RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780142|ref|YP_003064555.1| DNA-directed RNA polymerase
subunit beta' [Candidatus Liberibacter asiaticus str. psy62]
(1398 letters)
>gnl|CDD|30435 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 801 bits (2069), Expect = 0.0
Identities = 402/856 (46%), Positives = 502/856 (58%), Gaps = 78/856 (9%)
Query: 20 SVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRM 79
++ +ASP +I S GE+KKPETINYRT KPER GLF RIFGP KDYEC CGKYKR+
Sbjct: 6 DIKFGLASPEEIRS-WSGEVKKPETINYRT-KPERGGLFDERIFGPDKDYECTCGKYKRI 63
Query: 80 KYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERV 139
G HI+LA+PVAH WF KS+PS LL M+ RD ERV
Sbjct: 64 CPGGF-------------------GHIELAAPVAHIWFFKSIPS----LLDMTCRDCERV 100
Query: 140 LYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQNL 199
LYFE+YVV+ + LEK Q+L E EYV D F A GA+AI LL DL
Sbjct: 101 LYFEAYVVLG---TDLEKIQLLNETEYVY-------DSFCAHCGAEAIKILLEKPDL--- 147
Query: 200 ALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVALDF 259
T R++ + S + + KK++KRLK+VD+F+ SGN P WMI+ LPV PPDLRP + LD
Sbjct: 148 -ETEREEETLSPT--KVKKLLKRLKVVDAFLLSGNRPEWMILTVLPVPPPDLRPSIQLDG 204
Query: 260 GRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVT 319
GRFA SDLNDLYRRVI RNNRL RL L AP II+RNEKRMLQE+VDALFDN R R VT
Sbjct: 205 GRFAESDLNDLYRRVINRNNRLKRLLELAAP-IIVRNEKRMLQEAVDALFDNRR-PRAVT 262
Query: 320 GANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELF 379
G RPLKSLS LKGKQGRFR NLLGKRVDYSGRSVI GP L+L+QCG+PK MALELF
Sbjct: 263 GG--RPLKSLSQRLKGKQGRFRQNLLGKRVDYSGRSVISVGPNLKLNQCGVPKKMALELF 320
Query: 380 KPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLS-MQA 438
KPF+ +L +G + K AK+ VE+ PEVWDVL EV+ VLLNRAP+LHRLS MQA
Sbjct: 321 KPFVVTELNIEGLRTGAKYAKRMVERRLPEVWDVLREVIDGDPVLLNRAPTLHRLSIMQA 380
Query: 439 FEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASG 498
FEP + GKAI+LHPLVC YNADFDGD+MAV+ S EA EAR LM + N+L P G
Sbjct: 381 FEPVLPEGKAIRLHPLVCEAYNADFDGDEMAVHVPASGEAAAEARGLMGTQMNILTPHYG 440
Query: 499 APVTVPSQDMVLGLCYLSTVH----EGDPGEGML---FADMGEVYHALENKIVTLHSKIR 551
P+ P QD V G L+ V GE L +AD E A+ KI K+
Sbjct: 441 GPIVAPIQDTVGGPYLLTIVDAKLPSTPVGEIYLKDEYADDREKAEAIAKKIELTTGKVI 500
Query: 552 GRYKSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRH 611
S D + I TT GR I LP ++ I N ++IK I + TIYR
Sbjct: 501 VSTISPD---LAELSIIVTTDGRRIFNRGLPEDKDVLVKIVNGKLIKGVIDKKIVTIYRE 557
Query: 612 CGQ----KSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQ 667
G K+ V D L LG + GI G+ DI + K++I+ EA+ V + Q
Sbjct: 558 YGPEVASKALVKLLDKLKNLGIKGIGGFGIGIGRKDIEAEDEKDEIVIEAEGSVLKLILQ 617
Query: 668 YNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGA 727
Y +G +TR E+ N V + + + ++ IK + + I M SGA
Sbjct: 618 YEEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEE----QGLDFVDIRHMGLSGA 673
Query: 728 RGSIHQMRQLGGMRGLIAKPSGE-------------IIESPIRSHFKGGLCGFEFFQSCV 774
R +I Q+ QL G +G++ + E P S F GL E+F +
Sbjct: 674 RMNISQIVQLIGQQGVMGEKISVLARAAFEVTVKHLEAEGPGESSFLEGLTENEYFGHPI 733
Query: 775 GGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGS 834
GGR GL+D ++TA SGYL+RRLVDVAQ+ +V + DC T G+ + + G+ L
Sbjct: 734 GGRTGLVDTALKTADSGYLTRRLVDVAQDLIVQEDDCVT-DGIGVVIQFEYGEDGEDLTE 792
Query: 835 RVLGRTALDDIINPLT 850
R+LGR +D++ P+T
Sbjct: 793 RILGRVLEEDVLRPVT 808
