Hit NameLength (aa)HSP LengthHSP ScoreHSP Significance
KLLA0B08569g33733215570.0
Sklu_1926.434534010391e-142
Kwal_27.1259033834010081e-137
ADL323C34133610071e-137
Scas_667.203383339911e-134
YPR056W (TFB4)3383439721e-131
CAGL0D01650g3353249301e-125
AAR165W36233710.61
Kwal_27.1196439166653.7
Kwal_14.179636325628.4
BLASTP 2.2.26 [Sep-21-2011]

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.

Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= KLLA0B08569g
         (332 letters)

Database: blastdb 
           34,618 sequences; 16,596,109 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

KLLA0B08569g complement(756558..757571) similar to sgd|S0006260 ...   604   0.0  
Sklu_1926.4 YPR056W, Contig c1926 2998-4035 reverse complement        404   e-142
Kwal_27.12590                                                         392   e-137
ADL323C [1418] [Homologous to ScYPR056W (TFB4) - SH] (127631..12...   392   e-137
Scas_667.20                                                           386   e-134
YPR056W (TFB4) [5486] chr16 (671121..672137) RNA polymerase II t...   379   e-131
CAGL0D01650g complement(172035..173042) highly similar to tr|Q12...   362   e-125
AAR165W [353] [Homologous to ScYGL126W (SCS3) - SH] complement(6...    32   0.61 
Kwal_27.11964                                                          30   3.7  
Kwal_14.1796                                                           28   8.4  

>KLLA0B08569g complement(756558..757571) similar to sgd|S0006260
           Saccharomyces cerevisiae YPR056w TFB4 component of RNA
           polymerase transcription initiation TFIIH factor, start
           by similarity
          Length = 337

 Score =  604 bits (1557), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 296/332 (89%), Positives = 296/332 (89%)

Query: 1   MDAIADTVFQGTKSKTQEIEDTPSLLTVVVDTSIHSWVQLTKQQXXXXXXXXXXXKQLIE 60
           MDAIADTVFQGTKSKTQEIEDTPSLLTVVVDTSIHSWVQLTKQQ           KQLIE
Sbjct: 1   MDAIADTVFQGTKSKTQEIEDTPSLLTVVVDTSIHSWVQLTKQQSGSGSEGSSGEKQLIE 60

Query: 61  ALKSIVVFLNAHLAFNSGNQVCLIAAHSEGMKYLYPSADSKPSMSMVSSDMYRGFRNVDE 120
           ALKSIVVFLNAHLAFNSGNQVCLIAAHSEGMKYLYPSADSKPSMSMVSSDMYRGFRNVDE
Sbjct: 61  ALKSIVVFLNAHLAFNSGNQVCLIAAHSEGMKYLYPSADSKPSMSMVSSDMYRGFRNVDE 120

Query: 121 IVVEQWYRLFKEELEGQESKVXXXXXXXXXXXXXXTYVNRILKENENTSLRSRLLVITCG 180
           IVVEQWYRLFKEELEGQESKV              TYVNRILKENENTSLRSRLLVITCG
Sbjct: 121 IVVEQWYRLFKEELEGQESKVSMKSSLSGAMSSALTYVNRILKENENTSLRSRLLVITCG 180

Query: 181 TSQGKDEIFQYIPIMNCIFSATKMKCSIDVVKIGGGIESTFLQQATDATSGVYLHVENTR 240
           TSQGKDEIFQYIPIMNCIFSATKMKCSIDVVKIGGGIESTFLQQATDATSGVYLHVENTR
Sbjct: 181 TSQGKDEIFQYIPIMNCIFSATKMKCSIDVVKIGGGIESTFLQQATDATSGVYLHVENTR 240

