BLASTX 2.2.25 [Feb-01-2011]


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.

Query= Coptis25_contig00003643
         (2506 letters)

Database: ./nr 
           23,641,837 sequences; 8,123,359,852 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

emb|CBI40152.3| unnamed protein product [Vitis vinifera]              577   e-170
ref|XP_002265533.1| PREDICTED: DNA-directed RNA polymerase E sub...   577   e-170
ref|XP_004155767.1| PREDICTED: DNA-directed RNA polymerase E sub...   547   e-163
ref|XP_002879839.1| NRPD1b [Arabidopsis lyrata subsp. lyrata] gi...   528   e-159
gb|AAY89362.1| RNA polymerase IV largest subunit [Arabidopsis th...   514   e-158

>emb|CBI40152.3| unnamed protein product [Vitis vinifera]
          Length = 1890

 Score =  577 bits (1487), Expect(2) = e-170
 Identities = 306/572 (53%), Positives = 382/572 (66%), Gaps = 6/572 (1%)
 Frame = +3

Query: 3    PPGEPVGALAATAISNPSYKVVLDXXXXXNASWELMKEILFLKINFINDLNDRRVILYLK 182
            P GEPVG LAATA+SNP+YK VLD     N+SWELMKEIL  ++NF NDL DRRVILYL 
Sbjct: 887  PAGEPVGVLAATAMSNPAYKAVLDSSPSSNSSWELMKEILLCQVNFKNDLIDRRVILYLN 946

Query: 183  DCGCVKKYCKENAAYLIQNLLKRVSLRDITVNFQIEY--QRTSPEGSGTNANLVGHIHLD 356
            DC C +KYC+ENAAYL++N LK+ SL+D  V F IEY  Q      S     LVGHIHL+
Sbjct: 947  DCDCGRKYCRENAAYLVKNQLKKASLKDTAVEFMIEYVKQHAVSGSSEPGTGLVGHIHLN 1006

Query: 357  KKLLKDMNRSLQEVLQNCHETISFFRRRKKNSLGGFLKNISLSVSECCCLEQSNDTEWCK 536
            K LL+D+N S+QEV Q C ETI+ FR  KK ++G F K I LS  ECC  + S  ++   
Sbjct: 1007 KLLLQDLNVSMQEVCQKCEETINSFR--KKKNVGPFFKKIILSFRECCTFQHSCQSKGSD 1064

Query: 537  S-CLQFSWRLDISSLSLETTSQIMANMICPILLDTIIKGDCRVQEANIIWSSPDTTNWVK 713
              CL F W+ +    +LE    I+A+ ICP+LL TIIKGD RV   NIIW SPDTT W++
Sbjct: 1065 MPCLLFFWQGNRDD-NLEQILHILAHKICPVLLQTIIKGDSRVCTVNIIWISPDTTTWIR 1123

Query: 714  THSRAQHGELALEIVLEKKFVKQHGDAWRLALDSCLPVIHLIDTARSIPYGIRQVQELLG 893
               +++ GELAL+IVLEK  VKQ GDAWR+ LD+CLPV+HLIDT RSIPY I+QVQELLG
Sbjct: 1124 NPCKSRKGELALDIVLEKAAVKQRGDAWRIVLDACLPVLHLIDTRRSIPYAIKQVQELLG 1183

Query: 894  ISCAFDQAVLRLSSSIRKVNKGVLKKHLLLAANSMTCTGSLIGFNKAGYKALFRSLDVHI 1073
            ISCAFDQAV RLS S+  V KGVLK+HL+L ANSMTC G+LIGFN  GYKAL R+L++ +
Sbjct: 1184 ISCAFDQAVQRLSKSVTMVAKGVLKEHLILLANSMTCAGNLIGFNSGGYKALSRALNLQV 1243

Query: 1074 PFTEATLFTPRKCFERAAEKCHADALSGIVASCSWGKHVALGTGTPFEILWNKNEMGLDQ 1253
            PFTEATLFTPRKCFE+A+EKCH D+LS IVASCSWGKHV +GTG+ F++LW+  E+G  Q
Sbjct: 1244 PFTEATLFTPRKCFEKASEKCHTDSLSSIVASCSWGKHVTVGTGSRFDVLWDTKEIGPAQ 1303