Score = 42.6 bits (100), Expect = 9e-04
Identities = 27/224 (12%), Positives = 54/224 (24%), Gaps = 29/224 (12%)
Query: 714 KKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSC 773
K + S+ ++ ++ E I+ L E+
Sbjct: 84 KSIPSLL----DMTCRDCERVLYF--EAYVVLGTDLEKIQ---------LLNETEYVYDS 128
Query: 774 VGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLG 833
G + + + R + TK + + + S
Sbjct: 129 FCAHCGAEAIKILLEKPDLETEREEET---------LSPTKVKKLLKRLKVVDAFLLSGN 179
Query: 834 SRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESS-RGVC 892
+ + P I G ES +N++ + I L ++ V
Sbjct: 180 RPEWMILTVLPVPPPDLRPSIQLDGGRFAESDLNDLYRRVINRNNRLKRLLELAAPIIVR 239
Query: 893 VLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
A +L + + G P L+ R G
Sbjct: 240 NEKRMLQEAVDALFDNR-RPRAVTG---GRPLKSLSQRLKGKQG 279
Score = 41.8 bits (98), Expect = 0.001
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTV 940
A G AA++ G GTQ+ + T H GG +
Sbjct: 414 VPASGEAAAEARGLMGTQMNILTPHYGGPIVA 445
>gnl|CDD|176961 CHL00018, rpoC1, RNA polymerase beta' subunit.
Length = 663
Score = 704 bits (1820), Expect = 0.0
Identities = 264/648 (40%), Positives = 374/648 (57%), Gaps = 63/648 (9%)
Query: 14 DDRGFDSVRISIASPAKIASLSY---------GEIKKPETINYRTFKPERDGLFCARIFG 64
D +RI +ASP +I + + GE+ KP TI+Y+T KPE+DGLFC RIFG
Sbjct: 3 DRYKHQQLRIGLASPQQIRAWAERILPNGEIVGEVTKPYTIHYKTNKPEKDGLFCERIFG 62
Query: 65 PIKDYECICGKYKRM---KYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSL 121
PIK C CG Y+ + K CE+CGVE T S VRR RM +I LA PV H W+LK L
Sbjct: 63 PIKSGICACGNYRVIGDEKEDPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRL 122
Query: 122 PSRISTLLGMSLRDVERVLYFE-SYVVVDPGLSSLEKYQILTEEE---YVEAVSQF---- 173
PS I+ LL L+++E ++Y + S+ + + + L E E + ++ F
Sbjct: 123 PSYIANLLDKPLKELEGLVYCDFSFARPIAKKPTFLRLRGLFEYEIQSWKYSIPLFFSTQ 182
Query: 174 GQDQF----IAMMGADAIYELLIALDLQNLALTLRDQ---LSKSSSIF----------RR 216
G D F I+ GA AI E L LDL+ + + L + S R+
Sbjct: 183 GFDTFRNREIST-GAGAIREQLADLDLRIIIDNSLVEWKELGEEGSTGNEWEDRKIGRRK 241
Query: 217 KKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIG 276
+++R+K+ FI + P WM++ LPVLPP+LRP++ LD G+ +SDLN+LYRRVI
Sbjct: 242 DFLVRRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIY 301
Query: 277 RNNRLMRLKSLH--APEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLK 334
RNN L L + P ++ +K++LQE+VDAL DNG + + + +P KS SD+++
Sbjct: 302 RNNTLTDLLTTSRSTPGELVMCQKKLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIE 361
Query: 335 GKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVS 394
GK+GRFR NLLGKRVDYSGRSVIV GP L LHQCGLP+ +A+ELF+PF+ L ++ S
Sbjct: 362 GKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQPFVIRGLIRQHLAS 421
Query: 395 TVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPL 454
++ AK + ++ P VW++L EV+ H VLLNRAP+LHRL +QAF+P ++ G+AI LHPL
Sbjct: 422 NIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPL 481
Query: 455 VCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCY 514
VC G+NADFDGDQMAV+ +S EAQ EAR+LM S NLL PA G P++VPSQDM+LGL
Sbjct: 482 VCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYV 541
Query: 515 L-------------STVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDG 561
L + + + + F++ + A K + L S + R++ +
Sbjct: 542 LTIGNRRGIYANRYNPCNRKNSTKEPYFSNSYDALGAYRQKRINLDSPLWLRWRLDQRII 601
