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-002770
(1020 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_001029722.1| charged multivesicular body protein 2a [Bos ... 297 1e-80
Alignment gi|NP_001030549.1| charged multivesicular body protein 2b [Bos ... 85 1e-16
Alignment gi|NP_001014904.1| charged multivesicular body protein 1b [Bos ... 71 2e-12
Alignment gi|NP_001030223.2| charged multivesicular body protein 3 [Bos t... 64 3e-10
Alignment gi|NP_001178189.1| chromatin modifying protein 1A-like [Bos tau... 59 7e-09
>ref|NP_001029722.1| charged multivesicular body protein 2a [Bos taurus].
Length = 222
Score = 297 bits (760), Expect = 1e-80
Identities = 167/222 (75%), Positives = 167/222 (75%)
Frame = +3
Query: 213 MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVR 392
MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQE QGQMDAVR
Sbjct: 1 MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEKKIIADIKKMAKQGQMDAVR 60
Query: 393 IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP 572
IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP
Sbjct: 61 IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP 120
Query: 573 QIQKIMMEFERQAEIMDMKEEMMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELS 752
QIQKIMMEFERQAEIMDMKEEMMN VVAQVLDELGLSLTDELS
Sbjct: 121 QIQKIMMEFERQAEIMDMKEEMMNDAIDDAMGDEDDEEESDAVVAQVLDELGLSLTDELS 180
Query: 753 NLPSTGGSLXXXXXXXXXXXXXXXXXXXXXXXXXRLKNLRRD 878
NLPSTGGSL RLKNLRRD
Sbjct: 181 NLPSTGGSLSVAAGGKKAEATASALVDADADLEERLKNLRRD 222
>ref|NP_001030549.1| charged multivesicular body protein 2b [Bos taurus].
Length = 213
Score = 84.7 bits (208), Expect = 1e-16
Identities = 47/183 (25%), Positives = 89/183 (48%)
Frame = +3
Query: 231 RRKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDL 410
++KT ++++++ R L R + R+R LE QE G +A R++AK L
Sbjct: 6 KKKTVDDVIKEQNRELRGTQRAIIRDRAALEKQEKQLELEIKKMAKIGNKEACRVLAKQL 65
Query: 411 VRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIM 590
V R+ + + + + ++S + + + S MA AM K M +N+++ + + M
Sbjct: 66 VHLRKQKTRTFAVSSKVTSMSTQTKVMNSQMKMAGAMSTTAKTMQAVNKKMDPQKTLQTM 125
Query: 591 MEFERQAEIMDMKEEMMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELSNLPSTG 770
F+++ M+M EEM+N +V QVLDE+G+ ++ +++ PS
Sbjct: 126 QNFQKENMKMEMTEEMINDTLDDIFDGSDDEEESQDIVNQVLDEIGIEISGKMAKAPSAA 185
Query: 771 GSL 779
SL
Sbjct: 186 RSL 188
>ref|NP_001014904.1| charged multivesicular body protein 1b [Bos taurus].
Length = 199
Score = 70.9 bits (172), Expect = 2e-12
Identities = 41/158 (25%), Positives = 74/158 (46%)
Frame = +3
Query: 276 LNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDLVRTRRYVRKFVLMRA 455
L A +EL R +K + +E +G M+ RI A++ +R + F+ M A
Sbjct: 11 LKFAAKELGRSAKKCDKEEKAEKAKIKKAIQKGNMEVARIHAENAIRQKNQAVNFLRMSA 70
Query: 456 NIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIMDMKEE 635
+ AV+ ++QT + + ++M GV K+M + + L +I +M +FE Q E +D++ +
Sbjct: 71 RVDAVAARVQTAVTMGKVTKSMAGVVKSMDATLKTMNLEKISALMDKFEHQFETLDVQTQ 130
Query: 636 MMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDEL 749
M ++ ++ DE GL L EL
Sbjct: 131 QMEDTMSSTTTLTTPQGQVDMLLQEMADEAGLDLNMEL 168
>ref|NP_001030223.2| charged multivesicular body protein 3 [Bos taurus].
Length = 222
Score = 63.5 bits (153), Expect = 3e-10
Identities = 36/142 (25%), Positives = 76/142 (53%), Gaps = 2/142 (1%)
Frame = +3
Query: 222 LFGR--RKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRI 395
LFG+ K P+EL+ + + + MR +DR+ + ++ +E +GQ D +
Sbjct: 3 LFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCVV 62
Query: 396 MAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQ 575
+AK+++R+R+ V K +A++ +V + ++ + +A +++ T+ M M +K+P+
Sbjct: 63 LAKEMIRSRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPE 122
Query: 576 IQKIMMEFERQAEIMDMKEEMM 641
IQ M E ++ + EEM+
Sbjct: 123 IQATMRELSKEMMKAGIIEEML 144
>ref|NP_001178189.1| chromatin modifying protein 1A-like [Bos taurus].