Query: 241 GLIQYLSTAMFIDPSLRNVIIKPNQGSVDFRTSCFLTGKVVAVGFXXXXXXXXXXXIPPG 300
           GLIQYLSTAMFIDPSLRNVIIKPNQGSVDFRTSCFLTGKVVAVGF           IPPG
Sbjct: 241 GLIQYLSTAMFIDPSLRNVIIKPNQGSVDFRTSCFLTGKVVAVGFVCSVCLCVLSVIPPG 300

Query: 301 QKCPACDSPFDSKIIARLRRKPVLSNGVPKKK 332
           QKCPACDSPFDSKIIARLRRKPVLSNGVPKKK
Sbjct: 301 QKCPACDSPFDSKIIARLRRKPVLSNGVPKKK 332

>Sklu_1926.4 YPR056W, Contig c1926 2998-4035 reverse complement
          Length = 345

 Score =  404 bits (1039), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 201/340 (59%), Positives = 243/340 (71%), Gaps = 24/340 (7%)

Query: 1   MDAIADTVFQGTKSKTQEIEDTPSLLTVVVDTSIHSWVQLTKQQXXXXXXXXXXXKQLIE 60
           MDAI+D+ FQ TKSKT   E+ PSLLTVVVDT+   W +L K+              LI 
Sbjct: 1   MDAISDSTFQNTKSKTSITEENPSLLTVVVDTTPKLWAELDKESNSK--------GNLIS 52

Query: 61  ALKSIVVFLNAHLAFNSGNQVCLIAAHSEGMKYLYPSADS--------------KPSMSM 106
           AL+S++VFLNAHLAFN+ NQV +IAAHS G+KYLYP   +              +  +S+
Sbjct: 53  ALQSLIVFLNAHLAFNNSNQVAVIAAHSTGLKYLYPKTATTEGTGASSSSVVSGRKDLSI 112

Query: 107 VSSDMYRGFRNVDEIVVEQWYRLFKEELE--GQESKVXXXXXXXXXXXXXXTYVNRILKE 164
           +++DMYR FRNVDE VVE+ Y+LF++E E     S                TY+NR+ KE
Sbjct: 113 INNDMYRQFRNVDETVVEELYKLFQQEKEENNSTSNGVGRSTLSGAISAGLTYINRVNKE 172

Query: 165 NENTSLRSRLLVITCGTSQGKDEIFQYIPIMNCIFSATKMKCSIDVVKIGGGIESTFLQQ 224
           NEN +L+SRLLV TCG+S G+DEIFQYIPIMNCIF+ATKMKC IDVVKIGG  ESTFLQQ
Sbjct: 173 NENITLKSRLLVTTCGSSGGRDEIFQYIPIMNCIFTATKMKCPIDVVKIGGVQESTFLQQ 232

Query: 225 ATDATSGVYLHVENTRGLIQYLSTAMFIDPSLRNVIIKPNQGSVDFRTSCFLTGKVVAVG 284
           ATDAT+GVYLHV++T GLIQYL TAMFIDPSLR+VI+KPNQGSVDFRTSCFLTG+VVAVG
Sbjct: 233 ATDATNGVYLHVDSTEGLIQYLCTAMFIDPSLRHVIVKPNQGSVDFRTSCFLTGRVVAVG 292

Query: 285 FXXXXXXXXXXXIPPGQKCPACDSPFDSKIIARLRRKPVL 324
           F           IPPG KCPACD+ FD ++I +L+RKPV+
Sbjct: 293 FVCSVCLCVLSIIPPGNKCPACDAEFDERVITKLKRKPVV 332

>Kwal_27.12590
          Length = 338

 Score =  392 bits (1008), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 193/340 (56%), Positives = 239/340 (70%), Gaps = 16/340 (4%)

Query: 1   MDAIADTVFQGTKSKTQEIEDTPSLLTVVVDTSIHSWVQLTKQQXXXXXXXXXXXKQLIE 60
           MDAI+D  FQ TKSK    E+ PSLLTV+VDT    W +L K+              LI 
Sbjct: 1   MDAISDPSFQNTKSKIAVAEELPSLLTVIVDTMPKVWAELDKE--------GSQEGSLIS 52

