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-000790
(1252 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|NP_001029384.1| DNA-directed RNA polymerase II subunit RPB3 ... 530 e-150
Alignment gi|NP_001033213.1| DNA-directed RNA polymerases I and III subun... 98 2e-20
>ref|NP_001029384.1| DNA-directed RNA polymerase II subunit RPB3 [Bos taurus].
Length = 275
Score = 530 bits (1365), Expect = e-150
Identities = 260/275 (94%), Positives = 261/275 (94%)
Frame = +1
Query: 88 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 267
MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH
Sbjct: 1 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60
Query: 268 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 447
DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL
Sbjct: 61 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120
Query: 448 ISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 627
ISNSPRVIPVTSRNRDNDP+DYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct: 121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
Query: 628 GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR 807
GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR
Sbjct: 181 GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR 240
Query: 808 PETIVXXXXXXXXXXXXXXQTQLSHEIQSDVLTIN 912
PETIV QTQLSHEIQSDVLTIN
Sbjct: 241 PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN 275
>ref|NP_001033213.1| DNA-directed RNA polymerases I and III subunit RPAC1 [Bos taurus].
Length = 346
Score = 97.8 bits (242), Expect = 2e-20
Identities = 62/199 (31%), Positives = 104/199 (52%), Gaps = 11/199 (5%)
Frame = +1
Query: 112 VRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRL 291
V + + + +++F + D A+AN+ RR+ +AEVP +A++ V + N+S++ DE +AHRL
Sbjct: 51 VDVVHMDENSLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRL 110
Query: 292 GLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRC---------NEDQTRHVTSRD 444
GLIP+ +D + + + D E +++F L VRC + D +
Sbjct: 111 GLIPIHADPRLFEYRNQGD---EGGTEIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHR 167
Query: 445 LISNSPRVIPVTSRNRDNDPSDYVE--QDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 618
+ + +P+ D P + DDILI +LR GQE+ L + KG GK+HAK++
Sbjct: 168 VYTRHMTWVPL-GNQADLFPEGAIRPVHDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFS 226
Query: 619 PTAGVAFEYDPDNALRHTV 675
P A ++ PD L V
Sbjct: 227 PVATASYRLLPDITLLEPV 245
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: 49,679,472
Number of extensions: 1484705
Number of successful extensions: 6259
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 6232
Number of HSP's successfully gapped: 2
Length of query: 417
Length of database: 17,681,374
Length adjustment: 105
Effective length of query: 312
Effective length of database: 14,207,134
Effective search space: 4432625808
Effective search space used: 4432625808
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: 35 (18.1 bits)
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-000790
(1252 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_535283.2| PREDICTED: similar to polymerase (RNA) II (DNA ... 530 e-150
Alignment gi|XP_862568.1| PREDICTED: similar to DNA directed RNA polymera... 140 3e-33
Alignment gi|XP_865721.1| PREDICTED: similar to DNA-directed RNA polymera... 102 8e-22
Alignment gi|XP_865706.1| PREDICTED: similar to DNA-directed RNA polymera... 100 2e-21
Alignment gi|XP_532147.1| PREDICTED: similar to DNA-directed RNA polymera... 100 2e-21
Alignment gi|XP_865641.1| PREDICTED: similar to DNA-directed RNA polymera... 100 2e-21
Alignment gi|XP_865690.1| PREDICTED: similar to DNA-directed RNA polymera... 86 1e-16
Alignment gi|XP_865661.1| PREDICTED: similar to DNA-directed RNA polymera... 64 4e-10
>ref|XP_535283.2| PREDICTED: similar to polymerase (RNA) II (DNA directed)
polypeptide C (predicted) isoform 1 [Canis familiaris].
Length = 275
Score = 530 bits (1365), Expect = e-150
Identities = 260/275 (94%), Positives = 261/275 (94%)
Frame = +1
Query: 88 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 267
MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH
Sbjct: 1 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60
Query: 268 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 447
DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL
Sbjct: 61 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120
Query: 448 ISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 627
ISNSPRVIPVTSRNRDNDP+DYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct: 121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
Query: 628 GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR 807
GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR
Sbjct: 181 GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR 240
Query: 808 PETIVXXXXXXXXXXXXXXQTQLSHEIQSDVLTIN 912
PETIV QTQLSHEIQSDVLTIN
Sbjct: 241 PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN 275
>ref|XP_862568.1| PREDICTED: similar to DNA directed RNA polymerase II polypeptide C
isoform 2 [Canis familiaris].
