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-013431
(1043 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_542966.1| PREDICTED: similar to Protein c20orf178 [Canis ... 87 2e-17
Alignment gi|XP_535115.1| PREDICTED: similar to chromatin modifying prote... 72 1e-12
Alignment gi|XP_537387.1| PREDICTED: similar to chromatin modifying prote... 71 1e-12
>ref|XP_542966.1| PREDICTED: similar to Protein c20orf178 [Canis familiaris].
Length = 224
Score = 87.4 bits (215), Expect = 2e-17
Identities = 43/47 (91%), Positives = 44/47 (93%)
Frame = +3
Query: 210 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRGEL 350
PTPQ+AIQRLRDTEEMLSKKQEFLE KIEQELTAAKKHGTKNKR L
Sbjct: 20 PTPQDAIQRLRDTEEMLSKKQEFLETKIEQELTAAKKHGTKNKRAAL 66
>ref|XP_535115.1| PREDICTED: similar to chromatin modifying protein 4C isoform 1
[Canis familiaris].
Length = 236
Score = 71.6 bits (174), Expect = 1e-12
Identities = 32/47 (68%), Positives = 41/47 (87%)
Frame = +3
Query: 210 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRGEL 350
P+PQEA+ RLR+TEEMLSKKQE+LE ++++ELT AKKHGT+N R L
Sbjct: 20 PSPQEALARLRETEEMLSKKQEYLEARVQRELTLAKKHGTRNPRAAL 66
>ref|XP_537387.1| PREDICTED: similar to chromatin modifying protein 4A [Canis
familiaris].
Length = 265
Score = 71.2 bits (173), Expect = 1e-12
Identities = 33/47 (70%), Positives = 41/47 (87%)
Frame = +3
Query: 210 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRGEL 350
PTP+EAIQ+L++TE++L KKQEFLE+KI+QEL AKKHG KNKR L
Sbjct: 59 PTPEEAIQKLKETEKILIKKQEFLEQKIQQELQMAKKHGIKNKRAAL 105
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: 34,556,795
Number of extensions: 920304
Number of successful extensions: 4210
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 4179
Number of HSP's successfully gapped: 3
Length of query: 347
Length of database: 18,874,504
Length adjustment: 104
Effective length of query: 243
Effective length of database: 15,407,560
Effective search space: 3744037080
Effective search space used: 3744037080
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)
Animal-Genome cDNA 20110601C-013431
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-013431
(1043 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_001121978.1| charged multivesicular body protein 4b [Bos ... 91 2e-18
Alignment gi|NP_001121976.1| charged multivesicular body protein 4a [Bos ... 77 3e-14
Alignment gi|NP_001039441.1| charged multivesicular body protein 4C [Bos ... 66 4e-11
>ref|NP_001121978.1| charged multivesicular body protein 4b [Bos taurus].
Length = 224
Score = 90.9 bits (224), Expect = 2e-18
Identities = 45/47 (95%), Positives = 45/47 (95%)
Frame = +3
Query: 210 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRGEL 350
PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKR L
Sbjct: 20 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRAAL 66
>ref|NP_001121976.1| charged multivesicular body protein 4a [Bos taurus].
Length = 222
Score = 76.6 bits (187), Expect = 3e-14
Identities = 36/47 (76%), Positives = 43/47 (91%)
Frame = +3
Query: 210 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRGEL 350
PTP+EAIQ+L++TE++L KKQEFLE+KIEQEL AAKKHGTKNKR L
Sbjct: 17 PTPEEAIQKLKETEKILIKKQEFLEQKIEQELQAAKKHGTKNKRAAL 63
>ref|NP_001039441.1| charged multivesicular body protein 4C [Bos taurus].
Length = 236
Score = 66.2 bits (160), Expect = 4e-11
Identities = 30/47 (63%), Positives = 40/47 (85%)
Frame = +3
Query: 210 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRGEL 350
P+ QEA+ RLR+TEEML KKQE+LE +I++EL+ A+KHGT+NKR L
Sbjct: 20 PSAQEALARLRETEEMLGKKQEYLEGRIQRELSLARKHGTQNKRAAL 66
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: 33,535,094
Number of extensions: 992689
Number of successful extensions: 4136
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 4115
Number of HSP's successfully gapped: 3
Length of query: 347
Length of database: 17,681,374
Length adjustment: 103
Effective length of query: 244
Effective length of database: 14,273,310
Effective search space: 3482687640
Effective search space used: 3482687640
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-013431
(1043 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_003128593.2| PREDICTED: charged multivesicular body prote... 74 1e-13
Alignment gi|NP_001177119.1| charged multivesicular body protein 4c [Sus ... 71 9e-13
>ref|XP_003128593.2| PREDICTED: charged multivesicular body protein 4a-like [Sus
scrofa].