Query: 61  ALKSIVVFLNAHLAFNSGNQVCLIAAHSEGMKYLYPS--------ADSKPSMSMVSSDMY 112
           AL+S++VFLNAHL+FNS NQV +IAAHS G+KYL+P+        A   P +S+++S+MY
Sbjct: 53  ALQSLIVFLNAHLSFNSANQVAVIAAHSTGIKYLFPTPPSSQEEPAAKSPDLSIINSNMY 112

Query: 113 RGFRNVDEIVVEQWYRLFKEELEGQESKVXXXXXXXXXXXXXXTYVNRILKENENTSLRS 172
           R FRNVDE V+E+ Y+L ++E + +                  TY+NR++KE    SL++
Sbjct: 113 RQFRNVDETVLEELYKLLQDEKKRKIPSGFQKSTLSGAMSAGFTYINRVIKEQSTASLKA 172

Query: 173 RLLVITCGTSQGKDEIFQYIPIMNCIFSATKMKCSIDVVKIGGGIESTFLQQATDATSGV 232
           RL+V+TCG+S GKDEIFQYIPIMNCIFSATK+KC IDVVKIGG  ESTFLQQATDAT+GV
Sbjct: 173 RLMVMTCGSSGGKDEIFQYIPIMNCIFSATKLKCPIDVVKIGGSQESTFLQQATDATNGV 232

Query: 233 YLHVENTRGLIQYLSTAMFIDPSLRNVIIKPNQGSVDFRTSCFLTGKVVAVGFXXXXXXX 292
           YLHV +T GLIQYL+TAMFIDPSLR +++KPNQGSVDFRTSC+LTGKVVAVGF       
Sbjct: 233 YLHVPSTEGLIQYLTTAMFIDPSLRPIVVKPNQGSVDFRTSCYLTGKVVAVGFVCSVCLC 292

Query: 293 XXXXIPPGQKCPACDSPFDSKIIARLRRKPVLSNGVPKKK 332
               IPPG KCPACDS FD  +  +L+R+PV+     KKK
Sbjct: 293 VLSIIPPGNKCPACDSEFDEHVTTKLKRRPVVPGIAAKKK 332

>ADL323C [1418] [Homologous to ScYPR056W (TFB4) - SH]
           (127631..128656) [1026 bp, 341 aa]
          Length = 341

 Score =  392 bits (1007), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 197/336 (58%), Positives = 237/336 (70%), Gaps = 19/336 (5%)

Query: 1   MDAIADTVFQGTKSKTQEIEDTPSLLTVVVDTSIHSWVQLTKQQXXXXXXXXXXXKQLIE 60
           MDAIAD+ FQ  KSK Q +E+TPSLLT+V+DT+   W +  ++             QL++
Sbjct: 1   MDAIADSTFQINKSKVQLVEETPSLLTLVIDTNPKLWAEFDRE--------VGKKGQLMQ 52

Query: 61  ALKSIVVFLNAHLAFNSGNQVCLIAAHSEGMKYLYPSADSKPS---------MSMVSSDM 111
            LKS +VFLNAHL+FN+ NQV +IAA S G+KYLYP AD K            S+++ +M
Sbjct: 53  VLKSTIVFLNAHLSFNNSNQVSVIAACSRGIKYLYPQADDKEGSTKKKKSEDRSIINRNM 112

Query: 112 YRGFRNVDEIVVEQWYRLFKEELEGQESKVXX--XXXXXXXXXXXXTYVNRILKENENTS 169
           YRGFRNVDE VVE+ YR+F++E +  E  V                TY+NRI  E E  S
Sbjct: 113 YRGFRNVDEAVVEELYRVFQQESKQLEDGVPQPFRSTLSGAMSAGLTYINRITHETEGVS 172

