Search to RefSeqCP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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.
Query= 20110601C-013994
(976 letters)
Database: RefSeq49_CP.fasta
33,336 sequences; 18,874,504 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_852838.1| PREDICTED: similar to Exosome complex exonuclea... 389 e-108
Alignment gi|XP_857538.1| PREDICTED: similar to Exosome complex exonuclea... 71 2e-12
Alignment gi|XP_857497.1| PREDICTED: similar to Exosome complex exonuclea... 69 9e-12
Alignment gi|XP_539207.1| PREDICTED: similar to Exosome complex exonuclea... 67 2e-11
Alignment gi|XP_857418.1| PREDICTED: similar to Exosome complex exonuclea... 52 1e-06
>ref|XP_852838.1| PREDICTED: similar to Exosome complex exonuclease RRP46 (Ribosomal
RNA processing protein 46) (Exosome component 5) (p12B)
(Chronic myelogenous leukemia tumor antigen 28) [Canis
familiaris].
Length = 235
Score = 389 bits (999), Expect = e-108
Identities = 201/235 (85%), Positives = 208/235 (88%)
Frame = +1
Query: 34 MEESMQTETKVRPESGAESGPRSPSCTLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG 213
ME ++ + K ESG ESGPR P C+LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG
Sbjct: 1 MEGALPADAKTCAESGTESGPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG 60
Query: 214 PAEVKVRKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGALHPRTSITVVL 393
PAEVKV KEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLG LHPRTSITVVL
Sbjct: 61 PAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVL 120
Query: 394 QVISDAGSXXXXXXXXXXXXXVDAGVPMRALFCGVTCALDSDGTLMLDPTAKQEKEARAV 573
QV+SDAGS VDAGVPMRALFCGVTCAL+SDGTL+LDPTAKQEKEARAV
Sbjct: 121 QVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVTCALNSDGTLVLDPTAKQEKEARAV 180
Query: 574 LTFALDSVERKLLMSTTKGLYSDAELQQCLAAAQTASQHVFRFYRESLQRRYSKS 738
LTFALDSVERKLLMSTTKGLYS AELQQCLAAAQ ASQHVFRFYRESLQRRYSKS
Sbjct: 181 LTFALDSVERKLLMSTTKGLYSAAELQQCLAAAQAASQHVFRFYRESLQRRYSKS 235
>ref|XP_857538.1| PREDICTED: similar to Exosome complex exonuclease RRP41 (Ribosomal
RNA processing protein 41) (Exosome component 4) (p12A)
isoform 5 [Canis familiaris].
Length = 238
Score = 70.9 bits (172), Expect = 2e-12
Identities = 58/199 (29%), Positives = 84/199 (42%), Gaps = 6/199 (3%)
Frame = +1
Query: 115 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVRKEIFN----KATLEVILRPK 282
LR + ++ DGSA QG+T LA VYGP E + + N AT R +
Sbjct: 22 LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEASGHRALVNCQYSSATFSTGERKR 81
Query: 283 IGLPGVAEKSRER--LIRNTCEAVVLGALHPRTSITVVLQVISDAGSXXXXXXXXXXXXX 456
P KS E +R T EA +L LHPR+ I + +QV+ G
Sbjct: 82 --RPHGDRKSCEMGLHLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAV 139
Query: 457 VDAGVPMRALFCGVTCALDSDGTLMLDPTAKQEKEARAVLTFALDSVERKLLMSTTKGLY 636
+DAG+PMR C + D T + D + +E L AL ++ +
Sbjct: 140 LDAGIPMRDFVCACSAGF-VDNTALADLSHVEEAAGGPQLALALLPASGQIALLEMDARL 198
Query: 637 SDAELQQCLAAAQTASQHV 693
+ L+Q L AA A++ V
Sbjct: 199 HEDHLEQVLEAAARAARDV 217
>ref|XP_857497.1| PREDICTED: similar to Exosome complex exonuclease RRP41 (Ribosomal
RNA processing protein 41) (Exosome component 4) (p12A)
isoform 4 [Canis familiaris].