Query: 562 NSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIY 609
S R + E+ +I +I K+ + +IY
Sbjct: 602 AS----------REVPIEVQYESLGTYHEIYEHYLIVKSRKKEILSIY 639
>gnl|CDD|177040 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 334 bits (858), Expect = 1e-91
Identities = 145/379 (38%), Positives = 212/379 (55%), Gaps = 18/379 (4%)
Query: 592 CNQEMIKKNISAMVDTIYR---HCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPE 648
N+ + K A+ I H G T D L LGF+ A ++GIS G DD++ P
Sbjct: 10 HNKVIDKT---ALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPP 66
Query: 649 SKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDP 708
SK ++ +A++ E Y+ G + EK + +++W T++ + +EM + DP
Sbjct: 67 SKGWLVQDAEQQSLILEKHYHYGNVHAVEKLRQSIEIWYATSEYLKQEMNPNFR--MTDP 124
Query: 709 ETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFE 768
+N ++MMS SGARG+ Q+ QL GMRGL++ P G+II+ PI+S+F+ GL E
Sbjct: 125 -------LNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQIIDLPIQSNFREGLSLTE 177
Query: 769 FFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQV 828
+ SC G RKG++D +RTA +GYL+RRLV+V Q+ VV + DC T +G++++ + +
Sbjct: 178 YIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVS-PRNGMMI 236
Query: 829 VYSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESS 888
L ++GR DDI + + CI Q I N + + IRS LTC S+
Sbjct: 237 ERILIQTLIGRVLADDIY--IGSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRST 294
Query: 889 RGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIES 948
+C LCYG LA G LV +GEAVG+IA QSIGEPGTQLT+RTFH GG T + +
Sbjct: 295 SWICQLCYGWSLAHGDLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGVFTGGTAEQVRA 354
Query: 949 PCDGIVKIKNRNVCRNSTN 967
P +G +K V T
Sbjct: 355 PFNGKIKFNEDLVHPTRTR 373
Score = 192 bits (491), Expect = 5e-49
Identities = 90/262 (34%), Positives = 139/262 (53%), Gaps = 50/262 (19%)
Query: 1099 ALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTI- 1157
A + G+ + GD L L +++ DIT GLP+V +L EAR + IS +
Sbjct: 1102 ATVHGHYGEILYEGDTLVTLIYEKSRSGDITQGLPKVEQLLEARS------IDSISMNLE 1155
Query: 1158 -RIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDIL 1216
R++ + +R++ P+ F + + +
Sbjct: 1156 KRLEGWNERITRILGIPW---------------GFLIGAELSIAQ--------------S 1186
Query: 1217 RIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYIL-GDNV 1275
+I L+N++Q+VYR +GV I+ KHIE++VR M KV +++ + L G+ +
Sbjct: 1187 QI--------SLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGMSNVFLPGELI 1238
Query: 1276 DRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGK 1335
+ E +NR+L ++ + + PIL GITKASL T+SFIS ASFQETT+VL +AA+ G+
Sbjct: 1239 GLLRAERINRAL----EEAICYRPILLGITKASLNTQSFISEASFQETTRVLAKAALRGR 1294
Query: 1336 VDTLDGFKENVIVGRSIPAGTG 1357
+D L G KENVI+G IPAGTG
Sbjct: 1295 IDWLKGLKENVILGGLIPAGTG 1316
>gnl|CDD|147265 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1. RNA
polymerases catalyse 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 = 302 bits (776), Expect = 4e-82
Identities = 132/351 (37%), Positives = 172/351 (49%), Gaps = 44/351 (12%)
Query: 16 RGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGK 75
+ ++ IASP +I S GE+ KPET NY + KPE GL R+ K
Sbjct: 2 KKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEPGGLLDERMGT---------IK 52
