RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13846
(1423 letters)
>gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA
polymerase III (RNAP III), C-terminal domain. Eukaryotic
RNA polymerase III (RNAP III) is a large multi-subunit
complex responsible for the synthesis of tRNAs, 5SrRNA,
Alu-RNA, U6 snRNA, among others. Rpc1 is also known as
C160 in yeast. Structure studies suggest that different
RNA polymerase complexes share a similar crab-claw-shape
structure. The C-terminal domain of Rpb1, the largest
subunit of RNAP II, makes up part of the foot and jaw
structures of RNAP II. The similarity between this domain
and the C-terminal domain of Rpb1, its counterpart in
RNAP II, suggests a similar functional and structural
role.
Length = 300
Score = 350 bits (901), Expect = e-110
Identities = 150/308 (48%), Positives = 193/308 (62%), Gaps = 33/308 (10%)
Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG-----------EVCEYIE----- 1152
KY+RA++EP TAVGA+AAQSIGEPGTQMTLKTFHFAG + E I
Sbjct: 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNI 60
Query: 1153 -------EVFVPDD--SFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHS 1203
++ D S ++K +++ L + I ++ +
Sbjct: 61 STPIITAKLENDRDEKSARIVKGRIEKTYLGEV---ASYIEEVYSPD---DCYILIKLDK 114
Query: 1204 FLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNL 1263
+I K + S + + +K+ LP VV+ G+ + RAVI+++ +G KYKLLVEG L
Sbjct: 115 KIIEKLQLSKSNLYFLLQSLKRKLPDVVVSGIPEVKRAVINKDKKKG--KYKLLVEGYGL 172
Query: 1264 RDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVAD 1323
R VM T GV G + +SN+ EV K LGIEAARSTI+ EI+ M++HGMSID RH ML+AD
Sbjct: 173 RAVMNTPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLAD 232
Query: 1324 LMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLP 1383
LMT KGEVLGITR G+AKMKESVL LASFE T+DHLF+AA +G+ D I GVSECIIMG P
Sbjct: 233 LMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKP 292
Query: 1384 MNVGTGLI 1391
M +GTGL
Sbjct: 293 MPIGTGLF 300
Score = 287 bits (737), Expect = 7e-88
Identities = 129/273 (47%), Positives = 156/273 (57%), Gaps = 63/273 (23%)
Query: 725 FHFPQVYYERRRDYSVKVTASVKVTLELWNPGDYKLSQDGVPRIKEIINASRNISTPIIT 784
FHF V AS+ +TL GVPRIKEIINAS+NISTPIIT
Sbjct: 33 FHFAGV-------------ASMNITL-------------GVPRIKEIINASKNISTPIIT 66
Query: 785 AYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDDSFILIKLDMDRIRLLHLEVDI 844
A L+ D D ARIVKGR+E+T LGEV YIEEV+ PDD +ILIKLD I L L
Sbjct: 67 AKLENDRDEKSARIVKGRIEKTYLGEVASYIEEVYSPDDCYILIKLDKKIIEKLQL---- 122
Query: 845 DSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINR 904
S + + +K+ LP VV+ G+ + R
Sbjct: 123 -------------------------------SKSNLYFLLQSLKRKLPDVVVSGIPEVKR 151
Query: 905 AVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMT 964
AVI+++ +G KYKLLVEG LR VM T GV G + +SN+ EV K LGIEAARSTI+
Sbjct: 152 AVINKDKKKG--KYKLLVEGYGLRAVMNTPGVIGTRTTSNHIMEVEKVLGIEAARSTIIN 209
Query: 965 EIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
EI+ M++HGMSID RH ML+ADLMT KGEVLG
Sbjct: 210 EIQYTMKSHGMSIDPRHIMLLADLMTFKGEVLG 242
Score = 59.9 bits (146), Expect = 2e-09
Identities = 21/32 (65%), Positives = 25/32 (78%)
Query: 671 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLI 702
F+AA +G+ D I GVSECIIMG PM +GTGL
Sbjct: 269 FNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 264 bits (678), Expect = 9e-74
Identities = 102/270 (37%), Positives = 158/270 (58%), Gaps = 31/270 (11%)
Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
D D+VLFNRQPSLH++SIMAHR +VLP +TFR N VC PYNADFDGDEMN+H+PQTEEA
Sbjct: 414 DGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEA 473
Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
RAE A++LM + ++++PR G +I QD I+G YLLT+K+ F +
Sbjct: 474 RAE--------------ARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTK 519
Query: 461 AQTMRI-ASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
+ + + + I + + I+ N + WTGKQIFSL L + +
Sbjct: 520 EEALDLLRAAGIDELPEPEPAIE-------NGKPY------WTGKQIFSLFLPKDLNLEF 566
Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
A + + +E C D+YV+++N +LL G +DK +G+ + ++ +++++G +
Sbjct: 567 KAKICSGCD--ECKKEDCEHDAYVVIKNGKLLEGVIDKKAIGA-EQGSILDRIVKEYGPE 623
Query: 580 VAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
A + ++R+ ++M RGF+ GI D
Sbjct: 624 RARRFLDSVTRLAIRFIMLRGFTTGIDDED 653
Score = 148 bits (375), Expect = 5e-36
Identities = 72/245 (29%), Positives = 114/245 (46%), Gaps = 38/245 (15%)
Query: 91 DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
+ +++ S +I++ + Y D PI GL+D R+G C TCG +C GHFG+
Sbjct: 20 EEIRKMSVTKIITADTY--DDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGH 77
Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLK 210
I+L PV H+G+ + + +L++ C+ C R+ L EE+ + KL + L
Sbjct: 78 IELARPVIHVGFAKLIYKLLRATCRE--CGRLKLTEEEIEEYLEKLERLKEWGSLADDLI 135
Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
K++ + K VCPHCGE KI EK + E
Sbjct: 136 KEVKKEAAKRMVCPHCGEK--------QYKIKFEKPTT---------------FYEER-- 170
Query: 271 NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCI 330
+ K L P ++ + E IP ED+ LL +N E+++P ++LT L VPP +
Sbjct: 171 --KEGLVK-------LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTV 221
Query: 331 RPSVI 335
RPS+
Sbjct: 222 RPSIT 226
Score = 120 bits (304), Expect = 2e-27
Identities = 43/64 (67%), Positives = 56/64 (87%), Gaps = 1/64 (1%)
Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
GD+ +GFV++S+ SGLTPTEFFFH MGGREGLVDTAV+T+++GYMQRRL+ +L+DL
Sbjct: 773 GDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLK 832
Query: 665 VQYD 668
V+YD
Sbjct: 833 VEYD 836
Score = 57.2 bits (139), Expect = 6e-08
Identities = 16/47 (34%), Positives = 30/47 (63%)
Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
+LM + ++++PR G +I QD I+G YLLT+K+ F + + + +
Sbjct: 479 ILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDL 525
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 250 bits (642), Expect = 9e-74
Identities = 136/418 (32%), Positives = 213/418 (50%), Gaps = 96/418 (22%)
Query: 1031 LSNETLDSKEFLQDTSENFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQILSHQDKIGH 1090
+S ETL+ K L+D S + +K+ L E ++ +T E++ ++I
Sbjct: 2 MSEETLEEK--LEDASLELPQKLKEELREKLEERKLT----------EEEV----EEI-- 43
Query: 1091 GRESNPFPSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----- 1145
E +Y+R+ +EP AVG +AAQSIGEPGTQMT++TFH+AG
Sbjct: 44 ------------IEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEIN 91
Query: 1146 ---------------------------------------EVCEYIEEVFV---------- 1156
EV IE +
Sbjct: 92 VTLGLPRLIEIVDARKEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISVD 151
Query: 1157 PDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSF 1216
+ I+I+LD + L + +D ++ IE+ +G G + + G++ LI+ PK+ S
Sbjct: 152 LANMTIIIELDEEM--LEDRGLTVDDVKEAIEKKKG--GEVEIEGNT-LIISPKEPSYR- 205
Query: 1217 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 1276
++ ++ + + ++ IKG++GI R +I +E E Y + EG NL++V+ GV +
Sbjct: 206 --ELRKLAEKIRNIKIKGIKGIKRVIIRKEGDE----YVIYTEGSNLKEVLKVEGVDATR 259
Query: 1277 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITR 1336
++NN +E+ + LGIEAAR+ I+ EIK +E G+ +D RH MLVAD+MT GEV I R
Sbjct: 260 TTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGR 319
Query: 1337 HGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
HG++ K SVL A+FE T HL DAA G+ D + GV+E II+G P+ +GTG ++L
Sbjct: 320 HGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELT 377
Score = 169 bits (430), Expect = 1e-45
Identities = 82/234 (35%), Positives = 139/234 (59%), Gaps = 16/234 (6%)
Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
G+PR+ EI++A + STP++T YL + D + A V ++E TTL + + I
Sbjct: 95 GLPRLIEIVDARKEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDIS--VDL 152
Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
+ I+I+LD + L + +D ++ IE+ +G G + + G++ LI+ PK+ S
Sbjct: 153 ANMTIIIELDEEM--LEDRGLTVDDVKEAIEKKKG--GEVEIEGNT-LIISPKEPSYR-- 205
Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
++ ++ + + ++ IKG++GI R +I +E E Y + EG NL++V+ GV +
Sbjct: 206 -ELRKLAEKIRNIKIKGIKGIKRVIIRKEGDE----YVIYTEGSNLKEVLKVEGVDATRT 260
Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
++NN +E+ + LGIEAAR+ I+ EIK +E G+ +D RH MLVAD+MT GEV
Sbjct: 261 TTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEV 314
Score = 39.4 bits (93), Expect = 0.012
Identities = 16/35 (45%), Positives = 24/35 (68%)
Query: 671 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 705
DAA G+ D + GV+E II+G P+ +GTG ++L
Sbjct: 343 LDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELT 377
>gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP).
Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a
large multi-subunit complex responsible for the synthesis
of all RNAs in the cell. The relative positioning of the
RNAP core is highly conserved between archaeal RNAP and
the three classes of eukaryotic RNAPs. In archaea, the
largest subunit is split into two polypeptides, A' and
A'', which are encoded by separate genes in an operon.
Sequence alignments reveal that the archaeal A'' subunit
corresponds to the C-terminal one-third of the RNAPII
largest subunit (Rpb1). In subunit A'', several loops in
the jaw domain are shorter. The RNAPII Rpb1 interacts
with the second-largest subunit (Rpb2) to form the DNA
entry and RNA exit channels in addition to the catalytic
center of RNA synthesis.