Length = 196
Score = 58.9 bits (141), Expect = 7e-09
Identities = 34/157 (21%), Positives = 71/157 (45%)
Frame = +3
Query: 291 RELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDLVRTRRYVRKFVLMRANIQAV 470
++L++ +K E Q ++ R+ A++ +R + ++ M + + AV
Sbjct: 13 KQLEKLAKKAEKDSKAEQAKVKKALQQKNVECARVYAENAIRKKNEGVNWLRMASRVDAV 72
Query: 471 SLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIMDMKEEMMNXX 650
+ K+QT + + + M VTKA+ + L ++ +M FE+Q + +D+ +M
Sbjct: 73 ASKVQTAVTMKGVTKNMAQVTKALDRALSTMDLQKVSAVMDRFEQQVQNLDVHTSVMEDS 132
Query: 651 XXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELSNLP 761
++ Q+ +E GL + D+LS LP
Sbjct: 133 MSSATTLTTPQEQVDSLILQIAEENGLEVLDQLSQLP 169
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: 32,155,452
Number of extensions: 925952
Number of successful extensions: 6080
Number of sequences better than 1.0e-05: 5
Number of HSP's gapped: 5984
Number of HSP's successfully gapped: 5
Length of query: 340
Length of database: 17,681,374
Length adjustment: 103
Effective length of query: 237
Effective length of database: 14,273,310
Effective search space: 3382774470
Effective search space used: 3382774470
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 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-002770
(1020 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_533565.1| PREDICTED: similar to putative breast adenocarc... 296 3e-80
Alignment gi|XP_850536.1| PREDICTED: similar to putative breast adenocarc... 296 3e-80
Alignment gi|XP_861688.1| PREDICTED: similar to putative breast adenocarc... 251 1e-66
Alignment gi|XP_544799.2| PREDICTED: similar to chromatin modifying prote... 88 1e-17
Alignment gi|XP_532972.2| PREDICTED: similar to vacuolar protein sorting ... 64 3e-10
Alignment gi|XP_546776.2| PREDICTED: similar to Chromatin modifying prote... 57 2e-08
>ref|XP_533565.1| PREDICTED: similar to putative breast adenocarcinoma marker isoform
1 [Canis familiaris].
Length = 222
Score = 296 bits (757), Expect = 3e-80
Identities = 166/222 (74%), Positives = 167/222 (75%)
Frame = +3
Query: 213 MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVR 392
MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQE QGQMDAVR
Sbjct: 1 MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEKKIIADIKKMAKQGQMDAVR 60
Query: 393 IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP 572
IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP
Sbjct: 61 IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP 120
Query: 573 QIQKIMMEFERQAEIMDMKEEMMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELS 752
QIQKIMMEFERQAEIMDMKEEMMN VV+QVLDELGLSLTDELS
Sbjct: 121 QIQKIMMEFERQAEIMDMKEEMMNDAIDDAMGDEEDEEESDAVVSQVLDELGLSLTDELS 180
Query: 753 NLPSTGGSLXXXXXXXXXXXXXXXXXXXXXXXXXRLKNLRRD 878
NLPSTGGSL RLKNLRRD
Sbjct: 181 NLPSTGGSLSVAASGKKAEAAASALVDADADLEERLKNLRRD 222
>ref|XP_850536.1| PREDICTED: similar to putative breast adenocarcinoma marker isoform
2 [Canis familiaris].
Length = 222
Score = 296 bits (757), Expect = 3e-80
Identities = 166/222 (74%), Positives = 167/222 (75%)
Frame = +3
Query: 213 MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVR 392
MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQE QGQMDAVR
Sbjct: 1 MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEKKIIADIKKMAKQGQMDAVR 60
Query: 393 IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP 572
IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP
Sbjct: 61 IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP 120
Query: 573 QIQKIMMEFERQAEIMDMKEEMMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELS 752
QIQKIMMEFERQAEIMDMKEEMMN VV+QVLDELGLSLTDELS
Sbjct: 121 QIQKIMMEFERQAEIMDMKEEMMNDAIDDAMGDEEDEEESDAVVSQVLDELGLSLTDELS 180
Query: 753 NLPSTGGSLXXXXXXXXXXXXXXXXXXXXXXXXXRLKNLRRD 878
NLPSTGGSL RLKNLRRD
Sbjct: 181 NLPSTGGSLSVAASGKKAEAAASALVDADADLEERLKNLRRD 222
>ref|XP_861688.1| PREDICTED: similar to putative breast adenocarcinoma marker isoform
3 [Canis familiaris].
Length = 204
Score = 251 bits (640), Expect = 1e-66
Identities = 148/222 (66%), Positives = 149/222 (67%)
Frame = +3
Query: 213 MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVR 392
MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQE QGQMDAVR
Sbjct: 1 MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEKKIIADIKKMAKQGQMDAVR 60
Query: 393 IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP 572
IMAKDL AVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP
Sbjct: 61 IMAKDL------------------AVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP 102
Query: 573 QIQKIMMEFERQAEIMDMKEEMMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELS 752
QIQKIMMEFERQAEIMDMKEEMMN VV+QVLDELGLSLTDELS
Sbjct: 103 QIQKIMMEFERQAEIMDMKEEMMNDAIDDAMGDEEDEEESDAVVSQVLDELGLSLTDELS 162
Query: 753 NLPSTGGSLXXXXXXXXXXXXXXXXXXXXXXXXXRLKNLRRD 878
NLPSTGGSL RLKNLRRD
Sbjct: 163 NLPSTGGSLSVAASGKKAEAAASALVDADADLEERLKNLRRD 204
>ref|XP_544799.2| PREDICTED: similar to chromatin modifying protein 2B [Canis
familiaris].