Query: 76 YKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPS--RISTLLGMSL 133
K ICE CGVEVT HI+LA PV H F K + S R L SL
Sbjct: 53 KKS------ICETCGVEVT---ECPGHFGHIELAKPVFHIGFFKKILSILRCVCKLCSSL 103
Query: 134 RDVERVLYFESYVVVDP-GLSSLEKYQILTEEEYVEAVSQFG---------------QDQ 177
E V YF VV+DP G +S ++ + + +++
Sbjct: 104 LLNESVKYFFLKVVIDPKGKNSKKRLKKINNLCKKKSICSKCGEDNGGLKAFEGCGKYQP 163
Query: 178 FIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRR---KKIIKRLKIVDSFITSGN 234
I+ GA+AI LL ++++ L+++L K + KKI K + + F SGN
Sbjct: 164 KISKDGAEAIKALLKNIEIE----ELKEKLRKLNPEKVLQIFKKISKEDEEILGFNPSGN 219
Query: 235 NPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIII 294
P WMI+ LPV PP +RP V LD GRFA DL R +I RNNRL ++ AP II
Sbjct: 220 RPEWMILTVLPVPPPCIRPSVQLDGGRFAEDDLTHKLRDIIKRNNRLKKMLEEGAPSHII 279
Query: 295 RNEKRMLQESVDALFDNG-RHKRVVTGANRRPLKSLSDMLKGKQGRFRTNL 344
R EKR+LQE V LFDN + + RPLKS+S LKGK+GRFR NL
Sbjct: 280 REEKRLLQEHVATLFDNDIPGQPPALQKSGRPLKSISQRLKGKEGRFRGNL 330
>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 = 228 bits (584), Expect = 8e-60
Identities = 92/151 (60%), Positives = 111/151 (73%), Gaps = 2/151 (1%)
Query: 1209 NPVPQDILRIK--GVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPAD 1266
P D+LRIK G EA+ YL+ E+Q+VYR +GV IN KHIE++VR M KV+I DP D
Sbjct: 53 KINPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGD 112
Query: 1267 TEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKV 1326
+ ++ G+ VD E EE N+ L GKK + P+L GITKASL T+SFISAASFQETTKV
Sbjct: 113 SGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVLLGITKASLNTESFISAASFQETTKV 172
Query: 1327 LTEAAIAGKVDTLDGFKENVIVGRSIPAGTG 1357
LTEAAI GK+D L G KENVI+GR IPAGTG
Sbjct: 173 LTEAAIEGKIDWLRGLKENVILGRLIPAGTG 203
Score = 86.8 bits (216), Expect = 3e-17
Identities = 29/36 (80%), Positives = 31/36 (86%)
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVT 939
LV +GEAVG+IAAQSIGEPGTQLTMRTFH GG T
Sbjct: 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT 36
>gnl|CDD|35482 KOG0261, KOG0261, KOG0261, RNA polymerase III, large subunit
[Transcription].
Length = 1386
Score = 214 bits (546), Expect = 1e-55
Identities = 203/836 (24%), Positives = 333/836 (39%), Gaps = 161/836 (19%)
Query: 236 PGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRR---VIGRNNRLMRLKSLHAPEI 292
P +II ++PV P +RP V + A ++ +DL + +I N+ + + S P
Sbjct: 245 PENLIITRVPVPPVCIRPSVMSEDK--AGTNEDDLTMKLTEIILTNDVIKKHLSKGTPIN 302
Query: 293 IIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYS 352
+I + LQ V ++ + A ++P + LKGKQGRFR NL GKRVD+S
Sbjct: 303 LIMEDWDFLQLQVALYINSELPGIPINMAPKKPTRGFVQRLKGKQGRFRGNLSGKRVDFS 362
Query: 353 GRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKK----------------GYVSTV 396
GR+VI P L++ + G+P +A L P + + YV
Sbjct: 363 GRTVISPDPNLRIDEVGVPIRVAKILTFPERVTRANIRKLRQLVRNGPNVHPGANYVVQR 422
Query: 397 K-QAKKFVE-KERPEVWDVLA--EVVHQH-----VVLLNRAPSLHRLSMQAFEPKIISGK 447
K+F++ R ++ D L +VV +H VVL NR PSLH++S+ + K++ +
Sbjct: 423 GEGFKRFLKYGNRDKIADELKIGDVVERHLMDGDVVLFNRQPSLHKMSIMSHRAKVMPWR 482
Query: 448 AIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQD 507
+ + VC YNADFDGD+M ++ + EA+ EA VLM NNL+ P +G P+ +QD
Sbjct: 483 TFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALVLMGVKNNLVTPRNGEPIIAATQD 542