Length = 363
Score = 244 bits (624), Expect = 1e-71
Identities = 118/346 (34%), Positives = 174/346 (50%), Gaps = 64/346 (18%)
Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------- 1145
+ +Y+R+ IEP AVG +AAQSIGEPGTQMTL+TFH+AG
Sbjct: 25 IKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIV 84
Query: 1146 ---------------------------EVCEYIEEVFV----------PDDSFILIKLDM 1168
EV IEE + + I I+LD
Sbjct: 85 DARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISIDLFNMRITIELDE 144
Query: 1169 DRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLLP 1228
+ + + VD + IE+ + ++ + S K ++ ++ + +
Sbjct: 145 EMLEDRGITVD--DVLKAIEKLKKGKVGEEGDVTLIVLKAEEPSIK----ELRKLAEKIL 198
Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT 1288
+ IKG++GI R ++ +E+ E Y + EG NL+ V+ GV + ++NN +E+ +
Sbjct: 199 NTKIKGIKGIKRVIVRKEEDE----YVIYTEGSNLKAVLKVEGVDPTRTTTNNIHEIEEV 254
Query: 1289 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLN 1348
LGIEAAR+ I+ EIK +E G+ +D RH MLVAD+MT GEV I RHG+A K SVL
Sbjct: 255 LGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLA 314
Query: 1349 LASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
A+FE T HL DAA G+ D + GV E II+G P+ +GTG ++L
Sbjct: 315 RAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELT 360
Score = 168 bits (427), Expect = 2e-45
Identities = 76/234 (32%), Positives = 128/234 (54%), Gaps = 14/234 (5%)
Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
G+PR+ EI++A + STP +T YL+++ D + A V ++E TTL + E I
Sbjct: 76 GLPRLIEIVDARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDIS--IDL 133
Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
+ I I+LD + + + VD + IE+ + ++ + S K
Sbjct: 134 FNMRITIELDEEMLEDRGITVD--DVLKAIEKLKKGKVGEEGDVTLIVLKAEEPSIK--- 188
Query: 882 SKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKC 941
++ ++ + + + IKG++GI R ++ +E+ E Y + EG NL+ V+ GV +
Sbjct: 189 -ELRKLAEKILNTKIKGIKGIKRVIVRKEEDE----YVIYTEGSNLKAVLKVEGVDPTRT 243
Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
++NN +E+ + LGIEAAR+ I+ EIK +E G+ +D RH MLVAD+MT GEV
Sbjct: 244 TTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEV 297
Score = 38.8 bits (91), Expect = 0.016
Identities = 16/35 (45%), Positives = 23/35 (65%)
Query: 671 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 705
DAA G+ D + GV E II+G P+ +GTG ++L
Sbjct: 326 LDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELT 360
>gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A''.
This family consists of the archaeal A'' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein
[Transcription, DNA-dependent RNA polymerase].
Length = 367
Score = 231 bits (592), Expect = 2e-67
Identities = 123/347 (35%), Positives = 188/347 (54%), Gaps = 65/347 (18%)
Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------- 1145
+ E+Y+R+ I+P AVG +AAQSIGEPGTQMT++TFH+AG
Sbjct: 29 IKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIV 88
Query: 1146 ---------------------------EVCEYIEEVFVPD----------DSFILIKLDM 1168
EV + IE + D D ++I+LD
Sbjct: 89 DARKTPSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLADMTVIIELDE 148
Query: 1169 DRIRLLHLEVDIDSIRYCIERTR-GISGHLTVSGHSFLILKPKDSSKSFNSKMYQMKQLL 1227
++++ + VD + I++ + G + + G++ I PK S K ++ ++K+ +
Sbjct: 149 EQLKERGITVD--DVEKAIKKAKLGKVIEIDMDGNTITIKPPKPSLK----ELRKLKEKI 202
Query: 1228 PSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYK 1287
++ IKG++GI R VI +E E Y + EG NL++V+ GV + ++N+ +E+ +
Sbjct: 203 KNLHIKGIKGIKRVVIRKEGDE----YVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAE 258
Query: 1288 TLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVL 1347
LGIEAAR+ I+ EIK +E G+ +D RH MLVADLMT GEV I RHG++ K SVL
Sbjct: 259 VLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVL 318
Query: 1348 NLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
A+FE T HL DAA G+ D ++GV E II+G P+ +GTG + L+
Sbjct: 319 ARAAFEVTVKHLLDAAIRGEVDELAGVIENIIVGQPIPLGTGDVDLV 365
Score = 155 bits (393), Expect = 6e-41
Identities = 83/239 (34%), Positives = 139/239 (58%), Gaps = 15/239 (6%)
Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
G+PR+ EI++A + STP +T YL+ + D + A V ++E T L +V + I
Sbjct: 80 GLPRLIEIVDARKTPSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLA- 138
Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTR-GISGHLTVSGHSFLILKPKDSSKSF 880
D ++I+LD ++++ + VD + I++ + G + + G++ I PK S K
Sbjct: 139 -DMTVIIELDEEQLKERGITVD--DVEKAIKKAKLGKVIEIDMDGNTITIKPPKPSLK-- 193
Query: 881 NSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVK 940
++ ++K+ + ++ IKG++GI R VI +E E Y + EG NL++V+ GV +
Sbjct: 194 --ELRKLKEKIKNLHIKGIKGIKRVVIRKEGDE----YVIYTEGSNLKEVLKLEGVDKTR 247
Query: 941 CSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNG 999
++N+ +E+ + LGIEAAR+ I+ EIK +E G+ +D RH MLVADLMT GEV G
Sbjct: 248 TTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIG 306
Score = 36.6 bits (85), Expect = 0.089
Identities = 16/34 (47%), Positives = 24/34 (70%)
Query: 672 DAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 705
DAA G+ D ++GV E II+G P+ +GTG + L+
Sbjct: 332 DAAIRGEVDELAGVIENIIVGQPIPLGTGDVDLV 365
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'.
This family consists of the archaeal A' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein.
Length = 867
Score = 234 bits (599), Expect = 8e-64
Identities = 101/273 (36%), Positives = 150/273 (54%), Gaps = 37/273 (13%)
Query: 340 SDNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
D D+VLFNRQPSLH++S+M H+ KVLP +TFR N VC PYNADFDGDEMN+H+PQTEE
Sbjct: 409 IDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEE 468
Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
ARAE A+ LM + +++TPR G +I D+I+G YLLT K+ F
Sbjct: 469 ARAE--------------ARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFT 514
Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
+ + I I+ P + WTGKQIFS L P
Sbjct: 515 KEEVQTILGVAGYFGDPPEPAIE-------KPKEY------WTGKQIFSAFL------PE 555
Query: 520 NANLKTK---GRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDF 576
+ N + + + +E C D+YV+++N +LL G +DK +G+ K + + ++R++
Sbjct: 556 DLNFEGRAKICSSDACKKEECPHDAYVVIKNGKLLKGVIDKKAIGA-EKGKILHRIVREY 614
Query: 577 GEDVAVTAMWRLSRMTSFYLMNRGFSIGIGDVT 609
G + A + ++R+ ++ RGF+ GI D+
Sbjct: 615 GPEAARRFLDSVTRLFIRFITLRGFTTGIDDID 647
Score = 144 bits (365), Expect = 7e-35
Identities = 77/269 (28%), Positives = 130/269 (48%), Gaps = 49/269 (18%)
Query: 91 DRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGY 150
+ +++ S +++V+ + Y D PI GL+D R+G + C TCG + +C GHFG+
Sbjct: 15 EEIRKMSVVEVVTADTY--DDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGH 72
Query: 151 IDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRN-PALSYLVRKSL 209
I+L PV H+G+ + + IL++ C C R+ L EE+ + K+ + +L
Sbjct: 73 IELARPVVHVGFAKEIYKILRATC--RKCGRITLTEEEIEQYLEKINKLKEEGGDLASTL 130
Query: 210 KKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVK 269
+KI++ K CPHCGE E+ K + +K E+
Sbjct: 131 IEKIVKEAAKRMKCPHCGE---------------EQKKIKFEKPTYFYEE---------- 165
Query: 270 FNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNC 329
K G ++ L P E+ + E IP ED LL +N ++++P ++LT L VPP
Sbjct: 166 --------GKEGDVK-LTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVT 216
Query: 330 IRPSVI--SDLKSDNDVVLFNRQPSLHKL 356
+RPS+ + +S++D+ HKL
Sbjct: 217 VRPSITLETGERSEDDLT--------HKL 237
Score = 110 bits (277), Expect = 3e-24
Identities = 42/79 (53%), Positives = 57/79 (72%), Gaps = 7/79 (8%)
Query: 597 MNRGFS------IGIGDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAET 649
+ RG+ GD+ +GFV++SF GL PTE+FFH GGREGLVDTAV+T+++
Sbjct: 752 IRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQS 811
Query: 650 GYMQRRLVKSLEDLCVQYD 668
GYMQRRL+ +L+DL V+YD
Sbjct: 812 GYMQRRLINALQDLYVEYD 830
Score = 47.0 bits (112), Expect = 7e-05
Identities = 17/46 (36%), Positives = 27/46 (58%)
Query: 22 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
LM + +++TPR G +I D+I+G YLLT K+ F + + I
Sbjct: 476 LMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTI 521
>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase
subunit A'' fusion protein; Provisional.
