RPS-BLAST 2.2.26 [Sep-21-2011]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= psy10116
(298 letters)
>d2nn6h3 d.51.1.1 (H:168-293) Ribosomal RNA-processing protein 4,
RRP4 {Human (Homo sapiens) [TaxId: 9606]}
Length = 126
Score = 150 bits (380), Expect = 2e-46
Identities = 60/124 (48%), Positives = 84/124 (67%), Gaps = 3/124 (2%)
Query: 174 QGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYVWVSAI---DENKSGGFIQNMEVVK 230
QG+L+ V PSL++R K+HF +L CGA VILG NG++W+ E ++GGFI N+E V
Sbjct: 1 QGVLVQVSPSLVKRQKTHFHDLPCGASVILGNNGFIWIYPTPEHKEEEAGGFIANLEPVS 60
Query: 231 LSDRETITRLNNVIKALAESKVMLFDTSIQYAYEESLKYSTYDLLKPESKLDLVLCTAQK 290
L+DRE I+RL N I +L ++ML+DTSI Y YE SL + D+LKPE ++V+ T Q+
Sbjct: 61 LADREVISRLRNCIISLVTQRMMLYDTSILYCYEASLPHQIKDILKPEIMEEIVMETRQR 120
Query: 291 LQTL 294
L
Sbjct: 121 LLEQ 124
>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing
protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}
Length = 95
Score = 98.5 bits (245), Expect = 9e-27
Identities = 59/94 (62%), Positives = 80/94 (85%)
Query: 80 SRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMRE 139
+RYIGE+G++VVGR+T +Q ++W V+TNS L+S L L+S+NLPGGE RRRS +DE MR
Sbjct: 2 TRYIGEVGDIVVGRITEVQQKRWKVETNSRLDSVLLLSSMNLPGGELRRRSAEDELAMRG 61
Query: 140 FLKEGDLISAEIHQISTEGSLTLHTRSLKYGKLG 173
FL+EGDLISAE+ + ++G+++LHTRSLKYGKLG
Sbjct: 62 FLQEGDLISAEVQAVFSDGAVSLHTRSLKYGKLG 95
>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human
(Homo sapiens) [TaxId: 9606]}
Length = 125
Score = 77.2 bits (190), Expect = 2e-18
Identities = 16/92 (17%), Positives = 41/92 (44%), Gaps = 1/92 (1%)
Query: 80 SRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMRE 139
S+ + ++G +V +V+ + S+ V + L + E R + +D+ + +
Sbjct: 1 SQLLPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATEKDKVEIYK 60
Query: 140 FLKEGDLISAEIHQIS-TEGSLTLHTRSLKYG 170
+ GD++ A++ + + + L T + G
Sbjct: 61 SFRPGDIVLAKVISLGDAQSNYLLTTAENELG 92
>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3
(RRP40) {Saccharomyces cerevisiae [TaxId: 4932]}
Length = 90
Score = 71.8 bits (176), Expect = 1e-16
Identities = 22/98 (22%), Positives = 36/98 (36%), Gaps = 11/98 (11%)
Query: 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREF 140
RYI + + V+G + G S + V + S + P ++ R
Sbjct: 2 RYIPSVNDFVIGVIIGTFSDSYKVSLQNFSSSVSLS-YMAFPNASKK---------NRPT 51
Query: 141 LKEGDLISAEIHQISTEGSLTLHTRSLKYGK-LGQGIL 177
L+ GDL+ A + E + G+ G GIL
Sbjct: 52 LQVGDLVYARVCTAEKELEAEIECFDSTTGRDAGFGIL 89
>d2nn6h2 b.84.4.2 (H:25-72) Ribosomal RNA-processing protein 4,
RRP4 {Human (Homo sapiens) [TaxId: 9606]}
Length = 48
Score = 68.5 bits (168), Expect = 4e-16
Identities = 21/47 (44%), Positives = 35/47 (74%)
Query: 32 ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAM 78
++ PG+T+ G+M GHGT+ +E++ ASV G VE+VN+L+ V+A+
