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-004765
(1326 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_002694925.1| PREDICTED: DNA polymerase sigma-like [Bos ta... 648 0.0
Alignment gi|XP_001256516.1| PREDICTED: DNA polymerase sigma-like [Bos ta... 648 0.0
Alignment gi|NP_001153629.1| DNA polymerase sigma [Bos taurus]. 367 e-101
>ref|XP_002694925.1| PREDICTED: DNA polymerase sigma-like [Bos taurus].
Length = 467
Score = 648 bits (1672), Expect = 0.0
Identities = 338/442 (76%), Positives = 344/442 (77%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN
Sbjct: 72 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 131
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
VQNGVRAADLIKDFT QFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL
Sbjct: 132 VQNGVRAADLIKDFTKKYPVLPYLVLVLKQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 191
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS
Sbjct: 192 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 251
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR
Sbjct: 252 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 311
Query: 721 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK 900
VTDEVATYRDWISKQWGLQNRPEPSCNG ++ S+ + C+
Sbjct: 312 VTDEVATYRDWISKQWGLQNRPEPSCNG-------PVSSSSATQSSSSDVDSDATPCK-- 362
Query: 901 TXXXXXXXXXXXXXXXXXXXXXXXXXXXXVDSDATPCKTPKQLLCRPTPGNRVGSQDVSL 1080
TPKQLLCRP+ GNRVGSQDVSL
Sbjct: 363 --------------------------------------TPKQLLCRPSTGNRVGSQDVSL 384
Query: 1081 ESSQAVGKMXXXXXXXXXXXXXXXXHGSARLFRSSSKGFQGTTQTSHGSLMTNKPHQGKS 1260
ESSQ GKM HGS RLFRSSSKGFQGTTQTSHGSLMTNK HQGKS
Sbjct: 385 ESSQTGGKMQSTQTTNTPNSTNKSQHGSTRLFRSSSKGFQGTTQTSHGSLMTNKQHQGKS 444
Query: 1261 NNQYYHGKKRKHKRDAPLSDLC 1326
NNQYYHGKKRKHKRDAPLSDLC
Sbjct: 445 NNQYYHGKKRKHKRDAPLSDLC 466
>ref|XP_001256516.1| PREDICTED: DNA polymerase sigma-like [Bos taurus].
Length = 467
Score = 648 bits (1672), Expect = 0.0
Identities = 338/442 (76%), Positives = 344/442 (77%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN
Sbjct: 72 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 131
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
VQNGVRAADLIKDFT QFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL
Sbjct: 132 VQNGVRAADLIKDFTKKYPVLPYLVLVLKQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 191
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS
Sbjct: 192 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 251
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR
Sbjct: 252 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 311
Query: 721 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK 900
VTDEVATYRDWISKQWGLQNRPEPSCNG ++ S+ + C+
Sbjct: 312 VTDEVATYRDWISKQWGLQNRPEPSCNG-------PVSSSSATQSSSSDVDSDATPCK-- 362
Query: 901 TXXXXXXXXXXXXXXXXXXXXXXXXXXXXVDSDATPCKTPKQLLCRPTPGNRVGSQDVSL 1080
TPKQLLCRP+ GNRVGSQDVSL
Sbjct: 363 --------------------------------------TPKQLLCRPSTGNRVGSQDVSL 384
Query: 1081 ESSQAVGKMXXXXXXXXXXXXXXXXHGSARLFRSSSKGFQGTTQTSHGSLMTNKPHQGKS 1260
ESSQ GKM HGS RLFRSSSKGFQGTTQTSHGSLMTNK HQGKS
Sbjct: 385 ESSQTGGKMQSTQTTNTPNSTNKSQHGSTRLFRSSSKGFQGTTQTSHGSLMTNKQHQGKS 444
Query: 1261 NNQYYHGKKRKHKRDAPLSDLC 1326
NNQYYHGKKRKHKRDAPLSDLC
Sbjct: 445 NNQYYHGKKRKHKRDAPLSDLC 466
>ref|NP_001153629.1| DNA polymerase sigma [Bos taurus].