Query: 1254 DGVIDVYDFLQLVRMDPIG-DLNTSCLGRDTDELI-ENGVAELSLSPERNFDYSKPTFDD 1427
            DG ID+Y FL LVR    G + +T+CLG + ++LI E+   EL +SPE + ++ KP F+D
Sbjct: 1304 DGGIDIYSFLHLVRSGSYGKEPDTACLGAEVEDLILEDENLELGMSPEHSSNFEKPVFED 1363

Query: 1428 -AELQCKFDEHQVGDQGNTGDSRWEMDTSVVKDGGSSDWDAVKPGGSSDWSVVKAGGSSD 1604
             AE Q  ++ H  G  G                    DW AV     +  S +K    S 
Sbjct: 1364 SAEFQNTWENHVPGSGG--------------------DW-AVNQNKETTASTLKPSAWSS 1402

Query: 1605 WGTVKAVGSSDWGAENAFTESKPSDWECC*SW 1700
            WGT K      +        S+ + W+   +W
Sbjct: 1403 WGTDKVTMKDTFSTREPDESSRSAGWDDKGTW 1434



 Score = 50.4 bits (119), Expect(2) = e-170
 Identities = 68/289 (23%), Positives = 104/289 (35%), Gaps = 34/289 (11%)
 Frame = +1

Query: 1714 WGTVKAVGSS----------DWGAENAFTESKP----SDWGAT---AVKAGGSSDWGAV- 1839
            WGT KA  ++            G +  F + +P    S WG     A K G + + G   
Sbjct: 1434 WGTDKAQNTAFRRTHEDSPRSSGRDETFRDGRPQFASSAWGKKIDEADKTGWNKNDGKPQ 1493

Query: 1840 --KSGGSSDWGGENAFTGSKPSDWGA----TADKFQKQLCLSTEPSEGGPAA--GWNA-V 1992
              K   S DW  + A   +  S +G     T D  + +L +     +  P     W+A +
Sbjct: 1494 MDKLRESYDWDCKVAQEKTTQSTYGGISSTTGDWKKNELQMEVVQHDESPVNEHSWDANL 1553

Query: 1993 GSQKLPSKETVDTWGKQDEKSDTNDWVKHVKSQWEKEACDGGPASGWNASES-QKLHSNE 2169
                L    T   W    + S   DW K  K Q   E         W++S +  K  SN+
Sbjct: 1554 PEDPLAQATTSVGW----DSSTGKDWTKR-KLQSPSEQQRDPAIKSWSSSHNVMKEQSNQ 1608

Query: 2170 PFDA--WGKQAGKSNTDGWVKNIESQRGQPNESRESESSKSTGWNTIKSSSESPRTSNWN 2343
            P     W     K   D   ++  +QRG   ++ +SE   S GW      ++ P +  W 
Sbjct: 1609 PASTHGWDSPGAKGWNDVEEQSQWNQRGSAVKNDQSE--SSHGWGPSNEQNQLPSSQGWG 1666

Query: 2344 SLESQETPQMEPSDPW----GKKTEETKAGGWSGNDRHAQGVQWNKSPN 2478
            S  +    + E    W    GKK+    + GW  N+      +W    N
Sbjct: 1667 SPNAGAGHESETQSQWGQPSGKKSRPEGSRGWGSNN-----TEWKNKKN 1710


>ref|XP_002265533.1| PREDICTED: DNA-directed RNA polymerase E subunit 1 [Vitis vinifera]
          Length = 1830

 Score =  577 bits (1487), Expect(2) = e-170
 Identities = 306/572 (53%), Positives = 382/572 (66%), Gaps = 6/572 (1%)
 Frame = +3

Query: 3    PPGEPVGALAATAISNPSYKVVLDXXXXXNASWELMKEILFLKINFINDLNDRRVILYLK 182
            P GEPVG LAATA+SNP+YK VLD     N+SWELMKEIL  ++NF NDL DRRVILYL 
Sbjct: 827  PAGEPVGVLAATAMSNPAYKAVLDSSPSSNSSWELMKEILLCQVNFKNDLIDRRVILYLN 886

Query: 183  DCGCVKKYCKENAAYLIQNLLKRVSLRDITVNFQIEY--QRTSPEGSGTNANLVGHIHLD 356
            DC C +KYC+ENAAYL++N LK+ SL+D  V F IEY  Q      S     LVGHIHL+
Sbjct: 887  DCDCGRKYCRENAAYLVKNQLKKASLKDTAVEFMIEYVKQHAVSGSSEPGTGLVGHIHLN 946