Query: 170 LRSRLLVITCGTSQGKDEIFQYIPIMNCIFSATKMKCSIDVVKIGGGIESTFLQQATDAT 229
           L+SRLLVITCG+S  KDE+FQYIPIMNCIFSATKMKC IDVVK+GG  ESTFLQQATDAT
Sbjct: 173 LKSRLLVITCGSSASKDEVFQYIPIMNCIFSATKMKCPIDVVKVGGVKESTFLQQATDAT 232

Query: 230 SGVYLHVENTRGLIQYLSTAMFIDPSLRNVIIKPNQGSVDFRTSCFLTGKVVAVGFXXXX 289
           +G YLHV NT GLIQYLSTAMFIDPSLR  ++KPNQ SVDFRTSC+LTGKVVA+GF    
Sbjct: 233 NGNYLHVANTDGLIQYLSTAMFIDPSLRQWVVKPNQSSVDFRTSCYLTGKVVAIGFVCSV 292

Query: 290 XXXXXXXIPPGQKCPACDSPFDSKIIARLRRKPVLS 325
                  IPPG KCPACDS FD K++A+L RKPV++
Sbjct: 293 CLCVLSIIPPGNKCPACDSEFDEKVVAKLSRKPVIT 328

>Scas_667.20
          Length = 338

 Score =  386 bits (991), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 193/333 (57%), Positives = 236/333 (70%), Gaps = 18/333 (5%)

Query: 1   MDAIADTVFQGTKSKTQEIEDTPSLLTVVVDTSIHSWVQLTKQQXXXXXXXXXXXKQLIE 60
           MDAIAD  FQ TK ++   E+TPSLLTV+VD +   W +L ++              LI 
Sbjct: 1   MDAIADPTFQHTKVRSSITEETPSLLTVIVDITPKLWAELDEE--------INEKGNLIN 52

Query: 61  ALKSIVVFLNAHLAFNSGNQVCLIAAHSEGMKYLYPSAD--------SKPSMSMVSSDMY 112
            LKS++VFLNAHLAFNS NQV +IAAHS+G+KYL+P            K  +S+++ DMY
Sbjct: 53  VLKSLLVFLNAHLAFNSSNQVAVIAAHSQGIKYLFPKNSISVKGVNSGKKDLSIINKDMY 112

Query: 113 RGFRNVDEIVVEQWYRLFKEELEGQESKVXXXXXXXXXXXXXXTYVNRILKENENTSLRS 172
           R FRNVDE +V++ Y LF+EEL+ Q + V              TY+NR+ KE E  SL+S
Sbjct: 113 RRFRNVDETLVDELYALFEEELK-QVNTVTQKSTLSGAMSAGLTYINRVTKELEAISLKS 171

Query: 173 RLLVITCG-TSQGKDEIFQYIPIMNCIFSATKMKCSIDVVKIGGGIESTFLQQATDATSG 231
           RL+V+TCG   + KDEIFQYIPIMNCIFSATK+KC IDVVKIGG  ESTFLQQ TDAT+G
Sbjct: 172 RLMVLTCGGKGESKDEIFQYIPIMNCIFSATKIKCPIDVVKIGGSKESTFLQQTTDATNG 231

Query: 232 VYLHVENTRGLIQYLSTAMFIDPSLRNVIIKPNQGSVDFRTSCFLTGKVVAVGFXXXXXX 291
            YLHVE+T+GLIQYL+TAMFIDPSLR +I+KPN GSVDFRTSC+LTGKVVAVGF      
Sbjct: 232 AYLHVESTKGLIQYLATAMFIDPSLRQIIVKPNHGSVDFRTSCYLTGKVVAVGFICSVCL 291

Query: 292 XXXXXIPPGQKCPACDSPFDSKIIARLRRKPVL 324
                IPPG KCPACDS FD  +IA+L++KPV+
Sbjct: 292 CVLSIIPPGNKCPACDSEFDEHVIAKLKKKPVV 324

>YPR056W (TFB4) [5486] chr16 (671121..672137) RNA polymerase II
           transcription initiation factor TFIIH (factor b), 37 kDa
           subunit [1017 bp, 338 aa]
          Length = 338