Length = 541
Score = 367 bits (942), Expect = e-101
Identities = 184/266 (69%), Positives = 212/266 (79%), Gaps = 2/266 (0%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWE PL LE+ALRKH VA+ S+KVLDKATVPIIKLTD TEVKVDISFN
Sbjct: 47 DIDLVVFGKWERPPLQLLEQALRKHNVAEPGSIKVLDKATVPIIKLTDQETEVKVDISFN 106
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
++ GVRAA+ IK++ QFLLQRDLNEVFTGGI SYSL LMA+SFLQL
Sbjct: 107 METGVRAAEFIKNYMKKYSLLPYLILVLKQFLLQRDLNEVFTGGISSYSLILMAISFLQL 166
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPR DA + N G+LL+EFFELYGR+FNYLKTGIRIK+GG+Y+AK+E+ K M GYRPS
Sbjct: 167 HPRIDARRADENLGMLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSGYRPS 226
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
ML IEDPL PGNDVGRSSYGAMQVKQ FDYAY+VLSHAVSP+A+ YPN ++ES LGRII+
Sbjct: 227 MLCIEDPLLPGNDVGRSSYGAMQVKQVFDYAYIVLSHAVSPLARSYPNRDSESTLGRIIK 286
Query: 721 VTDEVATYRDWISKQWG--LQNRPEP 792
VT EV YR WI ++WG + P+P
Sbjct: 287 VTQEVIDYRTWIKEKWGGRVHAAPDP 312
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
0.317 0.134 0.398
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: 47,971,873
Number of extensions: 1207593
Number of successful extensions: 3479
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 3475
Number of HSP's successfully gapped: 5
Length of query: 442
Length of database: 17,681,374
Length adjustment: 105
Effective length of query: 337
Effective length of database: 14,207,134
Effective search space: 4787804158
Effective search space used: 4787804158
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 (21.6 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-004765
(1326 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_535307.2| PREDICTED: similar to PAP associated domain con... 749 0.0
Alignment gi|XP_545180.2| PREDICTED: similar to DNA polymerase sigma [Can... 369 e-102
>ref|XP_535307.2| PREDICTED: similar to PAP associated domain containing 5
(Topoisomerase-related function protein 4-2) (TRF4-2)
[Canis familiaris].
Length = 641
Score = 749 bits (1933), Expect = 0.0
Identities = 379/442 (85%), Positives = 381/442 (86%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN
Sbjct: 199 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 258
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
VQNGVRAADLIKDFT QFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL
Sbjct: 259 VQNGVRAADLIKDFTKKYPVLPYLVLVLKQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 318
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS
Sbjct: 319 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 378
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR
Sbjct: 379 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 438
Query: 721 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK 900
VTDEVATYRDWISKQWGLQ+ PEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK
Sbjct: 439 VTDEVATYRDWISKQWGLQSGPEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK 498
Query: 901 TXXXXXXXXXXXXXXXXXXXXXXXXXXXXVDSDATPCKTPKQLLCRPTPGNRVGSQDVSL 1080
T VDSDATPCKTPKQLLCRP+ GNRVGSQDVSL
Sbjct: 499 TSESLSKHSSNSSSGPVSSSSATQSSSSDVDSDATPCKTPKQLLCRPSTGNRVGSQDVSL 558
Query: 1081 ESSQAVGKMXXXXXXXXXXXXXXXXHGSARLFRSSSKGFQGTTQTSHGSLMTNKPHQGKS 1260
ESSQAVGKM HGSARLFRSSSKGFQGTTQTSHGSLMTNK HQGKS
Sbjct: 559 ESSQAVGKMQSTQTSNTSNSTNKSQHGSARLFRSSSKGFQGTTQTSHGSLMTNKQHQGKS 618
Query: 1261 NNQYYHGKKRKHKRDAPLSDLC 1326
NNQYYHGKKRKHKRDAPLSDLC
Sbjct: 619 NNQYYHGKKRKHKRDAPLSDLC 640
>ref|XP_545180.2| PREDICTED: similar to DNA polymerase sigma [Canis familiaris].
Length = 672
Score = 369 bits (948), Expect = e-102
Identities = 185/264 (70%), Positives = 212/264 (80%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWE PL LE+ALRKH VA+ S+KVLDKATVPIIKLTD TEVKVDISFN
Sbjct: 177 DIDLVVFGKWERPPLQLLEQALRKHNVAEPCSIKVLDKATVPIIKLTDQETEVKVDISFN 236
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
++ GVRAA+LIK++ QFLLQRDLNEVFTGGI SYSL LMA+SFLQL
Sbjct: 237 METGVRAAELIKNYMKKYSLLPYLILVLKQFLLQRDLNEVFTGGISSYSLILMAISFLQL 296
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPR DA + N G+LL+EFFELYGR+FNYLKTGIRIK+GG+Y+AK+E+ K M GYRPS
Sbjct: 297 HPRIDARRADENLGMLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSGYRPS 356
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
ML IEDPL PGNDVGRSSYGAMQVKQ FDYAY+VLSHAVSP+A+ YPN ++ES LGRII+
Sbjct: 357 MLCIEDPLLPGNDVGRSSYGAMQVKQVFDYAYIVLSHAVSPLARSYPNRDSESTLGRIIK 416
Query: 721 VTDEVATYRDWISKQWGLQNRPEP 792
VT EV YR WI ++WG + P P
Sbjct: 417 VTQEVIDYRRWIKEKWGGKAPPAP 440
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
0.317 0.134 0.398
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: 50,085,654
Number of extensions: 1242339
Number of successful extensions: 3639
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 3633
Number of HSP's successfully gapped: 2
Length of query: 442
Length of database: 18,874,504
Length adjustment: 106
Effective length of query: 336
Effective length of database: 15,340,888
Effective search space: 5154538368
Effective search space used: 5154538368
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 (21.6 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-004765
(1326 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_001035374.2| PAP-associated domain-containing protein 5 i... 752 0.0
Alignment gi|NP_001035375.2| PAP-associated domain-containing protein 5 i... 652 0.0
Alignment gi|NP_001165276.1| DNA polymerase sigma isoform 2 [Homo sapiens]. 372 e-103
Alignment gi|NP_008930.1| DNA polymerase sigma isoform 1 [Homo sapiens]. 372 e-103
Alignment gi|NP_001165277.1| DNA polymerase sigma isoform 3 [Homo sapiens]. 206 4e-53
>ref|NP_001035374.2| PAP-associated domain-containing protein 5 isoform a [Homo sapiens].