Query: 357  KKLLKDMNRSLQEVLQNCHETISFFRRRKKNSLGGFLKNISLSVSECCCLEQSNDTEWCK 536
            K LL+D+N S+QEV Q C ETI+ FR  KK ++G F K I LS  ECC  + S  ++   
Sbjct: 947  KLLLQDLNVSMQEVCQKCEETINSFR--KKKNVGPFFKKIILSFRECCTFQHSCQSKGSD 1004

Query: 537  S-CLQFSWRLDISSLSLETTSQIMANMICPILLDTIIKGDCRVQEANIIWSSPDTTNWVK 713
              CL F W+ +    +LE    I+A+ ICP+LL TIIKGD RV   NIIW SPDTT W++
Sbjct: 1005 MPCLLFFWQGNRDD-NLEQILHILAHKICPVLLQTIIKGDSRVCTVNIIWISPDTTTWIR 1063

Query: 714  THSRAQHGELALEIVLEKKFVKQHGDAWRLALDSCLPVIHLIDTARSIPYGIRQVQELLG 893
               +++ GELAL+IVLEK  VKQ GDAWR+ LD+CLPV+HLIDT RSIPY I+QVQELLG
Sbjct: 1064 NPCKSRKGELALDIVLEKAAVKQRGDAWRIVLDACLPVLHLIDTRRSIPYAIKQVQELLG 1123

Query: 894  ISCAFDQAVLRLSSSIRKVNKGVLKKHLLLAANSMTCTGSLIGFNKAGYKALFRSLDVHI 1073
            ISCAFDQAV RLS S+  V KGVLK+HL+L ANSMTC G+LIGFN  GYKAL R+L++ +
Sbjct: 1124 ISCAFDQAVQRLSKSVTMVAKGVLKEHLILLANSMTCAGNLIGFNSGGYKALSRALNLQV 1183

Query: 1074 PFTEATLFTPRKCFERAAEKCHADALSGIVASCSWGKHVALGTGTPFEILWNKNEMGLDQ 1253
            PFTEATLFTPRKCFE+A+EKCH D+LS IVASCSWGKHV +GTG+ F++LW+  E+G  Q
Sbjct: 1184 PFTEATLFTPRKCFEKASEKCHTDSLSSIVASCSWGKHVTVGTGSRFDVLWDTKEIGPAQ 1243

Query: 1254 DGVIDVYDFLQLVRMDPIG-DLNTSCLGRDTDELI-ENGVAELSLSPERNFDYSKPTFDD 1427
            DG ID+Y FL LVR    G + +T+CLG + ++LI E+   EL +SPE + ++ KP F+D
Sbjct: 1244 DGGIDIYSFLHLVRSGSYGKEPDTACLGAEVEDLILEDENLELGMSPEHSSNFEKPVFED 1303

Query: 1428 -AELQCKFDEHQVGDQGNTGDSRWEMDTSVVKDGGSSDWDAVKPGGSSDWSVVKAGGSSD 1604
             AE Q  ++ H  G  G                    DW AV     +  S +K    S 
Sbjct: 1304 SAEFQNTWENHVPGSGG--------------------DW-AVNQNKETTASTLKPSAWSS 1342

Query: 1605 WGTVKAVGSSDWGAENAFTESKPSDWECC*SW 1700
            WGT K      +        S+ + W+   +W
Sbjct: 1343 WGTDKVTMKDTFSTREPDESSRSAGWDDKGTW 1374



 Score = 50.4 bits (119), Expect(2) = e-170
 Identities = 68/289 (23%), Positives = 104/289 (35%), Gaps = 34/289 (11%)
 Frame = +1

Query: 1714 WGTVKAVGSS----------DWGAENAFTESKP----SDWGAT---AVKAGGSSDWGAV- 1839
            WGT KA  ++            G +  F + +P    S WG     A K G + + G   
Sbjct: 1374 WGTDKAQNTAFRRTHEDSPRSSGRDETFRDGRPQFASSAWGKKIDEADKTGWNKNDGKPQ 1433

Query: 1840 --KSGGSSDWGGENAFTGSKPSDWGA----TADKFQKQLCLSTEPSEGGPAA--GWNA-V 1992
              K   S DW  + A   +  S +G     T D  + +L +     +  P     W+A +
Sbjct: 1434 MDKLRESYDWDCKVAQEKTTQSTYGGISSTTGDWKKNELQMEVVQHDESPVNEHSWDANL 1493