 Score =  379 bits (972), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 189/343 (55%), Positives = 239/343 (69%), Gaps = 20/343 (5%)

Query: 1   MDAIADTVFQGTKSKTQEIEDTPSLLTVVVDTSIHSWVQLTKQQXXXXXXXXXXXKQLIE 60
           MDAI+D  F+  +S+ Q  E++PSLLTV+++ +   W    ++              +I+
Sbjct: 1   MDAISDPTFKHARSRKQVTEESPSLLTVIIEIAPKLWTTFDEEGNEKG--------SIIK 52

Query: 61  ALKSIVVFLNAHLAFNSGNQVCLIAAHSEGMKYLYPSADS-----------KPSMSMVSS 109
            L++++VFLNAHLAFNS N+V +IAA+S+G+KYLYP + S           +  + +++S
Sbjct: 53  VLEALIVFLNAHLAFNSANKVAVIAAYSQGIKYLYPESTSALKASESENKTRSDLKIINS 112

Query: 110 DMYRGFRNVDEIVVEQWYRLFKEELEGQESKVXXXXXXXXXXXXXXTYVNRILKENENTS 169
           DMYR FRNVDE +VE+ Y+LF+ E + Q  +               TYVNRI KE+  TS
Sbjct: 113 DMYRRFRNVDETLVEEIYKLFELE-KKQIEQNSQRSTLAGAMSAGLTYVNRISKESVTTS 171

Query: 170 LRSRLLVITCGTSQGKDEIFQYIPIMNCIFSATKMKCSIDVVKIGGGIESTFLQQATDAT 229
           L+SRLLV+TCG+   KDEIFQYIPIMNCIFSATKMKC IDVVKIGG  ESTFLQQ TDAT
Sbjct: 172 LKSRLLVLTCGSGSSKDEIFQYIPIMNCIFSATKMKCPIDVVKIGGSKESTFLQQTTDAT 231

Query: 230 SGVYLHVENTRGLIQYLSTAMFIDPSLRNVIIKPNQGSVDFRTSCFLTGKVVAVGFXXXX 289
           +GVYLHVE+T GLIQYL+TAMFIDPSLR +I+KPN GSVDFRTSC+LTG+VVAVGF    
Sbjct: 232 NGVYLHVESTEGLIQYLATAMFIDPSLRPIIVKPNHGSVDFRTSCYLTGRVVAVGFICSV 291

Query: 290 XXXXXXXIPPGQKCPACDSPFDSKIIARLRRKPVLSNGVPKKK 332
                  IPPG KCPACDS FD  +IA+L+RKPV+     KKK
Sbjct: 292 CLCVLSIIPPGNKCPACDSQFDEHVIAKLKRKPVVPRLKAKKK 334

>CAGL0D01650g complement(172035..173042) highly similar to tr|Q12004
           Saccharomyces cerevisiae YPR056w TFB4, start by
           similarity
          Length = 335

 Score =  362 bits (930), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 180/324 (55%), Positives = 226/324 (69%), Gaps = 17/324 (5%)

Query: 1   MDAIADTVFQGTKSKTQEIEDTPSLLTVVVDTSIHSWVQLTKQQXXXXXXXXXXXKQLIE 60
           MDAIAD  FQ TK ++   ED PSLLTVV+D S   W +   +            + +  
Sbjct: 1   MDAIADPNFQQTKLRSTATEDIPSLLTVVLDISPRLWAEFDHRSGEK--------QSVTT 52

Query: 61  ALKSIVVFLNAHLAFNSGNQVCLIAAHSEGMKYLYP--------SADSKPSMSMVSSDMY 112
            LKS++VFLN+HLAFNS NQV +IAA S+G++YLYP        +A +   +S++SS MY
Sbjct: 53  VLKSLIVFLNSHLAFNSANQVAVIAAFSQGIQYLYPRSSDTSEQNAGNSKDLSIISSHMY 112