Length = 793
Score = 88.2 bits (217), Expect = 1e-17
Identities = 53/198 (26%), Positives = 96/198 (48%)
Frame = +3
Query: 186 QAHRWAPAAMDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXX 365
+A R P M LF ++KT ++++++ R L R + R+R LE QE
Sbjct: 572 RAARARPLTMASLF-KKKTVDDVIKEQNRELRGTQRAIIRDRAALEKQEKQLELEIKKMA 630
Query: 366 XQGQMDAVRIMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMG 545
G +A R++AK LV R+ + + + + ++S + + + S MA AM K M
Sbjct: 631 KIGNKEACRVLAKQLVHLRKQKTRTFAVSSKVTSMSTQTKVMNSQMKMAGAMSTTAKTMQ 690
Query: 546 TMNRQLKLPQIQKIMMEFERQAEIMDMKEEMMNXXXXXXXXXXXXXXXXXXVVAQVLDEL 725
+N+++ + + M F+++ M+M EEM+N +V QVLDE+
Sbjct: 691 AVNKKMDPQKTLQTMQNFQKENMKMEMTEEMINDTLDDIFDGSDDEEESQDIVNQVLDEI 750
Query: 726 GLSLTDELSNLPSTGGSL 779
G+ ++ +++ PS SL
Sbjct: 751 GIEISGKMAKAPSAARSL 768
>ref|XP_532972.2| PREDICTED: similar to vacuolar protein sorting 24 isoform 1 isoform
1 [Canis familiaris].
Length = 221
Score = 63.5 bits (153), Expect = 3e-10
Identities = 36/142 (25%), Positives = 76/142 (53%), Gaps = 2/142 (1%)
Frame = +3
Query: 222 LFGR--RKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRI 395
LFG+ K P+EL+ + + + MR +DR+ + ++ +E +GQ D +
Sbjct: 3 LFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCVV 62
Query: 396 MAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQ 575
+AK+++R+R+ V K +A++ +V + ++ + +A +++ T+ M M +K+P+
Sbjct: 63 LAKEMIRSRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPE 122
Query: 576 IQKIMMEFERQAEIMDMKEEMM 641
IQ M E ++ + EEM+
Sbjct: 123 IQATMRELSKEMMKAGIIEEML 144
>ref|XP_546776.2| PREDICTED: similar to Chromatin modifying protein 1 (Charged
multivesicular body protein 1) (CHMP1) isoform 1 [Canis
familiaris].
Length = 196
Score = 57.4 bits (137), Expect = 2e-08
Identities = 33/157 (21%), Positives = 71/157 (45%)
Frame = +3
Query: 291 RELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDLVRTRRYVRKFVLMRANIQAV 470
++L++ +K E Q ++ R+ A++ +R + ++ M + + AV
Sbjct: 13 KQLEKLAKKAEKDSKAEQAKVKKALQQKNVECARVYAENAIRKKNEGVNWLRMASRVDAV 72
Query: 471 SLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIMDMKEEMMNXX 650
+ K+QT + + + M VTKA+ + L ++ +M FE+Q + +D+ +M
Sbjct: 73 ASKVQTAVTMKGVTKNMAQVTKALDRALSTMDLQKVSAVMDRFEQQVQNLDVHTAVMEDS 132
Query: 651 XXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELSNLP 761
++ Q+ +E GL + D+L+ LP
Sbjct: 133 MSSATTLTTPQEQVDSLIMQIAEENGLEVLDQLNQLP 169
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: 33,274,592
Number of extensions: 901566
Number of successful extensions: 5891
Number of sequences better than 1.0e-05: 6
Number of HSP's gapped: 5822
Number of HSP's successfully gapped: 6
Length of query: 340
Length of database: 18,874,504
Length adjustment: 103
Effective length of query: 237
Effective length of database: 15,440,896
Effective search space: 3659492352
Effective search space used: 3659492352
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-002770
(1020 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_940818.1| charged multivesicular body protein 2a [Homo sa... 296 3e-80
Alignment gi|NP_055268.1| charged multivesicular body protein 2a [Homo sa... 296 3e-80
Alignment gi|NP_054762.2| charged multivesicular body protein 2b [Homo sa... 84 3e-16
Alignment gi|NP_065145.2| charged multivesicular body protein 1b [Homo sa... 71 1e-12
Alignment gi|NP_057163.1| charged multivesicular body protein 3 isoform 1... 64 3e-10
Alignment gi|NP_002759.2| charged multivesicular body protein 1a isoform ... 59 5e-09
Alignment gi|NP_001185883.1| RNF103-VPS24 fusion protein [Homo sapiens]. 56 5e-08
>ref|NP_940818.1| charged multivesicular body protein 2a [Homo sapiens].
Length = 222
Score = 296 bits (757), Expect = 3e-80
Identities = 166/222 (74%), Positives = 167/222 (75%)
Frame = +3
Query: 213 MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVR 392
MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQE QGQMDAVR
Sbjct: 1 MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEKKIIADIKKMAKQGQMDAVR 60
Query: 393 IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP 572
IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP
Sbjct: 61 IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP 120
Query: 573 QIQKIMMEFERQAEIMDMKEEMMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELS 752
QIQKIMMEFERQAEIMDMKEEMMN VV+QVLDELGLSLTDELS
Sbjct: 121 QIQKIMMEFERQAEIMDMKEEMMNDAIDDAMGDEEDEEESDAVVSQVLDELGLSLTDELS 180
Query: 753 NLPSTGGSLXXXXXXXXXXXXXXXXXXXXXXXXXRLKNLRRD 878
NLPSTGGSL RLKNLRRD
Sbjct: 181 NLPSTGGSLSVAAGGKKAEAAASALADADADLEERLKNLRRD 222
>ref|NP_055268.1| charged multivesicular body protein 2a [Homo sapiens].