Length = 244
Score = 68.6 bits (166), Expect = 9e-12
Identities = 60/205 (29%), Positives = 86/205 (41%), Gaps = 12/205 (5%)
Frame = +1
Query: 115 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVK------VRKEIFN----KATLE 264
LR + ++ DGSA QG+T LA VYGP E + RK + N AT
Sbjct: 22 LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEARGVRTLTQRKALVNCQYSSATFS 81
Query: 265 VILRPKIGLPGVAEKSRER--LIRNTCEAVVLGALHPRTSITVVLQVISDAGSXXXXXXX 438
R + P KS E +R T EA +L LHPR+ I + +QV+ G
Sbjct: 82 TGERKR--RPHGDRKSCEMGLHLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVN 139
Query: 439 XXXXXXVDAGVPMRALFCGVTCALDSDGTLMLDPTAKQEKEARAVLTFALDSVERKLLMS 618
+DAG+PMR C + D T + D + +E L AL ++ +
Sbjct: 140 AATLAVLDAGIPMRDFVCACSAGF-VDNTALADLSHVEEAAGGPQLALALLPASGQIALL 198
Query: 619 TTKGLYSDAELQQCLAAAQTASQHV 693
+ L+Q L AA A++ V
Sbjct: 199 EMDARLHEDHLEQVLEAAARAARDV 223
>ref|XP_539207.1| PREDICTED: similar to Exosome complex exonuclease RRP41 (Ribosomal
RNA processing protein 41) (Exosome component 4) (p12A)
isoform 1 [Canis familiaris].
Length = 245
Score = 67.4 bits (163), Expect = 2e-11
Identities = 57/206 (27%), Positives = 86/206 (41%), Gaps = 13/206 (6%)
Frame = +1
Query: 115 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVRKEI-----------FNKATL 261
LR + ++ DGSA QG+T LA VYGP E++ + ++ AT
Sbjct: 22 LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATF 81
Query: 262 EVILRPKIGLPGVAEKSRER--LIRNTCEAVVLGALHPRTSITVVLQVISDAGSXXXXXX 435
R + P KS E +R T EA +L LHPR+ I + +QV+ G
Sbjct: 82 STGERKR--RPHGDRKSCEMGLHLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACV 139
Query: 436 XXXXXXXVDAGVPMRALFCGVTCALDSDGTLMLDPTAKQEKEARAVLTFALDSVERKLLM 615
+DAG+PMR C + D T + D + +E L AL ++ +
Sbjct: 140 NAATLAVLDAGIPMRDFVCACSAGF-VDNTALADLSHVEEAAGGPQLALALLPASGQIAL 198
Query: 616 STTKGLYSDAELQQCLAAAQTASQHV 693
+ L+Q L AA A++ V
Sbjct: 199 LEMDARLHEDHLEQVLEAAARAARDV 224
>ref|XP_857418.1| PREDICTED: similar to Exosome complex exonuclease RRP41 (Ribosomal
RNA processing protein 41) (Exosome component 4) (p12A)
isoform 3 [Canis familiaris].
Length = 226
Score = 51.6 bits (122), Expect = 1e-06
Identities = 34/123 (27%), Positives = 53/123 (43%)
Frame = +1
Query: 325 IRNTCEAVVLGALHPRTSITVVLQVISDAGSXXXXXXXXXXXXXVDAGVPMRALFCGVTC 504
+R T EA +L LHPR+ I + +QV+ G +DAG+PMR C +
Sbjct: 84 LRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSA 143
Query: 505 ALDSDGTLMLDPTAKQEKEARAVLTFALDSVERKLLMSTTKGLYSDAELQQCLAAAQTAS 684
D T + D + +E L AL ++ + + L+Q L AA A+
Sbjct: 144 GF-VDNTALADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLEQVLEAAARAA 202
Query: 685 QHV 693
+ V
Sbjct: 203 RDV 205
Database: RefSeq49_CP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,874,504
Number of sequences in database: 33,336
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 Sequences: 33336
Number of Hits to DB: 48,552,354
Number of extensions: 1629706
Number of successful extensions: 7765
Number of sequences better than 1.0e-05: 5
Number of HSP's gapped: 7725
Number of HSP's successfully gapped: 5
Length of query: 325
Length of database: 18,874,504
Length adjustment: 103
Effective length of query: 222
Effective length of database: 15,440,896
Effective search space: 3427878912
Effective search space used: 3427878912
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Animal-Genome cDNA 20110601C-013994
Search to RefSeqBP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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.
