TBLASTN 2.2.13 [Nov-27-2005]


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= gi|52630451|ref|NP_997954.2| type II iodothyronine deiodinase
[Danio rerio]
         (257 letters)

Database: /cursos/BI/genomes/project_2013/Gadus_morhua/genome.fa 
           398,859 sequences; 832,114,588 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

contig121407 dna:contig contig::contig121407:1:1277:1 REF             161   9e-39
GeneScaffold_4497 dna:genescaffold genescaffold:gadMor1:GeneScaf...   160   1e-38
GeneScaffold_2685 dna:genescaffold genescaffold:gadMor1:GeneScaf...   125   7e-28
contig152477 dna:contig contig::contig152477:1:1718:1 REF              99   4e-20
GeneScaffold_1484 dna:genescaffold genescaffold:gadMor1:GeneScaf...    60   3e-08

>contig121407 dna:contig contig::contig121407:1:1277:1 REF
          Length = 1277

 Score =  161 bits (407), Expect = 9e-39
 Identities = 91/262 (34%), Positives = 147/262 (56%), Gaps = 9/262 (3%)
 Frame = +1

Query: 1   MGLLSVDLLVTLQILPGFFSNCLFFVLYDSIVLVKRVVSLLSCSGSTG---------EWQ 51
           M L      + L +LP F    +   + D + + K+V+  +   G  G         +  
Sbjct: 52  MALALKHAALCLMLLPRFLLAAVMLWILDFLCIRKKVLLRMG-QGEGGPDDPPVCVSDSN 228

Query: 52  RMLTTAGVRSIWNSFLLDAYKQVKLGEAAPNSKVVKVTGINRCWSISGKTHNQCHLLDFE 111
           +M T   +R++W    LD +K   +G +APN++VV V           +      +LD  
Sbjct: 229 KMFTLESLRAVWYGQKLDFFKAAHVGHSAPNTEVVAV-----------QDRQTLRILDCM 375

Query: 112 SPDRPLVVNFGSATXPPFISQLPVFRRMVEEFSDVADFLLVYIDEAHPSDGWVGPPMENF 171
              RPL++NFGS + PPF+++L  FRR+  +++D+AD LLVYI+EAHPSDGWV     + 
Sbjct: 376 RGKRPLILNFGSCS*PPFMTRLAAFRRVASQYADIADSLLVYIEEAHPSDGWVS---SDA 546

Query: 172 SFEVRKHRNLEERMFAARTLLEHFSLPPQCQLVADCMDNNANIAYGVSYERVCIVQKNKI 231
            +++ KHR +E+R+ AA+ +L   S  P  Q+V D MDN++N AYG  +ER+ I++  ++
Sbjct: 547 PYQIPKHRCIEDRLRAAQLML---SEVPGSQVVIDTMDNSSNAAYGAYFERLYILRDQRV 717

Query: 232 AYLGGKGPFFYNLKDVRRWLEK 253
            Y GG+GP  Y + ++R WLE+
Sbjct: 718 VYQGGRGPEGYRISELRDWLEQ 783


>GeneScaffold_4497 dna:genescaffold genescaffold:gadMor1:GeneScaffold_4497:1:397058:1 REF
          Length = 397058

 Score =  160 bits (406), Expect = 1e-38
 Identities = 91/253 (35%), Positives = 142/253 (56%), Gaps = 10/253 (3%)
 Frame = +1

Query: 9     LVTLQILPGFFSNCLFFVLYDSIVLVKRVV---------SLLSCSGSTGEWQRMLTTAGV 59
             +V L +LP F    + F L D + + KRV            +       +  R+ T   +
Sbjct: 18622 IVCLVLLPRFLVAAVLFWLLDFLCIRKRVFFRMRPHEEGDAIDPPLCISDSNRLCTLESL 18801

Query: 60    RSIWNSFLLDAYKQVKLGEAAPNSKVVKVTGINRCWSISGKTHNQCHLLDFESPDRPLVV 119
             +++W+   LD  K  +LG  APN++VV++           +   +  +LD+   DRPL++
Sbjct: 18802 KAVWHGHKLDFLKAARLGCGAPNTEVVQL-----------RDQKRSRVLDYAQGDRPLIL 18948

