Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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.
Query= Dr_sW_012_C18
(399 letters)
Database: Non-redundant SwissProt sequences
184,735 sequences; 68,354,980 total letters
Score E
Sequences producing significant alignments: (bits) Value
sp|O26779|ECX1_METTH Probable exosome complex exonuclease 1 50 2e-06
sp|Q9NPD3|EXOS4_HUMAN Exosome complex exonuclease RRP41 (Ri... 48 8e-06
sp|Q921I9|EXOS4_MOUSE Exosome complex exonuclease RRP41 (Ri... 47 1e-05
sp|Q8ZVM9|ECX1_PYRAE Probable exosome complex exonuclease 1 45 4e-05
sp|O42872|RRP41_SCHPO Putative exosome complex exonuclease ... 40 0.002
sp|P46948|RRP41_YEAST Exosome complex exonuclease RRP41 (Ri... 38 0.008
sp|Q9YC03|ECX1_AERPE Probable exosome complex exonuclease 1 38 0.008
sp|Q17533|EXOS4_CAEEL Putative exosome complex exonuclease ... 32 0.35
sp|P47491|RPOD_MYCGE RNA polymerase sigma factor rpoD (Sigm... 30 1.3
sp|P78022|RPOD_MYCPN RNA polymerase sigma factor rpoD (Sigm... 30 1.7
>sp|O26779|ECX1_METTH Probable exosome complex exonuclease 1
Length = 240
Score = 50.1 bits (118), Expect = 2e-06
Identities = 32/111 (28%), Positives = 59/111 (53%), Gaps = 7/111 (6%)
Frame = +1
Query: 34 SKIEVYLMVLNDDGNAISAMVTCASLALIDANVEMYDILI-------GVSLISHVSNEDT 192
S I+V++ VL +G A +T AS+AL DA + M D+++ G ++ +S E+
Sbjct: 121 SVIDVFIEVLEAEGGTRCAGITAASVALADAGIPMRDMVVACAAGKVGDQVVLDLSEEED 180
Query: 193 NKKGQSISVAVLPNMRQIANIMSTYPCPVSEYEKLMRWDGPLKESLQIYEI 345
+ + VA+LP R+I + S E+E+ + D ++ L+I+E+
Sbjct: 181 KEGQADVPVAILPRTREITLLQSDGNLTPEEFERAL--DLAVEGCLRIHEV 229
>sp|Q9NPD3|EXOS4_HUMAN Exosome complex exonuclease RRP41 (Ribosomal RNA-processing protein
41) (Exosome component 4) (p12A)
Length = 245
Score = 47.8 bits (112), Expect = 8e-06
Identities = 28/90 (31%), Positives = 49/90 (54%), Gaps = 7/90 (7%)
Frame = +1
Query: 1 QSAINFSNHVHSKIEVYLMVLNDDGNAISAMVTCASLALIDANVEMYDILIGVS------ 162
++AI H S+I++Y+ VL DG +A V A+LA++DA + M D + S
Sbjct: 108 EAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDG 167
Query: 163 -LISHVSNEDTNKKGQSISVAVLPNMRQIA 249
++ +S+ + G +++A+LP QIA
Sbjct: 168 TALADLSHVEEAAGGPQLALALLPASGQIA 197
>sp|Q921I9|EXOS4_MOUSE Exosome complex exonuclease RRP41 (Ribosomal RNA-processing protein
41) (Exosome component 4)
Length = 245
Score = 47.4 bits (111), Expect = 1e-05
Identities = 28/90 (31%), Positives = 49/90 (54%), Gaps = 7/90 (7%)
Frame = +1
Query: 1 QSAINFSNHVHSKIEVYLMVLNDDGNAISAMVTCASLALIDANVEMYDILIGVS------ 162
++AI H S+I++Y+ VL DG +A V A+LA++DA + M D + S
Sbjct: 108 EAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVMDAGIPMRDFVCACSAGFVDG 167
Query: 163 -LISHVSNEDTNKKGQSISVAVLPNMRQIA 249
++ +S+ + G +++A+LP QIA
Sbjct: 168 TALADLSHVEEAAGGPQLALALLPASGQIA 197
>sp|Q8ZVM9|ECX1_PYRAE Probable exosome complex exonuclease 1
Length = 246
Score = 45.4 bits (106), Expect = 4e-05
Identities = 22/55 (40%), Positives = 36/55 (65%)
Frame = +1
Query: 1 QSAINFSNHVHSKIEVYLMVLNDDGNAISAMVTCASLALIDANVEMYDILIGVSL 165
+ AI + S+I+V++ +L DG+ A +T ASLAL DA + M D+++GVS+
Sbjct: 108 EPAIVLEQYPRSRIDVFVEILQADGSTRVASLTAASLALADAGIYMRDLVVGVSV 162
>sp|O42872|RRP41_SCHPO Putative exosome complex exonuclease RRP41 (Ribosomal
RNA-processing protein 41)
Length = 242