Query= 20110601C-013994
(976 letters)
Database: RefSeq49_BP.fasta
33,088 sequences; 17,681,374 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_002695041.1| PREDICTED: exosome component 5-like [Bos tau... 393 e-109
Alignment gi|XP_001790575.1| PREDICTED: exosome component 5-like [Bos tau... 393 e-109
Alignment gi|NP_001071554.1| exosome complex component RRP41 [Bos taurus]. 71 1e-12
Alignment gi|NP_001103659.1| exosome component 6 [Bos taurus]. 51 1e-06
>ref|XP_002695041.1| PREDICTED: exosome component 5-like [Bos taurus].
Length = 242
Score = 393 bits (1009), Expect = e-109
Identities = 205/242 (84%), Positives = 211/242 (87%), Gaps = 7/242 (2%)
Frame = +1
Query: 34 MEESMQTETKVRPESGAESGPRSPSCTLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG 213
ME MQTE+K+R +SG E GPR P C+LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG
Sbjct: 1 MEGEMQTESKIRADSGTEPGPRVPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG 60
Query: 214 PAEVKVRKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGALHPRTSITVVL 393
PAEVK+ KEIFNKATLEVILRPK GLPGVAEKSRERLIRNTCEAVVLGALHPRTSITVVL
Sbjct: 61 PAEVKISKEIFNKATLEVILRPKTGLPGVAEKSRERLIRNTCEAVVLGALHPRTSITVVL 120
Query: 394 QVISDAGS-------XXXXXXXXXXXXXVDAGVPMRALFCGVTCALDSDGTLMLDPTAKQ 552
QV+SDAGS VDAGVPMRALFCGVTCALDSDGTLMLDPTAKQ
Sbjct: 121 QVVSDAGSKLNHCLWLLACCLNAACMALVDAGVPMRALFCGVTCALDSDGTLMLDPTAKQ 180
Query: 553 EKEARAVLTFALDSVERKLLMSTTKGLYSDAELQQCLAAAQTASQHVFRFYRESLQRRYS 732
EKEARAVLTFALDSVERKLLMSTTKGLYSD ELQQCLAAAQTAS HVFRFYRESLQRRYS
Sbjct: 181 EKEARAVLTFALDSVERKLLMSTTKGLYSDTELQQCLAAAQTASTHVFRFYRESLQRRYS 240
Query: 733 KS 738
KS
Sbjct: 241 KS 242
>ref|XP_001790575.1| PREDICTED: exosome component 5-like [Bos taurus].
Length = 242
Score = 393 bits (1009), Expect = e-109
Identities = 205/242 (84%), Positives = 211/242 (87%), Gaps = 7/242 (2%)
Frame = +1
Query: 34 MEESMQTETKVRPESGAESGPRSPSCTLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG 213
ME MQTE+K+R +SG E GPR P C+LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG
Sbjct: 1 MEGEMQTESKIRADSGTEPGPRVPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG 60
Query: 214 PAEVKVRKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGALHPRTSITVVL 393
PAEVK+ KEIFNKATLEVILRPK GLPGVAEKSRERLIRNTCEAVVLGALHPRTSITVVL
Sbjct: 61 PAEVKISKEIFNKATLEVILRPKTGLPGVAEKSRERLIRNTCEAVVLGALHPRTSITVVL 120
Query: 394 QVISDAGS-------XXXXXXXXXXXXXVDAGVPMRALFCGVTCALDSDGTLMLDPTAKQ 552
QV+SDAGS VDAGVPMRALFCGVTCALDSDGTLMLDPTAKQ
Sbjct: 121 QVVSDAGSKLNHCLWLLACCLNAACMALVDAGVPMRALFCGVTCALDSDGTLMLDPTAKQ 180
Query: 553 EKEARAVLTFALDSVERKLLMSTTKGLYSDAELQQCLAAAQTASQHVFRFYRESLQRRYS 732
EKEARAVLTFALDSVERKLLMSTTKGLYSD ELQQCLAAAQTAS HVFRFYRESLQRRYS
Sbjct: 181 EKEARAVLTFALDSVERKLLMSTTKGLYSDTELQQCLAAAQTASTHVFRFYRESLQRRYS 240
Query: 733 KS 738
KS
Sbjct: 241 KS 242
>ref|NP_001071554.1| exosome complex component RRP41 [Bos taurus].