Query: 113 RGFRNVDEIVVEQWYRLFKEELEGQESKVXXXXXXXXXXXXXXTYVNRILKENENTSLRS 172
           R FRNVDE ++E++Y+L++ E E    K               TY NR+ KE E+ SLRS
Sbjct: 113 RRFRNVDETLIEEFYKLYQRE-ESLIDKPVQKSTLSGAMAAALTYTNRLTKEFESISLRS 171

Query: 173 RLLVITCGTSQGKDEIFQYIPIMNCIFSATKMKCSIDVVKIGGGIESTFLQQATDATSGV 232
           RLLVITCG+S+ KDEIFQYIPIMNCIFSATK+KC IDV+KIGG  +STFLQQ TDAT+GV
Sbjct: 172 RLLVITCGSSREKDEIFQYIPIMNCIFSATKLKCPIDVIKIGGNKQSTFLQQTTDATNGV 231

Query: 233 YLHVENTRGLIQYLSTAMFIDPSLRNVIIKPNQGSVDFRTSCFLTGKVVAVGFXXXXXXX 292
           Y+H+E+T G+IQYLSTAM IDPSLR +I++P QGSVDFRTSC+LTGKVVA+G+       
Sbjct: 232 YIHLESTNGIIQYLSTAMSIDPSLRQIIVRPTQGSVDFRTSCYLTGKVVAIGYICSVCLC 291

Query: 293 XXXXIPPGQKCPACDSPFDSKIIA 316
               IPPG KCPACDS FD ++IA
Sbjct: 292 VLSIIPPGNKCPACDSQFDERVIA 315

>AAR165W [353] [Homologous to ScYGL126W (SCS3) - SH]
           complement(639331..640419) [1089 bp, 362 aa]
          Length = 362

 Score = 32.0 bits (71), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 19/33 (57%)

Query: 189 FQYIPIMNCIFSATKMKCSIDVVKIGGGIESTF 221
           F   PIM+ +F++T   CS DV   G G+ S F
Sbjct: 100 FGIAPIMDQVFTSTGGHCSFDVFDTGMGLNSGF 132

>Kwal_27.11964
          Length = 391

 Score = 29.6 bits (65), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 17/66 (25%), Positives = 39/66 (59%), Gaps = 2/66 (3%)

Query: 216 GIESTFLQQATDATSGVYLHVENTRGLIQYLSTAMFIDPSLRNVIIKPNQGSVDFRTSCF 275
            +ES F+   ++ T+ + +H+  TRG++Q L +++  D  LR ++++  + S+ F     
Sbjct: 176 ALESIFISALSNLTAEMKVHLTVTRGILQDLESSITRD-KLRFLLVQNKKLSI-FNKKSM 233

Query: 276 LTGKVV 281
           L G+++
Sbjct: 234 LIGEMI 239

>Kwal_14.1796
          Length = 363

 Score = 28.5 bits (62), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 11/25 (44%), Positives = 16/25 (64%)

Query: 13  KSKTQEIEDTPSLLTVVVDTSIHSW 37
           K   Q I+ TPS L   +D+++HSW
Sbjct: 173 KEHLQSIDVTPSQLNSFIDSALHSW 197

  Database: blastdb
    Posted date:  Apr 3, 2006  3:33 PM
  Number of letters in database: 16,596,109
  Number of sequences in database:  34,618
  
Lambda     K      H
   0.319    0.133    0.384 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 

Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 34618
Number of Hits to DB: 8,961,261
Number of extensions: 315125
Number of successful extensions: 732
Number of sequences better than 10.0: 11
Number of HSP's gapped: 718
Number of HSP's successfully gapped: 11
Length of query: 332
Length of database: 16,596,109
Length adjustment: 102
Effective length of query: 230
Effective length of database: 13,065,073
Effective search space: 3004966790
Effective search space used: 3004966790
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (28.5 bits)