Length = 222
Score = 296 bits (757), Expect = 3e-80
Identities = 166/222 (74%), Positives = 167/222 (75%)
Frame = +3
Query: 213 MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVR 392
MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQE QGQMDAVR
Sbjct: 1 MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEKKIIADIKKMAKQGQMDAVR 60
Query: 393 IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP 572
IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP
Sbjct: 61 IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP 120
Query: 573 QIQKIMMEFERQAEIMDMKEEMMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELS 752
QIQKIMMEFERQAEIMDMKEEMMN VV+QVLDELGLSLTDELS
Sbjct: 121 QIQKIMMEFERQAEIMDMKEEMMNDAIDDAMGDEEDEEESDAVVSQVLDELGLSLTDELS 180
Query: 753 NLPSTGGSLXXXXXXXXXXXXXXXXXXXXXXXXXRLKNLRRD 878
NLPSTGGSL RLKNLRRD
Sbjct: 181 NLPSTGGSLSVAAGGKKAEAAASALADADADLEERLKNLRRD 222
>ref|NP_054762.2| charged multivesicular body protein 2b [Homo sapiens].
Length = 213
Score = 83.6 bits (205), Expect = 3e-16
Identities = 46/183 (25%), Positives = 89/183 (48%)
Frame = +3
Query: 231 RRKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDL 410
++KT ++++++ R L R + R+R LE QE G +A +++AK L
Sbjct: 6 KKKTVDDVIKEQNRELRGTQRAIIRDRAALEKQEKQLELEIKKMAKIGNKEACKVLAKQL 65
Query: 411 VRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIM 590
V R+ + + + + ++S + + + S MA AM K M +N+++ + + M
Sbjct: 66 VHLRKQKTRTFAVSSKVTSMSTQTKVMNSQMKMAGAMSTTAKTMQAVNKKMDPQKTLQTM 125
Query: 591 MEFERQAEIMDMKEEMMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELSNLPSTG 770
F+++ M+M EEM+N +V QVLDE+G+ ++ +++ PS
Sbjct: 126 QNFQKENMKMEMTEEMINDTLDDIFDGSDDEEESQDIVNQVLDEIGIEISGKMAKAPSAA 185
Query: 771 GSL 779
SL
Sbjct: 186 RSL 188
>ref|NP_065145.2| charged multivesicular body protein 1b [Homo sapiens].
Length = 199
Score = 71.2 bits (173), Expect = 1e-12
Identities = 41/158 (25%), Positives = 74/158 (46%)
Frame = +3
Query: 276 LNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDLVRTRRYVRKFVLMRA 455
L A +EL R +K + +E +G M+ RI A++ +R + F+ M A
Sbjct: 11 LKFAAKELSRSAKKCDKEEKAEKAKIKKAIQKGNMEVARIHAENAIRQKNQAVNFLRMSA 70
Query: 456 NIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIMDMKEE 635
+ AV+ ++QT + + ++M GV K+M + + L +I +M +FE Q E +D++ +
Sbjct: 71 RVDAVAARVQTAVTMGKVTKSMAGVVKSMDATLKTMNLEKISALMDKFEHQFETLDVQTQ 130
Query: 636 MMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDEL 749
M ++ ++ DE GL L EL
Sbjct: 131 QMEDTMSSTTTLTTPQNQVDMLLQEMADEAGLDLNMEL 168
>ref|NP_057163.1| charged multivesicular body protein 3 isoform 1 [Homo sapiens].
Length = 222
Score = 63.5 bits (153), Expect = 3e-10
Identities = 36/142 (25%), Positives = 76/142 (53%), Gaps = 2/142 (1%)
Frame = +3
Query: 222 LFGR--RKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRI 395
LFG+ K P+EL+ + + + MR +DR+ + ++ +E +GQ D +
Sbjct: 3 LFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCIV 62
Query: 396 MAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQ 575
+AK+++R+R+ V K +A++ +V + ++ + +A +++ T+ M M +K+P+
Sbjct: 63 LAKEMIRSRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPE 122
Query: 576 IQKIMMEFERQAEIMDMKEEMM 641
IQ M E ++ + EEM+
Sbjct: 123 IQATMRELSKEMMKAGIIEEML 144
>ref|NP_002759.2| charged multivesicular body protein 1a isoform 2 [Homo sapiens].
Length = 196
Score = 59.3 bits (142), Expect = 5e-09
Identities = 34/157 (21%), Positives = 71/157 (45%)
Frame = +3
Query: 291 RELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDLVRTRRYVRKFVLMRANIQAV 470
++L++ +K E Q ++ R+ A++ +R + ++ M + + AV
Sbjct: 13 KQLEKLAKKAEKDSKAEQAKVKKALLQKNVECARVYAENAIRKKNEGVNWLRMASRVDAV 72
Query: 471 SLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIMDMKEEMMNXX 650
+ K+QT + + + M VTKA+ + L ++ +M FE+Q + +D+ +M
Sbjct: 73 ASKVQTAVTMKGVTKNMAQVTKALDKALSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDS 132
Query: 651 XXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELSNLP 761
++ Q+ +E GL + D+LS LP
Sbjct: 133 MSSATTLTTPQEQVDSLIMQIAEENGLEVLDQLSQLP 169
>ref|NP_001185883.1| RNF103-VPS24 fusion protein [Homo sapiens].