Length = 245
Score = 71.2 bits (173), Expect = 1e-12
Identities = 59/206 (28%), Positives = 87/206 (42%), Gaps = 13/206 (6%)
Frame = +1
Query: 115 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVRKEI-----------FNKATL 261
LR + ++ DGSA QG+T LA VYGP E++ + ++ AT
Sbjct: 22 LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRPLVNCQYSSATF 81
Query: 262 EVILRPKIGLPGVAEKSRER--LIRNTCEAVVLGALHPRTSITVVLQVISDAGSXXXXXX 435
R + P KS E +R T EA +L LHPR+ I + +QV+ G
Sbjct: 82 STGERKR--RPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACV 139
Query: 436 XXXXXXXVDAGVPMRALFCGVTCALDSDGTLMLDPTAKQEKEARAVLTFALDSVERKLLM 615
+DAG+PMR C + DGT + D + +E L AL ++ +
Sbjct: 140 NAATLAVLDAGIPMRDFVCACSAGF-VDGTALADLSHVEEAAGGPQLALALLPASGQIAL 198
Query: 616 STTKGLYSDAELQQCLAAAQTASQHV 693
+ L+Q L AA AS+ V
Sbjct: 199 LEMDARLHEDHLEQVLEAAARASRDV 224
>ref|NP_001103659.1| exosome component 6 [Bos taurus].
Length = 272
Score = 51.2 bits (121), Expect = 1e-06
Identities = 61/208 (29%), Positives = 80/208 (38%), Gaps = 24/208 (11%)
Frame = +1
Query: 37 EESMQTETKVRPESGAESGPRSPSCTLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGP 216
EES + E G E PR P+ LR LLS+ GSA G T VL V GP
Sbjct: 12 EESQPPQLYAAGE-GEEPAPRDPA-RLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGP 69
Query: 217 ------------------AEVKVRKEI---FNKATLEVILRPKIGLPGVAEKSRERL-IR 330
A +R + F +A R + PG E+ L ++
Sbjct: 70 RPAEGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFSG--RRRRAPPGGGEERELALALQ 127
Query: 331 NTCEAVVLGALHPRTSITVVLQVISDAGSXXXXXXXXXXXXXVDAGVPMRALF--CGVTC 504
E V +PR + V ++ D GS DAGV M L CG++
Sbjct: 128 EALEPAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSR 187
Query: 505 ALDSDGTLMLDPTAKQEKEARAVLTFAL 588
A +LDPT +E+ A A LT AL
Sbjct: 188 APAPAPAWLLDPTLLEEERASAGLTVAL 215
Database: RefSeq49_BP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 17,681,374
Number of sequences in database: 33,088
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 Sequences: 33088
Number of Hits to DB: 46,851,220
Number of extensions: 1600610
Number of successful extensions: 7786
Number of sequences better than 1.0e-05: 4
Number of HSP's gapped: 7753
Number of HSP's successfully gapped: 4
Length of query: 325
Length of database: 17,681,374
Length adjustment: 102
Effective length of query: 223
Effective length of database: 14,306,398
Effective search space: 3190326754
Effective search space used: 3190326754
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqSP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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.
Query= 20110601C-013994
(976 letters)
Database: RefSeq49_SP.fasta
24,897 sequences; 11,343,932 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_003127206.2| PREDICTED: exosome complex component RRP46-l... 184 6e-47
Alignment gi|XP_003125499.1| PREDICTED: exosome complex component RRP41-l... 69 5e-12
>ref|XP_003127206.2| PREDICTED: exosome complex component RRP46-like [Sus scrofa].