Query: 120   NFGSATXPPFISQLPVFRRMVEEFSDVADFLLVYIDEAHPSDGWVGPPMENFSFEVRKHR 179
             NFGS T PPF+++L  F  +V++  DVAD+L+VYI+EAHPSDGWV     +  +++ KHR
Sbjct: 18949 NFGSCT*PPFMARLKAFHGLVQQHEDVADYLVVYIEEAHPSDGWVS---SDAPYQIPKHR 19119

Query: 180   NLEERMFAARTL-LEHFSLPPQCQLVADCMDNNANIAYGVSYERVCIVQKNKIAYLGGKG 238
              LE+R+ AA+ + LE     P C +V D M+N  N AYG  ++R+ I+   KI Y GG+G
Sbjct: 19120 CLEDRLSAAQLMRLE----VPGCAVVVDNMENATNAAYGAYFDRLYILHDGKIVYQGGRG 19287

Query: 239   PFFYNLKDVRRWL 251
             P  Y + ++R WL
Sbjct: 19288 PEGYRISELRDWL 19326


>GeneScaffold_2685 dna:genescaffold genescaffold:gadMor1:GeneScaffold_2685:1:119182:1
            REF
          Length = 119182

 Score =  125 bits (313), Expect = 7e-28
 Identities = 57/71 (80%), Positives = 63/71 (88%)
 Frame = -3

Query: 187  AARTLLEHFSLPPQCQLVADCMDNNANIAYGVSYERVCIVQKNKIAYLGGKGPFFYNLKD 246
            AAR L EHF LPPQC+LVAD MDNNAN AYGV+ ERVCIVQ+ KIAYLGGKGPFFYNLKD
Sbjct: 4454 AARRLTEHFGLPPQCRLVADSMDNNANAAYGVANERVCIVQRRKIAYLGGKGPFFYNLKD 4275

Query: 247  VRRWLEKCYGK 257
            VR+WLE+ YG+
Sbjct: 4274 VRQWLEQTYGR 4242


>contig152477 dna:contig contig::contig152477:1:1718:1 REF
          Length = 1718

 Score = 99.4 bits (246), Expect = 4e-20
 Identities = 52/77 (67%), Positives = 57/77 (74%), Gaps = 3/77 (3%)
 Frame = +3

Query: 1    MGLLSVDLLVTLQILPGFFSNCLFFVLYDSIVLVKRVVSLLSCSGST---GEWQRMLTTA 57
            MG    DLLV LQILPGFFSNCLF  LYDS++L+KR VSLL  S S    GEWQR LT+ 
Sbjct: 963  MGTGPEDLLVALQILPGFFSNCLFLALYDSVLLLKRAVSLLRASRSARGGGEWQRALTSE 1142

Query: 58   GVRSIWNSFLLDAYKQV 74
            G+RSIW  FLLDA KQV
Sbjct: 1143 GMRSIWKGFLLDANKQV 1193


>GeneScaffold_1484 dna:genescaffold genescaffold:gadMor1:GeneScaffold_1484:1:590555:1 REF
          Length = 590555

 Score = 60.1 bits (144), Expect = 3e-08
 Identities = 27/47 (57%), Positives = 38/47 (80%)
 Frame = -3

Query: 112    SPDRPLVVNFGSATXPPFISQLPVFRRMVEEFSDVADFLLVYIDEAH 158
              S +RPLV++FGS T PPF+ +L  F+ +V+++ DVADFL+VYI EAH
Sbjct: 485892 SGNRPLVLSFGSCT*PPFLFKLDEFKELVKDYRDVADFLVVYIAEAH 485752


  Database: /cursos/BI/genomes/project_2013/Gadus_morhua/genome.fa
    Posted date:  Oct 24, 2012  8:34 PM
  Number of letters in database: 832,114,588
  Number of sequences in database:  398,859
  
Lambda     K      H
   0.324    0.140    0.440 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 327,578,338
Number of Sequences: 398859
Number of extensions: 5242540
Number of successful extensions: 26176
Number of sequences better than 1.0e-04: 5
Number of HSP's better than  0.0 without gapping: 16924
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): 26168
length of query: 257
length of database: 277,371,529
effective HSP length: 119
effective length of query: 138
effective length of database: 229,907,308
effective search space: 31727208504
effective search space used: 31727208504
frameshift window, decay const: 40,  0.1
T: 13
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 114 (48.5 bits)