Query: 1993 GSQKLPSKETVDTWGKQDEKSDTNDWVKHVKSQWEKEACDGGPASGWNASES-QKLHSNE 2169
                L    T   W    + S   DW K  K Q   E         W++S +  K  SN+
Sbjct: 1494 PEDPLAQATTSVGW----DSSTGKDWTKR-KLQSPSEQQRDPAIKSWSSSHNVMKEQSNQ 1548

Query: 2170 PFDA--WGKQAGKSNTDGWVKNIESQRGQPNESRESESSKSTGWNTIKSSSESPRTSNWN 2343
            P     W     K   D   ++  +QRG   ++ +SE   S GW      ++ P +  W 
Sbjct: 1549 PASTHGWDSPGAKGWNDVEEQSQWNQRGSAVKNDQSE--SSHGWGPSNEQNQLPSSQGWG 1606

Query: 2344 SLESQETPQMEPSDPW----GKKTEETKAGGWSGNDRHAQGVQWNKSPN 2478
            S  +    + E    W    GKK+    + GW  N+      +W    N
Sbjct: 1607 SPNAGAGHESETQSQWGQPSGKKSRPEGSRGWGSNN-----TEWKNKKN 1650


>ref|XP_004155767.1| PREDICTED: DNA-directed RNA polymerase E subunit 1-like [Cucumis
            sativus]
          Length = 1959

 Score =  547 bits (1409), Expect(2) = e-163
 Identities = 281/569 (49%), Positives = 380/569 (66%), Gaps = 3/569 (0%)
 Frame = +3

Query: 3    PPGEPVGALAATAISNPSYKVVLDXXXXXNASWELMKEILFLKINFINDLNDRRVILYLK 182
            PPGEPVG LAATA+S P+YK VLD     N+SW++MKEIL  K++F N+  DRRVILYL 
Sbjct: 828  PPGEPVGVLAATAMSTPAYKAVLDSTPSSNSSWDMMKEILLCKVSFKNEPIDRRVILYLN 887

Query: 183  DCGCVKKYCKENAAYLIQNLLKRVSLRDITVNFQIEYQRTSPEGSGTNANLVGHIHLDKK 362
            +C C +KYC ENAAY++++ LK+V+L+D  ++F IEY R  P  SG    LVGH+HL++ 
Sbjct: 888  NCACGRKYCNENAAYVVKSHLKKVTLKDAAMDFMIEYNR-QPTPSGLGPGLVGHVHLNRM 946

Query: 363  LLKDMNRSLQEVLQNCHETISFFRRRKKNSLGGFLKNISLSVSECCCLEQSNDTEWCKSC 542
            LLK++N  + EVL+ C ET+S F+++KK         +  S+SE C   Q N  E     
Sbjct: 947  LLKELNIDMTEVLRRCQETMSSFKKKKKK----IAHALRFSISEHCAFHQWNGEESIDMP 1002

Query: 543  LQFSWRLDISSLSLETTSQIMANMICPILLDTIIKGDCRVQEANIIWSSPDTTNWVKTHS 722
                W      + LE T+ I+A+++ P+L +TIIKGD R++ A++IW SPD+T+W K  S
Sbjct: 1003 CLIFWH-QTRDVHLERTAHILADIVFPLLSETIIKGDPRIKSASVIWISPDSTSWQKNPS 1061

Query: 723  RAQHGELALEIVLEKKFVKQHGDAWRLALDSCLPVIHLIDTARSIPYGIRQVQELLGISC 902
            R Q GELAL++ LEK  VKQ+GDAWR  LD CLPV+HLIDT RS+PY I+QVQELLGISC
Sbjct: 1062 RWQDGELALDVCLEKSAVKQNGDAWRNVLDCCLPVLHLIDTRRSVPYAIKQVQELLGISC 1121

Query: 903  AFDQAVLRLSSSIRKVNKGVLKKHLLLAANSMTCTGSLIGFNKAGYKALFRSLDVHIPFT 1082
            AFDQ + RLS S+  V+KGVL  HL+L ANSMTCTG++IGFN  GYKAL R+L++ +PFT
Sbjct: 1122 AFDQMIQRLSKSVSMVSKGVLGDHLILLANSMTCTGNMIGFNSGGYKALSRALNIQVPFT 1181