Length = 109
Score = 184 bits (467), Expect = 6e-47
Identities = 93/94 (98%), Positives = 93/94 (98%)
Frame = +1
Query: 457 VDAGVPMRALFCGVTCALDSDGTLMLDPTAKQEKEARAVLTFALDSVERKLLMSTTKGLY 636
VDAGVPMRALFCGVTCALDSDGT MLDPTAKQEKEARAVLTFALDSVERKLLMSTTKGLY
Sbjct: 16 VDAGVPMRALFCGVTCALDSDGTFMLDPTAKQEKEARAVLTFALDSVERKLLMSTTKGLY 75
Query: 637 SDAELQQCLAAAQTASQHVFRFYRESLQRRYSKS 738
SDAELQQCLAAAQTASQHVFRFYRESLQRRYSKS
Sbjct: 76 SDAELQQCLAAAQTASQHVFRFYRESLQRRYSKS 109
>ref|XP_003125499.1| PREDICTED: exosome complex component RRP41-like isoform 1 [Sus
scrofa].
Length = 245
Score = 68.6 bits (166), Expect = 5e-12
Identities = 57/206 (27%), Positives = 86/206 (41%), Gaps = 13/206 (6%)
Frame = +1
Query: 115 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVRKEI-----------FNKATL 261
LR + ++ DGSA QG+T LA VYGP E++ + ++ AT
Sbjct: 22 LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRSRALPDRALVNCQYSSATF 81
Query: 262 EVILRPKIGLPGVAEKSRER--LIRNTCEAVVLGALHPRTSITVVLQVISDAGSXXXXXX 435
R + P KS E +R EA +L LHPR+ I + +QV+ G
Sbjct: 82 STGERKR--RPHGDRKSCEMGLQLRQAFEAAILTQLHPRSQIDIYVQVLQADGGIYAACV 139
Query: 436 XXXXXXXVDAGVPMRALFCGVTCALDSDGTLMLDPTAKQEKEARAVLTFALDSVERKLLM 615
+DAG+PMR C + DGT + D + +E L AL ++ +
Sbjct: 140 NVATLAVLDAGIPMRDFVCACSAGF-VDGTALADLSHVEEAAGGPQLALALLPASGQIAL 198
Query: 616 STTKGLYSDAELQQCLAAAQTASQHV 693
+ L+Q L AA A++ V
Sbjct: 199 LEMDARLHEDHLEQVLEAAAQAARDV 224
Database: RefSeq49_SP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 11,343,932
Number of sequences in database: 24,897
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 Sequences: 24897
Number of Hits to DB: 30,297,303
Number of extensions: 1037080
Number of successful extensions: 5217
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 5198
Number of HSP's successfully gapped: 2
Length of query: 325
Length of database: 11,343,932
Length adjustment: 99
Effective length of query: 226
Effective length of database: 8,879,129
Effective search space: 2006683154
Effective search space used: 2006683154
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqMP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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.
Query= 20110601C-013994
(976 letters)
Database: RefSeq49_MP.fasta
30,036 sequences; 15,617,559 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_613052.1| exosome complex component RRP46 [Mus musculus]. 382 e-106
Alignment gi|NP_780608.1| exosome complex component RRP41 [Mus musculus]. 70 2e-12
>ref|NP_613052.1| exosome complex component RRP46 [Mus musculus].
Length = 235
Score = 382 bits (982), Expect = e-106
Identities = 194/235 (82%), Positives = 207/235 (88%)
Frame = +1
Query: 34 MEESMQTETKVRPESGAESGPRSPSCTLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG 213
ME + + + + ++G ES PRSP C+LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG
Sbjct: 1 MEGAKRADANLLTDTGTESSPRSPVCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG 60
Query: 214 PAEVKVRKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGALHPRTSITVVL 393
PAEVKV KEIFNKATLEVILRPKIGLPGVAEKSRERL+RNTCEAVVLGALHPRTSITVVL
Sbjct: 61 PAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERLVRNTCEAVVLGALHPRTSITVVL 120
Query: 394 QVISDAGSXXXXXXXXXXXXXVDAGVPMRALFCGVTCALDSDGTLMLDPTAKQEKEARAV 573
QV+SDAGS VDAGVPMRALFCGVTCALDSDG L+LDPT KQEKEARA+
Sbjct: 121 QVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVTCALDSDGNLVLDPTTKQEKEARAI 180
Query: 574 LTFALDSVERKLLMSTTKGLYSDAELQQCLAAAQTASQHVFRFYRESLQRRYSKS 738
LTFALDS E+KLLMSTTKGLYSDAELQQCLAAAQ ASQH+FRFYRESLQRRYSKS
Sbjct: 181 LTFALDSAEQKLLMSTTKGLYSDAELQQCLAAAQAASQHIFRFYRESLQRRYSKS 235
>ref|NP_780608.1| exosome complex component RRP41 [Mus musculus].