Length = 251
Score = 56.2 bits (134), Expect = 5e-08
Identities = 31/129 (24%), Positives = 69/129 (53%)
Frame = +3
Query: 255 LRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDLVRTRRYVR 434
+R+ R ++R +R++ RE +K++ +GQ D ++AK+++R+R+ V
Sbjct: 52 IRKEMRVVDRQIRDIQREEEKVKRS-------VKDAAKKGQKDVCIVLAKEMIRSRKAVS 104
Query: 435 KFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAE 614
K +A++ +V + ++ + +A +++ T+ M M +K+P+IQ M E ++
Sbjct: 105 KLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMRELSKEMM 164
Query: 615 IMDMKEEMM 641
+ EEM+
Sbjct: 165 KAGIIEEML 173
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: 32,457,260
Number of extensions: 869774
Number of successful extensions: 5859
Number of sequences better than 1.0e-05: 7
Number of HSP's gapped: 5744
Number of HSP's successfully gapped: 7
Length of query: 340
Length of database: 18,297,164
Length adjustment: 103
Effective length of query: 237
Effective length of database: 14,901,872
Effective search space: 3531743664
Effective search space used: 3531743664
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-002770
(1020 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_081161.1| charged multivesicular body protein 2a [Mus mus... 296 2e-80
Alignment gi|NP_081155.1| charged multivesicular body protein 2b [Mus mus... 85 1e-16
Alignment gi|NP_080197.2| charged multivesicular body protein 1b-2 [Mus m... 71 2e-12
Alignment gi|NP_077152.1| charged multivesicular body protein 1b-1 [Mus m... 71 2e-12
Alignment gi|NP_080059.2| charged multivesicular body protein 3 [Mus musc... 62 7e-10
Alignment gi|NP_663581.1| charged multivesicular body protein 1a [Mus mus... 59 5e-09
>ref|NP_081161.1| charged multivesicular body protein 2a [Mus musculus].
Length = 222
Score = 296 bits (757), Expect = 2e-80
Identities = 166/222 (74%), Positives = 167/222 (75%)
Frame = +3
Query: 213 MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVR 392
MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQE QGQMDAVR
Sbjct: 1 MDLLFGRRKTPEELLRQNQRALNRAMRELDRERQKLETQEKKIIADIKKMAKQGQMDAVR 60
Query: 393 IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP 572
IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP
Sbjct: 61 IMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLP 120
Query: 573 QIQKIMMEFERQAEIMDMKEEMMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELS 752
QIQKIMMEFERQAEIMDMKEEMMN VV+QVLDELGLSLTDELS
Sbjct: 121 QIQKIMMEFERQAEIMDMKEEMMNDAIDDAMGDEEDEEESDAVVSQVLDELGLSLTDELS 180
Query: 753 NLPSTGGSLXXXXXXXXXXXXXXXXXXXXXXXXXRLKNLRRD 878
NLPSTGGSL RLKNLRRD
Sbjct: 181 NLPSTGGSLSVAAGGKKAEATASALADADADLEERLKNLRRD 222
>ref|NP_081155.1| charged multivesicular body protein 2b [Mus musculus].
Length = 213
Score = 84.7 bits (208), Expect = 1e-16
Identities = 47/183 (25%), Positives = 89/183 (48%)
Frame = +3
Query: 231 RRKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDL 410
++KT ++++++ R L R + R+R LE QE G +A R++AK L
Sbjct: 6 KKKTVDDVIKEQNRELRGTQRAIIRDRAALEKQEKQLELEIKKMAKIGNKEACRVLAKQL 65
Query: 411 VRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIM 590
V R+ + + + + ++S + + + S MA AM K M +N+++ + + M
Sbjct: 66 VHLRKQKTRTFAVSSKVTSMSTQTKVMNSQMKMAGAMSTTAKTMQAVNKKMDPQKTLQTM 125
Query: 591 MEFERQAEIMDMKEEMMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELSNLPSTG 770
F+++ M+M EEM+N +V QVLDE+G+ ++ +++ PS
Sbjct: 126 QNFQKENMKMEMTEEMINDTLDDIFDGSDDEEESQDIVNQVLDEIGIEISGKMAKAPSAA 185
Query: 771 GSL 779
SL
Sbjct: 186 RSL 188
>ref|NP_080197.2| charged multivesicular body protein 1b-2 [Mus musculus].
Length = 199
Score = 70.9 bits (172), Expect = 2e-12
Identities = 41/158 (25%), Positives = 74/158 (46%)
Frame = +3
Query: 276 LNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDLVRTRRYVRKFVLMRA 455
L A +EL+R +K + +E +G + RI A++ +R + F+ M A
Sbjct: 11 LKFAAKELNRNAKKCDKEEKAEKAKIKKAIQKGNTEVARIHAENAIRQKNQAINFLRMSA 70
Query: 456 NIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIMDMKEE 635
+ AV+ ++QT + + ++M GV K+M R + L +I +M +FE Q E +D++ +
Sbjct: 71 RVDAVAARVQTAVTMGKVTKSMAGVVKSMDATLRSMNLEKISALMDKFEHQFETLDVQTQ 130
Query: 636 MMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDEL 749
M ++ ++ DE GL L EL
Sbjct: 131 QMEDTMSSTTTLTTPQNQVDMLLQEMADEAGLDLNMEL 168
>ref|NP_077152.1| charged multivesicular body protein 1b-1 [Mus musculus].