Length = 222
Score = 73.9 bits (180), Expect = 1e-13
Identities = 34/47 (72%), Positives = 42/47 (89%)
Frame = +3
Query: 210 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRGEL 350
PTP+EAIQ+L++TE++L KKQEFLE+KI+QEL AKKHGTKNKR L
Sbjct: 17 PTPEEAIQKLKETEKILIKKQEFLEQKIQQELQTAKKHGTKNKRAAL 63
>ref|NP_001177119.1| charged multivesicular body protein 4c [Sus scrofa].
Length = 237
Score = 71.2 bits (173), Expect = 9e-13
Identities = 32/47 (68%), Positives = 41/47 (87%)
Frame = +3
Query: 210 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRGEL 350
P+PQEA+ RLR+TEEML KKQE+LE +I++EL+ AKKHGT+NKR L
Sbjct: 20 PSPQEALARLRETEEMLGKKQEYLENRIQRELSLAKKHGTQNKRAAL 66
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: 22,703,652
Number of extensions: 804834
Number of successful extensions: 2592
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 2583
Number of HSP's successfully gapped: 2
Length of query: 347
Length of database: 11,343,932
Length adjustment: 100
Effective length of query: 247
Effective length of database: 8,854,232
Effective search space: 2186995304
Effective search space used: 2186995304
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-013431
(1043 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_083638.1| charged multivesicular body protein 4b [Mus mus... 91 1e-18
Alignment gi|NP_079795.1| charged multivesicular body protein 4c [Mus mus... 67 3e-11
>ref|NP_083638.1| charged multivesicular body protein 4b [Mus musculus].
Length = 224
Score = 90.9 bits (224), Expect = 1e-18
Identities = 45/47 (95%), Positives = 45/47 (95%)
Frame = +3
Query: 210 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRGEL 350
PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKR L
Sbjct: 20 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRAAL 66
>ref|NP_079795.1| charged multivesicular body protein 4c [Mus musculus].
Length = 232
Score = 66.6 bits (161), Expect = 3e-11
Identities = 30/47 (63%), Positives = 40/47 (85%)
Frame = +3
Query: 210 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRGEL 350
P+ QEA+ RLR+TEEML+KKQE+LE +I++EL AKKHG++NKR L
Sbjct: 20 PSAQEALARLRETEEMLAKKQEYLENRIQRELALAKKHGSQNKRAAL 66
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: 28,189,682
Number of extensions: 726281
Number of successful extensions: 3203
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 3192
Number of HSP's successfully gapped: 2
Length of query: 347
Length of database: 15,617,559
Length adjustment: 102
Effective length of query: 245
Effective length of database: 12,553,887
Effective search space: 3075702315
Effective search space used: 3075702315
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-013431
(1043 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_789782.1| charged multivesicular body protein 4b [Homo sa... 91 2e-18
Alignment gi|NP_054888.2| charged multivesicular body protein 4a [Homo sa... 72 1e-12
Alignment gi|NP_689497.1| charged multivesicular body protein 4c [Homo sa... 70 4e-12
>ref|NP_789782.1| charged multivesicular body protein 4b [Homo sapiens].
Length = 224
Score = 90.9 bits (224), Expect = 2e-18
Identities = 45/47 (95%), Positives = 45/47 (95%)
Frame = +3
Query: 210 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRGEL 350
PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKR L
Sbjct: 20 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRAAL 66
>ref|NP_054888.2| charged multivesicular body protein 4a [Homo sapiens].
Length = 265
Score = 71.6 bits (174), Expect = 1e-12
Identities = 33/47 (70%), Positives = 42/47 (89%)
Frame = +3
Query: 210 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRGEL 350
PTP+EAIQ+L++TE++L KKQEFLE+KI+QEL AKK+GTKNKR L
Sbjct: 60 PTPEEAIQKLKETEKILIKKQEFLEQKIQQELQTAKKYGTKNKRAAL 106
>ref|NP_689497.1| charged multivesicular body protein 4c [Homo sapiens].