Length = 509
Score = 217 bits (555), Expect = 7e-61
Identities = 133/449 (29%), Positives = 206/449 (45%), Gaps = 94/449 (20%)
Query: 1003 ELKRLLDDIIAKNSSRSDPSLSAQEILALS--NETLDSKEFLQDTSENFVRDIKKFLEEF 1060
E KRL I+ +N S S L E N D + + D + R +EE
Sbjct: 90 EFKRLFGRILDENMSFSTGELLTAEEKEYYEENSNEDVLKVIDDVKKLGFRLPPSVIEEI 149
Query: 1061 SKKESVTSHQDKVSQPLREQILSHQDKIGHGRESNPFPSACKAEACREKYVRAQIEPATA 1120
+K D + + +I RE+Y RA+++P A
Sbjct: 150 AKAMKKKELSDDEYEEILRRI-------------------------REEYERARVDPYEA 184
Query: 1121 VGALAAQSIGEPGTQMTLKTFHFAG----------------------------------- 1145
VG +AAQSIGEPGTQMT++TFH+AG
Sbjct: 185 VGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARKKPSTPTMTIYLKKD 244
Query: 1146 ---------EVCEYIEEVFVPD---------DSFILIKLDMDRIRLLHLEVDIDSIRYCI 1187
EV + IE + D + ++++LD ++++ +E D I I
Sbjct: 245 YREDEEKVREVAKKIENTTLIDVADIITDIAEMSVVVELDEEKMKERLIEYD--DILAAI 302
Query: 1188 ERTRGISGHLTVSGHSFLIL--KPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHE 1245
+ TV +I + S K K+Y + + + S+ IKG++GI RA+ +
Sbjct: 303 SKLTFK----TVEIDDGIIRLKPQQPSFK----KLYLLAEKVKSLTIKGIKGIKRAIARK 354
Query: 1246 EDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLV 1305
E+ E ++ + +G NL+DV+ V + +N+ E+ LGIEAAR+ I+ E K
Sbjct: 355 ENDE--RRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRT 412
Query: 1306 MENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFY 1365
++ G+++D RH MLVAD+MT G V I RHG++ K SVL A+FE T HL A
Sbjct: 413 LQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKHLLRAGIL 472
Query: 1366 GQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
G+ D ++GV+E II+G P+ +GTG + L+
Sbjct: 473 GEVDKLAGVAENIIVGQPITLGTGAVSLV 501
Score = 148 bits (375), Expect = 2e-37
Identities = 77/236 (32%), Positives = 131/236 (55%), Gaps = 19/236 (8%)
Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
G+PR+ EI++A + STP +T YL KD D + R V ++E TTL +V + I ++
Sbjct: 218 GLPRLIEIVDARKKPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDVADIITDI--- 274
Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLIL--KPKDSSKS 879
+ ++++LD ++++ +E D I I + TV +I + S K
Sbjct: 275 AEMSVVVELDEEKMKERLIEYD--DILAAISKLTFK----TVEIDDGIIRLKPQQPSFK- 327
Query: 880 FNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV 939
K+Y + + + S+ IKG++GI RA+ +E+ E ++ + +G NL+DV+ V
Sbjct: 328 ---KLYLLAEKVKSLTIKGIKGIKRAIARKENDE--RRWVIYTQGSNLKDVLEIDEVDPT 382
Query: 940 KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
+ +N+ E+ LGIEAAR+ I+ E K ++ G+++D RH MLVAD+MT G V
Sbjct: 383 RTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSV 438
Score = 35.2 bits (81), Expect = 0.27
Identities = 14/34 (41%), Positives = 23/34 (67%)
Query: 672 DAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 705
A G+ D ++GV+E II+G P+ +GTG + L+
Sbjct: 468 RAGILGEVDKLAGVAENIIVGQPITLGTGAVSLV 501
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 211 bits (539), Expect = 2e-55
Identities = 106/270 (39%), Positives = 154/270 (57%), Gaps = 29/270 (10%)
Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
D D+V+FNRQPSLHKLSI+AHR KVLP TFR + VC PYNADFDGDEMN+H+PQ E+A
Sbjct: 430 DGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDA 489
Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNR 460
RAE A LM K NL++PR G +I A QDFIT YL+T+ +A F++
Sbjct: 490 RAE--------------AIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDK 535
Query: 461 AQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVN 520
+ IA + GI P + + WTGKQ+FSL L + +
Sbjct: 536 NEASNIAM--------LAGITDPLP----EPAIKTKDGPAWTGKQLFSLFLPKDFNFEGI 583
Query: 521 ANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSG--GKANVFYILLRDFGE 578
A + G+A A + C D YV+++ EL++G +D + +G+ ++ + +D+GE
Sbjct: 584 AKW-SAGKAGEAKDPSCLGDGYVLIKEGELISGVIDDNIIGALVEEPESLIDRIAKDYGE 642
Query: 579 DVAVTAMWRLSRMTSFYLMNRGFSIGIGDV 608
VA+ + ++ + +++ GFS G GD+
Sbjct: 643 AVAIEFLNKILIIAKKEILHYGFSNGPGDL 672
Score = 112 bits (281), Expect = 9e-25
Identities = 59/172 (34%), Positives = 96/172 (55%), Gaps = 6/172 (3%)
Query: 1232 IKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTLGI 1291
+KGV I RA + + +G ++ + G NL V+ + +N+ +E+ TLGI
Sbjct: 1146 VKGVPDIERAWVELVEKDGRDEWIIQTSGSNLAAVLEMKCIDIANTITNDCFEIAGTLGI 1205
Query: 1292 EAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGI------TRHGLAKMKES 1345
EAAR+ I E+ ++E+ G+ +D R+ MLVAD+M S+G + I RHG A K+S
Sbjct: 1206 EAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIGLQAAGVRHGFAGEKDS 1265
Query: 1346 VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLLQAV 1397
L A+FE T+ + AA G+ + I G+ + +IMG + +G+G + LL
Sbjct: 1266 PLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDF 1317
Score = 108 bits (272), Expect = 1e-23
Identities = 78/277 (28%), Positives = 125/277 (45%), Gaps = 54/277 (19%)
Query: 81 GLIEGTVTKEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQN 140
G+I G ++ D ++ +I + Y D P+ GLLD R+GT + C TCG
Sbjct: 11 GIIFGLISPAD-ARKIGFAEITAPEAY--DEDGLPVQGGLLDGRLGTIEPGQKCLTCGNL 67
Query: 141 LSDCVGHFGYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRA-KLRNP 199
++C GHFG+I+L PV HI + + ++L S C CA++ L +E F+ + +
Sbjct: 68 AANCPGHFGHIELAEPVIHIAFIDNIKDLLNSTCH--KCAKLKLPQEDLNVFKLIEEAHA 125
Query: 200 ALSYLVRKSLKKKILE--------TTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTK 251
A + K + +I+E KK CPHCG HE
Sbjct: 126 AARDIPEKRIDDEIIEEVRDQVKVYAKKAKECPHCG------------APQHE------- 166
Query: 252 KKDAIVEDLLAEYNEAVKF--NPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMN 309
E+ E F EIE H+ L P+E+ +FE I +D+ L+ +
Sbjct: 167 ----------LEFEEPTIFIEKTEIEEHR-------LLPIEIRDIFEKIIDDDLELIGFD 209
Query: 310 AELSKPSDLILTRLLVPPNCIRPSVI--SDLKSDNDV 344
+ ++P +L LVPP RPS+I + +S++D+
Sbjct: 210 PKKARPEWAVLQAFLVPPLTARPSIILETGERSEDDL 246
Score = 93.6 bits (232), Expect = 5e-19
Identities = 57/235 (24%), Positives = 109/235 (46%), Gaps = 10/235 (4%)
Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
G+ R E+++A STP + YLD + D++ A + L+ +V I + +
Sbjct: 1014 GLERFIELVDARAKPSTPTMDIYLDDECKEDIEKAIEIARNLKEL---KVRALIADSAID 1070
Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERT-RGISGHLTVSGHSFLI--LKPKDSSK 878
+ + I + R + ++ +G + + ++ ++ D K
Sbjct: 1071 NANEIKLIKPDKRALENGC-IPMERFAEIEAALAKGKKFEMELEDDLIILDLVEAADRDK 1129
Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
+ + ++L V KGV I RA + + +G ++ + G NL V+ +
Sbjct: 1130 PLATLIAIRNKILDKPV-KGVPDIERAWVELVEKDGRDEWIIQTSGSNLAAVLEMKCIDI 1188
Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
+N+ +E+ TLGIEAAR+ I E+ ++E+ G+ +D R+ MLVAD+M S+G
Sbjct: 1189 ANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRG 1243
Score = 91.6 bits (227), Expect = 2e-18
Identities = 35/64 (54%), Positives = 46/64 (71%), Gaps = 1/64 (1%)
Query: 606 GDVTP-GQGFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLC 664
GD P GFV+N++ GL EFFFH MGGREGL+D A +T ++GY QRRL +LED+
Sbjct: 809 GDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIR 868
Query: 665 VQYD 668
++YD
Sbjct: 869 LEYD 872
Score = 64.7 bits (157), Expect = 3e-10
Identities = 36/106 (33%), Positives = 52/106 (49%), Gaps = 12/106 (11%)
Query: 1048 NFVRDIKKFLEEFSKKESVTSHQDKVSQPLREQI--------LSHQDKIGHGRESNPFPS 1099
N R I+K E K + +D++ + +E D I
Sbjct: 904 NLERIIEKQKIEDRGKGAS---KDEIEELAKEYTKTFNANLPKLLADAIHGAELKEDELE 960
Query: 1100 ACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
A AE +E + +A++EP A+G ++AQSI EPGTQMTL+TFH AG
Sbjct: 961 AICAEG-KEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAG 1005
Score = 51.2 bits (122), Expect = 5e-06
Identities = 22/48 (45%), Positives = 31/48 (64%)
Query: 22 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIAS 69
LM K NL++PR G +I A QDFIT YL+T+ +A F++ + IA
Sbjct: 496 LMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAM 543
>gnl|CDD|218370 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 1, represents the clamp domain, which a
mobile domain involved in positioning the DNA,
maintenance of the transcription bubble and positioning
of the nascent RNA strand.
Length = 330
Score = 192 bits (490), Expect = 3e-54
Identities = 89/258 (34%), Positives = 128/258 (49%), Gaps = 24/258 (9%)
Query: 89 KEDRVQQQSHIQIVSKNLYCQDPQRTPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHF 148
+ +++ S ++ Y + P P GLLD RMGT +K++ C TCG +++C GHF
Sbjct: 13 SPEEIRKWSVGEVTKPETYNYGSLK-PEPGGLLDERMGTIKKKSICETCGVEVTECPGHF 71
Query: 149 GYIDLPLPVFHIGYFRCVINILQSICKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKS 208
G+I+L PVFHIG+F+ +++IL+ +CK C+ +LL E F + +P K
Sbjct: 72 GHIELAKPVFHIGFFKKILSILRCVCKL--CSSLLLNESVKYFFLKVVIDP--KGKNSKK 127
Query: 209 LKKKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKD---AIVEDLLAEYN 265
KKI KK S+C CGE NG +K K KD AI L
Sbjct: 128 RLKKINNLCKKKSICSKCGEDNGGLKAFEGCGKYQPKI-----SKDGAEAIKALLK---- 178
Query: 266 EAVKFNPEIEAHKKFGLIQTLNPLEVLQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLV 325
E++ + LNP +VLQ+F+ I ED +L N ++P +ILT L V
Sbjct: 179 --NIEIEELKEKLR-----KLNPEKVLQIFKKISKEDEEILGFNPSGNRPEWMILTVLPV 231
Query: 326 PPNCIRPSVISDLKSDND 343
PP CIRPSV D +
Sbjct: 232 PPPCIRPSVQLDGGRFAE 249
>gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase compared
to three in eukaryotes (not including mitochondrial. and
chloroplast polymerases). This domain, domain 5,
represents the discontinuous cleft domain that is
required to from the central cleft or channel where the
DNA is bound.
Length = 447
Score = 192 bits (491), Expect = 5e-53
Identities = 92/308 (29%), Positives = 127/308 (41%), Gaps = 61/308 (19%)
Query: 1101 CKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG--------------- 1145
C R+KY R+ +EP AVG +AAQSIGEPGTQMTL TFHFAG
Sbjct: 138 CFLCYGRDKYRRSLVEPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKE 197
Query: 1146 --------------------------------EVCEYIEEVFVP-------DDSFILIKL 1166
E + V DD +
Sbjct: 198 IINVAKNNKKPVITVLLIKNIVSDKARVKKQREEKTLLLLKKVTIIIVIYYDDDSESTVI 257
Query: 1167 DMDRIRLLHLEVDIDSI---RYCIERTRGISGHLTVSGHSFLILKPKDSSK--SFNSKMY 1221
DRI +L V + + G ++ + K + +
Sbjct: 258 KKDRIWVLAYFVIPEEVAEEVALAIIIIGKRKSRKRKKNNLGVAKDEKGLEEEELLLLNK 317
Query: 1222 QMKQLLPSVVIKGVQGINRAVI-HEEDVEGVTKYKLLVEGDNLRDVMATYGV-KGVKCSS 1279
+ + V GV + V H + ++ L EG+NL+ VM GV K S
Sbjct: 318 ILLVIPGIKVKYGVILTDGRVDPHTILEKLGKEWLLKTEGNNLQAVMRLQGVIDNDKTYS 377
Query: 1280 NNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGL 1339
N+ E+ K LGIEAAR +I+ EI+ V + G+ ++ RH L+ADLMT KGE+LGITR GL
Sbjct: 378 NDIREMLKKLGIEAARDSILLEIRNVFKFDGIYVNRRHLALLADLMTFKGELLGITRAGL 437
Query: 1340 AKMKESVL 1347
+ K S +
Sbjct: 438 NREKSSFI 445
Score = 169 bits (431), Expect = 3e-45
Identities = 78/241 (32%), Positives = 113/241 (46%), Gaps = 7/241 (2%)
Query: 764 GVPRIKEIINASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPDD 823
GVPR+KEIIN ++N P+IT L K+ D AR+ K R E+T L I V DD
Sbjct: 191 GVPRLKEIINVAKNNKKPVITVLLIKNIVSDKARVKKQREEKTLLLLKKVTIIIVIYYDD 250
Query: 824 SFILIKLDMDRIRLLHLEVDIDSI---RYCIERTRGISGHLTVSGHSFLILKPKDSSK-- 878
+ DRI +L V + + G ++ + K + +
Sbjct: 251 DSESTVIKKDRIWVLAYFVIPEEVAEEVALAIIIIGKRKSRKRKKNNLGVAKDEKGLEEE 310
Query: 879 SFNSKMYQMKQLLPSVVIKGVQGINRAVI-HEEDVEGVTKYKLLVEGDNLRDVMATYGV- 936
+ + V GV + V H + ++ L EG+NL+ VM GV
Sbjct: 311 ELLLLNKILLVIPGIKVKYGVILTDGRVDPHTILEKLGKEWLLKTEGNNLQAVMRLQGVI 370
Query: 937 KGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL 996
K SN+ E+ K LGIEAAR +I+ EI+ V + G+ ++ RH L+ADLMT KGE+L
Sbjct: 371 DNDKTYSNDIREMLKKLGIEAARDSILLEIRNVFKFDGIYVNRRHLALLADLMTFKGELL 430
Query: 997 G 997
G
Sbjct: 431 G 431
Score = 117 bits (294), Expect = 2e-27
Identities = 42/47 (89%), Positives = 45/47 (95%)
Query: 622 GLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYD 668
GLTP EFFFHTMGGREGL+DTAVKTAETGY+QRRLVK+LEDL VQYD
Sbjct: 1 GLTPQEFFFHTMGGREGLIDTAVKTAETGYLQRRLVKALEDLVVQYD 47
>gnl|CDD|214767 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus.
