RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy230
(222 letters)
>2nn6_G Exosome complex exonuclease RRP40; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1
Length = 289
Score = 195 bits (497), Expect = 1e-62
Identities = 89/217 (41%), Positives = 142/217 (65%), Gaps = 9/217 (4%)
Query: 7 SLNAEPRLILGPGLRRESSAILVSQSGILRHAKPF------TYYVDYIQRRYVPTRGDLV 60
+ R++ GPGLRR +LV++ G LRH +P Y+VD Q+RYVP +GD V
Sbjct: 72 RACSRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPVKGDHV 131
Query: 61 IGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESE 120
IG+VT++ GD ++VD+G +PA LSYL+FEGATK+N P V+ GD++ G+ + ANKDME E
Sbjct: 132 IGIVTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPE 191
Query: 121 MVCVDSRGKEFIMGIL-NDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNG 179
MVC+DS G+ MG++ DG L ++ L RKLL P C +++++ K +E+ GMNG
Sbjct: 192 MVCIDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGKLY--PLEIVFGMNG 249
Query: 180 KIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESI 216
+IW++ ++ T+ + N++ +CE ++ ++ + +
Sbjct: 250 RIWVKAKTIQQTLILANILEACEHMTSDQRKQIFSRL 286
>2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1
domain, KH domain, hydrolase, RNA-binding, nuclear
protein; 2.20A {Saccharomyces cerevisiae} SCOP: b.40.4.5
d.51.1.1
Length = 175
Score = 145 bits (368), Expect = 2e-44
Identities = 62/164 (37%), Positives = 98/164 (59%), Gaps = 5/164 (3%)
Query: 50 RRYVPTRGDLVIGVVTSRVGDNYRVDIGSH-DPAVLSYLAFEGATKKNPPKVETGDVVAG 108
+RY+P+ D VIGV+ D+Y+V + + LSY+AF A+KKN P ++ GD+V
Sbjct: 1 KRYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNASKKNRPTLQVGDLVYA 60
Query: 109 KLLTANKDMESEMVCVDSR-GKEFIMGILNDGYLLHTSISLC-RKLLNPKCPLLKQLAKR 166
++ TA K++E+E+ C DS G++ GIL DG ++ +++ + L N PLLK LA
Sbjct: 61 RVCTAEKELEAEIECFDSTTGRDAGFGILEDGMIIDVNLNFARQLLFNNDFPLLKVLAAH 120
Query: 167 SRQKMELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEIL 210
+ K E++IG+NGKIW++CE S+T+ IM C +
Sbjct: 121 T--KFEVAIGLNGKIWVKCEELSNTLACYRTIMECCQKNDTAAF 162
>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase,
exonuclease, phosphorolytic, exoribonuclease, RNA
degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus}
SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I*
3l7z_C
Length = 251
Score = 133 bits (335), Expect = 1e-38
Identities = 36/213 (16%), Positives = 78/213 (36%), Gaps = 12/213 (5%)
Query: 3 GDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIG 62
G+ L+ E ++ P + + +S + G+ + Y P D+VIG
Sbjct: 22 GELLA-EGEFQIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPLEGSFYYPKINDIVIG 80
Query: 63 VVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKV----ETGDVVAGKLLTANKDME 118
+V + VDI + A L G + + + GD V ++ ++ ++
Sbjct: 81 LVEDVEIYGWVVDIKAPYKAYLPASNLLGRSINVGEDLRRYLDVGDYVIARIENFDRSID 140
Query: 119 SEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMN 178
+ +G +++G ++ +++ + + L +S + + N
