ORF STATUS Function Best COG Functional category Pathways and functional systems
r_klactIII0774 suspect: LH AK KOG0132 RNA processing and modification RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains r_klactIII0774 suspect: LH AK KOG0132 Transcription RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains
Only best alignment is shown:
BLASTP 2.2.3 [May-13-2002]


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= r_klactIII0774  260473 258605 -623 
         (623 letters)

Database: KOG eukaryal database 04/03 
           60,738 sequences; 30,389,216 total letters

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

Color Key for Alignment Scores:   


                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

YNL251c [AK] KOG0132 RNA polymerase II C-terminal domain-binding...   415   e-115
SPAC222.09 [AK] KOG0132 RNA polymerase II C-terminal domain-bind...   152   1e-36

>YNL251c [AK] KOG0132 RNA polymerase II C-terminal domain-binding protein
           RA4 contains RPR and RRM domains
          Length = 575

 Score =  415 bits (1066), Expect = e-115
 Identities = 234/526 (44%), Positives = 306/526 (57%), Gaps = 32/526 (6%)

Query: 1   MMQSDEHEDFVATLESFKELKSGISGSRIRKLTDYAVNHGRNIEALLSFVIQYSKECPPT 60
           M Q D+ ++FVATLESFK+LKSGISGSRI+KLT YA++H      ++S +I YS+ CP +
Sbjct: 1   MQQDDDFQNFVATLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDS 60

Query: 61  HKLGSLYIVDSIVRALMSKSETVKQEEGEEGNYFLKGVELLNDNIQPLLIDGIERSDPAH 120
           HKLGSLYI+DSI RA + ++ +       +       +  L + IQ LL D I +S+  H
Sbjct: 61  HKLGSLYIIDSIGRAYLDETRSNSNSSSNKPGTCAHAINTLGEVIQELLSDAIAKSNQDH 120

Query: 121 LEKIQELINIWDKNNVFNNKPLNAARSRLSELVXXXXXXXXXXXXXXLTPRPAPSNDNKS 180
            EKI+ L++IWD++ +F    LNA RS+   +               L P+         
Sbjct: 121 KEKIRMLLDIWDRSGLFQKSYLNAIRSKCFAMDISNNTANTASQQLSLDPK--------- 171

Query: 181 SSGSKIDQVLNAIPKFENLP-GIQVPSGLFSEDISVQDSCLKELLGKLQVELTKNQKLVQ 239
               +  Q+L+ + K   L   I +P+ L S D + Q + L +++  LQ           
Sbjct: 172 ---QRSKQILSNLKKSPPLNLNISLPTDLTSTDPAKQQAALFQVIAALQKHFKTLPSHTS 228

Query: 240 VNKQAPRSIDNXXXXXXXXXXXXXXXQYVGXXXXXXXXXXXXXXKNDRSRAQATTSLHLS 299
           V   AP                    +Y                + +RSR+        S
Sbjct: 229 VGTVAPPQAHTITEYGSRRERERERERY--------------NSRRNRSRSPPAPFSQPS 274

Query: 300 --RXXXXXXXXXXXXXXXSINGQQG-NNHHLYPDEQNVPSNPHFRPKPVSFDPTVPRDHV 356
             R               + N   G NNHHLYPDE NV +NPH+RPKPVS+D T+P DH+
Sbjct: 275 TGRKDRYPSVAQDQYSIGAPNTTFGTNNHHLYPDELNVSNNPHYRPKPVSYDSTLPPDHI 334

Query: 357 KVYSRTLFVGGVPQNFKEHDIARMLRQFGEVQSVILNNARKHAFVKVYSRAEAERIMAHF 416
           KVYSRTLF+GGVP N KE D+A +L+ F EVQSVILNN+RKHAFVKVYSR EAE ++ +F
Sbjct: 335 KVYSRTLFIGGVPLNMKEWDLANVLKPFAEVQSVILNNSRKHAFVKVYSRHEAENVLQNF 394

Query: 417 TGGGNPTHGLRIRWAVGFGPRDCCDYQYGYSIIPLARLTEIDFKWSQSAEWGGTGGQPIQ 476
              G     LR RW VGFGPRDCCDYQ+GYSIIP+ RLT+ D KWS SA+WGGT GQP+ 
Sbjct: 395 NKDG--ALPLRTRWGVGFGPRDCCDYQHGYSIIPMHRLTDADKKWSVSAQWGGTSGQPLV 452