Length = 295
Score = 181 bits (462), Expect = 7e-51
Identities = 56/109 (51%), Positives = 74/109 (67%), Gaps = 14/109 (12%)
Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
D DVVLFNRQP+LH++SI AHR +VL +T R N VC+PYNADFDGDEMN+H+PQ+ EA
Sbjct: 201 DGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLHVPQSLEA 260
Query: 401 RAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGY 449
RAE A+ LM +N+++P+NG+ +I QD + G Y
Sbjct: 261 RAE--------------ARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
Score = 42.1 bits (100), Expect = 0.001
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGY 50
LM +N+++P+NG+ +I QD + G Y
Sbjct: 266 ELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
Score = 37.5 bits (88), Expect = 0.038
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 316 SDLILTRLLVPPNCIRPSVISD 337
+ILT L VPP C+RPSV D
Sbjct: 1 EWMILTVLPVPPPCLRPSVQLD 22
>gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA
polymerase I (RNAP I), C-terminal domain. RNA polymerase
I (RNAP I) is a multi-subunit protein complex responsible
for the synthesis of rRNA precursor. It consists of at
least 14 different subunits, and the largest one is
homologous to subunit Rpb1 of yeast RNAP II and subunit
beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in
yeast. Structure studies suggest that different RNAP
complexes share a similar crab-claw-shape structure. The
C-terminal domain of Rpb1, the largest subunit of RNAP
II, makes up part of the foot and jaw structures of RNAP
II. The similarity between this domain and the C-terminal
domain of Rpb1, its counterpart in RNAP II, suggests a
similar functional and structural role.
Length = 309
Score = 180 bits (458), Expect = 3e-50
Identities = 104/318 (32%), Positives = 148/318 (46%), Gaps = 41/318 (12%)
Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG----------------------- 1145
KY+R+ +EP AVG LAAQSIGEP TQMTL TFHFAG
Sbjct: 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKN 60
Query: 1146 ------EVCEYIEEVFVPDDSFILIKLDMDRIRLLHL--EVDIDSIRYCIERTRGISGHL 1197
+ ++ + + L K + R+ L + +V++ I IER
Sbjct: 61 IKTPSMTL--PLKNGKSAERAETLKK-RLSRVTLSDVVEKVEVTEILKTIERVFKKLLGK 117
Query: 1198 TVSGHSFLILKPKDSSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLL 1257
I P S K + +++L VI+ + GI R + EED G TKY ++
Sbjct: 118 WCE---VTIKLPLSSPK--LLLLSIVEKLARKAVIREIPGITRCFVVEEDKGGKTKYLVI 172
Query: 1258 VEGDNLRDVMATYGVKGV-KCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFR 1316
EG NL + + V + +N+ + + T GIEAAR I+ EI V + +G+++D R
Sbjct: 173 TEGVNLAALWKFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPR 232
Query: 1317 HPMLVADLMTSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSE 1376
H L+AD MT +G R G+ S L SFE T L A G D +S S
Sbjct: 233 HLSLIADYMTFEGGYRPFNRIGMES-STSPLQKMSFETTLAFLKKATLNGDIDNLSSPSS 291
Query: 1377 CIIMGLPMNVGTGLIKLL 1394
+++G P+N GTGL LL
Sbjct: 292 RLVVGKPVNGGTGLFDLL 309
Score = 117 bits (295), Expect = 2e-28
Identities = 71/234 (30%), Positives = 106/234 (45%), Gaps = 34/234 (14%)
Query: 764 GVPRIKEII-NASRNISTPIITAYLDKDTDLDYARIVKGRLERTTLGEVCEYIEEVFVPD 822
G+PR++EI+ AS+NI TP +T L + A +K RL R TL +V E +E
Sbjct: 46 GIPRLREILMTASKNIKTPSMTLPLKNGKSAERAETLKKRLSRVTLSDVVEKVE------ 99
Query: 823 DSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNS 882
+ I IER I P S K
Sbjct: 100 ---------------------VTEILKTIERVFKKLLGKWCE---VTIKLPLSSPK--LL 133
Query: 883 KMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGV-KC 941
+ +++L VI+ + GI R + EED G TKY ++ EG NL + + V +
Sbjct: 134 LLSIVEKLARKAVIREIPGITRCFVVEEDKGGKTKYLVITEGVNLAALWKFSDILDVNRI 193
Query: 942 SSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
+N+ + + T GIEAAR I+ EI V + +G+++D RH L+AD MT +G
Sbjct: 194 YTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGY 247
Score = 37.2 bits (87), Expect = 0.054
Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 8/45 (17%)
Query: 669 MSF--------DAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 705
MSF A G D +S S +++G P+N GTGL LL
Sbjct: 265 MSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFDLL 309
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 191 bits (487), Expect = 6e-50
Identities = 80/274 (29%), Positives = 113/274 (41%), Gaps = 41/274 (14%)
Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPH-RTFRFNECVCTPYNADFDGDEMNVHLPQTEE 399
D D VL NR P+LH+LSIM VLP + R + VC YNADFDGDEM VH+P + E
Sbjct: 360 DGDPVLLNRAPTLHRLSIMQAFEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASGE 419
Query: 400 ARAEALPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFN 459
A AE A+ LM + N++TP G ++A QD + G YLLT +A
Sbjct: 420 AAAE--------------ARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLP 465
Query: 460 RAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPV 519
I D + + + TGK I S I + +
Sbjct: 466 STPVGEIYL------KDEYADDREK------AEAIAKKIELTTGKVIVSTISPDLAELSI 513
Query: 520 NANLKTKGRAYTANEEFCHRDSYVILRNSELLAGSMDKSTLGSGGKANVFYILLRDFGED 579
+ E D V + N +L+ G +DK + R++G +
Sbjct: 514 IVTTDGRRIFNRGLPEDK--DVLVKIVNGKLIKGVIDKKI----------VTIYREYGPE 561
Query: 580 VAVTA-MWRLSRMTSFYLMNRG-FSIGIGDVTPG 611
VA A + L ++ + + G F IGIG
Sbjct: 562 VASKALVKLLDKLKNLGIKGIGGFGIGIGRKDIE 595
Score = 125 bits (316), Expect = 5e-29
Identities = 63/226 (27%), Positives = 91/226 (40%), Gaps = 59/226 (26%)
Query: 114 TPIPHGLLDRRMGTNQKEANCTTCGQNLSDCVGHFGYIDLPLPVFHIGYFRCVINILQSI 173
P GL D R+ K+ CT CG+ C G FG+I+L PV HI +F+ + ++L
Sbjct: 35 KPERGGLFDERIFGPDKDYECT-CGKYKRICPGGFGHIELAAPVAHIWFFKSIPSLLDMT 93
Query: 174 CKNPTCARVLLGEEKAAGFRAKLRNPALSYLVRKSLKKKILETTKKV--SVCPHCGEING 231
C++ C RVL F A + L K ++L T+ V S C HCG
Sbjct: 94 CRD--CERVLY-------FEAYV------VLGTDLEKIQLLNETEYVYDSFCAHCGAEAI 138
Query: 232 VVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHKKFGLIQTLNPLEV 291
+ DL E E TL+P +V
Sbjct: 139 KILLEKP--------------------DLETEREEE-----------------TLSPTKV 161
Query: 292 LQLFEAIPLEDIPLLLMNAELSKPSDLILTRLLVPPNCIRPSVISD 337
+L + + + D LL ++P +ILT L VPP +RPS+ D
Sbjct: 162 KKLLKRLKVVDAFLL----SGNRPEWMILTVLPVPPPDLRPSIQLD 203
Score = 112 bits (282), Expect = 6e-25
Identities = 32/58 (55%), Positives = 41/58 (70%)
Query: 613 GFVQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMS 670
G ++SF GLT E+F H +GGR GLVDTA+KTA++GY+ RRLV +DL VQ D
Sbjct: 713 GPGESSFLEGLTENEYFGHPIGGRTGLVDTALKTADSGYLTRRLVDVAQDLIVQEDDC 770
Score = 101 bits (254), Expect = 1e-21
Identities = 88/408 (21%), Positives = 151/408 (37%), Gaps = 71/408 (17%)
Query: 1047 ENFVRDIKKFLEEFSKKESVTSHQDKVSQP--LREQILSHQDKIG-HGRESNPFPSACKA 1103
E + ++ L E + V ++ P R I+ + + G+ P C+A
Sbjct: 345 ERRLPEVWDVLREVIDGDPVLLNR----APTLHRLSIMQAFEPVLPEGKAIRLHPLVCEA 400
Query: 1104 EACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEV----------CEYIEE 1153
A G AA++ G GTQM + T H+ G + +
Sbjct: 401 YNADF-DGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTI 459
Query: 1154 V--FVPDDSFILIKLDMD-------------RIRLLHLEVDIDSIRYC------------ 1186
V +P I L + +I L +V + +I
Sbjct: 460 VDAKLPSTPVGEIYLKDEYADDREKAEAIAKKIELTTGKVIVSTISPDLAELSIIVTTDG 519
Query: 1187 -----------------IERTRGISGHL-TVSGHSFLILKPKDSSKSFNSKMYQMKQLLP 1228
I + I G + + P+ +SK+ + ++K L
Sbjct: 520 RRIFNRGLPEDKDVLVKIVNGKLIKGVIDKKIVTIYREYGPEVASKALVKLLDKLKNL-- 577
Query: 1229 SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD--NLRDVMATYGVKGVKCSSNNTYEVY 1286
IKG+ G + ++ K ++++E + L+ ++ + NN E+
Sbjct: 578 --GIKGIGGFGIGIGRKDIEAEDEKDEIVIEAEGSVLKLILQYEEGDLTRTERNNIVEII 635
Query: 1287 KTLGIEAARSTIMTEIKLVMENHGMSI-DFRHPMLVADLMTSKGEVLGITRHGLAKMKES 1345
+ LGIEA R+ I+ EIK+ +E G+ D RH L M V I + G+ K S
Sbjct: 636 EVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMNISQIVQLIGQQGVMGEKIS 695
Query: 1346 VLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
VL A+FE T HL +A G++ + G++E G P+ TGL+
Sbjct: 696 VLARAAFEVTVKHL-EAEGPGESSFLEGLTENEYFGHPIGGRTGLVDT 742
Score = 61.1 bits (149), Expect = 3e-09
Identities = 59/238 (24%), Positives = 103/238 (43%), Gaps = 16/238 (6%)
Query: 761 SQD--GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIE 816
QD G P + I++A + STP+ YL + D + A + ++E TT + I
Sbjct: 447 IQDTVGGPYLLTIVDA-KLPSTPVGEIYLKDEYADDREKAEAIAKKIELTTGKVIVSTIS 505
Query: 817 EVFVPDDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHL-TVSGHSFLILKPKD 875
+ I++ D RI L D D + I + I G + + P+