Sbjct: 141 PVLSVKGKD-----LGRVSNGIVIDIMPVKVPRVIGKNKSMYETLTSKS--GCSIFVANN 193
Query: 179 GKIWIRCESFSDTVRVGNLIMSCELLSYEEILN 211
G+IW C S + I E S+ + L
Sbjct: 194 GRIWATCPSRFSEEILIEAIRKIENESHIKGLT 226
>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA
degradation, exoribonuclease, S1domain, KH domain,
archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5
b.84.4.2 d.51.1.1
Length = 229
Score = 127 bits (321), Expect = 7e-37
Identities = 41/209 (19%), Positives = 81/209 (38%), Gaps = 13/209 (6%)
Query: 3 GDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIG 62
GD LS N G G E + G+ + V ++ RY P+ GD+VIG
Sbjct: 8 GDLLSTNP---RAAGYGTYVEGGKVYAKIIGLFDQTET-HVRVIPLKGRYTPSVGDVVIG 63
Query: 63 VVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPK--VETGDVVAGKLLTANKDMESE 120
++ + + VDI S A L P ++ GD + K+L + M+
Sbjct: 64 IIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDIGDAIIAKVLNIDPKMKVT 123
Query: 121 MVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGMNGK 180
+ D + G ++ + + +++ K ++K L +++ +G NG
Sbjct: 124 LTMKDRIC-----RPIRFGRIVAINPARVPRVIGKKGSMIKLLKSEL--DVQIVVGQNGL 176
Query: 181 IWIRCESFSDTVRVGNLIMSCELLSYEEI 209
IW+ + ++ + + + E +
Sbjct: 177 IWVNGDRRKVSIAEEAIYLIEQEAHTEGL 205
>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein,
cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum
pernix} SCOP: b.40.4.5 d.51.1.1
Length = 235
Score = 125 bits (315), Expect = 8e-36
Identities = 46/220 (20%), Positives = 84/220 (38%), Gaps = 18/220 (8%)
Query: 3 GDTLSLNAEPRLILGPGLRRESSAILVSQSGILRH-AKPFTYYVDYIQRRYVPTRGDLVI 61
G+ L E P + + G+LR ++ YVP GD+VI
Sbjct: 15 GEPLPEEVE---ASPPYVIDYKGVKRATVVGLLREKGDGGGRAFVKLKEIYVPQAGDVVI 71
Query: 62 GVVTSRVGDNYRVDIGSHDPAVLSYLAFEG-----ATKKNPPKVETGDVVAGKLLTANKD 116
G++ S N+ VDI S AVLS F G A ++ GD + K++ +K
Sbjct: 72 GLIQSVGIMNWFVDINSPYVAVLSVQDFLGRPFNPAVDDMQSLLKVGDYIKAKVVAFDKT 131
Query: 117 MESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIG 176
+ +G + G ++ S + +++ K +LK L +++ + ++ +
Sbjct: 132 RSPLLTVQGEG-----LGRIVRGKIVEISPAKVPRVIGRKMSMLKTLEEKT--ECKIFVA 184
Query: 177 MNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLCESI 216
NG+I + C + I + L + I
Sbjct: 185 RNGRIHLECPNEDLEAIAVMAIKIID--EEAYTSGLTKRI 222
>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1
Length = 308
Score = 110 bits (277), Expect = 2e-29
Identities = 42/222 (18%), Positives = 79/222 (35%), Gaps = 27/222 (12%)
Query: 3 GDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIG 62
GDT++ + + G G ++ S +G + V ++ RY+ GD+V+G
Sbjct: 45 GDTIT--TDTGFMRGHGTYMGEEKLIASVAGSVERVNK-LICVKALKTRYIGEVGDIVVG 101
Query: 63 VVTSRVGDNYRVDIGSHDPAVL--SYLAFEGATKKNPPKVET---------GDVVAGKLL 111
+T ++V+ S +VL S + G + + GD+++ ++
Sbjct: 102 RITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRGFLQEGDLISAEVQ 161
Query: 112 TANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKM 171
D + + G L G L+ S SL ++ K