Query: 1083 EATLFTPRKCFERAAEKCHADALSGIVASCSWGKHVALGTGTPFEILWNKNEMGLDQDGV 1262
            EATLFTPRKCFE+AAEKCH D+LS IVASCSWGKHVA+GTG+ F+ILW++ E+G  QD V
Sbjct: 1182 EATLFTPRKCFEKAAEKCHKDSLSSIVASCSWGKHVAVGTGSRFDILWDQKELGCKQDDV 1241

Query: 1263 IDVYDFLQLVRMDPIGDLNTSCLGRDTDE-LIENGVAELSLSPERNFDYSKPTFDD-AEL 1436
            +DVY+FL +VR     +  ++CLG + ++ ++E+   EL+LSPE      KP F+D AE 
Sbjct: 1242 VDVYNFLHMVRSGKSEEPTSACLGEEIEDIMVEDEYGELTLSPEPFSTSEKPVFEDSAEF 1301

Query: 1437 QCKFDEHQVGDQGNTGDSRWEMDTSV-VKDGGSSDWDAVKPGGSSDWSVVKAGGSSDWGT 1613
            +   D +        G+S+WE   S+     G   W++ + G +++     +   +DW  
Sbjct: 1302 EHCLDNY-------PGESKWEKAPSLGAVSTGGGQWESNENGKATN-----SSDGNDWSG 1349

Query: 1614 VKAVGSSDWGAENAFTESKPSDWECC*SW 1700
                   D    NA   +  S W+   SW
Sbjct: 1350 WGRKAEPDVTVTNAQENTSNSAWDTTSSW 1378



 Score = 58.5 bits (140), Expect(2) = e-163
 Identities = 72/316 (22%), Positives = 112/316 (35%), Gaps = 47/316 (14%)
 Frame = +1

Query: 1693 KAGG---SSDWGT----------VKAVGSSDWGA---ENAFTESKPSDWGATAVKAGGSS 1824
            K+GG   +S WGT               SS W     + A T+         A K+GG  
Sbjct: 1412 KSGGWDSASTWGTKTKDDSFKRETAPKKSSQWSGLQKDKAETQDAFHKKAEMASKSGGWE 1471

Query: 1825 D--WGAVKSGGSSDWGGE-----NAF------TGSKPSDWGATADKFQKQLCLSTEPSEG 1965
            D  W    S    +W  +      +F        SK + WG+T           T+ S G
Sbjct: 1472 DKAWSRGTSKTEDNWSSQVKDKAESFQVQVQEVSSKTNGWGSTGGW--------TKNSGG 1523

Query: 1966 G--PAAGWNAVGSQKLPSKETVDTWGKQD----EKSDTNDW----VKHVKSQWEKEACDG 2115
                 AGWN  G   +  ++  D W ++     E   T+ W    V   K  +  +A D 
Sbjct: 1524 DHQSEAGWND-GQASMDREKVSDRWDRKATQKLESHQTSSWGSPTVGDSKDSFPSKAVDH 1582

Query: 2116 GPA---SGWNASESQKLHSNEPFDAWGKQAGKSNTDGWVKNIESQRGQPNESRESESSKS 2286
              +     W+  +S +       DAWG+Q  +      + N ES         ES     
Sbjct: 1583 SDSVVNHSWDRQKSPEASQGFGNDAWGQQKSRDVIKPSLANNESNLSGWGSQIESNEGSD 1642

Query: 2287 TGWNTIKSSSESPRTSNWNSLESQETP-----QMEPSDPWGKKTEETKAGGWSGNDRHAQ 2451
             G++ + +  +S  T  W+S E  + P      +E S  WG + +    G W    R ++
Sbjct: 1643 HGFDQVTNEQKSSDTRGWDSQEKTDKPWDKQKSLEASQSWGSQND--SLGSWGQPQRASE 1700

Query: 2452 GVQWNKSPNMNTNSSQ 2499
                    + +T  SQ
Sbjct: 1701 ECSRESQDDSSTQFSQ 1716


>ref|XP_002879839.1| NRPD1b [Arabidopsis lyrata subsp. lyrata] gi|297325678|gb|EFH56098.1|
            NRPD1b [Arabidopsis lyrata subsp. lyrata]
          Length = 1947

 Score =  528 bits (1360), Expect(2) = e-159
 Identities = 284/572 (49%), Positives = 369/572 (64%), Gaps = 15/572 (2%)
 Frame = +3