Sbjct: 506 PD--LAELSIIVTTDGRRIFNRGLPEDKDVLVK-IVNGKLIKGVIDKKIVTIYREYGPEV 562
Query: 876 SSKSFNSKMYQMKQLLPSVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGD--NLRDVMAT 933
+SK+ + ++K L IKG+ G + ++ K ++++E + L+ ++
Sbjct: 563 ASKALVKLLDKLKNL----GIKGIGGFGIGIGRKDIEAEDEKDEIVIEAEGSVLKLILQY 618
Query: 934 YGVKGVKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSI-DFRHPMLVADLMT 990
+ NN E+ + LGIEA R+ I+ EIK+ +E G+ D RH L M
Sbjct: 619 EEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGLSGARMN 676
Score = 51.9 bits (125), Expect = 3e-06
Identities = 16/47 (34%), Positives = 23/47 (48%)
Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRI 67
LM + N++TP G ++A QD + G YLLT +A I
Sbjct: 426 GLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEI 472
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 173 bits (441), Expect = 4e-44
Identities = 90/233 (38%), Positives = 138/233 (59%), Gaps = 12/233 (5%)
Query: 1164 IKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFNSKMYQM 1223
IK+++D L + I+S+ IE+ G+ + L LKPK S +
Sbjct: 623 IKVELDEETLADRGLTIESVEEAIEKKLGVK---IDRKGTVLYLKPKTPS------YKAL 673
Query: 1224 KQLLP---SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSN 1280
++ +P ++V+KG+ GI R ++ +E+ E +Y L +G NLR+V GV + ++N
Sbjct: 674 RKRIPKIKNIVLKGIPGIERVLVKKEEHENDEEYVLYTQGSNLREVFKIEGVDTSRTTTN 733
Query: 1281 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLA 1340
N E+ + LGIEAAR+ I+ E+ +E G+ +D RH MLVAD+MT+ GEV I RHG+A
Sbjct: 734 NIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGVA 793
Query: 1341 KMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 1393
K SVL A+FE T HL+DAA +G+ D + GV E +I+G P+ +GTG + L
Sbjct: 794 GEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDL 846
Score = 144 bits (365), Expect = 6e-35
Identities = 82/237 (34%), Positives = 131/237 (55%), Gaps = 18/237 (7%)
Query: 764 GVPRIKEIINASRNISTPIITAYLDKD--TDLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
G+PR+ EI++A + STPI+T +L + TD + A V ++E TLG+V I
Sbjct: 561 GLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAIDLWT 620
Query: 822 DDSFILIKLDMDRIRLLHLEVDIDSIRYCIERTRGISGHLTVSGHSFLILKPKDSSKSFN 881
IK+++D L + I+S+ IE+ G+ + L LKPK S
Sbjct: 621 QS----IKVELDEETLADRGLTIESVEEAIEKKLGVK---IDRKGTVLYLKPKTPS---- 669
Query: 882 SKMYQMKQLLP---SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKG 938
+++ +P ++V+KG+ GI R ++ +E+ E +Y L +G NLR+V GV
Sbjct: 670 --YKALRKRIPKIKNIVLKGIPGIERVLVKKEEHENDEEYVLYTQGSNLREVFKIEGVDT 727
Query: 939 VKCSSNNTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEV 995
+ ++NN E+ + LGIEAAR+ I+ E+ +E G+ +D RH MLVAD+MT+ GEV
Sbjct: 728 SRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEV 784
Score = 49.1 bits (117), Expect = 2e-05
Identities = 23/60 (38%), Positives = 31/60 (51%), Gaps = 10/60 (16%)
Query: 1103 AEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIEEVFVPDDSFI 1162
+ Y+ A +EP AVG +AAQSIGEPGTQM+L Y E++ V +
Sbjct: 42 IDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSLP----------YDEKIIVKEGGET 91
Score = 34.5 bits (79), Expect = 0.57
Identities = 15/34 (44%), Positives = 24/34 (70%)
Query: 671 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKL 704
+DAA +G+ D + GV E +I+G P+ +GTG + L
Sbjct: 813 YDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDL 846
>gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase
(RNAP), C-terminal domain. RNA polymerase (RNAP) is a
large multi-subunit complex responsible for the synthesis
of RNA. It is the principal enzyme of the transcription
process, and is the final target in many regulatory
pathways that control gene expression in all living
cells. At least three distinct RNAP complexes are found
in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for
the synthesis of ribosomal RNA precursor, mRNA precursor,
and 5S and tRNA, respectively. A single distinct RNAP
complex is found in prokaryotes and archaea, which may be
responsible for the synthesis of all RNAs. Structure
studies revealed that prokaryotic and eukaryotic RNAPs
share a conserved crab-claw-shape structure. The largest
and the second largest subunits each make up one clamp,
one jaw, and part of the cleft. The largest RNAP subunit
(Rpb1) interacts with the second-largest RNAP subunit
(Rpb2) to form the DNA entry and RNA exit channels in
addition to the catalytic center of RNA synthesis. The
region covered by this domain makes up part of the foot
and jaw structures. In archaea, some photosynthetic
organisms, and some organelles, this domain exists as a
separate subunit, while it forms the C-terminal region of
the RNAP largest subunit in eukaryotes and bacteria.
Length = 158
Score = 151 bits (383), Expect = 4e-42
Identities = 54/110 (49%), Positives = 73/110 (66%)
Query: 1281 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLA 1340
+ +E+ + LGIEAAR TI+ EI+ V+ + G+S+D RH L+AD+MT G + G+TR G
Sbjct: 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFR 108
Query: 1341 KMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGL 1390
K S L ASFE T+ HL DAA G+ D + GVSE II+G P +GTG
Sbjct: 109 ASKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
Score = 72.1 bits (177), Expect = 2e-14
Identities = 25/53 (47%), Positives = 38/53 (71%)
Query: 945 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
+ +E+ + LGIEAAR TI+ EI+ V+ + G+S+D RH L+AD+MT G + G
Sbjct: 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRG 101
Score = 60.5 bits (147), Expect = 2e-10
Identities = 24/26 (92%), Positives = 25/26 (96%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFHFAG 1145
AVG LAAQSIGEPGTQMTL+TFHFAG
Sbjct: 3 AVGVLAAQSIGEPGTQMTLRTFHFAG 28
Score = 47.0 bits (112), Expect = 9e-06
Identities = 16/31 (51%), Positives = 20/31 (64%)
Query: 671 FDAAFYGQTDCISGVSECIIMGLPMNVGTGL 701
DAA G+ D + GVSE II+G P +GTG
Sbjct: 128 LDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
>gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 3, represents the pore domain. The 3' end
of RNA is positioned close to this domain. The pore
delimited by this domain is thought to act as a channel
through which nucleotides enter the active site and/or
where the 3' end of the RNA may be extruded during
back-tracking.
Length = 158
Score = 149 bits (379), Expect = 1e-41
Identities = 57/182 (31%), Positives = 94/182 (51%), Gaps = 24/182 (13%)
Query: 427 NLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSW 486
N+++P+NG+ +I +QD + G YLLT+++ FF+R + M++ I
Sbjct: 1 NILSPQNGKPIIGPSQDMVLGLYLLTRRDTFFDREEVMQLLMYGIVL------------- 47
Query: 487 RSWNPVVFVRTAVIWTGKQIFSLILKPNRDCPVNANLKTKGRAYTANEEFCHRDSYVILR 546
+P + +WTGKQ FS +L N KG+ T E C DSYV++
Sbjct: 48 --PHPAILKPIKPLWTGKQTFSRLLPN------EINP--KGKPKTNEETLCENDSYVLIN 97
Query: 547 NSELLAGSMDKSTLGSGGKANVFYILLRDFGEDVAVTAMWRLSRMTSFYLMNRGFSIGIG 606
N EL++G +DK G ++ +I+ +++G + V + RL ++ YL GFSIGI
Sbjct: 98 NGELISGVIDKKLGG-KSLGSLIHIIYKEYGPEETVKFLDRLQKLGFRYLTKSGFSIGID 156
Query: 607 DV 608
D+
Sbjct: 157 DI 158
Score = 59.9 bits (146), Expect = 3e-10
Identities = 17/45 (37%), Positives = 32/45 (71%)
Query: 28 NLVTPRNGELLIAATQDFITGGYLLTQKNAFFNRAQTMRIASTLI 72
N+++P+NG+ +I +QD + G YLLT+++ FF+R + M++ I
Sbjct: 1 NILSPQNGKPIIGPSQDMVLGLYLLTRRDTFFDREEVMQLLMYGI 45
>gnl|CDD|216030 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 2, contains the active site. The
invariant motif -NADFDGD- binds the active site
magnesium ion.
Length = 165
Score = 149 bits (378), Expect = 2e-41
Identities = 46/65 (70%), Positives = 55/65 (84%)
Query: 341 DNDVVLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEA 400
D DVVL NRQP+LH++SIMAHR +VL +T R N VC+PYNADFDGDEMN+H+PQ+EEA
Sbjct: 96 DGDVVLLNRQPTLHRMSIMAHRPRVLEGKTIRLNPSVCSPYNADFDGDEMNLHVPQSEEA 155
Query: 401 RAEAL 405
RAEA
Sbjct: 156 RAEAR 160
Score = 39.5 bits (93), Expect = 0.004
Identities = 11/16 (68%), Positives = 15/16 (93%)
Query: 406 PSLHKLSIMAHRAKVL 421
P+LH++SIMAHR +VL
Sbjct: 106 PTLHRMSIMAHRPRVL 121
>gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA
polymerase II (RNAP II), C-terminal domain. RNA
polymerase II (RNAP II) is a large multi-subunit complex
responsible for the synthesis of mRNA. RNAP II consists
of a 10-subunit core enzyme and a peripheral heterodimer
of two subunits. The largest core subunit (Rpb1) of yeast
RNAP II is the best characterized member of this family.