Sbjct: 162 AVFSDGAVSLHTRSLK-----YGKLGQGVLVQVSPSLVKR--------QKTHFHDLPCGA 208
Query: 172 ELSIGMNGKIWIRCESFSDTVRVGNLIMSCELLSYEEILNLC 213
+ +G NG IWI G I + E +S + +
Sbjct: 209 SVILGNNGFIWIYPTPEHKEEEAGGFIANLEPVSLADREVIS 250
>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA,
exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A
{Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A
Length = 179
Score = 36.5 bits (84), Expect = 0.002
Identities = 18/118 (15%), Positives = 37/118 (31%), Gaps = 14/118 (11%)
Query: 3 GDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIG 62
GD + E + G G+ E + + +G L V+ I +GD+V+G
Sbjct: 7 GDRIGSAEE--YVKGEGVYEEGGELFAAVAGKLIIKDR-VAKVESISPIPEIVKGDVVLG 63
Query: 63 VVTSRVGDNYRVDIGSHDPAVLS-------YLAFEGATKKNPPKVET----GDVVAGK 109
V +++ S L + ++ D++ +
Sbjct: 64 RVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGYVKEISEAVGYLDILKAR 121
>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL,
phosphorolytic, hydrolase/transferase complex; 3.35A
{Homo sapiens} SCOP: b.40.4.5 b.84.4.2
Length = 209
Score = 33.1 bits (75), Expect = 0.037
Identities = 19/88 (21%), Positives = 28/88 (31%), Gaps = 7/88 (7%)
Query: 3 GDTLSLNAEPRLILGPGLRRESSAILVSQSGILRH-AKPFTYYVDYIQRR----YVPTRG 57
G+ L E G G I S +G L ++ V + R +P G
Sbjct: 25 GERLCNLEE--GSPGSGTYTRHGYIFSSLAGCLMKSSENGALPVVSVVRETESQLLPDVG 82
Query: 58 DLVIGVVTSRVGDNYRVDIGSHDPAVLS 85
+V V+S +V I L
Sbjct: 83 AIVTCKVSSINSRFAKVHILYVGSMPLK 110
>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 = 29.6 bits (66), Expect = 0.88
Identities = 28/162 (17%), Positives = 47/162 (29%), Gaps = 65/162 (40%)
Query: 18 PGLRRESSAILVS-QSGILRHAKPFT---------YYVDYIQ---RRYVPTRGDLVIGVV 64
P ++ +SA+ + G +A+ Y + ++ + Y GDL
Sbjct: 136 PFDKKSNSALFRAVGEG---NAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDL----- 187
Query: 65 TSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCV 124
I LS L + E K+ T ++ +
Sbjct: 188 -----------IKFSA-ETLSELI------RTTLDAE-------KVFTQGLNILEWLENP 222
Query: 125 DSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPL--LKQLA 164
+ + YLL IS CPL + QLA
Sbjct: 223 SNTP--------DKDYLLSIPIS---------CPLIGVIQLA 247
>2pkp_A Homoaconitase small subunit; beta barrel, amino-acid biosynthesis,
leucine biosynthesis, structural genomics, NPPSFA; 2.10A
{Methanocaldococcus jannaschii}
Length = 170
Score = 28.8 bits (65), Expect = 0.91
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 8/51 (15%)
Query: 67 RVGDNYRVD-------IGSHDPAVLSYLAFEGATKKNPPKVETGDV-VAGK 109
+ GD+ D + + DP L+ G + P KV+ GDV VAG+
Sbjct: 9 KFGDDVDTDAIIPGPYLRTTDPYELASHCMAGIDENFPKKVKEGDVIVAGE 59
>3d0f_A Penicillin-binding 1 transmembrane protein MRCA; BIG_1156.2, STR
genomics, PSI-2, protein structure initiative; 1.64A
{Nitrosomonas europaea atcc 19718}
Length = 106
Score = 27.2 bits (60), Expect = 2.3
Identities = 9/61 (14%), Positives = 19/61 (31%), Gaps = 7/61 (11%)