Length = 698
Score = 752 bits (1941), Expect = 0.0
Identities = 380/442 (85%), Positives = 382/442 (86%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN
Sbjct: 256 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 315
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
VQNGVRAADLIKDFT QFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL
Sbjct: 316 VQNGVRAADLIKDFTKKYPVLPYLVLVLKQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 375
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS
Sbjct: 376 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 435
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR
Sbjct: 436 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 495
Query: 721 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK 900
VTDEVATYRDWISKQWGL+NRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK
Sbjct: 496 VTDEVATYRDWISKQWGLKNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK 555
Query: 901 TXXXXXXXXXXXXXXXXXXXXXXXXXXXXVDSDATPCKTPKQLLCRPTPGNRVGSQDVSL 1080
T VDSDATPCKTPKQLLCRP+ GNRVGSQDVSL
Sbjct: 556 TSESLSKHSSNSSSGPVSSSSATQSSSSDVDSDATPCKTPKQLLCRPSTGNRVGSQDVSL 615
Query: 1081 ESSQAVGKMXXXXXXXXXXXXXXXXHGSARLFRSSSKGFQGTTQTSHGSLMTNKPHQGKS 1260
ESSQAVGKM HGSARLFRSSSKGFQGTTQTSHGSLMTNK HQGKS
Sbjct: 616 ESSQAVGKMQSTQTTNTSNSTNKSQHGSARLFRSSSKGFQGTTQTSHGSLMTNKQHQGKS 675
Query: 1261 NNQYYHGKKRKHKRDAPLSDLC 1326
NNQYYHGKKRKHKRDAPLSDLC
Sbjct: 676 NNQYYHGKKRKHKRDAPLSDLC 697
>ref|NP_001035375.2| PAP-associated domain-containing protein 5 isoform b [Homo sapiens].
Length = 651
Score = 652 bits (1683), Expect = 0.0
Identities = 340/442 (76%), Positives = 347/442 (78%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN
Sbjct: 256 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 315
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
VQNGVRAADLIKDFT QFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL
Sbjct: 316 VQNGVRAADLIKDFTKKYPVLPYLVLVLKQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 375
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS
Sbjct: 376 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 435
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR
Sbjct: 436 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 495
Query: 721 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK 900
VTDEVATYRDWISKQWGL+NRPEPSCNG ++ S+ + C+
Sbjct: 496 VTDEVATYRDWISKQWGLKNRPEPSCNG-------PVSSSSATQSSSSDVDSDATPCK-- 546
Query: 901 TXXXXXXXXXXXXXXXXXXXXXXXXXXXXVDSDATPCKTPKQLLCRPTPGNRVGSQDVSL 1080
TPKQLLCRP+ GNRVGSQDVSL
Sbjct: 547 --------------------------------------TPKQLLCRPSTGNRVGSQDVSL 568
Query: 1081 ESSQAVGKMXXXXXXXXXXXXXXXXHGSARLFRSSSKGFQGTTQTSHGSLMTNKPHQGKS 1260
ESSQAVGKM HGSARLFRSSSKGFQGTTQTSHGSLMTNK HQGKS
Sbjct: 569 ESSQAVGKMQSTQTTNTSNSTNKSQHGSARLFRSSSKGFQGTTQTSHGSLMTNKQHQGKS 628
Query: 1261 NNQYYHGKKRKHKRDAPLSDLC 1326
NNQYYHGKKRKHKRDAPLSDLC
Sbjct: 629 NNQYYHGKKRKHKRDAPLSDLC 650
>ref|NP_001165276.1| DNA polymerase sigma isoform 2 [Homo sapiens].
Length = 541
Score = 372 bits (954), Expect = e-103
Identities = 188/292 (64%), Positives = 220/292 (75%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWE PL LE+ALRKH VA+ S+KVLDKATVPIIKLTD TEVKVDISFN
Sbjct: 47 DIDLVVFGKWERPPLQLLEQALRKHNVAEPCSIKVLDKATVPIIKLTDQETEVKVDISFN 106
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
++ GVRAA+ IK++ QFLLQRDLNEVFTGGI SYSL LMA+SFLQL
Sbjct: 107 METGVRAAEFIKNYMKKYSLLPYLILVLKQFLLQRDLNEVFTGGISSYSLILMAISFLQL 166
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPR DA + N G+LL+EFFELYGR+FNYLKTGIRIK+GG+Y+AK+E+ K M GYRPS
Sbjct: 167 HPRIDARRADENLGMLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSGYRPS 226
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
ML IEDPL PGNDVGRSSYGAMQVKQ FDYAY+VLSHAVSP+A+ YPN + ES LGRII+
Sbjct: 227 MLCIEDPLLPGNDVGRSSYGAMQVKQVFDYAYIVLSHAVSPLARSYPNRDAESTLGRIIK 286
Query: 721 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENE 876
VT EV YR WI ++WG + P P + I +++ CN ++ E
Sbjct: 287 VTQEVIDYRRWIKEKWGSKAHPSPGMDSR----IKIKERIATCNGEQTQNRE 334
>ref|NP_008930.1| DNA polymerase sigma isoform 1 [Homo sapiens].