Structure studies suggest that RNAP complexes from
different organisms share a crab-claw-shape structure. In
yeast, Rpb1 and Rpb2, the largest and the second largest
subunits, each makes up one clamp, one jaw, and part of
the cleft. Rpb1 interacts with Rpb2 to form the DNA entry
and RNA exit channels in addition to the catalytic center
of RNA synthesis. The C-terminal domain of Rpb1 makes up
part of the foot and jaw structures.
Length = 410
Score = 148 bits (377), Expect = 2e-38
Identities = 58/165 (35%), Positives = 96/165 (58%)
Query: 1230 VVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKTL 1289
V + + I + + ++ L +G NLR+V++ GV + +SN+ E+++ L
Sbjct: 244 KVFIREENKKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVL 303
Query: 1290 GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLAKMKESVLNL 1349
GIEAAR ++ E++ V+ G +++RH L+ D+MT +G ++ ITRHG+ + L
Sbjct: 304 GIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMR 363
Query: 1350 ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 1394
SFE T D L +AA +G+TD + GVSE I++G +GTG LL
Sbjct: 364 CSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGCFDLL 408
Score = 134 bits (339), Expect = 2e-33
Identities = 69/281 (24%), Positives = 122/281 (43%), Gaps = 51/281 (18%)
Query: 764 GVPRIKEIINASRNISTPIITAYLDKDT--DLDYARIVKGRLERTTLGEVCEYIEEVFVP 821
GVPR+KEIIN ++NI TP +T YL+ D + A+ ++ RLE TTL +V E + P
Sbjct: 63 GVPRLKEIINVAKNIKTPSLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDP 122
Query: 822 DD----------------------------SFILIKLDMDRIRLLHLEVDIDSIRYCIER 853
D S L+++++DR ++ ++ ++ I I+
Sbjct: 123 DPQNTVIEEDKEFVESYFEFPDEDVEQDRLSPWLLRIELDRKKMTDKKLSMEQIAKKIKE 182
Query: 854 TRGISGHLTVS-----------------GHSFLILKPKDSSKSFNSKMYQMKQL----LP 892
++ S + K S M L
Sbjct: 183 EFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEEDSEDDVFLKKIESNMLSDMTLKGIEGI 242
Query: 893 SVVIKGVQGINRAVIHEEDVEGVTKYKLLVEGDNLRDVMATYGVKGVKCSSNNTYEVYKT 952
V + + I + + ++ L +G NLR+V++ GV + +SN+ E+++
Sbjct: 243 RKVFIREENKKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEV 302
Query: 953 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKG 993
LGIEAAR ++ E++ V+ G +++RH L+ D+MT +G
Sbjct: 303 LGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRG 343
Score = 74.9 bits (185), Expect = 8e-14
Identities = 23/37 (62%), Positives = 28/37 (75%)
Query: 1109 KYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
++ R+ + P VG +AAQSIGEP TQMTL TFHFAG
Sbjct: 18 RFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAG 54
Score = 41.4 bits (98), Expect = 0.003
Identities = 16/35 (45%), Positives = 23/35 (65%)
Query: 671 FDAAFYGQTDCISGVSECIIMGLPMNVGTGLIKLL 705
+AA +G+TD + GVSE I++G +GTG LL
Sbjct: 374 LEAAAFGETDDLKGVSENIMLGQLAPIGTGCFDLL 408
>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit,
predominant form. Bacteria have a single DNA-directed
RNA polymerase, with required subunits that include
alpha, beta, and beta-prime. This model describes the
predominant architecture of the beta-prime subunit in
most bacteria. This model excludes from among the
bacterial mostly sequences from the cyanobacteria, where
RpoC is replaced by two tandem genes homologous to it
but also encoding an additional domain [Transcription,
DNA-dependent RNA polymerase].
Length = 1140
Score = 96.7 bits (241), Expect = 5e-20
Identities = 41/109 (37%), Positives = 63/109 (57%), Gaps = 14/109 (12%)
Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
VL NR P+LH+L I A ++ + R + VCT +NADFDGD+M VH+P + EA+AE
Sbjct: 403 VLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAE- 461
Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
A+ LM +N++ P++G+ ++ +QD + G Y LT
Sbjct: 462 -------------ARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTT 497
Score = 66.2 bits (162), Expect = 1e-10
Identities = 31/75 (41%), Positives = 42/75 (56%), Gaps = 13/75 (17%)
Query: 618 SFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAAFYG 677
SF GLT E+F T G R+GL DTA+KTA++GY+ RRLV +D+ V+ +
Sbjct: 720 SFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREE--------- 770
Query: 678 QTDCISGVSECIIMG 692
DC G E I +
Sbjct: 771 --DC--GTEEGIEVE 781
Score = 55.8 bits (135), Expect = 2e-07
Identities = 20/31 (64%), Positives = 25/31 (80%)
Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
+E AVG +AAQSIGEPGTQ+T++TFH G
Sbjct: 868 VEIGEAVGVIAAQSIGEPGTQLTMRTFHTGG 898
Score = 45.0 bits (107), Expect = 3e-04
Identities = 38/148 (25%), Positives = 64/148 (43%), Gaps = 42/148 (28%)
Query: 1283 YEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK-------------G 1329
+++ + GI+A + ++ E++ V G+ I+ +H ++ M K G
Sbjct: 990 HDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPG 1049
Query: 1330 E---------------------------VLGITRHGLAKMKESVLNLASFENTSDHLFDA 1362
E +LGIT+ L ES L+ ASF+ T+ L DA
Sbjct: 1050 ELIDIHEFNEENRKLLEQGKKPASAIPQLLGITKASLNT--ESFLSAASFQETTKVLTDA 1107
Query: 1363 AFYGQTDCISGVSECIIMGLPMNVGTGL 1390
A G+ D + G+ E +I+G + GTGL
Sbjct: 1108 AIKGKVDYLLGLKENVIIGNLIPAGTGL 1135
Score = 32.3 bits (74), Expect = 2.5
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 21 VLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 54
LM +N++ P++G+ ++ +QD + G Y LT
Sbjct: 464 ALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTT 497
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 93.4 bits (232), Expect = 7e-19
Identities = 43/108 (39%), Positives = 62/108 (57%), Gaps = 14/108 (12%)
Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
VL NR P+LH+L I A ++ + + + VCT +NADFDGD+M VH+P + +A+AE
Sbjct: 499 VLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAE- 557
Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLT 452
A+VLM + +N+ +P +G L TQD I G Y LT
Sbjct: 558 -------------ARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLT 592
Score = 58.0 bits (140), Expect = 4e-08
Identities = 24/52 (46%), Positives = 38/52 (73%)
Query: 615 VQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQ 666
++ +F GL+ E+F T G R+GLVDTA++TA++GY+ RRLV +D+ V+
Sbjct: 825 IKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVR 876
Score = 53.7 bits (129), Expect = 8e-07
Identities = 26/52 (50%), Positives = 33/52 (63%), Gaps = 7/52 (13%)
Query: 1101 CKAE--ACREKY-----VRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
C AE C++ Y R + TAVG +AAQSIGEPGTQ+T++TFH G
Sbjct: 950 CHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGG 1001
Score = 46.4 bits (110), Expect = 1e-04
Identities = 27/60 (45%), Positives = 40/60 (66%), Gaps = 2/60 (3%)
Query: 1331 VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGL 1390
+LGIT+ LA +S L+ ASF+ T+ L DAA G+ D ++G+ E +I+G P+ GTGL
Sbjct: 1179 LLGITKASLAT--DSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGL 1236
Score = 33.7 bits (77), Expect = 1.00
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 20 QVLMANKSNLVTPRNGELLIAATQDFITGGYLLT 53
+VLM + +N+ +P +G L TQD I G Y LT
Sbjct: 559 RVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLT 592
Score = 31.4 bits (71), Expect = 4.6
Identities = 14/30 (46%), Positives = 21/30 (70%)
Query: 672 DAAFYGQTDCISGVSECIIMGLPMNVGTGL 701
DAA G+ D ++G+ E +I+G P+ GTGL
Sbjct: 1207 DAAIEGKVDHLAGLKENVIIGKPIPAGTGL 1236
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit.
Length = 663
Score = 89.6 bits (223), Expect = 4e-18
Identities = 42/111 (37%), Positives = 63/111 (56%), Gaps = 14/111 (12%)
Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
VL NR P+LH+L I A + ++ R + VC +NADFDGD+M VH+P + EA+AE
Sbjct: 450 VLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAE- 508
Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN 455
A++LM + NL++P G+ + +QD + G Y+LT N
Sbjct: 509 -------------ARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGN 546
Score = 31.4 bits (72), Expect = 3.7
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 22 LMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN 56
LM + NL++P G+ + +QD + G Y+LT N
Sbjct: 512 LMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGN 546
>gnl|CDD|235055 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma;
Provisional.
Length = 627
Score = 89.0 bits (221), Expect = 7e-18
Identities = 42/111 (37%), Positives = 64/111 (57%), Gaps = 14/111 (12%)
Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
VL NR P+LH+L I A ++ R + + VC +NADFDGD+M VH+P + EA+AE
Sbjct: 429 VLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAE- 487
Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN 455
A++LM +N+++P GE ++ +QD + G Y LT +N
Sbjct: 488 -------------ARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAEN 525
Score = 32.4 bits (74), Expect = 2.3
Identities = 13/37 (35%), Positives = 24/37 (64%)
Query: 20 QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN 56
++LM +N+++P GE ++ +QD + G Y LT +N
Sbjct: 489 RLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAEN 525
>gnl|CDD|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit.
The RNA polymerase gamma subunit, encoded by the rpoC1
gene, is found in cyanobacteria and corresponds to the
N-terminal region the beta' subunit, encoded by rpoC, in
other bacteria. The equivalent subunit in plastids and
chloroplasts is designated beta', while the product of
the rpoC2 gene is designated beta''.