Query: 9    GEPVGALAATAISNPSYKVVLDXXXXXNASWELMKEILFLKINFINDLNDRRVILYLKDC 188
            GEPVG LAATA+SNP+YK VLD     N+SWE MKE+L  K+NF N  NDRRVILYL +C
Sbjct: 825  GEPVGVLAATAMSNPAYKAVLDSTANSNSSWEQMKEVLLCKVNFQNTTNDRRVILYLNEC 884

Query: 189  GCVKKYCKENAAYLIQNLLKRVSLRDITVNFQIEY--QRTSPEGSGTNANLVGHIHLDKK 362
             C K++C+ENAAY ++N LK+VSL+D  V F +EY  Q+T  E  G ++ L GHIHLDK 
Sbjct: 885  HCGKRFCQENAAYTVRNKLKKVSLKDTAVEFLVEYRKQQTISEIFGIDSCLHGHIHLDKT 944

Query: 363  LLKDMNRSLQEVLQNCHETISFFRRRKKNSLGGFLKNISLSVSECCCLEQS---NDTEWC 533
            LL+D N S+Q++LQ C + I+   ++KK       K  SLSVSECC  +      D++  
Sbjct: 945  LLQDWNISMQDILQKCEDVINSLGQKKKKKATDDFKRTSLSVSECCSFQDPCGRKDSDM- 1003

Query: 534  KSCLQFSWRLDISSLSLETTSQIMANMICPILLDTIIKGDCRVQEANIIWSSPDTTNWVK 713
              CL FS+    +   LE T  ++ N I P+LL+T+IKGD R+  ANIIW+S D T W++
Sbjct: 1004 -PCLMFSY--SATDPDLERTLDVLCNTIYPVLLETVIKGDPRICSANIIWNSSDMTTWIR 1060

Query: 714  THSRAQHGELALEIVLEKKFVKQHGDAWRLALDSCLPVIHLIDTARSIPYGIRQVQELLG 893
                ++ GE  L++ +EK  VKQ GDAWR+ +D+CL V+HLIDT RSIPY I+QVQELLG
Sbjct: 1061 NCHASRRGEWVLDVTVEKSAVKQSGDAWRVVIDACLSVLHLIDTKRSIPYSIKQVQELLG 1120

Query: 894  ISCAFDQAVLRLSSSIRKVNKGVLKKHLLLAANSMTCTGSLIGFNKAGYKALFRSLDVHI 1073
            +SCAF+QAV RLS+S+R V+KGVLK+H++L AN+MTC+G+++GFN  GYKAL RSL++  
Sbjct: 1121 LSCAFEQAVQRLSASVRMVSKGVLKEHIILLANNMTCSGNMLGFNSGGYKALTRSLNIKA 1180

Query: 1074 PFTEATLFTPRKCFERAAEKCHADALSGIVASCSWGKHVALGTGTPFEILWNKNEMGLDQ 1253
            PFTEATL TPR+CFE+AAEKCH D+LS +V SCSWGK V +GTG+ FE+LWN+ E GLD 
Sbjct: 1181 PFTEATLITPRRCFEKAAEKCHTDSLSTVVGSCSWGKRVDVGTGSQFELLWNQKETGLDD 1240

Query: 1254 DGVIDVYDFLQLVRMDPIGDLNTSCLGRDTDELIENGVAELSLSPERNFDYSKPTFDD-A 1430
                DVY FLQ+VR     D   S  G D   + E  +AE + SPER+    +P F+D A
Sbjct: 1241 KEETDVYSFLQMVRSTTNADAYVSSPGFD---VTEEEMAEWAESPERDSALGEPKFEDSA 1297

Query: 1431 ELQCKFDEHQVGDQGNTGDSRWEMDTSVVKDGGSSDWDAVKPGGSSDWSVVK-----AGG 1595
            E Q       + D+G   +S WE          SS WD    GG S+W V K     A  
Sbjct: 1298 EFQ------NLHDEGKPSESNWEK---------SSSWDNGCSGG-SEWGVSKNTGGEANP 1341

Query: 1596 SSDWGTVKAVGSSD----WGAENAFTESKPSD 1679
             S+W     V   D    W  +    ES  SD
Sbjct: 1342 ESNWEKTTNVEKEDAWSSWNTKKDAQESSKSD 1373



 Score = 63.5 bits (153), Expect(2) = e-159
 Identities = 68/258 (26%), Positives = 100/258 (38%), Gaps = 19/258 (7%)
 Frame = +1