Length = 245
Score = 70.1 bits (170), Expect = 2e-12
Identities = 58/206 (28%), Positives = 87/206 (42%), Gaps = 13/206 (6%)
Frame = +1
Query: 115 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVRKEI-----------FNKATL 261
LR + ++ DGSA QG+T LA VYGP E++ + ++ AT
Sbjct: 22 LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRSRALPDRALVNCQYSSATF 81
Query: 262 EVILRPKIGLPGVAEKSRER--LIRNTCEAVVLGALHPRTSITVVLQVISDAGSXXXXXX 435
R + P KS E +R T EA +L LHPR+ I + +QV+ G
Sbjct: 82 STGERKR--RPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACV 139
Query: 436 XXXXXXXVDAGVPMRALFCGVTCALDSDGTLMLDPTAKQEKEARAVLTFALDSVERKLLM 615
+DAG+PMR C + DGT + D + +E L AL ++ +
Sbjct: 140 NAATLAVMDAGIPMRDFVCACSAGF-VDGTALADLSHVEEAAGGPQLALALLPASGQIAL 198
Query: 616 STTKGLYSDAELQQCLAAAQTASQHV 693
+ L+Q L AA A++ V
Sbjct: 199 LEMDSRLHEDHLEQVLEAAAQAARGV 224
Database: RefSeq49_MP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 15,617,559
Number of sequences in database: 30,036
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 Sequences: 30036
Number of Hits to DB: 39,891,575
Number of extensions: 1301942
Number of successful extensions: 5964
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 5938
Number of HSP's successfully gapped: 2
Length of query: 325
Length of database: 15,617,559
Length adjustment: 102
Effective length of query: 223
Effective length of database: 12,553,887
Effective search space: 2799516801
Effective search space used: 2799516801
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqHP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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.
Query= 20110601C-013994
(976 letters)
Database: RefSeq49_HP.fasta
32,964 sequences; 18,297,164 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_064543.3| exosome complex component RRP46 [Homo sapiens]. 389 e-108
Alignment gi|NP_061910.1| exosome complex component RRP41 [Homo sapiens]. 69 8e-12
Alignment gi|NP_478126.1| exosome complex component MTR3 [Homo sapiens]. 50 2e-06
>ref|NP_064543.3| exosome complex component RRP46 [Homo sapiens].
Length = 235
Score = 389 bits (1000), Expect = e-108
Identities = 199/235 (84%), Positives = 207/235 (88%)
Frame = +1
Query: 34 MEESMQTETKVRPESGAESGPRSPSCTLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG 213
MEE T+ K+R E+G S PR P C+LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG
Sbjct: 1 MEEETHTDAKIRAENGTGSSPRGPGCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYG 60
Query: 214 PAEVKVRKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGALHPRTSITVVL 393
PAEVKV KEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLG LHPRTSITVVL
Sbjct: 61 PAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVL 120
Query: 394 QVISDAGSXXXXXXXXXXXXXVDAGVPMRALFCGVTCALDSDGTLMLDPTAKQEKEARAV 573
QV+SDAGS VDAGVPMRALFCGV CALDSDGTL+LDPT+KQEKEARAV
Sbjct: 121 QVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEARAV 180
Query: 574 LTFALDSVERKLLMSTTKGLYSDAELQQCLAAAQTASQHVFRFYRESLQRRYSKS 738
LTFALDSVERKLLMS+TKGLYSD ELQQCLAAAQ ASQHVFRFYRESLQRRYSKS
Sbjct: 181 LTFALDSVERKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRRYSKS 235
>ref|NP_061910.1| exosome complex component RRP41 [Homo sapiens].