Length = 542
Score = 372 bits (954), Expect = e-103
Identities = 188/292 (64%), Positives = 220/292 (75%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWE PL LE+ALRKH VA+ S+KVLDKATVPIIKLTD TEVKVDISFN
Sbjct: 47 DIDLVVFGKWERPPLQLLEQALRKHNVAEPCSIKVLDKATVPIIKLTDQETEVKVDISFN 106
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
++ GVRAA+ IK++ QFLLQRDLNEVFTGGI SYSL LMA+SFLQL
Sbjct: 107 METGVRAAEFIKNYMKKYSLLPYLILVLKQFLLQRDLNEVFTGGISSYSLILMAISFLQL 166
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPR DA + N G+LL+EFFELYGR+FNYLKTGIRIK+GG+Y+AK+E+ K M GYRPS
Sbjct: 167 HPRIDARRADENLGMLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSGYRPS 226
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
ML IEDPL PGNDVGRSSYGAMQVKQ FDYAY+VLSHAVSP+A+ YPN + ES LGRII+
Sbjct: 227 MLCIEDPLLPGNDVGRSSYGAMQVKQVFDYAYIVLSHAVSPLARSYPNRDAESTLGRIIK 286
Query: 721 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENE 876
VT EV YR WI ++WG + P P + I +++ CN ++ E
Sbjct: 287 VTQEVIDYRRWIKEKWGSKAHPSPGMDSR----IKIKERIATCNGEQTQNRE 334
>ref|NP_001165277.1| DNA polymerase sigma isoform 3 [Homo sapiens].
Length = 362
Score = 206 bits (524), Expect = 4e-53
Identities = 98/158 (62%), Positives = 120/158 (75%)
Frame = +1
Query: 403 VLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPSMLYIEDPLQPGNDV 582
+LL+EFFELYGR+FNYLKTGIRIK+GG+Y+AK+E+ K M GYRPSML IEDPL PGNDV
Sbjct: 1 MLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSGYRPSMLCIEDPLLPGNDV 60
Query: 583 GRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIRVTDEVATYRDWISK 762
GRSSYGAMQVKQ FDYAY+VLSHAVSP+A+ YPN + ES LGRII+VT EV YR WI +
Sbjct: 61 GRSSYGAMQVKQVFDYAYIVLSHAVSPLARSYPNRDAESTLGRIIKVTQEVIDYRRWIKE 120
Query: 763 QWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENE 876
+WG + P P + I +++ CN ++ E
Sbjct: 121 KWGSKAHPSPGMDSR----IKIKERIATCNGEQTQNRE 154
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
0.317 0.134 0.398
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: 49,270,118
Number of extensions: 1238977
Number of successful extensions: 3385
Number of sequences better than 1.0e-05: 5
Number of HSP's gapped: 3378
Number of HSP's successfully gapped: 7
Length of query: 442
Length of database: 18,297,164
Length adjustment: 106
Effective length of query: 336
Effective length of database: 14,802,980
Effective search space: 4973801280
Effective search space used: 4973801280
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 (21.6 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-004765
(1326 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_001157970.1| PAP-associated domain-containing protein 5 i... 728 0.0
Alignment gi|NP_001157969.1| PAP-associated domain-containing protein 5 i... 728 0.0
Alignment gi|NP_001157971.1| PAP-associated domain-containing protein 5 i... 656 0.0
Alignment gi|NP_001162602.1| DNA polymerase sigma isoform 2 [Mus musculus]. 370 e-102
Alignment gi|NP_941002.2| DNA polymerase sigma isoform 1 [Mus musculus]. 370 e-102
>ref|NP_001157970.1| PAP-associated domain-containing protein 5 isoform a [Mus musculus].
Length = 680
Score = 728 bits (1880), Expect = 0.0
Identities = 369/442 (83%), Positives = 373/442 (84%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN
Sbjct: 238 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 297
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
VQNGVRAADLIKDFT QFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL
Sbjct: 298 VQNGVRAADLIKDFTKKYPVLPYLVLVLKQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 357
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS
Sbjct: 358 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 417
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR
Sbjct: 418 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 477
Query: 721 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK 900
VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEE EALGKCRS
Sbjct: 478 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEEKEALGKCRSN 537
Query: 901 TXXXXXXXXXXXXXXXXXXXXXXXXXXXXVDSDATPCKTPKQLLCRPTPGNRVGSQDVSL 1080
VDSDATPCKTPKQLLCRP RVGSQDVSL
Sbjct: 538 ASEPLSKHSSNSSSGPVSSSSATQSSSSDVDSDATPCKTPKQLLCRPPTVTRVGSQDVSL 597
Query: 1081 ESSQAVGKMXXXXXXXXXXXXXXXXHGSARLFRSSSKGFQGTTQTSHGSLMTNKPHQGKS 1260
E SQAVGKM HGSARLFRSSSKGFQGT QTSHG+LMT+K HQGKS
Sbjct: 598 EVSQAVGKMQSTQTTNTPNNANKSQHGSARLFRSSSKGFQGTAQTSHGALMTSKQHQGKS 657
Query: 1261 NNQYYHGKKRKHKRDAPLSDLC 1326
N QYYHGKKR+HKRDAPLS+LC
Sbjct: 658 NTQYYHGKKRRHKRDAPLSELC 679
>ref|NP_001157969.1| PAP-associated domain-containing protein 5 isoform a [Mus musculus].