Query: 508 MVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGNSISKI 567
+ G YL T + F D E L S + +D +I K
Sbjct: 543 FITGG-YLLTHKD-------TFLDRAEFSQ--------LCSYMSDAMTHIDLPPPAILKP 586
Query: 568 YDTTPGRMIIGEILPRHHEI-------------------SFDICNQE---MIKKN--ISA 603
+ G+ + ++ + + SF++C + +I+ + IS
Sbjct: 587 VELWTGKQLFSVLIRPNDDSPVRVNLDAKNKNFSLVKGKSFEMCPNDGYVIIRNSELISG 646
Query: 604 MVD--------------TIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDI----I 645
++D + R G + + L +L R+ + G S G DD+ I
Sbjct: 647 VLDKSTLGSGKKDSLFYILLRDYGSMAAADAMNRLAKLCARFLGNRGFSIGIDDVQPGEI 706
Query: 646 VPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVE 705
+ + KE+++ E +YN G + N+ +T + ++ I+
Sbjct: 707 LSQEKEELVNRGYAKCDEKIEEYNKGKLQLQPGCNE-----EETLEAEILSELSTIREEA 761
Query: 706 FDPETGRQKKMNSIFMMSHSGARGS---IHQMRQLGGMRGLIAK--PSGEIIES-P---- 755
NS +M+ G++GS I QM G + + P G S P
Sbjct: 762 GKICIRELHPRNSPLIMALCGSKGSKINISQMVACVGQQIISGHRVPDGFEDRSLPHFER 821
Query: 756 ----------IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDV----- 800
+ + F GL EFF + GR+GL+D ++TA +GY+ RRL+
Sbjct: 822 HSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKSLEDLS 881
Query: 801 ---------AQNCVV-------------------------------NQVDCNTKKGLTIT 820
+ VV L+
Sbjct: 882 VQYDGTVRNSNGDVVQFTYGGDGLDPAMMEGKDQPVNFNRVFDHAKAIFPHRHDPPLSSE 941
Query: 821 HIVDSGQVVYSLGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIR 880
+ ++ + G + ++ + + K +L + K +
Sbjct: 942 ELDETLEEELLRKFTEKGDPFVHELREFIAS-LSKKIKKLQDKYGDECGPKFCPDLLYQI 1000
Query: 881 SALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
S LT + C D + V G AVG IAAQSIGEPGTQ+T++TFH G
Sbjct: 1001 SRLTEKQLEKFVERC--LDKYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAG 1054
Score = 48.4 bits (115), Expect = 1e-05
Identities = 33/140 (23%), Positives = 56/140 (40%), Gaps = 42/140 (30%)
Query: 1220 GVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIE 1279
G+EA + +I+E+ G++I+ +HI ++ M + E+
Sbjct: 1255 GIEAARTTIISEIGYTMSNHGMSIDPRHIMLLADVMTYRGEVL----------------- 1297
Query: 1280 VEELNRSLAQQGKKLVSFSPILQGITKASLQ--TKSFISAASFQETTKVLTEAAIAGKVD 1337
GIT+ L S + ASF++T L +AA GK D
Sbjct: 1298 -----------------------GITRFGLAKMKDSVLMLASFEKTADHLFDAAAYGKKD 1334
Query: 1338 TLDGFKENVIVGRSIPAGTG 1357
++G E +I+G + GTG
Sbjct: 1335 AIEGVSECIILGIPMCIGTG 1354
>gnl|CDD|144278 pfam00623, RNA_pol_Rpb1_2, RNA polymerase Rpb1, domain 2. RNA
polymerases catalyse 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 = 210 bits (538), Expect = 2e-54
Identities = 73/165 (44%), Positives = 100/165 (60%), Gaps = 22/165 (13%)
Query: 346 GKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKG-------------- 391
GKRVD+SGRSVI P L+L + G+P MALEL KP + +L K
Sbjct: 1 GKRVDFSGRSVITPDPNLKLDEVGVPIEMALELTKPEIVTKLNIKKLRKLVSNGPNVPPG 60
Query: 392 --YVSTVKQAKKFVEKER---PEVW---DVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKI 443
Y+ +K AK+ +E ++ E+W VL V+ VVLLNR P+LHR+S+ A P++
Sbjct: 61 AKYIKRIKGAKRDLEYKKRIAIELWYGDIVLRHVIDGDVVLLNRQPTLHRMSIMAHRPRV 120
Query: 444 ISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLS 488
+ GK I+L+P VC+ YNADFDGD+M ++ S EA+ EAR LML
Sbjct: 121 LEGKTIRLNPSVCSPYNADFDGDEMNLHVPQSEEARAEARELMLV 165
>gnl|CDD|35481 KOG0260, KOG0260, KOG0260, RNA polymerase II, large subunit
[Transcription].