Length = 72
Score = 140 bits (352), Expect = 3e-33
Identities = 70/70 (100%), Positives = 70/70 (100%)
Frame = +1
Query: 88 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 267
MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH
Sbjct: 1 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60
Query: 268 DEFIAHRLGL 297
DEFIAHRLGL
Sbjct: 61 DEFIAHRLGL 70
>ref|XP_865721.1| PREDICTED: similar to DNA-directed RNA polymerase I 40 kDa
polypeptide (RPA40) (RPA39) isoform 6 [Canis
familiaris].
Length = 328
Score = 102 bits (254), Expect = 8e-22
Identities = 75/258 (29%), Positives = 126/258 (48%), Gaps = 21/258 (8%)
Frame = +1
Query: 112 VRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRL 291
V + + + +++F + D A+AN+ RR+ +AEVP +A++ V + N+S++ DE +AHRL
Sbjct: 51 VDVVHMDENSLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRL 110
Query: 292 GLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRC---------NEDQTRHVTSRD 444
GLIP+ +D + + + D +E +++F L VRC + D +
Sbjct: 111 GLIPIHADPRLFEYRNQGD---DEGTEIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHK 167
Query: 445 LISNSPRVIPVTSRNRDNDPSDYVE--QDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 618
+ S +P+ D P + DDILI +LR GQE+ L + KG GK+HAK++
Sbjct: 168 VYSRHMTWVPL-GNQADLFPEGTIRPVHDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFS 226
Query: 619 PTAGVAFEYDPDNALRHTVYPKPEEWPKSEYSE--LDEDESQAPYDPNGKP--------E 768
P A ++ PD L V E +S ++ E Q K +
Sbjct: 227 PVATASYRLLPDITLLEPVEGDAAEELSRCFSPGVIEVQEVQVFRKEKLKKVVRLARVRD 286
Query: 769 RFYYNVESCGSLRPETIV 822
+ ++VES G L P+ +V
Sbjct: 287 HYIFSVESTGVLPPDVLV 304
>ref|XP_865706.1| PREDICTED: similar to DNA-directed RNA polymerase I 40 kDa
polypeptide (RPA40) (RPA39) isoform 5 [Canis
familiaris].
Length = 338
Score = 100 bits (250), Expect = 2e-21
Identities = 63/199 (31%), Positives = 105/199 (52%), Gaps = 11/199 (5%)
Frame = +1
Query: 112 VRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRL 291
V + + + +++F + D A+AN+ RR+ +AEVP +A++ V + N+S++ DE +AHRL
Sbjct: 51 VDVVHMDENSLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRL 110
Query: 292 GLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRC---------NEDQTRHVTSRD 444
GLIP+ +D + + + D +E +++F L VRC + D +
Sbjct: 111 GLIPIHADPRLFEYRNQGD---DEGTEIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHK 167
Query: 445 LISNSPRVIPVTSRNRDNDPSDYVE--QDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 618
+ S +P+ D P + DDILI +LR GQE+ L + KG GK+HAK++
Sbjct: 168 VYSRHMTWVPL-GNQADLFPEGTIRPVHDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFS 226
Query: 619 PTAGVAFEYDPDNALRHTV 675
P A ++ PD L V
Sbjct: 227 PVATASYRLLPDITLLEPV 245
>ref|XP_532147.1| PREDICTED: similar to DNA-directed RNA polymerase I 40 kDa
polypeptide (RPA40) (RPA39) isoform 1 [Canis
familiaris].
Length = 346
Score = 100 bits (250), Expect = 2e-21
Identities = 63/199 (31%), Positives = 105/199 (52%), Gaps = 11/199 (5%)
Frame = +1
Query: 112 VRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRL 291
V + + + +++F + D A+AN+ RR+ +AEVP +A++ V + N+S++ DE +AHRL
Sbjct: 51 VDVVHMDENSLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRL 110
Query: 292 GLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRC---------NEDQTRHVTSRD 444
GLIP+ +D + + + D +E +++F L VRC + D +
Sbjct: 111 GLIPIHADPRLFEYRNQGD---DEGTEIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHK 167
Query: 445 LISNSPRVIPVTSRNRDNDPSDYVE--QDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 618
+ S +P+ D P + DDILI +LR GQE+ L + KG GK+HAK++
Sbjct: 168 VYSRHMTWVPL-GNQADLFPEGTIRPVHDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFS 226
Query: 619 PTAGVAFEYDPDNALRHTV 675
P A ++ PD L V
Sbjct: 227 PVATASYRLLPDITLLEPV 245
>ref|XP_865641.1| PREDICTED: similar to DNA-directed RNA polymerase I 40 kDa
polypeptide (RPA40) (RPA39) isoform 2 [Canis
familiaris].