Query: 477 TNMVYEEPDIIVGEGVSSKAISQKMPTDKGVLGPKSGKVGQATAVS 522
           T +V+EEPDIIVGEGVSSKAISQKMPTD G  GP+SGK  ++ ++S
Sbjct: 453 TGIVFEEPDIIVGEGVSSKAISQKMPTDSGRNGPRSGKPNKSGSIS 498


>SPAC222.09 [AK] KOG0132 RNA polymerase II C-terminal domain-binding protein
           RA4 contains RPR and RRM domains
          Length = 620

 Score =  152 bits (385), Expect = 1e-36
 Identities = 75/173 (43%), Positives = 107/173 (61%), Gaps = 1/173 (0%)

Query: 329 PDEQNVPS-NPHFRPKPVSFDPTVPRDHVKVYSRTLFVGGVPQNFKEHDIARMLRQFGEV 387
           P    VP   P   P+    DPT+P D +KVYSRTLF+GG+ ++ +E  +  M  +FG V
Sbjct: 373 PPADGVPKPTPDGFPRRFERDPTIPPDSIKVYSRTLFLGGITRSVREPVLRSMFERFGSV 432

Query: 388 QSVILNNARKHAFVKVYSRAEAERIMAHFTGGGNPTHGLRIRWAVGFGPRDCCDYQYGYS 447
           QS+ILN+  +H F+K++ R  AE+              +R +W VGFGPR+C D+  G S
Sbjct: 433 QSLILNHNYRHGFLKMFRRDAAEKAQVAMENVPFADTTIRTKWGVGFGPRECSDFSTGIS 492

Query: 448 IIPLARLTEIDFKWSQSAEWGGTGGQPIQTNMVYEEPDIIVGEGVSSKAISQK 500
           +IP+  LT+ D  W  +AE+GGTGG PI   +  +EPDI +G G+SSKAIS++
Sbjct: 493 VIPIRLLTDADRTWLVTAEYGGTGGLPITPGIALDEPDIEIGLGISSKAISKR 545



 Score = 85.5 bits (210), Expect = 2e-16
 Identities = 51/148 (34%), Positives = 85/148 (56%), Gaps = 9/148 (6%)

Query: 9   DFVATLESFKELKSGISGSRIRKLTDYAVNHGRNIEALLSFVIQYSKECPPTHKLGSLYI 68
           +F   L+S +  K+GISGS+I KLT+ ++ +       ++ V +Y+K  P THKLG+LYI
Sbjct: 6   EFDGILDSLEHSKTGISGSKILKLTNLSMENVSENAQFVASVYKYAKRAPVTHKLGALYI 65

Query: 69  VDSIVRALM--SKSETVKQEEGEEGNY---FLKGVELLNDNIQPLLIDGIERSDPAHLEK 123
           +DSIVR+    +K      E   + ++   + K  E+ +     L+ D I+ +  AHL K
Sbjct: 66  LDSIVRSFQDGAKKNNESFENPVDASFSGGWCKAAEITDS----LVADAIQHAPSAHLPK 121

Query: 124 IQELINIWDKNNVFNNKPLNAARSRLSE 151
           I +L +IW+K + F  + L + RS+L +
Sbjct: 122 ILKLCDIWEKASTFPPEKLESLRSKLKD 149


  Database: KOG eukaryal database 04/03
    Posted date:  Apr 14, 2003  1:07 PM
  Number of letters in database: 30,389,216
  Number of sequences in database:  60,738
  
Lambda     K      H
   0.315    0.133    0.385 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 30,618,174
Number of Sequences: 60738
Number of extensions: 1247368
Number of successful extensions: 2606
Number of sequences better than 1.0e-05: 2
Number of HSP's better than  0.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 2598
Number of HSP's gapped (non-prelim): 5
length of query: 623
length of database: 30,389,216
effective HSP length: 112
effective length of query: 511
effective length of database: 23,586,560
effective search space: 12052732160
effective search space used: 12052732160
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)