Miyakogusa Predicted Gene

Lj0g3v0353889.2
Show Alignment:  
BLASTP 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.

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= Lj0g3v0353889.2 tr|D7KU36|D7KU36_ARALL DNA-directed RNA
polymerase OS=Arabidopsis lyrata subsp. lyrata
GN=ARALYDRAFT,27.49,4e-18,seg,NULL; beta and beta-prime subunits of
DNA dependent RNA-polymerase,NULL,CUFF.24477.2
         (788 letters)

Database: TAIR10_pep 
           35,386 sequences; 14,482,855 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AT2G40030.1 | Symbols: NRPD1B, DRD3, ATNRPD1B, DMS5, NRPE1 | nuc...   391   e-108
AT1G63020.2 | Symbols: NRPD1A | nuclear RNA polymerase D1A | chr...   106   6e-23
AT1G63020.1 | Symbols: NRPD1A, POL IVA, SDE4, NRPD1, SMD2 | nucl...   106   6e-23

>AT2G40030.1 | Symbols: NRPD1B, DRD3, ATNRPD1B, DMS5, NRPE1 | nuclear
            RNA polymerase D1B | chr2:16715089-16723406 FORWARD
            LENGTH=1976
          Length = 1976

 Score =  391 bits (1005), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 298/856 (34%), Positives = 438/856 (51%), Gaps = 113/856 (13%)

Query: 1    MLEELKINMAEVFQRCQEKLRSLNRKRKYYQT--LKSTELFFSESCA------SPNFSSP 52
            +L++  I+M ++ Q+C++ + SL +K+K   T   K T L  SE C+      S     P
Sbjct: 945  LLQDWNISMQDIHQKCEDVINSLGQKKKKKATDDFKRTSLSVSECCSFRDPCGSKGSDMP 1004

Query: 53   CVTFI--SLDGDGLDKTTEILADVICPVLLGTIIQGDPRISSANITWINPDSNAWVRNPS 110
            C+TF   + D D L++T ++L + + PVLL  +I+GD RI SANI W + D   W+RN  
Sbjct: 1005 CLTFSYNATDPD-LERTLDVLCNTVYPVLLEIVIKGDSRICSANIIWNSSDMTTWIRNRH 1063

Query: 111  KSSNGELALDIILEEAAVKQSGDAWRIVLDSCLPVLNLIDTRRSIPYAIKQVQELLGISC 170
             S  GE  LD+ +E++AVKQSGDAWR+V+DSCL VL+LIDT+RSIPY++KQVQELLG+SC
Sbjct: 1064 ASRRGEWVLDVTVEKSAVKQSGDAWRVVIDSCLSVLHLIDTKRSIPYSVKQVQELLGLSC 1123

Query: 171  TFDQAIQRLAASVKMVAKGVLREHLILLASSMTCGGNLVGFNTGGYKALARQLNIQVPFT 230
             F+QA+QRL+ASV+MV+KGVL+EH+ILLA++MTC G ++GFN+GGYKAL R LNI+ PFT
Sbjct: 1124 AFEQAVQRLSASVRMVSKGVLKEHIILLANNMTCSGTMLGFNSGGYKALTRSLNIKAPFT 1183

Query: 231  DATLFTPKKCFERAAEKCHTDSLSSIVASCSWGKPVAVGTGSRFDVLWDAKERKSNELEG 290
            +ATL  P+KCFE+AAEKCHTDSLS++V SCSWGK V VGTGS+F++LW+ KE   ++ E 
Sbjct: 1184 EATLIAPRKCFEKAAEKCHTDSLSTVVGSCSWGKRVDVGTGSQFELLWNQKETGLDDKEE 1243

Query: 291  MDVYNFLHMVKSLINGEEENDACXXXXXXXXXXXXNADYSLSPQHTSGV-DAVFEETFEA 349
             DVY+FL MV S  N     DA              A+++ SP+  S + +  FE++ + 
Sbjct: 1244 TDVYSFLQMVISTTNA----DAFVSSPGFDVTEEEMAEWAESPERDSALGEPKFEDSADF 1299

Query: 350  MN-----GPESNGWGATT--DRTETKSTQWSAWESNKAETK-----DGGSQRVHEDSWTS 397
             N      P    W  ++  D   +  ++W   +S   E       +  +    ED+W+S
Sbjct: 1300 QNLHDEGKPSGANWEKSSSWDNGCSGGSEWGVSKSTGGEANPESNWEKTTNVEKEDAWSS 1359

Query: 398  RDVMKDDSQMTNAWDGNVEQTKTISNDWTAWGKNKSEIQDNVAEKAEGECGSSEMWKTAV 457
             +  KD             Q  + S+   AWG    +   +     E    +S   K ++
Sbjct: 1360 WNTRKD------------AQESSKSDSGGAWGIKTKDADADTTPNWE----TSPAPKDSI 1403

Query: 458  IQEGSSK-SNAW--KSNIEQRSDEDSWTSQKLKADVIQDSSKPSSWGAKPKSN-----DS 509
            + E +   S+ W  KS  ++  D+ +W ++   A     S+  + WG+  K N     D+
Sbjct: 1404 VPENNEPTSDVWGHKSVSDKSWDKKNWGTE--SAPAAWGSTDAAVWGSSDKKNSETESDA 1461

Query: 510  SNWGRNKDEIQDVVSRRAEDDSWSSKKQLSSDATQEDSSKFSFWGGNKDTTKPKSNDWSS 569
            + WG       DV S       W+ K       + E  S  + WG + D TK  +  W+S
Sbjct: 1462 AAWGSRDKNNSDVGSGAGVLGPWNKK-------SSETESNGATWGSS-DKTKSGAAAWNS 1513