Sbjct: 2 LVVPGDTITTDTGFMRGHGTYMGEEKLIASVAGSVERVNKLICVKAL 48
>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3
(RRP40) {Human (Homo sapiens) [TaxId: 9606]}
Length = 88
Score = 66.8 bits (163), Expect = 6e-15
Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 16/99 (16%)
Query: 81 RYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREF 140
RY+ G+ V+G VT + VD ++L ++ G +R R
Sbjct: 1 RYVPVKGDHVIGIVTAKSGDIFKVDVGGSEPASLSY--LSFEGATKR---------NRPN 49
Query: 141 LKEGDLISAEIHQISTEGSLTL-----HTRSLKYGKLGQ 174
++ GDLI + + + + R+ G +GQ
Sbjct: 50 VQVGDLIYGQFVVANKDMEPEMVCIDSCGRANGMGVIGQ 88
>d2ba0a2 b.84.4.2 (A:2-52) Exosome complex RNA-binding protein 1,
ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}
Length = 51
Score = 56.1 bits (136), Expect = 2e-11
Identities = 11/50 (22%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 32 ILTPGETVEYLEGYMTGHGTFPDDEEIKASVGGVVEKVNQLVSVRAMNSR 81
I+ PG+ + G+GT+ + ++ A + G+ ++ V V + R
Sbjct: 3 IVLPGDLLS-TNPRAAGYGTYVEGGKVYAKIIGLFDQTETHVRVIPLKGR 51
>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex
RNA-binding protein 1, ECR1 {Sulfolobus solfataricus
[TaxId: 2287]}
Length = 87
Score = 57.3 bits (138), Expect = 2e-11
Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 7/93 (7%)
Query: 80 SRYIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMRE 139
S Y +I ++V+G V ++ WVVD + ++ L + RS+ E +R
Sbjct: 1 SFYYPKINDIVIGLVEDVEIYGWVVDIKAPYKAYLPAS-------NLLGRSINVGEDLRR 53
Query: 140 FLKEGDLISAEIHQISTEGSLTLHTRSLKYGKL 172
+L GD + A I L + G++
Sbjct: 54 YLDVGDYVIARIENFDRSIDPVLSVKGKDLGRV 86
>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex
RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId:
56636]}
Length = 88
Score = 56.4 bits (136), Expect = 3e-11
Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 6/91 (6%)
Query: 82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFL 141
Y+ + G+VV+G + + W VD NS + L + R + M+ L
Sbjct: 3 YVPQAGDVVIGLIQSVGIMNWFVDINSPYVAVLSVQDFL------GRPFNPAVDDMQSLL 56
Query: 142 KEGDLISAEIHQISTEGSLTLHTRSLKYGKL 172
K GD I A++ S L + G++
Sbjct: 57 KVGDYIKAKVVAFDKTRSPLLTVQGEGLGRI 87
>d2je6i2 b.84.4.2 (I:7-65) Exosome complex RNA-binding protein 1,
ECR1 {Sulfolobus solfataricus [TaxId: 2287]}
Length = 59
Score = 45.8 bits (109), Expect = 9e-08
Identities = 8/48 (16%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 32 ILTPGETVEYLEGYMT-GHGTFPDDEEIKASVGGVVEKVNQLVSVRAM 78
I+ PGE + E + + + ++V G+ + + V +
Sbjct: 10 IVVPGELLAEGEFQIPWSPYILKINSKYYSTVVGLFDVKDTQFEVIPL 57
>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex
RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus
[TaxId: 2234]}
Length = 83
Score = 45.4 bits (107), Expect = 3e-07
Identities = 19/91 (20%), Positives = 37/91 (40%), Gaps = 9/91 (9%)
Query: 82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFL 141
Y +G+VV+G + + + W VD S ++ L + ++ + E L