Length = 680
Score = 728 bits (1880), Expect = 0.0
Identities = 369/442 (83%), Positives = 373/442 (84%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN
Sbjct: 238 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 297
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
VQNGVRAADLIKDFT QFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL
Sbjct: 298 VQNGVRAADLIKDFTKKYPVLPYLVLVLKQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 357
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS
Sbjct: 358 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 417
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR
Sbjct: 418 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 477
Query: 721 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK 900
VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEE EALGKCRS
Sbjct: 478 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEEKEALGKCRSN 537
Query: 901 TXXXXXXXXXXXXXXXXXXXXXXXXXXXXVDSDATPCKTPKQLLCRPTPGNRVGSQDVSL 1080
VDSDATPCKTPKQLLCRP RVGSQDVSL
Sbjct: 538 ASEPLSKHSSNSSSGPVSSSSATQSSSSDVDSDATPCKTPKQLLCRPPTVTRVGSQDVSL 597
Query: 1081 ESSQAVGKMXXXXXXXXXXXXXXXXHGSARLFRSSSKGFQGTTQTSHGSLMTNKPHQGKS 1260
E SQAVGKM HGSARLFRSSSKGFQGT QTSHG+LMT+K HQGKS
Sbjct: 598 EVSQAVGKMQSTQTTNTPNNANKSQHGSARLFRSSSKGFQGTAQTSHGALMTSKQHQGKS 657
Query: 1261 NNQYYHGKKRKHKRDAPLSDLC 1326
N QYYHGKKR+HKRDAPLS+LC
Sbjct: 658 NTQYYHGKKRRHKRDAPLSELC 679
>ref|NP_001157971.1| PAP-associated domain-containing protein 5 isoform b [Mus musculus].
Length = 637
Score = 656 bits (1693), Expect = 0.0
Identities = 339/442 (76%), Positives = 344/442 (77%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN
Sbjct: 238 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 297
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
VQNGVRAADLIKDFT +L
Sbjct: 298 VQNGVRAADLIKDFT-------------------------------------------KL 314
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS
Sbjct: 315 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 374
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR
Sbjct: 375 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 434
Query: 721 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK 900
VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEE EALGKCRS
Sbjct: 435 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEEKEALGKCRSN 494
Query: 901 TXXXXXXXXXXXXXXXXXXXXXXXXXXXXVDSDATPCKTPKQLLCRPTPGNRVGSQDVSL 1080
VDSDATPCKTPKQLLCRP RVGSQDVSL
Sbjct: 495 ASEPLSKHSSNSSSGPVSSSSATQSSSSDVDSDATPCKTPKQLLCRPPTVTRVGSQDVSL 554
Query: 1081 ESSQAVGKMXXXXXXXXXXXXXXXXHGSARLFRSSSKGFQGTTQTSHGSLMTNKPHQGKS 1260
E SQAVGKM HGSARLFRSSSKGFQGT QTSHG+LMT+K HQGKS
Sbjct: 555 EVSQAVGKMQSTQTTNTPNNANKSQHGSARLFRSSSKGFQGTAQTSHGALMTSKQHQGKS 614
Query: 1261 NNQYYHGKKRKHKRDAPLSDLC 1326
N QYYHGKKR+HKRDAPLS+LC
Sbjct: 615 NTQYYHGKKRRHKRDAPLSELC 636
>ref|NP_001162602.1| DNA polymerase sigma isoform 2 [Mus musculus].
Length = 541
Score = 370 bits (951), Expect = e-102
Identities = 188/292 (64%), Positives = 220/292 (75%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWE PL LE+ALRKH VA+ S+KVLDKATVPIIKLTD TEVKVDISFN
Sbjct: 47 DIDLVVFGKWERPPLQLLEQALRKHNVAEPCSIKVLDKATVPIIKLTDQETEVKVDISFN 106
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
++ GVRAA+ IK++ QFLLQRDLNEVFTGGI SYSL LMA+SFLQL
Sbjct: 107 METGVRAAEFIKNYMKKYSLLPYLILVLKQFLLQRDLNEVFTGGISSYSLILMAISFLQL 166
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPR DA + N G+LL+EFFELYGR+FNYLKTGIRIK+GG+Y+AK+E+ K M GYRPS
Sbjct: 167 HPRIDARRADENLGMLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSGYRPS 226
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
ML IEDPL PGNDVGRSSYGAMQVKQ FDYAY+VLSHAVSP+A+ YPN ++ES LGRII+
Sbjct: 227 MLCIEDPLLPGNDVGRSSYGAMQVKQVFDYAYIVLSHAVSPLARSYPNRDSESTLGRIIK 286
Query: 721 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENE 876
VT EV YR WI ++WG + P P + I +++ CN + E
Sbjct: 287 VTQEVIDYRRWIKEKWGSRILPSPDLDNR----IKIKERITTCNGEQMQSRE 334
>ref|NP_941002.2| DNA polymerase sigma isoform 1 [Mus musculus].
