Animal-Genome cDNA 20060611S-012985


Search to RefSeqSP

BLASTX 2.2.10 [Oct-19-2004]


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= 20060611S-012985
         (938 letters)

Database: RefSeqSP 
           1040 sequences; 434,620 total letters

Searching...done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_999143.1| beta 2-microglobulin [Sus scrofa]                    101   2e-23

>ref|NP_999143.1| beta 2-microglobulin [Sus scrofa]
          Length = 118

 Score =  101 bits (252), Expect = 2e-23
 Identities = 55/100 (55%), Positives = 66/100 (66%), Gaps = 1/100 (1%)
 Frame = +1

Query: 82  DAVARPPKVHVYSLHPPQNGKRHYLNCYVSGFHPPDIEIDLLKNGDKMKFVTTLTCLSTR 261
           DAVARPPKV VYS HP +NGK +YLNCYVSGFHPP IEIDLLKNG+KM      + LS  
Sbjct: 19  DAVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMN--AEQSDLSFS 76

Query: 262 TGLSTFWTPVTSLLTLWINIAACE-KNVTLDKPIMLGWDR 378
              S +    T      ++  +C  K+VTLDKP ++ WDR
Sbjct: 77  KDWSFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDR 116


  Database: RefSeqSP
    Posted date:  Aug 1, 2006  7:14 PM
  Number of letters in database: 434,620
  Number of sequences in database:  1040
  
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 Hits to DB: 858,228
Number of Sequences: 1040
Number of extensions: 20532
Number of successful extensions: 74
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 61
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 72
length of database: 434,620
effective HSP length: 77
effective length of database: 354,540
effective search space used: 83316900
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqBP

BLASTX 2.2.10 [Oct-19-2004]


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= 20060611S-012985
         (938 letters)

Database: RefSeqBP 
           33,508 sequences; 16,112,626 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_776318.1| beta-2-microglobulin [Bos taurus]                     92   8e-19

>ref|NP_776318.1| beta-2-microglobulin [Bos taurus]
          Length = 118

 Score = 91.7 bits (226), Expect = 8e-19
 Identities = 48/100 (48%), Positives = 65/100 (65%), Gaps = 1/100 (1%)
 Frame = +1

Query: 82  DAVARPPKVHVYSLHPPQNGKRHYLNCYVSGFHPPDIEIDLLKNGDKMKFVTTLTCLSTR 261
           DA+ RPPK+ VYS HPP++GK +YLNCYV GFHPP IEIDLLKNG+K+K  +  + LS  
Sbjct: 19  DAIQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIK--SEQSDLSFS 76

Query: 262 TGLSTFWTPVTSLLTLWINIAACE-KNVTLDKPIMLGWDR 378
              S +            +  +C  K+VTL++P ++ WDR
Sbjct: 77  KDWSFYLLSHAEFTPNSKDQYSCRVKHVTLEQPRIVKWDR 116


  Database: RefSeqBP
    Posted date:  Aug 1, 2006  7:14 PM
  Number of letters in database: 16,112,626
  Number of sequences in database:  33,508
  
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 Hits to DB: 31,642,670
Number of Sequences: 33508
Number of extensions: 767230
Number of successful extensions: 2677
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 2451
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 2674
length of database: 16,112,626
effective HSP length: 101
effective length of database: 12,728,318
effective search space used: 2685675098
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqHP

BLASTX 2.2.10 [Oct-19-2004]


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= 20060611S-012985
         (938 letters)

Database: RefSeqHP 
           39,411 sequences; 17,774,539 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_004039.1| beta-2-microglobulin precursor [Homo sapiens]         86   4e-17

>ref|NP_004039.1| beta-2-microglobulin precursor [Homo sapiens]
          Length = 119

 Score = 85.9 bits (211), Expect = 4e-17
 Identities = 46/100 (46%), Positives = 63/100 (63%), Gaps = 1/100 (1%)
 Frame = +1

Query: 82  DAVARPPKVHVYSLHPPQNGKRHYLNCYVSGFHPPDIEIDLLKNGDKMKFVTTLTCLSTR 261
           +A+ R PK+ VYS HP +NGK ++LNCYVSGFHP DIE+DLLKNG++++ V   + LS  
Sbjct: 19  EAIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEH-SDLSFS 77

Query: 262 TGLSTFWTPVTSLLTLWINIAACEKN-VTLDKPIMLGWDR 378
              S +    T       +  AC  N VTL +P ++ WDR
Sbjct: 78  KDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDR 117


  Database: RefSeqHP
    Posted date:  Aug 2, 2006 12:57 AM
  Number of letters in database: 17,774,539
  Number of sequences in database:  39,411
  
