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|320165142|gb|EFW42041.1| sec tRNA synthase [Capsaspora
owczarzaki ATCC 30864]
         (470 letters)

Database: N.gruberi/genome.fa 
           784 sequences; 40,964,085 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gb|GG738847.1| Naegleria gruberi genomic scaffold NAEGRscaffold_...   338   7e-93

>gb|GG738847.1| Naegleria gruberi genomic scaffold NAEGRscaffold_3, whole genome shotgun
              sequence
          Length = 941567

 Score =  338 bits (867), Expect = 7e-93
 Identities = 186/465 (40%), Positives = 289/465 (62%), Gaps = 13/465 (2%)
 Frame = +3

Query: 19     YIQQGADAIRTRQNLVKSLLAQRKWPELGWDEMSIELLLSDLAQMDSNNFPANIGAGERE 78
              +++Q   A+  +Q + K+LL+QR+ P+ G+ +  IE LLS  A MD+NN+  +IG GERE
Sbjct: 822930 HVKQALQAVNKQQKMYKTLLSQRQLPKEGFSDQQIESLLSFFASMDTNNYENHIGIGERE 823109

Query: 79     ARVYSDLVARRHFRMAHGIGRSGDIAAIQPKAAGSSLIMKLVNIMCLDVIRLAGVHAANA 138
               RV+S LV +RHF ++HGIGRSG++ + QPKAAGSS+I++L N +    I+LAG      
Sbjct: 823110 GRVFSKLVEKRHFYLSHGIGRSGELTSNQPKAAGSSIILQLCNYLVNHAIQLAGCKNVKK 823289

Query: 139    CIALPLATGMAMVMTLLTLAQT-RPPSARKVLWLRIDQKSCIKAITACGFEVVVVDNAIE 197
               I +P+ TGM + + L +LA +   P+ + V+W RIDQ+S +K+I   GF  +V++N + 
Sbjct: 823290 SIVVPMCTGMTLALCLRSLANSLEQPNKKYVIWPRIDQQSVLKSIDTAGFTPIVIENVLN 823469

Query: 198    GD-EVRTDLSALQHQVNTVGKDNILCIVSTTSCFAPRCPDRIVEIAKICATESIPHVINN 256
               D  +  +L +++ ++  VG +NILC++STTSCFAPR PD + EI KIC    I  V+NN
Sbjct: 823470 EDGSIEANLQSIESKIQQVGAENILCVLSTTSCFAPRVPDDVFEIGKICFKYGIGQVVNN 823649

Query: 257    AYGIQSSKITALIQD--AHKAGRVDAFVQSSDKNLMVPVGGALV-AGHDRAFIKRIGEMY 313
              AYG+QS  I   I    A     +  FVQS+DKN MVPVGGA+V +G D  FI ++ ++Y
Sbjct: 823650 AYGVQSKIIMERINKTIASSKSTITCFVQSTDKNFMVPVGGAVVSSGSDITFIDKVSKIY 823829

Query: 314    PGRASAAPSVDIFITLLSMGQQGFRSLLKQRKVVFE----QLRAKL----GAFAVSQGER 365
               GRAS  P +D+FITLLSMG+ G+  LL +R+V+F+    ++ +KL      F++ +G  
Sbjct: 823830 AGRASMTPILDLFITLLSMGKDGWEKLLAEREVLFQHFVSEIESKLTNTQSKFSLIRG-- 824003

Query: 366    LLETPHNPISLAITLSTFGSDATRLGSFLFTRCVSGTRVVAADRAAATTSVGPVSLSNFG 425
                    N IS A+++     +A ++G  LF R  +G RVV   + ++ T +  +S   +G
Sbjct: 824004 --SLQRNQISFALSIDLPKEEALKVGVSLFYRNCTGPRVVL--KGSSKTVLPHLSFVGYG 824171

Query: 426    AHHSAYHGAYLTAAAAIGMTEQEVDALIDRLTAAFKDLRAAMNQP 470
              +H  +Y   Y+T A AIG+ ++E+++ +  L      L+   + P
Sbjct: 824172 SHTDSYPHHYITLACAIGIEKEEIESFLTLLNKV*SRLQYISHHP 824306


  Database: N.gruberi/genome.fa
    Posted date:  Feb 9, 2011  9:02 AM
  Number of letters in database: 40,964,085
  Number of sequences in database:  784
  
Lambda     K      H
   0.321    0.133    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,870,765
Number of Sequences: 784
Number of extensions: 204916
Number of successful extensions: 830
Number of sequences better than 1.0e-05: 1
Number of HSP's better than  0.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 752
Number of HSP's gapped (non-prelim): 223
length of query: 470
length of database: 13,654,695
effective HSP length: 106
effective length of query: 364
effective length of database: 13,571,591
effective search space: 4940059124
effective search space used: 4940059124
frameshift window, decay const: 40,  0.1
T: 13
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 115 (48.9 bits)