Length = 281
Score = 100 bits (250), Expect = 2e-21
Identities = 63/199 (31%), Positives = 105/199 (52%), Gaps = 11/199 (5%)
Frame = +1
Query: 112 VRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRL 291
V + + + +++F + D A+AN+ RR+ +AEVP +A++ V + N+S++ DE +AHRL
Sbjct: 51 VDVVHMDENSLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRL 110
Query: 292 GLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRC---------NEDQTRHVTSRD 444
GLIP+ +D + + + D +E +++F L VRC + D +
Sbjct: 111 GLIPIHADPRLFEYRNQGD---DEGTEIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHK 167
Query: 445 LISNSPRVIPVTSRNRDNDPSDYVE--QDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 618
+ S +P+ D P + DDILI +LR GQE+ L + KG GK+HAK++
Sbjct: 168 VYSRHMTWVPL-GNQADLFPEGTIRPVHDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFS 226
Query: 619 PTAGVAFEYDPDNALRHTV 675
P A ++ PD L V
Sbjct: 227 PVATASYRLLPDITLLEPV 245
>ref|XP_865690.1| PREDICTED: similar to DNA-directed RNA polymerase I 40 kDa
polypeptide (RPA40) (RPA39) isoform 4 [Canis
familiaris].
Length = 296
Score = 85.5 bits (210), Expect = 1e-16
Identities = 55/178 (30%), Positives = 94/178 (52%), Gaps = 11/178 (6%)
Frame = +1
Query: 112 VRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRL 291
V + + + +++F + D A+AN+ RR+ +AEVP +A++ V + N+S++ DE +AHRL
Sbjct: 51 VDVVHMDENSLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRL 110
Query: 292 GLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRC---------NEDQTRHVTSRD 444
GLIP+ +D + + + D +E +++F L VRC + D +
Sbjct: 111 GLIPIHADPRLFEYRNQGD---DEGTEIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHK 167
Query: 445 LISNSPRVIPVTSRNRDNDPSDYVE--QDDILIVKLRKGQELRLRAYAKKGFGKEHAK 612
+ S +P+ D P + DDILI +LR GQE+ L + KG GK+ A+
Sbjct: 168 VYSRHMTWVPL-GNQADLFPEGTIRPVHDDILIAQLRPGQEIDLLMHCVKGIGKKVAR 224
>ref|XP_865661.1| PREDICTED: similar to DNA-directed RNA polymerase I 40 kDa
polypeptide (RPA40) (RPA39) isoform 3 [Canis
familiaris].
Length = 144
Score = 63.5 bits (153), Expect = 4e-10
Identities = 27/68 (39%), Positives = 48/68 (70%)
Frame = +1
Query: 112 VRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRL 291
V + + + +++F + D A+AN+ RR+ +AEVP +A++ V + N+S++ DE +AHRL
Sbjct: 51 VDVVHMDENSLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRL 110
Query: 292 GLIPLTSD 315
GLIP+ +D
Sbjct: 111 GLIPIHAD 118
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: 51,902,705
Number of extensions: 1532995
Number of successful extensions: 6464
Number of sequences better than 1.0e-05: 8
Number of HSP's gapped: 6421
Number of HSP's successfully gapped: 8
Length of query: 417
Length of database: 18,874,504
Length adjustment: 105
Effective length of query: 312
Effective length of database: 15,374,224
Effective search space: 4796757888
Effective search space used: 4796757888
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: 35 (18.1 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-000790
(1252 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_116558.1| DNA-directed RNA polymerase II subunit RPB3 [Ho... 528 e-150
Alignment gi|NP_976035.1| DNA-directed RNA polymerases I and III subunit ... 101 2e-21
>ref|NP_116558.1| DNA-directed RNA polymerase II subunit RPB3 [Homo sapiens].