Length = 542
Score = 370 bits (951), Expect = e-102
Identities = 188/292 (64%), Positives = 220/292 (75%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWE PL LE+ALRKH VA+ S+KVLDKATVPIIKLTD TEVKVDISFN
Sbjct: 47 DIDLVVFGKWERPPLQLLEQALRKHNVAEPCSIKVLDKATVPIIKLTDQETEVKVDISFN 106
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
++ GVRAA+ IK++ QFLLQRDLNEVFTGGI SYSL LMA+SFLQL
Sbjct: 107 METGVRAAEFIKNYMKKYSLLPYLILVLKQFLLQRDLNEVFTGGISSYSLILMAISFLQL 166
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPR DA + N G+LL+EFFELYGR+FNYLKTGIRIK+GG+Y+AK+E+ K M GYRPS
Sbjct: 167 HPRIDARRADENLGMLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSGYRPS 226
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
ML IEDPL PGNDVGRSSYGAMQVKQ FDYAY+VLSHAVSP+A+ YPN ++ES LGRII+
Sbjct: 227 MLCIEDPLLPGNDVGRSSYGAMQVKQVFDYAYIVLSHAVSPLARSYPNRDSESTLGRIIK 286
Query: 721 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENE 876
VT EV YR WI ++WG + P P + I +++ CN + E
Sbjct: 287 VTQEVIDYRRWIKEKWGSRILPSPDLDNR----IKIKERITTCNGEQMQSRE 334
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
0.317 0.134 0.398
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: 42,126,771
Number of extensions: 1059184
Number of successful extensions: 2929
Number of sequences better than 1.0e-05: 5
Number of HSP's gapped: 2922
Number of HSP's successfully gapped: 6
Length of query: 442
Length of database: 15,617,559
Length adjustment: 104
Effective length of query: 338
Effective length of database: 12,493,815
Effective search space: 4222909470
Effective search space used: 4222909470
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 (21.6 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-004765
(1326 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_003361170.1| PREDICTED: PAP-associated domain-containing ... 758 0.0
Alignment gi|XP_003134203.2| PREDICTED: DNA polymerase sigma [Sus scrofa]. 373 e-103
>ref|XP_003361170.1| PREDICTED: PAP-associated domain-containing protein 5-like [Sus
scrofa].
Length = 511
Score = 758 bits (1957), Expect = 0.0
Identities = 383/442 (86%), Positives = 383/442 (86%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN
Sbjct: 69 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 128
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
VQNGVRAADLIKDFT QFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL
Sbjct: 129 VQNGVRAADLIKDFTKKYPVLPYLVLVLKQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 188
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS
Sbjct: 189 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 248
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR
Sbjct: 249 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 308
Query: 721 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK 900
VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK
Sbjct: 309 VTDEVATYRDWISKQWGLQNRPEPSCNGNGVTLIVDTQQLDKCNNNLSEENEALGKCRSK 368
Query: 901 TXXXXXXXXXXXXXXXXXXXXXXXXXXXXVDSDATPCKTPKQLLCRPTPGNRVGSQDVSL 1080
T VDSDATPCKTPKQLLCRPTPGNRVGSQDVSL
Sbjct: 369 TSESLSKHSSNSSSGPVSSSSATQSSSSDVDSDATPCKTPKQLLCRPTPGNRVGSQDVSL 428
Query: 1081 ESSQAVGKMXXXXXXXXXXXXXXXXHGSARLFRSSSKGFQGTTQTSHGSLMTNKPHQGKS 1260
ESSQAVGKM HGSARLFRSSSKGFQGTTQTSHGSLMTNK HQGKS
Sbjct: 429 ESSQAVGKMQSAQATSTSNSTNKSQHGSARLFRSSSKGFQGTTQTSHGSLMTNKQHQGKS 488
Query: 1261 NNQYYHGKKRKHKRDAPLSDLC 1326
NNQYYHGKKRKHKRDAPLSDLC
Sbjct: 489 NNQYYHGKKRKHKRDAPLSDLC 510
>ref|XP_003134203.2| PREDICTED: DNA polymerase sigma [Sus scrofa].