Length = 199
Score = 70.9 bits (172), Expect = 2e-12
Identities = 41/158 (25%), Positives = 75/158 (47%)
Frame = +3
Query: 276 LNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDLVRTRRYVRKFVLMRA 455
L A +EL+R +K + +E +G M+ RI A++ +R + F+ M A
Sbjct: 11 LKFAAKELNRSSKKCDKEEKAEKAKIKKAIQKGNMEVARIHAENAIRQKNQGVNFLRMSA 70
Query: 456 NIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIMDMKEE 635
+ AV+ ++QT + + ++M GV K+M + + L +I +M +FE Q E +D++ +
Sbjct: 71 RVDAVAARVQTAVTMGKVTKSMAGVVKSMDATLKSMNLEKISALMDKFEHQFETLDVQTQ 130
Query: 636 MMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDEL 749
M ++ ++ DE GL L EL
Sbjct: 131 QMEDTMSSTTTLTTPQNQVDMLLQEMADEAGLDLNMEL 168
>ref|NP_080059.2| charged multivesicular body protein 3 [Mus musculus].
Length = 224
Score = 62.0 bits (149), Expect = 7e-10
Identities = 35/142 (24%), Positives = 76/142 (53%), Gaps = 2/142 (1%)
Frame = +3
Query: 222 LFGR--RKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRI 395
LFG+ K P+EL+ + + + MR +DR+ + ++ +E +GQ + +
Sbjct: 3 LFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKEVCVV 62
Query: 396 MAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQ 575
+AK+++R+R+ V K +A++ +V + ++ + +A +++ T+ M M +K+P+
Sbjct: 63 LAKEMIRSRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPE 122
Query: 576 IQKIMMEFERQAEIMDMKEEMM 641
IQ M E ++ + EEM+
Sbjct: 123 IQATMRELSKEMMKAGIIEEML 144
>ref|NP_663581.1| charged multivesicular body protein 1a [Mus musculus].
Length = 196
Score = 59.3 bits (142), Expect = 5e-09
Identities = 34/157 (21%), Positives = 71/157 (45%)
Frame = +3
Query: 291 RELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDLVRTRRYVRKFVLMRANIQAV 470
++L++ +K E Q ++ R+ A++ +R + ++ M + + AV
Sbjct: 13 KQLEKLAKKAEKDSKAEQAKVKKALQQKNVECARVYAENAIRKKNEGVNWLRMASRVDAV 72
Query: 471 SLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIMDMKEEMMNXX 650
+ K+QT + + + M VTKA+ + L ++ +M FE+Q + +D+ +M
Sbjct: 73 ASKVQTAVTMKGVTKNMAQVTKALDKALSAMDLQKVSAVMDRFEQQVQNLDVHTSVMEDS 132
Query: 651 XXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELSNLP 761
++ Q+ +E GL + D+LS LP
Sbjct: 133 VSSATTLTTPQEQVDSLIVQIAEENGLEVLDQLSQLP 169
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: 27,157,308
Number of extensions: 708685
Number of successful extensions: 4333
Number of sequences better than 1.0e-05: 6
Number of HSP's gapped: 4261
Number of HSP's successfully gapped: 6
Length of query: 340
Length of database: 15,617,559
Length adjustment: 102
Effective length of query: 238
Effective length of database: 12,553,887
Effective search space: 2987825106
Effective search space used: 2987825106
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-002770
(1020 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_003361783.1| PREDICTED: charged multivesicular body prote... 217 9e-57
Alignment gi|XP_003132778.1| PREDICTED: charged multivesicular body prote... 85 7e-17
Alignment gi|XP_003356398.1| PREDICTED: charged multivesicular body prote... 71 1e-12
Alignment gi|XP_003354782.1| PREDICTED: charged multivesicular body prote... 64 2e-10
Alignment gi|NP_001230289.1| chromatin modifying protein 1A [Sus scrofa]. 59 4e-09
Alignment gi|XP_003125011.2| PREDICTED: charged multivesicular body prote... 56 3e-08
Alignment gi|XP_003354783.1| PREDICTED: charged multivesicular body prote... 54 1e-07
>ref|XP_003361783.1| PREDICTED: charged multivesicular body protein 2a-like, partial
[Sus scrofa].
Length = 177
Score = 217 bits (552), Expect = 9e-57
Identities = 123/166 (74%), Positives = 123/166 (74%)
Frame = +3
Query: 381 DAVRIMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQ 560
DAVRIMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQ
Sbjct: 12 DAVRIMAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQ 71
Query: 561 LKLPQIQKIMMEFERQAEIMDMKEEMMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLT 740
LKLPQIQKIMMEFERQAEIMDMKEEMMN VVAQVLDELGLSLT
Sbjct: 72 LKLPQIQKIMMEFERQAEIMDMKEEMMNDAIDDAMGDEEDEEESDAVVAQVLDELGLSLT 131
Query: 741 DELSNLPSTGGSLXXXXXXXXXXXXXXXXXXXXXXXXXRLKNLRRD 878
DELSNLPSTGGSL RLKNLRRD
Sbjct: 132 DELSNLPSTGGSLSVAASGKKAEAAASALVDADADLEERLKNLRRD 177
>ref|XP_003132778.1| PREDICTED: charged multivesicular body protein 2b-like [Sus
scrofa].