Length = 1605
Score = 209 bits (534), Expect = 3e-54
Identities = 201/876 (22%), Positives = 328/876 (37%), Gaps = 121/876 (13%)
Query: 16 RGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGK 75
R SV+ I SP +I +S EI+ PET +P+ GL R+ G
Sbjct: 13 RTVKSVQFGILSPDEIRRMSVAEIEFPET--MEGGRPKLGGLMDPRL-----------GT 59
Query: 76 YKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTL----LGM 131
R +C+ CG + HI+LA PV HP FLK + + + +
Sbjct: 60 IDRD----SLCQTCGGNMF---ECPGHFGHIELAKPVFHPGFLKKVKKILRCVCFYCSKI 112
Query: 132 SLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIAMMGADAIYELL 191
L + + E D + G
Sbjct: 113 LKDKFNPKEDQILRKRYCSKGRLLMVLDVCKGKVVCEGGIDVESDGR-SGCGLKQPSIRR 171
Query: 192 IALDLQN-LALTLRDQLSKSSSIFRR--KKIIKRLKIVDSFITSGN----NPGWMIIRKL 244
+ LDL D + +I KR+ D P WMI+ L
Sbjct: 172 LGLDLWAFWKQGDEDSQESKRKLSAERVLEIFKRISDEDIDQLGFKPKIARPEWMILTVL 231
Query: 245 PVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQES 304
PV PP +RP + + DL +I +N L R + AP II +++LQ
Sbjct: 232 PVPPPAVRPEIVMQGSARGEDDLTHKLADIIKKNIGLKRNEENGAPAHIIEEYEQLLQFH 291
Query: 305 VDALFDNG-RHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPEL 363
V DN + + RPLKS+S LKGK+GR R NL+GKRVD+S R+VI P L
Sbjct: 292 VATYVDNDIPGQPQADQKSGRPLKSISARLKGKEGRIRGNLMGKRVDFSARTVITGDPNL 351
Query: 364 QLHQCGLPKLMAL-----ELFKPFLYAQLEK-----------KGYVSTVKQAKKFVEKER 407
L + G+P+ +A E PF +L++ Y+ + +
Sbjct: 352 SLDEVGVPRSIAKRLTFPEHVTPFNIDRLQELVRRGLLEHPGAKYI-IRDNGDRIDLRYH 410
Query: 408 PEVWDV---LAEVVHQH-----VVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGY 459
D+ V +H VVL NR PSLH++SM A +++ +L+ V + Y
Sbjct: 411 KRAGDIHLQPGYKVERHLMDGDVVLFNRQPSLHKMSMMAHRVRVLPYSTFRLNLSVTSPY 470
Query: 460 NADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVH 519
NADFDGD+M ++ S E + E L + ++ P S PV QD + T
Sbjct: 471 NADFDGDEMNLHVPQSLETKAELEELAMVPKQIISPQSNKPVMGIVQDTLTA-VRKMTKR 529
Query: 520 EG--DPGEGMLFADMGEVYHA-------------------LENKIVTLHSKIRGRYKSVD 558
+ + + M + + + I+ + +
Sbjct: 530 DVFLNRAQVMNLLMYVPDWDGPPPAKPAILKPKPLWTGKQIFSLIIPGGINYIRDHSTHP 589
Query: 559 KDGNSISKIYDTTPGRMII--GEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKS 616
+ + DT R++I GE+ + +C + + + +V I+ G K
Sbjct: 590 DSEDELISPGDT---RVLIEGGEL------LIGVLCKKTV-GSSAGGLVHVIFLEKGPKI 639
Query: 617 TVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRG 676
F D + L + G S G D I + +I + + + + R
Sbjct: 640 ARGFFDSIQTLINSWLLREGFSIGIGDTIADAATMCVIQNT--IKEAKRDVLA---VIRE 694
Query: 677 EKYNKVVDLWGKTTDKVTEEMMARI-KRVEFDPETGRQK---KMNSIFMMSHSGARGSIH 732
+ N++ G+T + E + R+ + QK + N+ M +G++GS
Sbjct: 695 AQNNELEPTPGRTLRETFENKVNRVLNDARDKSGSSAQKSLSESNNFKTMVVAGSKGSFI 754
Query: 733 QMRQLG---------GMR---GLIAKPSGEIIESP--------IRSHFKGGLCGFEFFQS 772
+ Q+ G R G + + + + + GL EFF
Sbjct: 755 NISQVSACVGQQNVEGKRIPFGFPKRTLPHFSKDDYSPESRGFVENSYLTGLTPQEFFFH 814
Query: 773 CVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQ 808
+GGR+GL+D ++TA +GY+ RRL+ ++ +V
Sbjct: 815 AMGGREGLIDTAVKTAETGYIQRRLMKAMEDIMVAY 850
Score = 55.4 bits (133), Expect = 1e-07