Length = 619
Score = 88.9 bits (220), Expect = 7e-18
Identities = 40/111 (36%), Positives = 62/111 (55%), Gaps = 14/111 (12%)
Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
V+ NR P+LH+L I A ++ R + + VC +NADFDGD+M VH+P + EA+ E
Sbjct: 422 VMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTE- 480
Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN 455
A++LM +N+++P GE ++ +QD + G Y LT N
Sbjct: 481 -------------ARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALN 518
Score = 33.4 bits (76), Expect = 0.94
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 20 QVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQKN 56
++LM +N+++P GE ++ +QD + G Y LT N
Sbjct: 482 RLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALN 518
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 89.0 bits (222), Expect = 1e-17
Identities = 43/109 (39%), Positives = 66/109 (60%), Gaps = 14/109 (12%)
Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
VL NR P+LH+L I A ++ + + + VCT +NADFDGD+M VH+P + EA+AE
Sbjct: 411 VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAE- 469
Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLTQ 453
A+VLM + +N+++P NG+ +I +QD + G Y LT+
Sbjct: 470 -------------ARVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTR 505
Score = 57.8 bits (141), Expect = 5e-08
Identities = 23/40 (57%), Positives = 30/40 (75%)
Query: 618 SFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLV 657
+F GLT E+F T G R+GL DTA+KTA++GY+ RRLV
Sbjct: 729 NFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLV 768
Score = 57.4 bits (140), Expect = 6e-08
Identities = 18/28 (64%), Positives = 23/28 (82%)
Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFH 1142
+ AVG +AAQSIGEPGTQ+T++TFH
Sbjct: 876 VNIGEAVGVIAAQSIGEPGTQLTMRTFH 903
Score = 37.4 bits (88), Expect = 0.062
Identities = 27/65 (41%), Positives = 40/65 (61%), Gaps = 2/65 (3%)
Query: 1326 TSKGEVLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMN 1385
T + +LGIT+ LA ES L+ ASF+ T+ L +AA G+ D + G+ E +I+G +
Sbjct: 1075 TGRPVLLGITKASLAT--ESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIP 1132
Query: 1386 VGTGL 1390
GTGL
Sbjct: 1133 AGTGL 1137
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 83.1 bits (205), Expect = 9e-16
Identities = 41/108 (37%), Positives = 63/108 (58%), Gaps = 14/108 (12%)
Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
VL NR P+LH+L I A ++ + + + VCT +NADFDGD+M VH+P + EA+ E
Sbjct: 1854 VLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLE- 1912
Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLT 452
A+VLM + +N+++P NG +I ++D + G Y LT
Sbjct: 1913 -------------ARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLT 1947
Score = 53.5 bits (128), Expect = 1e-06
Identities = 63/253 (24%), Positives = 109/253 (43%), Gaps = 66/253 (26%)
Query: 1189 RTRGISGHLTVSGHSFLILKPK--------DSSKSFNSKMYQMKQLLPSVVIKGVQGINR 1240
+TR I+G L F +PK D +F+ K + K+ S++IK V +
Sbjct: 2549 KTRDITGGLPRVIELFEARRPKEHAIVSEIDGYVAFSEKDRRGKR---SILIKPV---DE 2602
Query: 1241 AVIHEEDVEGVTKYKLLVEGDNLR--DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI 1298
+ E + +K+ ++ EGD +R D++ + +++ + LG+EA +
Sbjct: 2603 QISPVEYLVSRSKHVIVNEGDFVRKGDLLMD--------GDPDLHDILRVLGLEALAHYM 2654
Query: 1299 MTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVL-------------------------- 1332
++EI+ V G+ ID +H ++ M K E+
Sbjct: 2655 ISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDRENDAMS 2714
Query: 1333 --------------GITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECI 1378
GITR L S ++ ASF+ T+ L +AAF G++D +SG+ E +
Sbjct: 2715 NSGKRPAHYLPILQGITRASLET--SSFISAASFQETTKVLTEAAFCGKSDPLSGLKENV 2772
Query: 1379 IMGLPMNVGTGLI 1391
I+G + GTGLI
Sbjct: 2773 IVGRLIPAGTGLI 2785
Score = 48.1 bits (114), Expect = 4e-05
Identities = 22/41 (53%), Positives = 29/41 (70%)
Query: 617 NSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLV 657
++F GL E+F T G R+GL DTA+KTA +GY+ RRLV
Sbjct: 2182 SNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLV 2222
Score = 48.1 bits (114), Expect = 5e-05
Identities = 22/55 (40%), Positives = 31/55 (56%)
Query: 1098 PSACKAEACREKYVRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEYIE 1152
P C R+ + AVG +AAQS+GEPGTQ+T++TFH G + +E
Sbjct: 2313 PGVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRGVE 2367
Score = 32.7 bits (74), Expect = 2.1
Identities = 15/31 (48%), Positives = 23/31 (74%)
Query: 672 DAAFYGQTDCISGVSECIIMGLPMNVGTGLI 702
+AAF G++D +SG+ E +I+G + GTGLI
Sbjct: 2755 EAAFCGKSDPLSGLKENVIVGRLIPAGTGLI 2785
Score = 32.3 bits (73), Expect = 2.5
Identities = 39/162 (24%), Positives = 74/162 (45%), Gaps = 24/162 (14%)
Query: 853 RTRGISGHLTVSGHSFLILKPK--------DSSKSFNSKMYQMKQLLPSVVIKGVQGINR 904
+TR I+G L F +PK D +F+ K + K+ S++IK V +
Sbjct: 2549 KTRDITGGLPRVIELFEARRPKEHAIVSEIDGYVAFSEKDRRGKR---SILIKPV---DE 2602
Query: 905 AVIHEEDVEGVTKYKLLVEGDNLR--DVMATYGVKGVKCSSNNTYEVYKTLGIEAARSTI 962
+ E + +K+ ++ EGD +R D++ + +++ + LG+EA +
Sbjct: 2603 QISPVEYLVSRSKHVIVNEGDFVRKGDLLMD--------GDPDLHDILRVLGLEALAHYM 2654
Query: 963 MTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGNGTPVEL 1004
++EI+ V G+ ID +H ++ M K E+ G + L
Sbjct: 2655 ISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYL 2696
Score = 32.3 bits (73), Expect = 2.8
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 20 QVLMANKSNLVTPRNGELLIAATQDFITGGYLLT 53
+VLM + +N+++P NG +I ++D + G Y LT
Sbjct: 1914 RVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLT 1947
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 81.9 bits (202), Expect = 2e-15
Identities = 41/108 (37%), Positives = 62/108 (57%), Gaps = 14/108 (12%)
Query: 345 VLFNRQPSLHKLSIMAHRAKVLPHRTFRFNECVCTPYNADFDGDEMNVHLPQTEEARAEA 404
VL NR P+LHK SI A K++ + + + VC+ +NADFDGD+M VH+P ++EA AE
Sbjct: 1810 VLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAE- 1868
Query: 405 LPSLHKLSIMAHRAKVLMANKSNLVTPRNGELLIAATQDFITGGYLLT 452
KVLM + N++ P +G+ + +QD + G Y L+
Sbjct: 1869 -------------CKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLS 1903
Score = 57.6 bits (139), Expect = 5e-08
Identities = 29/74 (39%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 1098 PSACKAE--ACREKY-----VRAQIEPATAVGALAAQSIGEPGTQMTLKTFHFAGEVCEY 1150
P CKA C + Y P AVG +AAQSIGEPGTQ+TL+TFH G
Sbjct: 2250 PVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309
Query: 1151 IEE--VFVPDDSFI 1162
+E + + F+
Sbjct: 2310 QDEREIVASKEGFV 2323
Score = 46.8 bits (111), Expect = 9e-05
Identities = 20/41 (48%), Positives = 28/41 (68%)
Query: 617 NSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLV 657
++F GL E+F T G R+GL DTA+KTA GY+ R+L+
Sbjct: 2126 SNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLI 2166
Score = 39.9 bits (93), Expect = 0.014
Identities = 20/62 (32%), Positives = 38/62 (61%), Gaps = 2/62 (3%)
Query: 1331 VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGL 1390
+LGITR + +S+++ ASF+ T+ L +A+ + D + + E +++G + VGTG+
Sbjct: 2816 LLGITRAAIGS--DSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGM 2873
Query: 1391 IK 1392
K
Sbjct: 2874 YK 2875
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 62.3 bits (152), Expect = 2e-09
Identities = 21/36 (58%), Positives = 25/36 (69%), Gaps = 4/36 (11%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFH----FAGEVCEYI 1151
AVG +A QSIGEPGTQ+TL+TFH F G E +
Sbjct: 317 AVGIIAGQSIGEPGTQLTLRTFHTGGVFTGGTAEQV 352
Score = 52.2 bits (126), Expect = 2e-06
Identities = 22/42 (52%), Positives = 31/42 (73%)
Query: 616 QNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLV 657
Q++F GL+ TE+ G R+G+VDTAV+TA+ GY+ RRLV
Sbjct: 166 QSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLV 207
Score = 33.4 bits (77), Expect = 1.1
Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 1331 VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTGL 1390
+LGIT+ L +S ++ ASF+ T+ L AA G+ D + G+ E +I+G + GTG
Sbjct: 1260 LLGITKASLNT--QSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGF 1317
Query: 1391 IKL 1393
L
Sbjct: 1318 KGL 1320
>gnl|CDD|132721 cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacterial
DNA-dependent RNA polymerase (RNAP), C-terminal domain.
Bacterial RNA polymerase (RNAP) is a large multi-subunit
complex responsible for the synthesis of all RNAs in the
cell. This family also includes the eukaryotic
plastid-encoded RNAP beta" subunit. Structure studies
suggest that RNAP complexes from different organisms
share a crab-claw-shape structure with two pincers
defining a central cleft. Beta' and beta, the largest and
the second largest subunits of bacterial RNAP, each makes
up one pincer and part of the base of the cleft. The
C-terminal domain includes a G loop that forms part of
the floor of the downstream DNA-binding cavity. The
position of the G loop may determine the switch of the
bridge helix between flipped-out and normal alpha-helical
conformations.
Length = 204
Score = 57.9 bits (141), Expect = 3e-09
Identities = 20/31 (64%), Positives = 25/31 (80%)
Query: 1115 IEPATAVGALAAQSIGEPGTQMTLKTFHFAG 1145
+E AVG +AAQSIGEPGTQ+T++TFH G
Sbjct: 3 VELGEAVGIIAAQSIGEPGTQLTMRTFHTGG 33
Score = 52.1 bits (126), Expect = 3e-07
Identities = 41/145 (28%), Positives = 65/145 (44%), Gaps = 42/145 (28%)
Query: 1286 YKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK-------------GE-- 1330
K LG EA + ++ EI+ V + G++I+ +H ++ MTSK GE
Sbjct: 62 IKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELV 121
Query: 1331 -------------------------VLGITRHGLAKMKESVLNLASFENTSDHLFDAAFY 1365
+LGIT+ L ES ++ ASF+ T+ L +AA
Sbjct: 122 DLNEFEEENKRLLLLGKKPAKYEPVLLGITKASLNT--ESFISAASFQETTKVLTEAAIE 179
Query: 1366 GQTDCISGVSECIIMGLPMNVGTGL 1390
G+ D + G+ E +I+G + GTGL
Sbjct: 180 GKIDWLRGLKENVILGRLIPAGTGL 204
>gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit.
The family consists of the product of the rpoC2 gene, a
subunit of DNA-directed RNA polymerase of cyanobacteria
and chloroplasts. RpoC2 corresponds largely to the
C-terminal region of the RpoC (the beta' subunit) of
other bacteria. Members of this family are designated
beta'' in chloroplasts/plastids, and beta' (confusingly)
in Cyanobacteria, where RpoC1 is called beta' in
chloroplasts/plastids and gamma in Cyanobacteria. We
prefer to name this family beta'', after its organellar
members, to emphasize that this RpoC1 and RpoC2 together
replace RpoC in other bacteria [Transcription,
DNA-dependent RNA polymerase].