Length = 625
Score = 373 bits (957), Expect = e-103
Identities = 185/264 (70%), Positives = 213/264 (80%)
Frame = +1
Query: 1 DIDLVVFGKWENLPLWTLEEALRKHKVADEDSVKVLDKATVPIIKLTDSFTEVKVDISFN 180
DIDLVVFGKWE PL LE+ALRKHKVA+ S+KVLDKATVPIIKLTD TEVKVDISFN
Sbjct: 130 DIDLVVFGKWERPPLQLLEQALRKHKVAEPCSIKVLDKATVPIIKLTDQETEVKVDISFN 189
Query: 181 VQNGVRAADLIKDFTXXXXXXXXXXXXXXQFLLQRDLNEVFTGGIGSYSLFLMAVSFLQL 360
++ GVRAA+ IK++ QFLLQRDLNEVFTGGI SYSL LMA+SFLQL
Sbjct: 190 METGVRAAEFIKNYMKKYSLLPYLILVLKQFLLQRDLNEVFTGGISSYSLILMAISFLQL 249
Query: 361 HPREDACIPNTNYGVLLIEFFELYGRHFNYLKTGIRIKDGGSYVAKDEVQKNMLDGYRPS 540
HPR DA + N G+LL+EFFELYGR+FNYLKTGIRIK+GG+Y+AK+E+ K M GYRPS
Sbjct: 250 HPRIDARRADENLGMLLVEFFELYGRNFNYLKTGIRIKEGGAYIAKEEIMKAMTSGYRPS 309
Query: 541 MLYIEDPLQPGNDVGRSSYGAMQVKQAFDYAYVVLSHAVSPIAKYYPNNETESILGRIIR 720
ML IEDPL PGNDVGRSSYGAMQVKQ FDYAY+VLSHAVSP+A+ YPN ++ES LGRI++
Sbjct: 310 MLCIEDPLLPGNDVGRSSYGAMQVKQVFDYAYIVLSHAVSPLARSYPNRDSESTLGRIVK 369
Query: 721 VTDEVATYRDWISKQWGLQNRPEP 792
VT EV YR WI ++WG + RP P
Sbjct: 370 VTQEVIDYRRWIKEKWGSRARPAP 393
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
0.317 0.134 0.398
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: 30,825,405
Number of extensions: 771657
Number of successful extensions: 2237
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 2234
Number of HSP's successfully gapped: 2
Length of query: 442
Length of database: 11,343,932
Length adjustment: 102
Effective length of query: 340
Effective length of database: 8,804,438
Effective search space: 2993508920
Effective search space used: 2993508920
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 (21.6 bits)
S2: 35 (18.1 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-004765
(1326 letters)
Database: Sscrofa_10.2.fasta
4582 sequences; 2,808,509,378 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
gb|GL893669.1| Sus scrofa unplaced genomic scaffold chrU_scaffol... 434 e-119
Sscrofa_Chr16 62 8e-07
>gb|GL893669.1| Sus scrofa unplaced genomic scaffold chrU_scaffold2410
Length = 136349
Score = 434 bits (219), Expect = e-119
Identities = 219/219 (100%)
Strand = Plus / Minus
Query: 356 agttacatcccagggaagatgcttgcatccccaatacaaactatggtgttctcttaatag 415
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 69571 agttacatcccagggaagatgcttgcatccccaatacaaactatggtgttctcttaatag 69512
Query: 416 aattttttgaattatatggacgacacttcaattatttaaagactggcatccggataaagg 475
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 69511 aattttttgaattatatggacgacacttcaattatttaaagactggcatccggataaagg 69452
Query: 476 atggtggttcctatgtggccaaagatgaagtacagaaaaatatgctagatggctacaggc 535
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 69451 atggtggttcctatgtggccaaagatgaagtacagaaaaatatgctagatggctacaggc 69392
Query: 536 catcaatgctttatattgaagatcctttacaaccaggta 574
|||||||||||||||||||||||||||||||||||||||
Sbjct: 69391 catcaatgctttatattgaagatcctttacaaccaggta 69353
Score = 377 bits (190), Expect = e-101
Identities = 190/190 (100%)
Strand = Plus / Minus
Query: 802 ggaaatggtgttaccttgatagtagatactcagcagttagataaatgtaataataatcta 861
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 67465 ggaaatggtgttaccttgatagtagatactcagcagttagataaatgtaataataatcta 67406
Query: 862 tctgaagaaaatgaagcccttggaaaatgtagaagtaaaacttcggaatctcttagtaaa 921
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 67405 tctgaagaaaatgaagcccttggaaaatgtagaagtaaaacttcggaatctcttagtaaa 67346
Query: 922 cactcttcaaactcttcatcaggtccagtgtcttcctcctctgccacacagtccagctct 981
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 67345 cactcttcaaactcttcatcaggtccagtgtcttcctcctctgccacacagtccagctct 67286
Query: 982 agtgacgttg 991
||||||||||
Sbjct: 67285 agtgacgttg 67276
Score = 337 bits (170), Expect = 9e-90
Identities = 173/174 (99%)
Strand = Plus / Minus
Query: 1153 cagcatggatcagcaaggctctttcgttcttccagcaaaggcttccaaggtacaacccaa 1212
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 64274 cagcatggatcagcaaggctctttcgttcttccagcaaaggcttccaaggtacaacccaa 64215
Query: 1213 acaagccatggttccttgatgacaaacaaaccacatcaaggcaaatcaaataatcagtat 1272
||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||
Sbjct: 64214 acaagccatggttccttgatgacaaacaaacaacatcaaggcaaatcaaataatcagtat 64155
Query: 1273 taccatggcaaaaagaggaaacacaagagggacgcccccctctcagacctttgt 1326
||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 64154 taccatggcaaaaagaggaaacacaagagggacgcccccctctcagacctttgt 64101