Sbjct: 1 YTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPV---------SENPEMKPNKKPNEVL 51
Query: 142 KEGDLISAEIHQISTEGSLTLHTRSLKYGKL 172
GD I A++ I + +TL + +
Sbjct: 52 DIGDAIIAKVLNIDPKMKVTLTMKDRICRPI 82
>d2nn6i2 b.84.4.2 (I:6-60) Exosome component 1, EXOSC1 {Human
(Homo sapiens) [TaxId: 9606]}
Length = 55
Score = 39.3 bits (92), Expect = 2e-05
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 35 PGETVEYLEGYMTGHGTFPDDEEIKASVGGVV--EKVNQLVSV 75
PGE + LE G GT+ I +S+ G + N + V
Sbjct: 5 PGERLCNLEEGSPGSGTYTRHGYIFSSLAGCLMKSSENGALPV 47
>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide
phosphorylase, PNPase {Escherichia coli [TaxId: 562]}
Length = 76
Score = 33.6 bits (77), Expect = 0.003
Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 13/84 (15%)
Query: 85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEG 144
E+G V G+VT + V E +H + + + E + ++L+ G
Sbjct: 4 EVGRVYTGKVTRIVDFGAFVAIGGGKEGLVH----------ISQIADKRVEKVTDYLQMG 53
Query: 145 DLISAEIHQISTEGSLTLHTRSLK 168
+ ++ ++ +G + L S+K
Sbjct: 54 QEVPVKVLEVDRQGRIRL---SIK 74
>d2ja9a2 d.51.1.1 (A:152-236) Ribosomal RNA-processing protein 40,
RRP40 {Saccharomyces cerevisiae [TaxId: 4932]}
Length = 85
Score = 30.1 bits (68), Expect = 0.067
Identities = 9/48 (18%), Positives = 20/48 (41%), Gaps = 7/48 (14%)
Query: 175 GILLTVPPSLIRR----SKSHFCNL---ACGAQVILGCNGYVWVSAID 215
G+++ V + R+ + + +V +G NG +WV +
Sbjct: 2 GMIIDVNLNFARQLLFNNDFPLLKVLAAHTKFEVAIGLNGKIWVKCEE 49
>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II
subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces
cerevisiae) [TaxId: 4932]}
Length = 91
Score = 28.3 bits (63), Expect = 0.30
Identities = 9/73 (12%), Positives = 21/73 (28%), Gaps = 1/73 (1%)
Query: 85 EIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFLKEG 144
GEVV G V + V + + + + + + + +
Sbjct: 2 FKGEVVDGTVVSCSQHGFEVQVGPM-KVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIK 60
Query: 145 DLISAEIHQISTE 157
I +I ++
Sbjct: 61 SRIRVKIEGCISQ 73
>g1pya.1 d.155.1.1 (A:,B:) Histidine decarboxylase {Lactobacillus
sp., strain 30a [TaxId: 1591]}
Length = 310
Score = 27.9 bits (62), Expect = 1.4
Identities = 27/109 (24%), Positives = 44/109 (40%), Gaps = 23/109 (21%)
Query: 4 EKDKPVIEIMLASDRIDPLIEIHEFTDPILTPGETVEYLEGYMTGHGTFPDDEEIKASVG 63
E D + ++ + I P ++T + PG GY+TG +K G
Sbjct: 2 ELDAKLNKLGVDRIAISPY---KQWTRGYMEPGN---IGNGYVTG---------LKVDAG 46
Query: 64 GVVEK-----VNQLVSV-RA-MNSRYIGEIGEVVVGRVTGLQSQKWVVD 105
V +K ++ +VS RA + YIG+I TG+Q + D
Sbjct: 47 -VRDKSDDDVLDGIVSYDRAETKNAYIGQINMTTASXFTGVQGRVIGYD 94
>d1u3em1 d.4.1.3 (M:1-105) Intron-encoded homing endonuclease I-HmuI
{Bacteriophage SP01 [TaxId: 10685]}
Length = 105
Score = 26.1 bits (57), Expect = 2.3
Identities = 14/80 (17%), Positives = 26/80 (32%), Gaps = 3/80 (3%)