Length = 1227
Score = 57.6 bits (139), Expect = 5e-08
Identities = 32/90 (35%), Positives = 49/90 (54%), Gaps = 14/90 (15%)
Query: 615 VQNSFFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCVQYDMSFDAA 674
++ +F GLT TE+ + G R+GLVDTA++TA++GY+ RRLV +D+ V+
Sbjct: 158 IKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVR-------- 209
Query: 675 FYGQTDCISGVSECIIMGLPMNVGTGLIKL 704
+ DC G I++ M G I L
Sbjct: 210 ---EEDC--GTERSIVVR-AMTEGDKKISL 233
Score = 51.8 bits (124), Expect = 3e-06
Identities = 28/61 (45%), Positives = 37/61 (60%), Gaps = 11/61 (18%)
Query: 1098 PSACKA--EACREKYVRA-----QIEPATAVGALAAQSIGEPGTQMTLKTFH----FAGE 1146
P C+A CR+ Y + ++ AVG +AAQSIGEPGTQ+T++TFH F GE
Sbjct: 282 PLTCEAARSVCRKCYGWSLAHAHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGE 341
Query: 1147 V 1147
V
Sbjct: 342 V 342
Score = 41.4 bits (97), Expect = 0.004
Identities = 33/140 (23%), Positives = 61/140 (43%), Gaps = 42/140 (30%)
Query: 1290 GIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK-------------GEV----- 1331
++ + ++ E++ V ++ G+ I +H ++ MTSK GE+
Sbjct: 1084 SLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQ 1143
Query: 1332 ----------------------LGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQTD 1369
LGIT+ L +S ++ ASF+ T+ L +AA G++D
Sbjct: 1144 VEQVNEAMAITGGAPAQYTPVLLGITKASLNT--DSFISAASFQETTRVLTEAAIEGKSD 1201
Query: 1370 CISGVSECIIMGLPMNVGTG 1389
+ G+ E +I+G + GTG
Sbjct: 1202 WLRGLKENVIIGRLIPAGTG 1221
>gnl|CDD|132724 cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) of Higher plant RNA
polymerase IV, C-terminal domain. Higher plants have
five multi-subunit nuclear RNA polymerases: RNAP I, RNAP
II and RNAP III, which are essential for viability; plus
the two isoforms of the non-essential polymerase RNAP IV
(IVa and IVb), which specialize in small RNA-mediated
gene silencing pathways. RNAP IVa and/or RNAP IVb might
be involved in RNA-directed DNA methylation of endogenous
repetitive elements, silencing of transgenes, regulation
of flowering-time genes, inducible regulation of adjacent
gene pairs, and spreading of mobile silencing signals.
NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b
is the largest subunit of RNAP IVb. The full subunit
compositions of RNAP IVa and RNAP IVb are not known, nor
are their templates or enzymatic products. However, it
has been shown that RNAP IVa and, to a lesser extent,
RNAP IVb are crucial for several RNA-mediated gene
silencing phenomena.
Length = 381
Score = 56.7 bits (137), Expect = 5e-08
Identities = 34/115 (29%), Positives = 52/115 (45%), Gaps = 7/115 (6%)
Query: 1281 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLGITRHGLA 1340
+ ++ LGI+AA + ++ + G S+ H +LVAD MT GE +G+ G
Sbjct: 261 SIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYK 320
Query: 1341 KMKESVLNL------ASFENTSDHLFDAAFYGQTDCISGVSECIIMGLPMNVGTG 1389
+ S L + A F + AA G +D +SGV + G VGTG
Sbjct: 321 AQRRS-LKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTG 374
Score = 37.4 bits (87), Expect = 0.054
Identities = 17/53 (32%), Positives = 28/53 (52%)
Query: 945 NTYEVYKTLGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSKGEVLG 997
+ ++ LGI+AA + ++ + G S+ H +LVAD MT GE +G
Sbjct: 261 SIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVG 313
>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1331
Score = 56.9 bits (138), Expect = 8e-08
Identities = 23/40 (57%), Positives = 28/40 (70%), Gaps = 4/40 (10%)
Query: 1120 AVGALAAQSIGEPGTQMTLKTFH----FAGEVCEYIEEVF 1155
AVG +AAQSIGEPGTQ+T++TFH F GEV + F
Sbjct: 313 AVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSPF 352
Score = 55.8 bits (135), Expect = 2e-07
Identities = 24/47 (51%), Positives = 34/47 (72%)
Query: 619 FFSGLTPTEFFFHTMGGREGLVDTAVKTAETGYMQRRLVKSLEDLCV 665
F GLT TE+ + G R+GLVDTA++TA++GY+ RRLV +D+ V
Sbjct: 163 FREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIV 209
Score = 36.9 bits (86), Expect = 0.095
Identities = 33/141 (23%), Positives = 61/141 (43%), Gaps = 42/141 (29%)
Query: 1289 LGIEAARSTIMTEIKLVMENHGMSIDFRHPMLVADLMTSK-------------GEV---- 1331
++ + ++ E++ V ++ G+ I +H ++ MTSK GE+
Sbjct: 1084 EALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIELR 1143
Query: 1332 -----------------------LGITRHGLAKMKESVLNLASFENTSDHLFDAAFYGQT 1368
LGIT+ L +S ++ ASF+ T+ L +AA G++
Sbjct: 1144 QVEQVNEAMAITGGAPAEYTPVLLGITKASLNT--DSFISAASFQETTRVLTEAAIEGKS 1201
Query: 1369 DCISGVSECIIMGLPMNVGTG 1389
D + G+ E +I+G + GTG
Sbjct: 1202 DWLRGLKENVIIGRLIPAGTG 1222
>gnl|CDD|233209 TIGR00958, 3a01208, Conjugate Transporter-2 (CT2) Family protein.
[Transport and binding proteins, Other].
Length = 711
Score = 33.2 bits (76), Expect = 1.1
Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 6/64 (9%)
Query: 450 LLTQKNAFFNRAQTMRIASTLIADTSDICGIIKRFSWRSWNPVVFVRTAVIWTGKQIFSL 509
LL Q FF+ +T + S L +DT + S N V +R V+ G F L
Sbjct: 244 LLRQDLGFFDENKTGELTSRLSSDTQTMS------RSLSLNVNVLLRNLVMLLGLLGFML 297
Query: 510 ILKP 513
L P
Sbjct: 298 WLSP 301
>gnl|CDD|232968 TIGR00420, trmU, tRNA
(5-methylaminomethyl-2-thiouridylate)-methyltransferase.
tRNA
(5-methylaminomethyl-2-thiouridylate)-methyltransferase
(trmU, asuE, or mnmA) is involved in the biosynthesis of
the modified nucleoside
5-methylaminomethyl-2-thiouridine (mnm5s2U34) present in
the wobble position of some tRNAs. This enzyme appears
not to occur in the Archaea [Protein synthesis, tRNA and
rRNA base modification].
Length = 352
Score = 32.7 bits (75), Expect = 1.2
Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 223 CPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKFNPEIEAHK--KF 280
C ++ C L I EK + + + + E + EY E NP+I +K KF
Sbjct: 46 CTSAEDLRDAQAICEKLGIPLEKVNFQKEYWNKVFEPFIQEYKEGRTPNPDILCNKFIKF 105
Query: 281 GL 282
G
Sbjct: 106 GA 107
>gnl|CDD|217339 pfam03054, tRNA_Me_trans, tRNA methyl transferase. This family
represents
tRNA(5-methylaminomethyl-2-thiouridine)-
methyltransferase which is involved in the biosynthesis
of the modified nucleoside
5-methylaminomethyl-2-thiouridine present in the wobble
position of some tRNAs.
Length = 355
Score = 31.8 bits (73), Expect = 2.7
Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 2/74 (2%)
Query: 211 KKILETTKKVSVCPHCGEINGVVKKCGLLKISHEKYKNRTKKKDAIVEDLLAEYNEAVKF 270
K E ++ C ++ + C L I + + + E L EY
Sbjct: 33 KNWDEEDEEGHGCCSEEDLADAQRVCEQLGIPLYVVNFEKEYWEKVFEPFLDEYKNGRTP 92
Query: 271 NPEIEAHK--KFGL 282
NP+I ++ KFG
Sbjct: 93 NPDILCNREIKFGA 106
>gnl|CDD|222253 pfam13597, NRDD, Anaerobic ribonucleoside-triphosphate reductase.
Length = 542
Score = 31.8 bits (73), Expect = 3.1
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 200 ALSYLVRKSLKKKI--LETTKKVSVCPHCGEINGVVKKC 236
AL LV+K+ K + T S+C CG I+G + +C
Sbjct: 465 ALKKLVKKAAKTGLPYFTITPTFSICNDCGYIDGELNRC 503
>gnl|CDD|237296 PRK13188, PRK13188, bifunctional UDP-3-O-[3-hydroxymyristoyl]
N-acetylglucosamine
deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein]
dehydratase; Reviewed.
Length = 464
Score = 31.4 bits (72), Expect = 4.0
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 1311 MSID---FRHPMLVADLMTSKGEVLGITRHGLAKMK 1343
M ID FR ++ D + K E+L R G+ +M+
Sbjct: 405 MKIDKVKFRQKVVPGDTLIFKVELLSPIRRGICQMQ 440
>gnl|CDD|188690 cd08736, RGS_RhoGEF-like, Regulator of G protein signaling (RGS)
domain found in the Rho guanine nucleotide exchange
factor (RhoGEF) protein. The RGS domain found in the Rho
guanine nucleotide exchange factor (RhoGEF) protein
subfamily of the RGS domain containing protein family,
which is a diverse group of multifunctional proteins that
regulate cellular signaling events downstream of
G-protein coupled receptors (GPCRs). RhoGEFs link signals
from heterotrimeric G-alpha12/13 protein-coupled
receptors to Rho GTPase activation, leading to various
cellular responses, such as actin reorganization and gene
expression. The RGS domain of the RhoGEFs has very little
sequence similarity with the canonical RGS domain of the
RGS proteins and therefore is often refered to as the RH
(RGS Homology) domain. The RGS-GEFs subfamily includes
the leukemia-associated RhoGEF (LARG), p115RhoGEF, and
PDZ-RhoGEF. RGS proteins play critical regulatory role as
GTPase activating proteins (GAPs) of the heterotrimeric
G-protein G-alpha-subunits. RGS proteins play critical
regulatory role as GTPase activating proteins (GAPs) of
the heterotrimeric G-protein G-alpha-subunits. RGS
proteins regulate many aspects of embryonic development
such as glial differentiation, embryonic axis formation,
skeletal and muscle development, cell migration during
early embryogenesis, as well as apoptosis, cell
proliferation, and modulation of cardiac development.
Length = 120
Score = 29.5 bits (67), Expect = 4.2
Identities = 17/81 (20%), Positives = 40/81 (49%), Gaps = 9/81 (11%)
Query: 994 EVLGNGTPVELKRLLDDI----IAKNS---SRSDPSLSAQ--EILALSNETLDSKEFLQD 1044
++ G P ++++ +I + KN+ + SL+A+ + L + D + Q+
Sbjct: 30 DLYKQGNPKDMRKWAYEIYSTFLEKNAPLKVKVPESLAAEIDKRLPNLIDEEDLRRVFQE 89
Query: 1045 TSENFVRDIKKFLEEFSKKES 1065
E + +I++ LE+F +K +
Sbjct: 90 AQERAMPEIQEQLEDFRQKRT 110
>gnl|CDD|223059 PHA03367, PHA03367, single-stranded DNA binding protein;
Provisional.
Length = 1115
Score = 30.4 bits (69), Expect = 9.2
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 154 PLPVFHIGYFRCVINILQSICKNPTC 179
P PVF Y+R ++ I+Q I P C
Sbjct: 608 PCPVFLNLYYRSILTIIQDIAL-PIC 632
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.136 0.396
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 72,096,507
Number of extensions: 7266725
Number of successful extensions: 6066
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5982
Number of HSP's successfully gapped: 135
Length of query: 1423
Length of database: 10,937,602
Length adjustment: 109
Effective length of query: 1314
Effective length of database: 6,103,016
Effective search space: 8019363024
Effective search space used: 8019363024
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: 65 (28.6 bits)