Length = 275
Score = 528 bits (1359), Expect = e-150
Identities = 259/275 (94%), Positives = 260/275 (94%)
Frame = +1
Query: 88 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 267
MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH
Sbjct: 1 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60
Query: 268 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 447
DEFIAHRLGLIPL SDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL
Sbjct: 61 DEFIAHRLGLIPLISDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120
Query: 448 ISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 627
ISNSPRVIPVTSRNRDNDP+DYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct: 121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
Query: 628 GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR 807
GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR
Sbjct: 181 GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR 240
Query: 808 PETIVXXXXXXXXXXXXXXQTQLSHEIQSDVLTIN 912
PETIV QTQLSHEIQSDVLTIN
Sbjct: 241 PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN 275
>ref|NP_976035.1| DNA-directed RNA polymerases I and III subunit RPAC1 [Homo
sapiens].
Length = 346
Score = 101 bits (251), Expect = 2e-21
Identities = 64/199 (32%), Positives = 105/199 (52%), Gaps = 11/199 (5%)
Frame = +1
Query: 112 VRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRL 291
V + + + +++F + D A+AN+ RR+ +AEVP +A++ V + N+S++ DE +AHRL
Sbjct: 51 VDVVHMDENSLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRL 110
Query: 292 GLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRC---------NEDQTRHVTSRD 444
GLIP+ +D + + + D EE +++F L VRC + D +
Sbjct: 111 GLIPIHADPRLFEYRNQGD---EEGTEIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHK 167
Query: 445 LISNSPRVIPVTSRNRDNDPSDYVE--QDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 618
+ + IP+ D P + DDILI +LR GQE+ L + KG GK+HAK++
Sbjct: 168 VYTRHMTWIPL-GNQADLFPEGTIRPVHDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFS 226
Query: 619 PTAGVAFEYDPDNALRHTV 675
P A ++ PD L V
Sbjct: 227 PVATASYRLLPDITLLEPV 245
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: 50,847,200
Number of extensions: 1499790
Number of successful extensions: 6406
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 6373
Number of HSP's successfully gapped: 2
Length of query: 417
Length of database: 18,297,164
Length adjustment: 105
Effective length of query: 312
Effective length of database: 14,835,944
Effective search space: 4628814528
Effective search space used: 4628814528
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: 35 (18.1 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-000790
(1252 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_033116.2| DNA-directed RNA polymerase II subunit RPB3 [Mu... 528 e-150
Alignment gi|NP_033111.2| DNA-directed RNA polymerases I and III subunit ... 99 5e-21
>ref|NP_033116.2| DNA-directed RNA polymerase II subunit RPB3 [Mus musculus].
Length = 275
Score = 528 bits (1361), Expect = e-150
Identities = 259/275 (94%), Positives = 261/275 (94%)
Frame = +1
Query: 88 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 267
MPYANQPTVRITELT+ENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH
Sbjct: 1 MPYANQPTVRITELTEENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60
Query: 268 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 447
DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL
Sbjct: 61 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120
Query: 448 ISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 627
ISNSPRVIPVTSRNRDNDP+DYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct: 121 ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
Query: 628 GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR 807
GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR
Sbjct: 181 GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR 240
Query: 808 PETIVXXXXXXXXXXXXXXQTQLSHEIQSDVLTIN 912
PETIV QTQLSHEIQSDVLTIN
Sbjct: 241 PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN 275
>ref|NP_033111.2| DNA-directed RNA polymerases I and III subunit RPAC1 [Mus
musculus].
Length = 346
Score = 99.4 bits (246), Expect = 5e-21
Identities = 62/190 (32%), Positives = 103/190 (54%), Gaps = 10/190 (5%)
Frame = +1
Query: 112 VRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRL 291
V + ++ ++ ++F + D A+AN+ RR+ +AEVP +A++ V + N+S++ DE +AHRL
Sbjct: 51 VDVVQMDEDTLEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRL 110
Query: 292 GLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRD----LISNS 459
GLIP+ +D +L R+ EE +++F L VRC + S D +++
Sbjct: 111 GLIPILAD---PRLFEYRNQGEEEGTEIDTLQFRLQVRCTRNPNAAKDSSDPNELYVNHK 167
Query: 460 PRVIPVTSRNRDNDPSDYVE------QDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP 621
+T N + E DDILI +LR GQE+ L + KG GK+HAK++P
Sbjct: 168 VYTRHMTWVPLGNQADVFPEGTIRPVHDDILIAQLRPGQEIDLMMHCVKGIGKDHAKFSP 227
Query: 622 TAGVAFEYDP 651
A ++ P
Sbjct: 228 VATASYRLLP 237
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: 42,800,904
Number of extensions: 1239733
Number of successful extensions: 5165
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 5126
Number of HSP's successfully gapped: 2
Length of query: 417
Length of database: 15,617,559
Length adjustment: 104
Effective length of query: 313
Effective length of database: 12,493,815
Effective search space: 3910564095
Effective search space used: 3910564095
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: 35 (18.1 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-000790
(1252 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_003355849.1| PREDICTED: DNA-directed RNA polymerase II su... 531 e-151
>ref|XP_003355849.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Sus
scrofa].