Score = 40.0 bits (92), Expect = 0.002
Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 6/77 (7%)
Frame = +1
Query: 34 SKIEVYLMVLNDDGNAISAMVTCASLALIDANVEMYDILI--GVSLISHVSNEDTNKKGQ 207
S+I VYL VL DDG +++ + +LALIDA + + D + ++ D N +
Sbjct: 118 SQISVYLHVLQDDGAVMASCINATTLALIDAGIPVKDFVCCSTAGIVESDMLLDLNSLEE 177
Query: 208 S----ISVAVLPNMRQI 246
S ++VAVL N++++
Sbjct: 178 SALSWLTVAVLGNIKKV 194
>sp|P46948|RRP41_YEAST Exosome complex exonuclease RRP41 (Ribosomal RNA-processing protein
41) (SKI6 protein)
Length = 246
Score = 37.7 bits (86), Expect = 0.008
Identities = 15/42 (35%), Positives = 28/42 (66%)
Frame = +1
Query: 40 IEVYLMVLNDDGNAISAMVTCASLALIDANVEMYDILIGVSL 165
I++ + VL DG + +++ +LALIDA + M+D + G+S+
Sbjct: 122 IDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISV 163
>sp|Q9YC03|ECX1_AERPE Probable exosome complex exonuclease 1
Length = 246
Score = 37.7 bits (86), Expect = 0.008
Identities = 20/42 (47%), Positives = 28/42 (66%)
Frame = +1
Query: 40 IEVYLMVLNDDGNAISAMVTCASLALIDANVEMYDILIGVSL 165
I+V+L VL DG +A VT ASLAL DA + M ++ GV++
Sbjct: 123 IDVFLEVLQADGGTRTAAVTAASLALADAGIPMRALVGGVAV 164
>sp|Q17533|EXOS4_CAEEL Putative exosome complex exonuclease RRP41 (Ribosomal
RNA-processing protein 41)
Length = 240
Score = 32.3 bits (72), Expect = 0.35
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 8/62 (12%)
Frame = +1
Query: 34 SKIEVYLMVLNDDGNAISAMVTCASLALIDANVEMYDI--------LIGVSLISHVSNED 189
S+++++ V+ DG+ ++A V SLAL DA + M I + G ++ S E+
Sbjct: 114 SQLDIFCEVIQGDGSNLAACVNATSLALADAGIPMKGIASAATCGVVDGKPIVDLTSREE 173
Query: 190 TN 195
T+
Sbjct: 174 TD 175
>sp|P47491|RPOD_MYCGE RNA polymerase sigma factor rpoD (Sigma-A)
Length = 497
Score = 30.4 bits (67), Expect = 1.3
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 11/64 (17%)
Frame = +1
Query: 127 NVEMYDILIGVSLISHVSNEDTN-----------KKGQSISVAVLPNMRQIANIMSTYPC 273
N++++DIL G SL SH+ N+DTN KK + + + ++I ++++ +
Sbjct: 91 NLKLFDILEG-SLKSHIENDDTNTVINLLTEAWEKKSKKKQKNITLSNKEIISVLAKFEL 149
Query: 274 PVSE 285
P E
Sbjct: 150 PEDE 153
>sp|P78022|RPOD_MYCPN RNA polymerase sigma factor rpoD (Sigma-A)
Length = 499
Score = 30.0 bits (66), Expect = 1.7
Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 11/64 (17%)
Frame = +1
Query: 127 NVEMYDILIGVSLISHVSNEDTN-----------KKGQSISVAVLPNMRQIANIMSTYPC 273
N++++DIL G SL SH N+DTN KK + L N + I N++S +
Sbjct: 94 NLKLFDILEG-SLKSHTENDDTNKVISLLVEVWEKKNKKKDNNSLSN-KDIVNVLSKFEL 151
Query: 274 PVSE 285
P E
Sbjct: 152 PDDE 155
Database: Non-redundant SwissProt sequences
Posted date: Dec 6, 2005 7:40 AM
Number of letters in database: 68,354,980
Number of sequences in database: 184,735
Database: swissprot.01
Posted date: Dec 6, 2005 8:18 AM
Number of letters in database: 66,202,850
Number of sequences in database: 184,431
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 41,779,627
Number of Sequences: 369166
Number of extensions: 775799
Number of successful extensions: 1650
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 1640
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 1650
length of database: 68,354,980
effective HSP length: 98
effective length of database: 50,250,950
effective search space used: 1708532300
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)