Identities = 44/205 (21%), Positives = 79/205 (38%), Gaps = 49/205 (23%)
Query: 1161 RNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPV---PQDILR 1217
R + +V + P EDG F P ++ DG ++ + D +P D++
Sbjct: 1253 RGIPDIFKVYMSPTEDG-----EFKPVDEWDLETDGVNLRRVLSEPDVDPARTTSNDLVE 1307
Query: 1218 I---KGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDN 1274
I G+EA+ L+ E+ V +G +N++H+ ++ M + + I
Sbjct: 1308 IAEVLGIEAVRKALLRELLNVISFDGSYVNYRHLALLCDVMTARGHLMA------ITRHG 1361
Query: 1275 VDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAG 1334
++R + L R SF+ET +L +AA
Sbjct: 1362 INRQDTGALMRC--------------------------------SFEETVDILMDAAAHA 1389
Query: 1335 KVDTLDGFKENVIVGRSIPAGTGAI 1359
+ D G EN+++G+ P GTG
Sbjct: 1390 EKDPCRGVSENIMLGQLAPMGTGCF 1414
Score = 46.5 bits (110), Expect = 5e-05
Identities = 18/33 (54%), Positives = 24/33 (72%)
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
+ + GE VG +AAQS+GEP TQ+T+ TFH G
Sbjct: 1047 AEASPGEMVGALAAQSVGEPATQMTLNTFHYAG 1079
>gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5. RNA
polymerases catalyse 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 = 184 bits (469), Expect = 2e-46
Identities = 86/309 (27%), Positives = 126/309 (40%), Gaps = 31/309 (10%)
Query: 768 EFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQ 827
EFF +GGR+GL+D ++TA +GYL RRLV ++ VV D G I +
Sbjct: 6 EFFFHTMGGREGLIDTAVKTAETGYLQRRLVKALEDLVVQYDDTVRNSGGEIVQFLYGED 65
Query: 828 VVYSLGSRVLGRT--------ALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRI 879
+ L GR L + ++ + + + + GI S R+
Sbjct: 66 GLDPLKIEGQGRFTIEDSDLKLEKKFKIDLNDVLLLLSEFSLSTLLFEILLRSGIESKRV 125
Query: 880 RSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVT 939
RS LTC S GVC LCYGRD R SLV GEAVG+IAAQSIGEPGTQ+T+ TFH G +
Sbjct: 126 RSELTCNSKAGVCFLCYGRDKYRRSLVEPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVAS 185
Query: 940 VMDRSFIESPCDGIVKIKN-----RNVCRNSTNDLISMGRNTTLQ---ILDMSGQEQYSH 991
+ G+ ++K +N + L+ +
Sbjct: 186 ----KNVTL---GVPRLKEIINVAKNNKKPVITVLLIKNIVSDKARVKKQREEKTLLLLK 238
Query: 992 RIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTG 1051
++ ++ DD ++ W F I E + I IG+
Sbjct: 239 KVTIIIVIYYDDDSESTVIKKDRIWVLAYFVIPE--------EVAEEVALAIIIIGKRKS 290
Query: 1052 IAKRKVIDW 1060
++K
Sbjct: 291 RKRKKNNLG 299
Score = 105 bits (263), Expect = 1e-22
Identities = 51/171 (29%), Positives = 71/171 (41%), Gaps = 4/171 (2%)
Query: 1149 ILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDG 1208
LA I R R K + V + + E + NK + G V+ G + DG
Sbjct: 279 ALAIIIIGKRKSRKRKKNNLGVAKDEK--GLEEEELLLLNKILLVIPGIKVKYGVILTDG 336
Query: 1209 NPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTE 1268
P IL G E L N +Q V RL+GV N K +R ML+K+ I D+
Sbjct: 337 RVDPHTILEKLGKEWLLKTEGNNLQAVMRLQGVIDNDKTYSNDIREMLKKLGIEAARDSI 396
Query: 1269 YILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQT--KSFISA 1317
+ NV + + +NR L++F L GIT+A L SFI
Sbjct: 397 LLEIRNVFKFDGIYVNRRHLALLADLMTFKGELLGITRAGLNREKSSFILM 447
>gnl|CDD|35483 KOG0262, KOG0262, KOG0262, RNA polymerase I, large subunit
[Transcription].