Length = 245
Score = 68.6 bits (166), Expect = 8e-12
Identities = 57/206 (27%), Positives = 87/206 (42%), Gaps = 13/206 (6%)
Frame = +1
Query: 115 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVRKEI-----------FNKATL 261
LR + ++ DGSA QG+T LA VYGP E++ + ++ AT
Sbjct: 22 LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRALVNCQYSSATF 81
Query: 262 EVILRPKIGLPGVAEKSRER--LIRNTCEAVVLGALHPRTSITVVLQVISDAGSXXXXXX 435
R + P KS E +R T EA +L LHPR+ I + +QV+ G
Sbjct: 82 STGERKR--RPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACV 139
Query: 436 XXXXXXXVDAGVPMRALFCGVTCALDSDGTLMLDPTAKQEKEARAVLTFALDSVERKLLM 615
+DAG+PMR C + DGT + D + +E L AL ++ +
Sbjct: 140 NAATLAVLDAGIPMRDFVCACSAGF-VDGTALADLSHVEEAAGGPQLALALLPASGQIAL 198
Query: 616 STTKGLYSDAELQQCLAAAQTASQHV 693
+ L++ L AA A++ V
Sbjct: 199 LEMDARLHEDHLERVLEAAAQAARDV 224
>ref|NP_478126.1| exosome complex component MTR3 [Homo sapiens].
Length = 272
Score = 50.4 bits (119), Expect = 2e-06
Identities = 60/208 (28%), Positives = 81/208 (38%), Gaps = 24/208 (11%)
Frame = +1
Query: 37 EESMQTETKVRPESGAESGPRSPSCTLRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGP 216
EES + E A G R P+ LR LLS+ GSA G T VL V GP
Sbjct: 12 EESQPPQLYAADEEEAP-GTRDPT-RLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVSGP 69
Query: 217 AEVK------------------VRKEI---FNKATLEVILRPKIGLPGVAEKSRERL-IR 330
+ + +R + F +A R + PG E+ L ++
Sbjct: 70 RQAEGGERGGGPAGAGGEAPAALRGRLLCDFRRAPFAG--RRRRAPPGGCEERELALALQ 127
Query: 331 NTCEAVVLGALHPRTSITVVLQVISDAGSXXXXXXXXXXXXXVDAGVPMRALF--CGVTC 504
E V +PR + V ++ D GS DAGV M L CG++
Sbjct: 128 EALEPAVRLGRYPRAQLEVSALLLEDGGSALAAALTAAALALADAGVEMYDLVVGCGLSL 187
Query: 505 ALDSDGTLMLDPTAKQEKEARAVLTFAL 588
A T +LDPT +E+ A A LT AL
Sbjct: 188 APGPAPTWLLDPTRLEEERAAAGLTVAL 215
Database: RefSeq49_HP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,297,164
Number of sequences in database: 32,964
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 Sequences: 32964
Number of Hits to DB: 47,567,274
Number of extensions: 1587639
Number of successful extensions: 7250
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 7228
Number of HSP's successfully gapped: 3
Length of query: 325
Length of database: 18,297,164
Length adjustment: 103
Effective length of query: 222
Effective length of database: 14,901,872
Effective search space: 3308215584
Effective search space used: 3308215584
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to Sscrofa10_2
BLASTN 2.2.24 [Aug-08-2010]
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.