Length = 275
Score = 531 bits (1368), Expect = e-151
Identities = 261/275 (94%), Positives = 261/275 (94%)
Frame = +1
Query: 88 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 267
MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH
Sbjct: 1 MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH 60
Query: 268 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 447
DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL
Sbjct: 61 DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL 120
Query: 448 ISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 627
ISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
Sbjct: 121 ISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
Query: 628 GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR 807
GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR
Sbjct: 181 GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR 240
Query: 808 PETIVXXXXXXXXXXXXXXQTQLSHEIQSDVLTIN 912
PETIV QTQLSHEIQSDVLTIN
Sbjct: 241 PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN 275
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: 32,056,220
Number of extensions: 960707
Number of successful extensions: 3963
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 3952
Number of HSP's successfully gapped: 1
Length of query: 417
Length of database: 11,343,932
Length adjustment: 101
Effective length of query: 316
Effective length of database: 8,829,335
Effective search space: 2790069860
Effective search space used: 2790069860
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-000790
(1252 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 771 0.0
>Sscrofa_Chr06
|| Length = 157765593
Score = 771 bits (389), Expect = 0.0
Identities = 462/485 (95%), Gaps = 1/485 (0%)
Strand = Plus / Plus
Query: 769 aggttttactacaacgtggaatcttgtggctctctgcgccctgaaaccattgtcctctca 828
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17390473 aggttttactacaacgtggaatcttgtggctctctgcgccctgaaaccattgtcctctca 17390532
Query: 829 gcactttctggattaaagaagaaactgagtgacttacagacccaattaagccatgagatc 888
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17390533 gcactttctggattaaagaagaaactgagtgacttacagacccaattaagccatgagatc 17390592
Query: 889 cagagtgacgtcctgaccataaactagccgcagctcacctgtctcagcagaaacagctct 948
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17390593 cagagtgacgtcctgaccataaactagccgcagctcacctgtctcagcagaaacagctct 17390652
Query: 949 tgaatttcaggcctctcctgagacttttgctcctggggactggacagctgttgctcaagc 1008
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17390653 tgaatttcaggcctctcctgagacttttgctcctggggactggacagctgttgctcaagc 17390712
Query: 1009 ttcctggcacacctgcagtactggcta-aaaggtaacgatgggggagggcaggccatccc 1067
||||||||||||||||||||||||||| ||||||| || |||||||||||||||||||||
Sbjct: 17390713 ttcctggcacacctgcagtactggctagaaaggtagcggtgggggagggcaggccatccc 17390772
Query: 1068 aggctggcaccgtccccagttgccgggggtgccactgctgtccgaagcggaaaagtctcc 1127
|||||||||||||| | |||||||||||||||||||||||| || ||||||||||||||
Sbjct: 17390773 aggctggcaccgtcgcaggttgccgggggtgccactgctgtcggaggcggaaaagtctcc 17390832
Query: 1128 tacatcccttgagcatccgtgggcccgcctgctgaagggcaatggtgctcttcacaacgc 1187
||||||| |||||||||||||| || ||||||||| ||||| ||||||||| ||||||||
Sbjct: 17390833 tacatccattgagcatccgtggccctgcctgctgatgggcagtggtgctctccacaacgc 17390892
Query: 1188 ccgaagtggcctcaggggccctggggtcccccggttgaaaaccactgagctggaacctcc 1247
| || ||| | |||||||||||| ||||||||||||| ||||||||||||||| ||||
Sbjct: 17390893 cggatgtgcctccaggggccctggcgtcccccggttgagaaccactgagctggactctcc 17390952
Query: 1248 ttttc 1252
|||||
Sbjct: 17390953 ttttc 17390957
Score = 339 bits (171), Expect = 2e-90
Identities = 171/171 (100%)
Strand = Plus / Plus
Query: 526 gacatcctcatcgtcaagctgaggaagggccaggagctgagacttcgcgcctacgccaaa 585