Query: 152 HQISTEGSL--TLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGAQVILGCNGYV 209
+Q+S G + ++LK+ G + + K+ + G +
Sbjct: 13 YQVSNTGEVYSIKSGKTLKHQIPKDGYH-RIGLFKGGKGKTFQVHRLVAIHFCEGYEEGL 71
Query: 210 WVSAIDENKSGGFIQNMEVV 229
V D NK N+ V
Sbjct: 72 VVDHKDGNKDNNLSTNLRWV 91
>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima
[TaxId: 2336]}
Length = 72
Score = 25.4 bits (56), Expect = 2.7
Identities = 13/77 (16%), Positives = 21/77 (27%), Gaps = 17/77 (22%)
Query: 82 YIGEIGEVVVGRVTGLQSQKWVVDTNSILESALHLTSVNLPGGEQRRRSVQDEEMMREFL 141
Y G V V + + + LP + E + E +
Sbjct: 4 YSELKGTVTTAEVIRVMGEWADIRIGK--------LETRLP---------KKEWIPGEEI 46
Query: 142 KEGDLISAEIHQISTEG 158
K GDL+ I +
Sbjct: 47 KAGDLVKVYIIDVVKTT 63
>d2z0sa2 d.51.1.1 (A:148-234) Exosome complex RNA-binding protein 1,
ECR1 {Aeropyrum pernix [TaxId: 56636]}
Length = 87
Score = 25.4 bits (56), Expect = 3.5
Identities = 7/51 (13%), Positives = 20/51 (39%), Gaps = 6/51 (11%)
Query: 174 QGILLTVPPSLIRR------SKSHFCNLACGAQVILGCNGYVWVSAIDENK 218
+G ++ + P+ + R S ++ + NG + + +E+
Sbjct: 1 RGKIVEISPAKVPRVIGRKMSMLKTLEEKTECKIFVARNGRIHLECPNEDL 51
>d2nn6g3 d.51.1.1 (G:195-274) Ribosomal RNA-processing protein 40,
RRP40 {Human (Homo sapiens) [TaxId: 9606]}
Length = 80
Score = 24.6 bits (54), Expect = 5.1
Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 15/85 (17%)
Query: 175 GILLTVPPSLIRRSKSHFCNL------ACGAQVILGCNGYVWVSAIDENKS---GGFIQN 225
G+L V LIR+ + C + +++ G NG +WV A ++ ++
Sbjct: 2 GLLFKVTLGLIRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVKAKTIQQTLILANILEA 61
Query: 226 MEVVKLSDRETITRLNNVIKALAES 250
E + R+ I LAES
Sbjct: 62 CEHMTSDQRKQI------FSRLAES 80
>d2nwia1 d.190.1.3 (A:1-160) Hypothetical protein AF1396
{Archaeoglobus fulgidus [TaxId: 2234]}
Length = 160
Score = 25.4 bits (55), Expect = 7.3
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 6/66 (9%)
Query: 154 ISTEGSLTLHTRSLKYGKLGQGILLTVPPSLIRRSKSHFCNLACGA-----QVILGCNGY 208
++T+GS+T ++ K+ + L R + + G V L NG
Sbjct: 9 MTTDGSITAIIEAVTQKKV-EVETLEQKIIRADRELAELLEIDEGDEVNYRVVYLRANGE 67
Query: 209 VWVSAI 214
++ AI
Sbjct: 68 IYAKAI 73
Database: scop70_1_75
Posted date: Mar 27, 2010 6:21 PM
Number of letters in database: 2,407,596
Number of sequences in database: 13,730
Lambda K H
0.316 0.134 0.375
Gapped
Lambda K H
0.267 0.0610 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,065,338
Number of extensions: 48668
Number of successful extensions: 251
Number of sequences better than 10.0: 1
Number of HSP's gapped: 246
Number of HSP's successfully gapped: 24
Length of query: 298
Length of database: 2,407,596
Length adjustment: 85
Effective length of query: 213
Effective length of database: 1,240,546
Effective search space: 264236298
Effective search space used: 264236298
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: 53 (24.5 bits)