Query: 1705 SSDWGTVKAVGSSDWGAENAFTESKPSDWGATAVKAGGSSDWGAVKSGGSSDWGGENAFT 1884
            S  WG  K+     W  +N  TES P+ WG+T     GSSD              +N+ T
Sbjct: 1412 SDVWGH-KSGSDKSWDKKNGGTESAPAAWGSTDAAVWGSSD-------------KKNSET 1457

Query: 1885 GSKPSDWGATADKFQKQLCLSTEPSEGGPAAG-WNAVGSQKLPSKETVDTWGKQDE-KSD 2058
             S  + WG+   K       ++E   G    G WN   S+   ++    TWG  D+ KS 
Sbjct: 1458 ESDAAAWGSRDKK-------NSEVGSGAGVLGPWNKKSSK---TESDGATWGSSDKTKSG 1507

Query: 2059 TNDWVKHVKSQWEKE--ACDGGPASGWNASESQKLHSNEPFDAWG-----KQAGKSNTDG 2217
               W     S W+K+    D  PA+ W +    K  +      WG     K   +S   G
Sbjct: 1508 AAAW-----SSWDKKNMETDSEPAA-WGSQSKNKPETESGPSTWGAWDTKKSETESGPAG 1561

Query: 2218 WVKNIESQRGQPNESRESESSKSTGWNTIKSSSE-------SPRTSNWNSLESQETPQME 2376
            W   I  ++   N   ES  +    W+  KS++E       S   + W   +   +    
Sbjct: 1562 W--GIVDKK---NSETESGPAAMGNWDKKKSNTESGPAAWGSTDAAVWGFSDKNNSETES 1616

Query: 2377 PSDPWG---KKTEETKAG 2421
             +  WG   KKT ET++G
Sbjct: 1617 DAAAWGSRDKKTSETESG 1634


>gb|AAY89362.1| RNA polymerase IV largest subunit [Arabidopsis thaliana]
          Length = 1976

 Score =  514 bits (1324), Expect(2) = e-158
 Identities = 275/573 (47%), Positives = 363/573 (63%), Gaps = 16/573 (2%)
 Frame = +3

Query: 9    GEPVGALAATAISNPSYKVVLDXXXXXNASWELMKEILFLKINFINDLNDRRVILYLKDC 188
            GEPVG LAATA+SNP+YK VLD     N+SWELMKE+L  K+NF N  NDRRVILYL +C
Sbjct: 825  GEPVGVLAATAMSNPAYKAVLDSSPNSNSSWELMKEVLLCKVNFQNTTNDRRVILYLNEC 884

Query: 189  GCVKKYCKENAAYLIQNLLKRVSLRDITVNFQIEYQR--TSPEGSGTNANLVGHIHLDKK 362
             C K++C+ENAA  ++N L +VSL+D  V F +EY++  T  E  G ++ L GHIHL+K 
Sbjct: 885  HCGKRFCQENAACTVRNKLNKVSLKDTAVEFLVEYRKQPTISEIFGIDSCLHGHIHLNKT 944

Query: 363  LLKDMNRSLQEVLQNCHETISFFRRRKKNSLGGFLKNISLSVSECC-----CLEQSNDTE 527
            LL+D N S+Q++ Q C + I+   ++KK       K  SLSVSECC     C  + +D  
Sbjct: 945  LLQDWNISMQDIHQKCEDVINSLGQKKKKKATDDFKRTSLSVSECCSFRDPCGSKGSDMP 1004

Query: 528  WCKSCLQFSWRLDISSLSLETTSQIMANMICPILLDTIIKGDCRVQEANIIWSSPDTTNW 707
                CL FS+  + +   LE T  ++ N + P+LL+ +IKGD R+  ANIIW+S D T W
Sbjct: 1005 ----CLTFSY--NATDPDLERTLDVLCNTVYPVLLEIVIKGDSRICSANIIWNSSDMTTW 1058

Query: 708  VKTHSRAQHGELALEIVLEKKFVKQHGDAWRLALDSCLPVIHLIDTARSIPYGIRQVQEL 887
            ++    ++ GE  L++ +EK  VKQ GDAWR+ +DSCL V+HLIDT RSIPY ++QVQEL
Sbjct: 1059 IRNRHASRRGEWVLDVTVEKSAVKQSGDAWRVVIDSCLSVLHLIDTKRSIPYSVKQVQEL 1118