Length = 213
Score = 84.7 bits (208), Expect = 7e-17
Identities = 47/183 (25%), Positives = 89/183 (48%)
Frame = +3
Query: 231 RRKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDL 410
++KT ++++++ R L R + R+R LE QE G +A R++AK L
Sbjct: 6 KKKTVDDVIKEQNRELRGTQRAIIRDRAALEKQEKQLELEIKKMAKIGNKEACRVLAKQL 65
Query: 411 VRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIM 590
V R+ + + + + ++S + + + S MA AM K M +N+++ + + M
Sbjct: 66 VHLRKQKTRTFAVSSKVTSMSTQTKVMNSQMKMAGAMSTTAKTMQAVNKKMDPQKTLQTM 125
Query: 591 MEFERQAEIMDMKEEMMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELSNLPSTG 770
F+++ M+M EEM+N +V QVLDE+G+ ++ +++ PS
Sbjct: 126 QNFQKENMKMEMTEEMINDTLDDIFDGSDDEEESQDIVNQVLDEIGIEISGKMAKAPSAA 185
Query: 771 GSL 779
SL
Sbjct: 186 RSL 188
>ref|XP_003356398.1| PREDICTED: charged multivesicular body protein 1b-like [Sus
scrofa].
Length = 199
Score = 70.9 bits (172), Expect = 1e-12
Identities = 41/158 (25%), Positives = 74/158 (46%)
Frame = +3
Query: 276 LNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDLVRTRRYVRKFVLMRA 455
L A +EL R +K + +E +G M+ RI A++ +R + F+ M A
Sbjct: 11 LKFAAKELGRSAKKCDKEEKAEKAKIKKAIQKGNMEVARIHAENAIRQKNQAVNFLRMSA 70
Query: 456 NIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIMDMKEE 635
+ AV+ ++QT + + ++M GV K+M + + L +I +M +FE Q E +D++ +
Sbjct: 71 RVDAVAARVQTAVTMGKVTKSMAGVVKSMDATLKTMNLEKISALMDKFEHQFETLDVQTQ 130
Query: 636 MMNXXXXXXXXXXXXXXXXXXVVAQVLDELGLSLTDEL 749
M ++ ++ DE GL L EL
Sbjct: 131 QMEDTMSSTTTLTTPQGQVDMLLQEMADEAGLDLNMEL 168
>ref|XP_003354782.1| PREDICTED: charged multivesicular body protein 3-like isoform 2
[Sus scrofa].
Length = 221
Score = 63.5 bits (153), Expect = 2e-10
Identities = 36/142 (25%), Positives = 76/142 (53%), Gaps = 2/142 (1%)
Frame = +3
Query: 222 LFGR--RKTPEELLRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRI 395
LFG+ K P+EL+ + + + MR +DR+ + ++ +E +GQ D +
Sbjct: 3 LFGKTQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCVV 62
Query: 396 MAKDLVRTRRYVRKFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQ 575
+AK+++R+R+ V K +A++ +V + ++ + +A +++ T+ M M +K+P+
Sbjct: 63 LAKEMIRSRKAVSKLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPE 122
Query: 576 IQKIMMEFERQAEIMDMKEEMM 641
IQ M E ++ + EEM+
Sbjct: 123 IQATMRELSKEMMKAGIIEEML 144
>ref|NP_001230289.1| chromatin modifying protein 1A [Sus scrofa].
Length = 196
Score = 58.9 bits (141), Expect = 4e-09
Identities = 34/157 (21%), Positives = 72/157 (45%)
Frame = +3
Query: 291 RELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDLVRTRRYVRKFVLMRANIQAV 470
++L++ +K E Q ++ R+ A++ +R + ++ M + + AV
Sbjct: 13 KQLEKLAKKAEKDSKAEQAKVKKALQQKNVECARVYAENAIRKKNEGVNWLRMASRVDAV 72
Query: 471 SLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIMDMKEEMMNXX 650
+ K+QT + + + M VTKA+ + L ++ +M +FE+Q + +D+ +M
Sbjct: 73 ASKVQTAVTMKGVTKNMAQVTKALDRALSTMDLQKVSAVMDKFEQQVQNLDVHTAVMEDS 132
Query: 651 XXXXXXXXXXXXXXXXVVAQVLDELGLSLTDELSNLP 761
++ Q+ +E GL + D+LS LP
Sbjct: 133 MSSATTLTTPQEQVDSLIMQIAEENGLEVLDQLSQLP 169
>ref|XP_003125011.2| PREDICTED: charged multivesicular body protein 3-like isoform 1
[Sus scrofa].
Length = 213
Score = 56.2 bits (134), Expect = 3e-08
Identities = 31/129 (24%), Positives = 69/129 (53%)
Frame = +3
Query: 255 LRQNQRALNRAMRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDLVRTRRYVR 434
+R+ R ++R +R++ RE +K++ +GQ D ++AK+++R+R+ V
Sbjct: 15 IRKEMRVVDRQIRDIQREEEKVKRS-------VKDAAKKGQKDVCVVLAKEMIRSRKAVS 67
Query: 435 KFVLMRANIQAVSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAE 614
K +A++ +V + ++ + +A +++ T+ M M +K+P+IQ M E ++
Sbjct: 68 KLYASKAHMNSVLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMRELSKEMM 127
Query: 615 IMDMKEEMM 641
+ EEM+
Sbjct: 128 KAGIIEEML 136
>ref|XP_003354783.1| PREDICTED: charged multivesicular body protein 3-like isoform 3
[Sus scrofa].
