>YNL299W TRF5 SGDID:S000005243, Chr XIV from 66517-68445, Verified
           ORF, "Poly (A) polymerase involved in nuclear RNA
           quality control based on: homology with Trf4p, genetic
           interactions with TRF4 mutants, physical interaction
           with Mtr4p (TRAMP subunit), and by direct assay;
           disputed role as a sigma DNA polymerase"
          Length = 642

 Score = 91.7 bits (226), Expect = 1e-22
 Identities = 65/230 (28%), Positives = 108/230 (46%), Gaps = 7/230 (3%)

Query: 468 IEVFGSYTSGLSLPSSDIDVCIMNIKENELD---CLYILAYALIKLNIACDIRIIKDARV 524
           + VFGS+ + L LP SDID C++N +  + +    +Y LA  L    +A  + +I   RV
Sbjct: 217 LHVFGSFATDLYLPGSDID-CVVNSRNRDKEDRNYIYELARHLKNKGLAIRMEVIVKTRV 275

Query: 525 KILKYIDKELGVQIDICINQKSSKETTDFIITQMKKYIYXXXXXXXXXXXXHSRNLNETY 584
            I+K+I+ +  + ID+   + +  E    I   ++                HSR LN  +
Sbjct: 276 PIIKFIEPQSQLHIDVSFERTNGLEAAKLIREWLRDSPGLRELVLIIKQFLHSRRLNNVH 335

Query: 585 IGGIGSFLLSCMVLHFLQMHTSTFDNNHFNNTYLIKLLIEFFYFYSIDFKLHDACIVVR- 643
            GG+G F + C+V  FL MH     N+      L  LLI+FF  Y  +F   D  I +  
Sbjct: 336 TGGLGGFTVICLVYSFLNMHPRIKSNDIDVLDNLGVLLIDFFELYGKNFGYDDVAISISD 395

Query: 644 GLGHVLPRRLRKEYEYNDQR--LCFENPIDTSIDIGRNTYRIKYILYLFS 691
           G    +P+   +  E +  +  L  ++P D + +I R ++ +K I   F+
Sbjct: 396 GYASYIPKSCWRTLEPSRSKFSLAIQDPGDPNNNISRGSFNMKDIKKAFA 445

 Score = 25.0 bits (53), Expect = 0.014
 Identities = 14/56 (25%), Positives = 30/56 (53%), Gaps = 5/56 (8%)

Query: 1   MEDDYYFFLFQ---EEESEQVKEAKQDLHNALKKNREKIKNVSNNKPM--EKASNI 51
           +ED+  F  F    E+E+EQ+KE   +  + L  +  ++  +++ + +  E A N+
Sbjct: 101 LEDNQDFIAFSDSSEDETEQIKEDDDERSSFLLTDEHEVSKLTSQQSLNTESACNV 156

 Score = 21.2 bits (43), Expect = 0.21
 Identities = 28/126 (22%), Positives = 46/126 (36%), Gaps = 9/126 (7%)

Query: 11  QEEESEQVKEAKQDLHNALKKNREKIKNVSNNKPMEKASNIIWLGQDDDNLKNEYKKHNE 70
           + +E +  K  ++      +K  E   +  N     K  ++    +DDD   N     N+
Sbjct: 14  KRKEDKHTKRMRKSSFTRTQKMLEVFND--NRSHFNKYESLAIDVEDDDTFGNLVLMEND 71

Query: 71  GKHNRD-----RKKSAEDINILSSDKRNIINRRNDEFTKKYEQDKYHSYDGRHDNDDNVD 125
            K + D        S+ED     S KRN     N +F    +  +  +   + D DD   
Sbjct: 72  -KSDVDIPVIEEVTSSEDEQRAESSKRNNSLEDNQDFIAFSDSSEDETEQIKED-DDERS 129

Query: 126 SFPFND 131
           SF   D
Sbjct: 130 SFLLTD 135

 Score = 20.4 bits (41), Expect = 0.36
 Identities = 12/41 (29%), Positives = 18/41 (43%)

Query: 291 SKDSNNIIIEGSGYNMKKKSLSRNKSYKEEKRKNSSFLLND 331
           SK +N++            S    +  KE+  + SSFLL D
Sbjct: 95  SKRNNSLEDNQDFIAFSDSSEDETEQIKEDDDERSSFLLTD 135

 Score = 19.6 bits (39), Expect = 0.61
 Identities = 9/44 (20%), Positives = 27/44 (61%), Gaps = 1/44 (2%)

Query: 133 QNKKRKKETSYSKNE-MEYGYCEHKDSFDKYNNKKKIRKNDDMY 175
           ++ KR +++S+++ + M   + +++  F+KY +     ++DD +
Sbjct: 19  KHTKRMRKSSFTRTQKMLEVFNDNRSHFNKYESLAIDVEDDDTF 62

 Score = 18.9 bits (37), Expect = 1.0
 Identities = 9/37 (24%), Positives = 17/37 (45%)

Query: 816 SYVNMDYMIMNTSSMLYANIDKIFSHSFDVYNNIFKY 852
           S++NM   I +    +  N+  +    F++Y   F Y
Sbjct: 350 SFLNMHPRIKSNDIDVLDNLGVLLIDFFELYGKNFGY 386

 Score = 18.1 bits (35), Expect = 1.8
 Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 59  DNLKNEYKKHNEGKHNRDRKKSAEDINILSSDKRNIIN-RRNDEFTKKYEQDKYHSYDG 116
           D ++N+    NE  H R  +   ED+ I  ++   +    + DE  KK ++ K    +G
Sbjct: 490 DLVQNKAIIENERYHKRRTRIVQEDLFINDTEDLPVEEIYKLDEPAKKKQKAKKDKREG 548

Lambda     K      H
   0.318    0.135    0.397 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1434
Number of extensions: 94
Number of successful extensions: 14
Number of sequences better than 10.0: 1
Number of HSP's gapped: 9
Number of HSP's successfully gapped: 8
Length of query: 858
Length of database: 642
Length adjustment: 40
Effective length of query: 818
Effective length of database: 602
Effective search space:   492436
Effective search space used:   492436
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 29 (16.2 bits)
S2: 29 (15.8 bits)