Query: 570  WGGNRDGIQDGGSKRAQDDSWSSQKDVTRESSSKVDAWGA---NNEASNPKSNDWSA--- 623
            W  ++  I+      A    W SQ     E+ S   AWGA       + P    W     
Sbjct: 1514 W--DKKNIETDSEPAA----WGSQGKKNSETESGPAAWGAWDKKKSETEPGPAGWGMGDK 1567

Query: 624  --------------WGKNKDGTQDGGSERAQDDSSSLGKW-KAESQVEADTVQEDSSKSK 668
                          W K K  T+ G +     D+++ G   K  S+ E+D     S   K
Sbjct: 1568 KNSETELGPAAMGNWDKKKSDTKSGPAAWGSTDAAAWGSSDKNNSETESDAAAWGSRNKK 1627

Query: 669  AWERNSDNVKVGNSSWGKPKFPETQAWDPQKETNQGAGSRGWDS--QIASANSDSDRNFQ 726
              E     ++ G  +WG    P   A D  K+TN+      W S  +  S   D     Q
Sbjct: 1628 TSE-----IESGAGAWGSWGQPSPTAED--KDTNED-DRNPWVSLKETKSREKDDKERSQ 1679

Query: 727  WGKQGRESFKKSQGWGSNAGDMK-NKNRPGRAP------GP-------RLDMYSSEEQDI 772
            WG   ++             D K N+N   R P       P       RLD ++SEEQ++
Sbjct: 1680 WGNPAKKFPSSGGWSNGGGADWKGNRNHTPRPPRSEDNLAPMFTATRQRLDSFTSEEQEL 1739

Query: 773  LKDIEPIVQSIRRIMQ 788
            L D+EP+++++R+IM 
Sbjct: 1740 LSDVEPVMRTLRKIMH 1755


>AT1G63020.2 | Symbols: NRPD1A | nuclear RNA polymerase D1A |
            chr1:23355329-23361126 REVERSE LENGTH=1453
          Length = 1453

 Score =  106 bits (265), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 118/233 (50%), Gaps = 12/233 (5%)

Query: 74   VICPVLLGTIIQGDPRISSANITWINPDSNAWVRNPSKSSN---GELALDIILEEAAVKQ 130
            V+ P LL + ++GD  I   NI W +       + P ++ N   GEL L + +     K+
Sbjct: 1066 VLIPFLLDSPVKGDQGIKKVNILWTDRP-----KAPKRNGNHLAGELYLKVTMYGDRGKR 1120

Query: 131  SGDAWRIVLDSCLPVLNLIDTRRSIPYAIKQVQELLGISCTFDQAIQRLAASVKMVAKGV 190
              + W  +L++CLP++++ID  RS P  I+Q   + GI       +  L ++V    K +
Sbjct: 1121 --NCWTALLETCLPIMDMIDWGRSHPDNIRQCCSVYGIDAGRSIFVANLESAVSDTGKEI 1178

Query: 191  LREHLILLASSMTCGGNLVGFNTGGYKALARQLNIQVPFTDATLFTPKKCFERAAEKCHT 250
            LREHL+L+A S++  G  V  N  G+    +  +   PFT A   +P +CF +AA++   
Sbjct: 1179 LREHLLLVADSLSVTGEFVALNAKGWSKQRQVESTPAPFTQACFSSPSQCFLKAAKEGVR 1238

Query: 251  DSLSSIVASCSWGKPVAVGTGSRFDVLWDAKERKSNELEGMDVYNFLHMVKSL 303
            D L   + + +WGK    GTG +F+++   K         +DVY+ L   K++
Sbjct: 1239 DDLQGSIDALAWGKVPGFGTGDQFEIIISPKVHGFT--TPVDVYDLLSSTKTM 1289


>AT1G63020.1 | Symbols: NRPD1A, POL IVA, SDE4, NRPD1, SMD2 | nuclear
            RNA polymerase D1A | chr1:23355329-23361126 REVERSE
            LENGTH=1453
          Length = 1453

 Score =  106 bits (265), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 118/233 (50%), Gaps = 12/233 (5%)

Query: 74   VICPVLLGTIIQGDPRISSANITWINPDSNAWVRNPSKSSN---GELALDIILEEAAVKQ 130
            V+ P LL + ++GD  I   NI W +       + P ++ N   GEL L + +     K+
Sbjct: 1066 VLIPFLLDSPVKGDQGIKKVNILWTDRP-----KAPKRNGNHLAGELYLKVTMYGDRGKR 1120

Query: 131  SGDAWRIVLDSCLPVLNLIDTRRSIPYAIKQVQELLGISCTFDQAIQRLAASVKMVAKGV 190
              + W  +L++CLP++++ID  RS P  I+Q   + GI       +  L ++V    K +
Sbjct: 1121 --NCWTALLETCLPIMDMIDWGRSHPDNIRQCCSVYGIDAGRSIFVANLESAVSDTGKEI 1178

Query: 191  LREHLILLASSMTCGGNLVGFNTGGYKALARQLNIQVPFTDATLFTPKKCFERAAEKCHT 250
            LREHL+L+A S++  G  V  N  G+    +  +   PFT A   +P +CF +AA++   
Sbjct: 1179 LREHLLLVADSLSVTGEFVALNAKGWSKQRQVESTPAPFTQACFSSPSQCFLKAAKEGVR 1238

Query: 251  DSLSSIVASCSWGKPVAVGTGSRFDVLWDAKERKSNELEGMDVYNFLHMVKSL 303
            D L   + + +WGK    GTG +F+++   K         +DVY+ L   K++
Sbjct: 1239 DDLQGSIDALAWGKVPGFGTGDQFEIIISPKVHGFT--TPVDVYDLLSSTKTM 1289