Query: 53 VPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSY--LAFEGATKKNPPK-----VETGDV 105
+ D++ VV S + + ++ L N PK + G +
Sbjct: 30 IGNSDDILAAVVLSATPGAVEAFRKNGETIRITGDGLKAAHRFLSNDPKIGEKRIRPGAL 89
Query: 106 V 106
+
Sbjct: 90 I 90
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces
cerevisiae}
Length = 1030
Score = 28.3 bits (63), Expect = 2.4
Identities = 11/65 (16%), Positives = 18/65 (27%), Gaps = 8/65 (12%)
Query: 57 GDLVIGVVTSRVGDNY-RVDIGSHDPAVL--SYLAFEGATKKNPPK--VETGDVVAGKLL 111
G ++ V R N S V+ A + P E G K++
Sbjct: 906 GSIIPVRVE-RFWHNDIICTTNSEVECVVNAQRHAGAQL--RRPANEIYEIGKTYPAKVI 962
Query: 112 TANKD 116
+
Sbjct: 963 YIDYA 967
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces
cerevisiae}
Length = 1219
Score = 28.3 bits (63), Expect = 2.4
Identities = 11/66 (16%), Positives = 19/66 (28%), Gaps = 8/66 (12%)
Query: 56 RGDLVIGVVTSRVGDNY-RVDIGSHDPAVL--SYLAFEGATKKNPPK--VETGDVVAGKL 110
+G ++ V R N S V+ A + P E G K+
Sbjct: 902 KGSIIPVRVE-RFWHNDIICTTNSEVECVVNAQRHAGAQL--RRPANEIYEIGKTYPAKV 958
Query: 111 LTANKD 116
+ +
Sbjct: 959 IYIDYA 964
>3hdi_A Processing protease; CAGE structure, M16B peptidase,
metallopeptidase, peptidasome, protease, hydrolase;
2.70A {Bacillus halodurans c-125}
Length = 421
Score = 27.5 bits (62), Expect = 3.6
Identities = 10/76 (13%), Positives = 19/76 (25%), Gaps = 16/76 (21%)
Query: 45 VDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYL--AFEGATKKNPPKVET 102
Y+ R Y +VI V G+ ++ + F
Sbjct: 172 RHYMDRFYTGDY--VVISVA------------GNVHDELIDKIKETFSQVKPTTYNYQGE 217
Query: 103 GDVVAGKLLTANKDME 118
+ + K+ E
Sbjct: 218 KPMFLPNRIVRKKETE 233
>1v7l_A 3-isopropylmalate dehydratase small subunit; beta barrel, lyase;
1.98A {Pyrococcus horikoshii} SCOP: c.8.2.1
Length = 163
Score = 26.1 bits (58), Expect = 8.0
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 67 RVGDNYRVD-------IGSHDPAVLSYLAFEGATKKNPPKVETGDV-VAGK 109
+ GD+ D + DP L+ +AF V GDV VAGK
Sbjct: 9 KFGDDISTDEITPGRYNLTKDPKELAKIAFIEVRPDFARNVRPGDVVVAGK 59
>1k3r_A Conserved protein MT0001; beta barrel, structural genomics, PSI;
2.30A {Methanothermobacter
thermautotrophicusorganism_taxid} SCOP: b.40.4.10
c.116.1.2
Length = 268
Score = 26.0 bits (57), Expect = 9.1
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 54 PTRGDLVIGVVTSRVGDNYRVDIGSHDPAVL 84
P G+ G+ RV VDIG+ A+
Sbjct: 100 PVTGEYRQGLTVKRVKKGTLVDIGADKLALC 130
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 0.138 0.404
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,339,591
Number of extensions: 192871
Number of successful extensions: 424
Number of sequences better than 10.0: 1
Number of HSP's gapped: 410
Number of HSP's successfully gapped: 23
Length of query: 222
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 132
Effective length of database: 4,188,903
Effective search space: 552935196
Effective search space used: 552935196
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 (25.0 bits)