Score = 327 bits (165), Expect = 9e-87
Identities = 165/165 (100%)
Strand = Plus / Minus
Query: 991 gattccgacgcgacgccatgcaaaacccccaaacagctgctctgccgtccgacccctggg 1050
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 65609 gattccgacgcgacgccatgcaaaacccccaaacagctgctctgccgtccgacccctggg 65550
Query: 1051 aatcgagtagggtcgcaggatgtgtccttggaatcctctcaggcagtgggaaaaatgcag 1110
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 65549 aatcgagtagggtcgcaggatgtgtccttggaatcctctcaggcagtgggaaaaatgcag 65490
Query: 1111 agcgcccaggccactagcacctccaacagcaccaacaaatcccag 1155
|||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 65489 agcgcccaggccactagcacctccaacagcaccaacaaatcccag 65445
Score = 260 bits (131), Expect = 2e-66
Identities = 131/131 (100%)
Strand = Plus / Minus
Query: 227 agaaatatcctgtattaccctacttggttttagtattgaaacaattcttattacagaggg 286
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 70424 agaaatatcctgtattaccctacttggttttagtattgaaacaattcttattacagaggg 70365
Query: 287 accttaatgaagtatttacaggtgggattggttcttacagtctctttttaatggcagtca 346
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 70364 accttaatgaagtatttacaggtgggattggttcttacagtctctttttaatggcagtca 70305
Query: 347 gtttccttcag 357
|||||||||||
Sbjct: 70304 gtttccttcag 70294
Score = 248 bits (125), Expect = 7e-63
Identities = 128/129 (99%)
Strand = Plus / Minus
Query: 570 aggtaatgatgttggaaggagttcctatggggccatgcaggtgaagcaggccttcgatta 629
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 67900 aggtaatgatgttggaaggagttcctatggggccatgcaggtgaagcaggccttcgatta 67841
Query: 630 tgcctatgtggtcttgagtcatgctgtatcgcccatagcaaagtactatcccaacaacga 689
|||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 67840 tgcctacgtggtcttgagtcatgctgtatcgcccatagcaaagtactatcccaacaacga 67781
Query: 690 aacggagag 698
|||||||||
Sbjct: 67780 aacggagag 67772
Score = 244 bits (123), Expect = 1e-61
Identities = 123/123 (100%)
Strand = Plus / Minus
Query: 1 gacatcgatctcgtggtgtttgggaagtgggagaacctccccctttggaccttggaagaa 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 75349 gacatcgatctcgtggtgtttgggaagtgggagaacctccccctttggaccttggaagaa 75290
Query: 61 gctcttcggaagcataaggttgcagatgaagattcggtgaaagttctagacaaagcaact 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 75289 gctcttcggaagcataaggttgcagatgaagattcggtgaaagttctagacaaagcaact 75230
Query: 121 gta 123
|||
Sbjct: 75229 gta 75227
Score = 214 bits (108), Expect = 9e-53
Identities = 108/108 (100%)
Strand = Plus / Minus
Query: 121 gtacctattattaaattaacagattcttttaccgaagtgaaagttgatatcagctttaat 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 73505 gtacctattattaaattaacagattcttttaccgaagtgaaagttgatatcagctttaat 73446
Query: 181 gtacaaaatggtgtgagagcagctgacctcatcaaagattttaccaag 228
||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 73445 gtacaaaatggtgtgagagcagctgacctcatcaaagattttaccaag 73398
Score = 212 bits (107), Expect = 4e-52
Identities = 107/107 (100%)
Strand = Plus / Minus
Query: 697 agcatcttaggtagaatcattagagtaacggatgaagttgccacatacagagattggata 756
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 67673 agcatcttaggtagaatcattagagtaacggatgaagttgccacatacagagattggata 67614
Query: 757 tcaaagcagtggggcttgcagaataggcctgagccttcatgcaatgg 803
|||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 67613 tcaaagcagtggggcttgcagaataggcctgagccttcatgcaatgg 67567
>Sscrofa_Chr16
|| Length = 86898991
Score = 61.9 bits (31), Expect = 8e-07
Identities = 79/95 (83%)
Strand = Plus / Minus
Query: 247 tacttggttttagtattgaaacaattcttattacagagggaccttaatgaagtatttaca 306
|||||| |||||||| ||||||| ||| | | ||||||||||| || ||||| ||||||
Sbjct: 81593480 tacttgattttagtactgaaacagttcctcctgcagagggacctgaacgaagtttttaca 81593421
Query: 307 ggtgggattggttcttacagtctctttttaatggc 341
||||| ||| | || ||||| ||| ||||||||||
Sbjct: 81593420 ggtggaattagctcgtacagcctcattttaatggc 81593386
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: 43,195,230
Number of extensions: 286
Number of successful extensions: 286
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 286
Number of HSP's successfully gapped: 10
Length of query: 1326
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1305
Effective length of database: 2,808,413,156
Effective search space: 3664979168580
Effective search space used: 3664979168580
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)