Length = 195
Score = 53.9 bits (128), Expect = 1e-07
Identities = 29/118 (24%), Positives = 63/118 (53%)
Frame = +3
Query: 288 MRELDRERQKLETQEXXXXXXXXXXXXQGQMDAVRIMAKDLVRTRRYVRKFVLMRANIQA 467
MR +DR+ + ++ +E +GQ D ++AK+++R+R+ V K +A++ +
Sbjct: 1 MRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCVVLAKEMIRSRKAVSKLYASKAHMNS 60
Query: 468 VSLKIQTLKSNNSMAQAMKGVTKAMGTMNRQLKLPQIQKIMMEFERQAEIMDMKEEMM 641
V + ++ + +A +++ T+ M M +K+P+IQ M E ++ + EEM+
Sbjct: 61 VLMGMKNQLAVLRVAGSLQKSTEVMKAMQSLVKIPEIQATMRELSKEMMKAGIIEEML 118
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: 21,277,544
Number of extensions: 671159
Number of successful extensions: 3894
Number of sequences better than 1.0e-05: 7
Number of HSP's gapped: 3825
Number of HSP's successfully gapped: 7
Length of query: 340
Length of database: 11,343,932
Length adjustment: 100
Effective length of query: 240
Effective length of database: 8,854,232
Effective search space: 2125015680
Effective search space used: 2125015680
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-002770
(1020 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|GL895345.1| Sus scrofa unplaced genomic scaffold chrU_scaffol... 367 8e-99
gb|GL895557.1| Sus scrofa unplaced genomic scaffold chrU_scaffol... 256 2e-65
>gb|GL895345.1| Sus scrofa unplaced genomic scaffold chrU_scaffold392
Length = 986
Score = 367 bits (185), Expect = 8e-99
Identities = 185/185 (100%)
Strand = Plus / Minus
Query: 754 acctcccctccaccggaggttccctcagtgtggctgccagtgggaagaaggccgaggccg 813
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 185 acctcccctccaccggaggttccctcagtgtggctgccagtgggaagaaggccgaggccg 126
Query: 814 cagcctcggccctagttgatgcagacgcagatctggaggagcggctcaagaaccttcgaa 873
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 125 cagcctcggccctagttgatgcagacgcagatctggaggagcggctcaagaaccttcgaa 66
Query: 874 gggactgattgctccctgtgccaccccagggaaccagcagatggcccagcattttcactg 933
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 65 gggactgattgctccctgtgccaccccagggaaccagcagatggcccagcattttcactg 6
Query: 934 tacct 938
|||||
Sbjct: 5 tacct 1
Score = 359 bits (181), Expect = 2e-96
Identities = 181/181 (100%)
Strand = Plus / Minus
Query: 380 ggatgcggtgcgcatcatggcaaaagacctggtgcgcacccggcggtacgtgcgcaagtt 439
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 841 ggatgcggtgcgcatcatggcaaaagacctggtgcgcacccggcggtacgtgcgcaagtt 782
Query: 440 cgtgttgatgcgggccaacatccaggccgtgtccctcaagatccagacgctcaagtctaa 499
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 781 cgtgttgatgcgggccaacatccaggccgtgtccctcaagatccagacgctcaagtctaa 722
Query: 500 caactccatggcacaagccatgaagggcgtcaccaaggccatgggcaccatgaacagaca 559
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 721 caactccatggcacaagccatgaagggcgtcaccaaggccatgggcaccatgaacagaca 662
Query: 560 g 560
|
Sbjct: 661 g 661
Score = 266 bits (134), Expect = 2e-68
Identities = 134/134 (100%)
Strand = Plus / Minus
Query: 558 cagctcaagctgccccagatccagaagatcatgatggagtttgagcggcaggcggagatc 617
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 589 cagctcaagctgccccagatccagaagatcatgatggagtttgagcggcaggcggagatc 530
Query: 618 atggacatgaaggaggagatgatgaacgatgccatcgacgacgccatgggggacgaggag 677
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 529 atggacatgaaggaggagatgatgaacgatgccatcgacgacgccatgggggacgaggag 470
Query: 678 gacgaggaggagag 691
||||||||||||||
Sbjct: 469 gacgaggaggagag 456
Score = 127 bits (64), Expect = 1e-26
Identities = 64/64 (100%)
Strand = Plus / Minus
Query: 690 agcgatgccgtcgtggctcaggtcctggatgagctggggttgagcctgacagatgagctg 749
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 372 agcgatgccgtcgtggctcaggtcctggatgagctggggttgagcctgacagatgagctg 313
Query: 750 tcaa 753
||||
Sbjct: 312 tcaa 309
>gb|GL895557.1| Sus scrofa unplaced genomic scaffold chrU_scaffold411
Length = 1310
Score = 256 bits (129), Expect = 2e-65
Identities = 129/129 (100%)
Strand = Plus / Plus
Query: 2 ggtttaatccggaaacggcggcgacggcagaggcgacagaaccaaggggctgtggttggt 61
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1092 ggtttaatccggaaacggcggcgacggcagaggcgacagaaccaaggggctgtggttggt 1151
Query: 62 gggcgctccagggagccgagccagaggagcgtgacccggaagtggaagcgaacccccgtc 121
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1152 gggcgctccagggagccgagccagaggagcgtgacccggaagtggaagcgaacccccgtc 1211
Query: 122 ccagctccg 130
|||||||||
Sbjct: 1212 ccagctccg 1220
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: 23,896,080
Number of extensions: 292
Number of successful extensions: 292
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 292
Number of HSP's successfully gapped: 5
Length of query: 1020
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 999
Effective length of database: 2,808,413,156
Effective search space: 2805604742844
Effective search space used: 2805604742844
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)