Query= 20110601C-013994
(976 letters)
Database: Sscrofa_10.2.fasta
4582 sequences; 2,808,509,378 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Sscrofa_Chr06 599 e-168
>Sscrofa_Chr06
|| Length = 157765593
Score = 599 bits (302), Expect = e-168
Identities = 330/334 (98%), Gaps = 4/334 (1%)
Strand = Plus / Minus
Query: 647 agctccagcagtgcctggctgcagcccagactgcctcccaacacgtcttccgcttctacc 706
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 45166845 agctccagcagtgcctggctgcagcccagactgcctcccaacacgtcttccgcttctacc 45166786
Query: 707 gggaatcgctgcagaggcgttactccaagagctgaggcagccaagagctgaggcaggcca 766
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 45166785 gggaatcgctgcagaggcgttactccaagagctgaggcagccaagagctgaggcaggcca 45166726
Query: 767 gggcaggtgcccctcccgccaccgcccactccctccagtaccaactaaaccagcagcccg 826
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 45166725 gggcaggtgcccctcccgccaccgcccactccctccagtaccaactaaaccagcagcccg 45166666
Query: 827 gccctgcctgtctgtccttgtgcgtgggggtgagcttgtggctctgtcactgcaggagcc 886
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 45166665 gccctgcctgtctgtccttgtgcgtgggggtgagcttgtggctctgtcactgcaggagcc 45166606
Query: 887 cctaacctgccaggaatgtgtggctaatagccccagggtctgccccacccc-agaaaacg 945
||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||
Sbjct: 45166605 cctaacctgccaggaatgtgtggctaatagccccagggtctgccccaccccaagaaaacg 45166546
Query: 946 ga-tgtgcatttattg-atg-acctactcatctc 976
|| ||||||||||||| ||| |||||||||||||
Sbjct: 45166545 gattgtgcatttattgaatgaacctactcatctc 45166512
Score = 359 bits (181), Expect = 2e-96
Identities = 181/181 (100%)
Strand = Plus / Minus
Query: 2 gacagtccctgctgcacgtgggctccccggcgatggaggagtcgatgcagactgaaacca 61
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 45273437 gacagtccctgctgcacgtgggctccccggcgatggaggagtcgatgcagactgaaacca 45273378
Query: 62 aggtacgccccgagtctggagcagagtctggccctcggagccccagctgtactctccggc 121
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 45273377 aggtacgccccgagtctggagcagagtctggccctcggagccccagctgtactctccggc 45273318
Query: 122 actttgcctgcgaacaaaacttgttgtcccggcccgatggctctgcctctttcctgcaag 181
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 45273317 actttgcctgcgaacaaaacttgttgtcccggcccgatggctctgcctctttcctgcaag 45273258
Query: 182 g 182
|
Sbjct: 45273257 g 45273257
Score = 274 bits (138), Expect = 8e-71
Identities = 141/142 (99%)
Strand = Plus / Minus
Query: 418 ctcctggcctgctgcctgaatgctgcctgcatggcactggtggatgcgggtgtgcccatg 477
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 45169088 ctcctggcctgctgcctgaatgctgcctgcatggcactggtggatgcgggtgtgcccatg 45169029
Query: 478 cgggccctcttctgtggggtcacctgtgctctggactccgatgggaccctcatgctggac 537
|||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||
Sbjct: 45169028 cgggccctcttctgtggggtcacctgtgctctggactccgatgggaccttcatgctggac 45168969
Query: 538 cccacagccaagcaagaaaagg 559
||||||||||||||||||||||
Sbjct: 45168968 cccacagccaagcaagaaaagg 45168947
Score = 182 bits (92), Expect = 2e-43
Identities = 92/92 (100%)
Strand = Plus / Minus
Query: 557 aggaggcccgggcggtcctgacctttgctcttgacagtgtggaacggaagctgctgatgt 616
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 45167653 aggaggcccgggcggtcctgacctttgctcttgacagtgtggaacggaagctgctgatgt 45167594
Query: 617 ccaccaccaagggactctactcagatgctgag 648
||||||||||||||||||||||||||||||||
Sbjct: 45167593 ccaccaccaagggactctactcagatgctgag 45167562
Database: Sscrofa_10.2.fasta
Posted date: Nov 16, 2011 10:34 AM
Number of letters in database: 2,808,509,378
Number of sequences in database: 4582
Lambda K H
1.37 0.711 1.31
Gapped
Lambda K H
1.37 0.711 1.31
Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 4582
Number of Hits to DB: 25,604,188
Number of extensions: 170
Number of successful extensions: 170
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 170
Number of HSP's successfully gapped: 4
Length of query: 976
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 955
Effective length of database: 2,808,413,156
Effective search space: 2682034563980
Effective search space used: 2682034563980
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 50 (99.1 bits)
S1: 18 (36.2 bits)
S2: 29 (58.0 bits)