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 Hits to DB: 35,674,653
Number of Sequences: 39411
Number of extensions: 886184
Number of successful extensions: 3427
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 2928
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 3411
length of database: 17,774,539
effective HSP length: 102
effective length of database: 13,754,617
effective search space used: 2888469570
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqCP

BLASTX 2.2.10 [Oct-19-2004]


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= 20060611S-012985
         (938 letters)

Database: RefSeqCP 
           33,732 sequences; 19,266,565 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|XP_535458.1| PREDICTED: similar to beta-2-microglobulin prec...    91   2e-18
Alignment   gi|XP_850148.1| PREDICTED: similar to beta-2-microglobulin prec...    91   2e-18

>ref|XP_535458.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 2
           [Canis familiaris]
          Length = 125

 Score = 90.5 bits (223), Expect = 2e-18
 Identities = 49/104 (47%), Positives = 62/104 (59%), Gaps = 5/104 (4%)
 Frame = +1

Query: 82  DAVARPPKVHVYSLHPPQNGKRHYLNCYVSGFHPPDIEIDLLKNGDKMKFVTTLTCLSTR 261
           DAV  PPK+ VYS HP +NGK ++LNCYVSGFHPP+IEIDLLKNG +MK         T 
Sbjct: 26  DAVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMK------AEQTD 79

Query: 262 TGLSTFWTPVTSLLTLWI-----NIAACEKNVTLDKPIMLGWDR 378
              S  WT    + T +        +   K+VTL +P ++ WDR
Sbjct: 80  LSFSKDWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWDR 123


>ref|XP_850148.1| PREDICTED: similar to beta-2-microglobulin precursor isoform 3
           [Canis familiaris]
          Length = 125

 Score = 90.5 bits (223), Expect = 2e-18
 Identities = 49/104 (47%), Positives = 62/104 (59%), Gaps = 5/104 (4%)
 Frame = +1

Query: 82  DAVARPPKVHVYSLHPPQNGKRHYLNCYVSGFHPPDIEIDLLKNGDKMKFVTTLTCLSTR 261
           DAV  PPK+ VYS HP +NGK ++LNCYVSGFHPP+IEIDLLKNG +MK         T 
Sbjct: 26  DAVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPPEIEIDLLKNGKEMK------AEQTD 79

Query: 262 TGLSTFWTPVTSLLTLWI-----NIAACEKNVTLDKPIMLGWDR 378
              S  WT    + T +        +   K+VTL +P ++ WDR
Sbjct: 80  LSFSKDWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVKWDR 123


  Database: RefSeqCP
    Posted date:  Aug 1, 2006  9:25 PM
  Number of letters in database: 19,266,565
  Number of sequences in database:  33,732
  
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 Hits to DB: 37,106,906
Number of Sequences: 33732
Number of extensions: 894666
Number of successful extensions: 3203
Number of sequences better than 1.0e-05: 2
Number of HSP's better than  0.0 without gapping: 2845
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 3192
length of database: 19,266,565
effective HSP length: 103
effective length of database: 15,792,169
effective search space used: 3300563321
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)

Search to RefSeqMP

BLASTX 2.2.10 [Oct-19-2004]


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= 20060611S-012985
         (938 letters)

Database: RefSeqMP 
           45,328 sequences; 21,768,885 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_033865.2| beta-2-microglobulin [Mus musculus]                   73   4e-13

>ref|NP_033865.2| beta-2-microglobulin [Mus musculus]
          Length = 119

 Score = 73.2 bits (178), Expect = 4e-13
 Identities = 39/99 (39%), Positives = 58/99 (58%), Gaps = 1/99 (1%)
 Frame = +1

Query: 85  AVARPPKVHVYSLHPPQNGKRHYLNCYVSGFHPPDIEIDLLKNGDKMKFVTTLTCLSTRT 264
           A+ + P++ VYS HPP+NGK + LNCYV+ FHPP IEI +LKNG K+  V  ++ +S   
Sbjct: 20  AIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKV-EMSDMSFSK 78

Query: 265 GLSTFWTPVTSLLTLWINIAACE-KNVTLDKPIMLGWDR 378
             S +    T       +  AC  K+ ++ +P  + WDR
Sbjct: 79  DWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDR 117


  Database: RefSeqMP
    Posted date:  Aug 2, 2006 12:58 AM
  Number of letters in database: 21,768,885
  Number of sequences in database:  45,328
  
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 Hits to DB: 42,803,272
Number of Sequences: 45328
Number of extensions: 1038399
Number of successful extensions: 3635
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 3243
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 3627
length of database: 21,768,885
effective HSP length: 103
effective length of database: 17,100,101
effective search space used: 3573921109
frameshift window, decay const: 40,  0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)