K+ + I L + IK E K+
Sbjct: 201 RFSEEILIEAIR--KIENESHIKGLTDRIKQFIEEKL 235
>pdb|2JEB|I Chain I, Structure Of A 9-Subunit Archaeal Exosome Bound To Mn Ions
Length = 251
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/157 (24%), Positives = 67/157 (42%), Gaps = 15/157 (9%)
Query: 102 WVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT 161
WVVD + ++ +L + NL G RS+ E +R +L GD + A I
Sbjct: 90 WVVDIKAPYKA--YLPASNLLG-----RSINVGEDLRRYLDVGDYVIARIENFDRSIDPV 142
Query: 162 LHTRSLKYGKLGQGILLTV----PPSLIRRSKSHFCNLA--CGAQVILGCNGYVWVSAID 215
L + G++ GI++ + P +I ++KS + L G + + NG +W +
Sbjct: 143 LSVKGKDLGRVSNGIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPS 202
Query: 216 ENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKV 252
I+ + K+ + I L + IK E K+
Sbjct: 203 RFSEEILIEAIR--KIENESHIKGLTDRIKQFIEEKL 237
>pdb|2JE6|I Chain I, Structure Of A 9-Subunit Archaeal Exosome
pdb|2JEA|I Chain I, Structure Of A 9-Subunit Archaeal Exosome Bound To Rna
pdb|4BA1|I Chain I, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
pdb|4BA2|I Chain I, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
Length = 251
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/157 (24%), Positives = 67/157 (42%), Gaps = 15/157 (9%)
Query: 102 WVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLT 161
WVVD + ++ +L + NL G RS+ E +R +L GD + A I
Sbjct: 90 WVVDIKAPYKA--YLPASNLLG-----RSINVGEDLRRYLDVGDYVIARIENFDRSIDPV 142
Query: 162 LHTRSLKYGKLGQGILLTV----PPSLIRRSKSHFCNLA--CGAQVILGCNGYVWVSAID 215
L + G++ GI++ + P +I ++KS + L G + + NG +W +
Sbjct: 143 LSVKGKDLGRVSNGIVIDIMPVKVPRVIGKNKSMYETLTSKSGCSIFVANNGRIWATCPS 202
Query: 216 ENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKV 252
I+ + K+ + I L + IK E K+
Sbjct: 203 RFSEEILIEAIR--KIENESHIKGLTDRIKQFIEEKL 237
>pdb|2BA0|A Chain A, Archaeal Exosome Core
pdb|2BA0|B Chain B, Archaeal Exosome Core
pdb|2BA0|C Chain C, Archaeal Exosome Core
Length = 229
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 35/178 (19%), Positives = 73/178 (41%), Gaps = 25/178 (14%)
Query: 47 TGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSRYXXXXXXXXXXRVTGLQSQKWVVDT 106
G+GT+ + ++ A + G+ ++ V V + RY + + + W VD
Sbjct: 18 AGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGRYTPSVGDVVIGIIREVAANGWAVDI 77
Query: 107 NSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEIHQISTEGSLTLH--- 163
S ++ L ++ ++ + E L GD I A++ I + +TL
Sbjct: 78 YSPYQAFLPVSE---------NPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVTLTMKD 128
Query: 164 --TRSLKYGKLGQGILLTVPPSLIRR---SKSHFCNL---ACGAQVILGCNGYVWVSA 213
R +++G+ ++ + P+ + R K L Q+++G NG +WV+
Sbjct: 129 RICRPIRFGR-----IVAINPARVPRVIGKKGSMIKLLKSELDVQIVVGQNGLIWVNG 181
>pdb|1J3P|A Chain A, Crystal Structure Of Thermococcus Litoralis Phosphoglucose
Isomerase
pdb|1J3P|B Chain B, Crystal Structure Of Thermococcus Litoralis Phosphoglucose
Isomerase
pdb|1J3Q|A Chain A, Crystal Structure Of Thermococcus Litoralis Phosphogrucose
Isomerase Soaked With Feso4
pdb|1J3Q|B Chain B, Crystal Structure Of Thermococcus Litoralis Phosphogrucose
Isomerase Soaked With Feso4
pdb|1J3R|A Chain A, Crystal Structure Of Thermococcus Litoralis Phosphogrucose
Isomerase Complexed With Gluconate-6-Phosphate
pdb|1J3R|B Chain B, Crystal Structure Of Thermococcus Litoralis Phosphogrucose
Isomerase Complexed With Gluconate-6-Phosphate
Length = 190
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 12/78 (15%)
Query: 133 DEEMMREFLKEGDLISAEIHQI---STEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSK 189
DEE ++ ++EGD + E++ I EG L T L GK+G +T K
Sbjct: 37 DEEAWKKMVEEGDPVVYEVYAIEQEEKEGDLNFATTVLYPGKVGNEFFMT---------K 87
Query: 190 SHFCNLACGAQVILGCNG 207
H+ + A+V G
Sbjct: 88 GHYHSKIDRAEVYFALKG 105
>pdb|1UKY|A Chain A, Substrate Specificity And Assembly Of Catalytic Center
Derived From Two Structures Of Ligated Uridylate Kinase
pdb|1UKZ|A Chain A, Substrate Specificity And Assembly Of Catalytic Center
Derived From Two Structures Of Ligated Uridylate Kinase
Length = 203
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 96 GLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEGDLISAEI 151
G Q +K V D S +HL++ +L EQ R Q E+++ +KEG ++ EI
Sbjct: 29 GTQCEKLVKDY-----SFVHLSAGDLLRAEQGRAGSQYGELIKNCIKEGQIVPQEI 79
>pdb|2C9J|A Chain A, Structure Of The Fluorescent Protein Cmfp512 At 1.35a From
Cerianthus Membranaceus
pdb|2C9J|B Chain B, Structure Of The Fluorescent Protein Cmfp512 At 1.35a From
Cerianthus Membranaceus
pdb|2C9J|C Chain C, Structure Of The Fluorescent Protein Cmfp512 At 1.35a From
Cerianthus Membranaceus
pdb|2C9J|D Chain D, Structure Of The Fluorescent Protein Cmfp512 At 1.35a From
Cerianthus Membranaceus
pdb|2C9J|E Chain E, Structure Of The Fluorescent Protein Cmfp512 At 1.35a From
Cerianthus Membranaceus
pdb|2C9J|F Chain F, Structure Of The Fluorescent Protein Cmfp512 At 1.35a From
Cerianthus Membranaceus
pdb|2C9J|G Chain G, Structure Of The Fluorescent Protein Cmfp512 At 1.35a From
Cerianthus Membranaceus
pdb|2C9J|H Chain H, Structure Of The Fluorescent Protein Cmfp512 At 1.35a From
Cerianthus Membranaceus
Length = 223
Score = 27.7 bits (60), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 27/58 (46%)
Query: 206 NGYVWVSAIDENKSGGFIQNMEVVKLSDRETITRLNNVIKALAESKVMLFDTSIQYAY 263
+G VW ++ +G ++N V++ ET+T N V+ +L D S Y +
Sbjct: 113 HGDVWALGVNFPPNGPVMKNEIVMEEPAEETLTAKNGVLVGFCPKAYLLKDGSYYYGH 170
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.133 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,046,284
Number of Sequences: 62578
Number of extensions: 298243
Number of successful extensions: 937
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 926
Number of HSP's gapped (non-prelim): 10
length of query: 298
length of database: 14,973,337
effective HSP length: 98
effective length of query: 200
effective length of database: 8,840,693
effective search space: 1768138600
effective search space used: 1768138600
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)