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17389324 gacatcctcatcgtcaagctgaggaagggccaggagctgagacttcgcgcctacgccaaa 17389383
Query: 586 aagggctttggcaaggaacacgccaagtggaaccccactgcaggggtggcttttgaatat 645
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17389384 aagggctttggcaaggaacacgccaagtggaaccccactgcaggggtggcttttgaatat 17389443
Query: 646 gatcccgacaatgccctgaggcacacggtgtaccccaagccggaggaatgg 696
|||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17389444 gatcccgacaatgccctgaggcacacggtgtaccccaagccggaggaatgg 17389494
Score = 262 bits (132), Expect = 4e-67
Identities = 132/132 (100%)
Strand = Plus / Plus
Query: 345 ggactgcacttgtgaggagttctgccccgagtgctcggtggagttcaccctcgatgtgcg 404
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17388549 ggactgcacttgtgaggagttctgccccgagtgctcggtggagttcaccctcgatgtgcg 17388608
Query: 405 gtgcaacgaagaccagacgcgtcacgtcacatcccgagacctcatctccaacagcccccg 464
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17388609 gtgcaacgaagaccagacgcgtcacgtcacatcccgagacctcatctccaacagcccccg 17388668
Query: 465 ggtcattccggt 476
||||||||||||
Sbjct: 17388669 ggtcattccggt 17388680
Score = 244 bits (123), Expect = 1e-61
Identities = 123/123 (100%)
Strand = Plus / Plus
Query: 52 aaccgacccccaaggccccgcgagcagtctggcgcgatgccgtatgccaaccagccaacc 111
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17383948 aaccgacccccaaggccccgcgagcagtctggcgcgatgccgtatgccaaccagccaacc 17384007
Query: 112 gtgcggatcaccgagctcaccgacgagaatgtcaagttcattatcgagaatacggacctg 171
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17384008 gtgcggatcaccgagctcaccgacgagaatgtcaagttcattatcgagaatacggacctg 17384067
Query: 172 gcg 174
|||
Sbjct: 17384068 gcg 17384070
Score = 155 bits (78), Expect = 7e-35
Identities = 78/78 (100%)
Strand = Plus / Plus
Query: 695 ggccaaagagtgagtactcggagctggatgaggatgagtcacaggcgccctacgacccca 754
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17389651 ggccaaagagtgagtactcggagctggatgaggatgagtcacaggcgccctacgacccca 17389710
Query: 755 acggcaagccagagaggt 772
||||||||||||||||||
Sbjct: 17389711 acggcaagccagagaggt 17389728
Score = 145 bits (73), Expect = 7e-32
Identities = 73/73 (100%)
Strand = Plus / Plus
Query: 221 tagcaattgactgggttcagattgatgccaattcctcagtccttcacgacgagttcattg 280
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17385501 tagcaattgactgggttcagattgatgccaattcctcagtccttcacgacgagttcattg 17385560
Query: 281 ctcacaggcttgg 293
|||||||||||||
Sbjct: 17385561 ctcacaggcttgg 17385573
Score = 109 bits (55), Expect = 4e-21
Identities = 55/55 (100%)
Strand = Plus / Plus
Query: 292 ggattaatccccctcactagtgacgacattgtggacaagctgcagtactcccggg 346
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17385722 ggattaatccccctcactagtgacgacattgtggacaagctgcagtactcccggg 17385776
Score = 105 bits (53), Expect = 6e-20
Identities = 53/53 (100%)
Strand = Plus / Plus
Query: 474 ggtgacatcccggaaccgagataatgaccccagtgactacgtggagcaggacg 526
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17389140 ggtgacatcccggaaccgagataatgaccccagtgactacgtggagcaggacg 17389192
Score = 99.6 bits (50), Expect = 4e-18
Identities = 50/50 (100%)
Strand = Plus / Plus
Query: 174 ggtggcgaattctatccggagggtcttcatcgctgaggtgcccataatag 223
||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 17384253 ggtggcgaattctatccggagggtcttcatcgctgaggtgcccataatag 17384302
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: 28,885,712
Number of extensions: 141
Number of successful extensions: 141
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 140
Number of HSP's successfully gapped: 9
Length of query: 1252
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1231
Effective length of database: 2,808,413,156
Effective search space: 3457156595036
Effective search space used: 3457156595036
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 50 (99.1 bits)
S1: 18 (36.2 bits)
S2: 30 (60.0 bits)