Query: 888  LGISCAFDQAVLRLSSSIRKVNKGVLKKHLLLAANSMTCTGSLIGFNKAGYKALFRSLDV 1067
            LG+SCAF+QAV RLS+S+R V+KGVLK+H++L AN+MTC+G+++GFN  GYKAL RSL++
Sbjct: 1119 LGLSCAFEQAVQRLSASVRMVSKGVLKEHIILLANNMTCSGTMLGFNSGGYKALTRSLNI 1178

Query: 1068 HIPFTEATLFTPRKCFERAAEKCHADALSGIVASCSWGKHVALGTGTPFEILWNKNEMGL 1247
              PFTEATL  PRKCFE+AAEKCH D+LS +V SCSWGK V +GTG+ FE+LWN+ E GL
Sbjct: 1179 KAPFTEATLIAPRKCFEKAAEKCHTDSLSTVVGSCSWGKRVDVGTGSQFELLWNQKETGL 1238

Query: 1248 DQDGVIDVYDFLQLVRMDPIGDLNTSCLGRDTDELIENGVAELSLSPERNFDYSKPTFDD 1427
            D     DVY FLQ+V      D   S  G D   + E  +AE + SPER+    +P F+D
Sbjct: 1239 DDKEETDVYSFLQMVISTTNADAFVSSPGFD---VTEEEMAEWAESPERDSALGEPKFED 1295

Query: 1428 AELQCKFDEHQVGDQGNTGDSRWEMDTSVVKDGGSSDWDAVKPGGSSDWSVVKAGG---- 1595
            +      D   + D+G    + WE          SS WD    GG S+W V K+ G    
Sbjct: 1296 SA-----DFQNLHDEGKPSGANWEK---------SSSWDNGCSGG-SEWGVSKSTGGEAN 1340

Query: 1596 -SSDWGTVKAVGSSD----WGAENAFTESKPSD 1679
              S+W     V   D    W       ES  SD
Sbjct: 1341 PESNWEKTTNVEKEDAWSSWNTRKDAQESSKSD 1373



 Score = 73.9 bits (180), Expect(2) = e-158
 Identities = 80/328 (24%), Positives = 118/328 (35%), Gaps = 61/328 (18%)
 Frame = +1

Query: 1705 SSDWGTVKAVGSSDWGAENAFTESKPSDWGATAVKAGGSSD------------WGA---- 1836
            S  WG  K+V    W  +N  TES P+ WG+T     GSSD            WG+    
Sbjct: 1412 SDVWGH-KSVSDKSWDKKNWGTESAPAAWGSTDAAVWGSSDKKNSETESDAAAWGSRDKN 1470

Query: 1837 ---VKSG---------------------GSSD-----------WGGENAFTGSKPSDWGA 1911
               V SG                     GSSD           W  +N  T S+P+ WG+
Sbjct: 1471 NSDVGSGAGVLGPWNKKSSETESNGATWGSSDKTKSGAAAWNSWDKKNIETDSEPAAWGS 1530

Query: 1912 TADKFQKQLCLSTEPSEGGPAAGWNAVGSQKLPSKETVDTWGKQDEKSDTNDWVKHVKSQ 2091
               K           +E GPAA W A   +K  ++     WG  D+K+   +        
Sbjct: 1531 QGKK--------NSETESGPAA-WGAWDKKKSETEPGPAGWGMGDKKNSETELGPAAMGN 1581

Query: 2092 WEKEACD--GGP-------ASGWNASESQKLHSNEPFDAWGKQAGKSNTDGWVKNIESQR 2244
            W+K+  D   GP       A+ W +S+     +     AWG +  K++            
Sbjct: 1582 WDKKKSDTKSGPAAWGSTDAAAWGSSDKNNSETESDAAAWGSRNKKTSEIESGAGAWGSW 1641

Query: 2245 GQPNESRESESSKSTGWNTIKSSSESPRTSNWNSLESQETPQMEPSDPWGKKTEE-TKAG 2421
            GQP+ + E + +     N   S  E+         +S+E    E S  WG   ++   +G
Sbjct: 1642 GQPSPTAEDKDTNEDDRNPWVSLKET---------KSREKDDKERSQ-WGNPAKKFPSSG 1691

Query: 2422 GWSGNDRHAQGVQWNKSPNMNTNSSQEE 2505
            GWS    +  G  W  + N      + E
Sbjct: 1692 GWS----NGGGADWKGNRNHTPRPPRSE 1715