Length = 233
Score = 69.7 bits (169), Expect = 4e-12
Identities = 31/47 (65%), Positives = 40/47 (85%)
Frame = +3
Query: 210 PTPQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKRGEL 350
P+PQEA+ RLR+TEEML KKQE+LE +I++E+ AKKHGT+NKR L
Sbjct: 20 PSPQEALVRLRETEEMLGKKQEYLENRIQREIALAKKHGTQNKRAAL 66
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: 33,626,908
Number of extensions: 879762
Number of successful extensions: 4013
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 3990
Number of HSP's successfully gapped: 3
Length of query: 347
Length of database: 18,297,164
Length adjustment: 103
Effective length of query: 244
Effective length of database: 14,901,872
Effective search space: 3636056768
Effective search space used: 3636056768
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 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-013431
(1043 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_Chr17 1647 0.0
>Sscrofa_Chr17
|| Length = 69701581
Score = 1647 bits (831), Expect = 0.0
Identities = 837/839 (99%)
Strand = Plus / Plus
Query: 1 ctgtgggaggtggctcggccgggcccagctgcggggcggaggtggcgaagaggcctgcgg 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42214650 ctgtgggaggtggctcggccgggcccagctgcggggcggaggtggcgaagaggcctgcgg 42214709
Query: 61 cggcagggagcagcagggctgggagcaggcgccggaaccgagccgagccgagccgaagcg 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42214710 cggcagggagcagcagggctgggagcaggcgccggaaccgagccgagccgagccgaagcg 42214769
Query: 121 ggcggcgcaggccggcgcggcgagcagcaaccatgtcggtgtttgggaagctgttcgggg 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42214770 ggcggcgcaggccggcgcggcgagcagcaaccatgtcggtgtttgggaagctgttcgggg 42214829
Query: 181 ctggagggggtaaggccggcaagggcggcccgaccccccaggaggccatccagagactgc 240
|||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct: 42214830 ctggagggggtaaggccggcgagggcggcccgaccccccaggaggccatccagagactgc 42214889
Query: 241 gggacacagaggagatgctaagtaagaaacaggaattcctggagaagaagatcgaacagg 300
||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42214890 gggacacagaggatatgctaagtaagaaacaggaattcctggagaagaagatcgaacagg 42214949
Query: 301 aactgacggccgccaagaagcacggcactaaaaacaagcgcggtgagttggcccggcccc 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42214950 aactgacggccgccaagaagcacggcactaaaaacaagcgcggtgagttggcccggcccc 42215009
Query: 361 ctcagacttccctggcctggactccaccttcgccagactcgcgctagtgtttgctcggat 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42215010 ctcagacttccctggcctggactccaccttcgccagactcgcgctagtgtttgctcggat 42215069
Query: 421 cctggacctcttacccggtcagactcccttcagtgtcgccccctggacttcttcattaga 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42215070 cctggacctcttacccggtcagactcccttcagtgtcgccccctggacttcttcattaga 42215129
Query: 481 ctgtcattccagccctcttctcccaggctctccccactctgccaggccctttcagaccct 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42215130 ctgtcattccagccctcttctcccaggctctccccactctgccaggccctttcagaccct 42215189
Query: 541 cgtttcacagcacttccttcgtcctcactctgttcctttctcctccacatttccccctcc 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42215190 cgtttcacagcacttccttcgtcctcactctgttcctttctcctccacatttccccctcc 42215249
Query: 601 ctctggtctgtcctcacccagcttcccagatactgccgccgcctccttcttgtctccttt 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42215250 ctctggtctgtcctcacccagcttcccagatactgccgccgcctccttcttgtctccttt 42215309
Query: 661 ctgccctccattctaacacttgtgtccttcctgtcccactcctaccctctgccaacccct 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42215310 ctgccctccattctaacacttgtgtccttcctgtcccactcctaccctctgccaacccct 42215369
Query: 721 ctggggaatccatgagctgtccctggcctctctccccatccccctgactcagaattctcc 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42215370 ctggggaatccatgagctgtccctggcctctctccccatccccctgactcagaattctcc 42215429
Query: 781 tttagaagcctcctgaatggagagaaaaaggaactgggaggagaggaggtcccctgttc 839
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 42215430 tttagaagcctcctgaatggagagaaaaaggaactgggaggagaggaggtcccctgttc 42215488
Score = 151 bits (76), Expect = 9e-34
Identities = 90/92 (97%), Gaps = 2/92 (2%)
Strand = Plus / Plus
Query: 953 acctctggtttcc-tcataaccaggttttatcagagtttcacgtagcgcaagccttcacg 1011
||||||||||||| ||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct: 42215602 acctctggtttccctcataac-aggttttatcagagtttcacgtagcgcaagccttcacg 42215660
Query: 1012 cggtgactcacggcttcctgatcccggtgtac 1043
||||||||||||||||||||||||||||||||
Sbjct: 42215661 cggtgactcacggcttcctgatcccggtgtac 42215692
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: 27,396,748
Number of extensions: 362
Number of successful extensions: 362
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 362
Number of HSP's successfully gapped: 2
Length of query: 1043
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1022
Effective length of database: 2,808,413,156
Effective search space: 2870198245432
Effective search space used: 2870198245432
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)