Length = 1640
Score = 128 bits (324), Expect = 7e-30
Identities = 85/338 (25%), Positives = 149/338 (44%), Gaps = 60/338 (17%)
Query: 235 NPGWMI-IRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRV------IGRNNRLMRLKSL 287
+P M + L V P RP L + +V I + + M+ K
Sbjct: 323 DPSDMFFLDNLLVPPTRFRPPSMLG-DEVHENPQTLNLNKVLESSVLIRKLLKDMKGKLD 381
Query: 288 HAPEIIIRNEKRM----------LQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQ 337
++I+ + + LQ SV+ LFD+ + +R + +L+ K+
Sbjct: 382 EELKLILERLRGIFSKLINAWLQLQASVNVLFDSKMASK----WSRDSPPGIKQILEKKE 437
Query: 338 GRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKP-----FLYAQL----- 387
G FR +++GKRV+Y+ RSVI P ++ ++ G+P + A +L P + +L
Sbjct: 438 GLFRKHMMGKRVNYAARSVISPDPNIETNEIGIPPVFAKKLTYPEPVTPWNVNELRKAVI 497
Query: 388 -------------EKKGYVS-----TVKQ----AKKFVEKERPEVWDVLAEVVHQH---- 421
++ G ++ T +Q A + + + + VH+H
Sbjct: 498 NGPDVHPGATYIQDEDGTLTLLSPMTDEQREALANQLLTPSTGNPTEFGTKKVHRHVKNG 557
Query: 422 -VVLLNRAPSLHRLSMQAFEPKIISG-KAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQ 479
VVL+NR P+LH+ S+ A + +++ G K ++LH C YNADFDGD+M V+ S A+
Sbjct: 558 DVVLMNRQPTLHKPSIMAHKARVLPGEKTLRLHYANCKAYNADFDGDEMNVHFPQSEIAR 617
Query: 480 LEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLST 517
EA + + + L P G P+ QD ++ L+
Sbjct: 618 AEAYNIANTDSQYLVPTDGTPLRGLIQDHIVSGVLLTM 655
Score = 60.4 bits (146), Expect = 3e-09
Identities = 22/33 (66%), Positives = 26/33 (78%)
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
SL + GE VGV+AAQSIGEP TQ+T+ TFH G
Sbjct: 1148 SLADPGEPVGVLAAQSIGEPSTQMTLNTFHFAG 1180
Score = 52.7 bits (126), Expect = 7e-07
Identities = 51/217 (23%), Positives = 85/217 (39%), Gaps = 48/217 (22%)
Query: 624 LMRLGFRYACSSGISFGKDDIIVPES----KEKIIAEA----DKMVKEYENQYNDGLIT- 674
RL Y G + G DD+++ + + +I+ E+ ++ KE D
Sbjct: 786 FSRLFTAYLQMHGFTLGVDDLLLDKDADKKRREILRESRNVGNQAAKEAFGLDVDAPPDE 845
Query: 675 ----------RGEKYNKVVDLWGKT-TDKVTEEMMARIKRVEFDPETGRQKKM--NSIFM 721
+ ++D K+ + T E++ + G KK N++ +
Sbjct: 846 LRSRLEAIYLKDADKLAMLDRVMKSELNGYTSEIVKKCV------PDGLLKKFPENNMQL 899
Query: 722 MSHSGARGSIHQMRQLGGMRGLIAK--------------PSGEIIE-SP-----IRSHFK 761
M SGA+GS Q+ + G PS E SP I F
Sbjct: 900 MIQSGAKGSNVNTSQISCLLGQQELEGKRVPLMVSGKTLPSFAPYETSPRAGGFIDGRFL 959
Query: 762 GGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLV 798
G+ E+F C+ GR+GL+D ++T+ SGYL R L+
Sbjct: 960 TGIKPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLI 996
Score = 46.1 bits (109), Expect = 7e-05
Identities = 39/197 (19%), Positives = 76/197 (38%), Gaps = 54/197 (27%)
Query: 1162 NYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGV 1221
+ + V++ +GV F H + D + + D IL GV
Sbjct: 1487 DDVKEKSVLLT---EGVNLPALF----DHADILDVNRLYSNDI--------HAILNTYGV 1531
Query: 1222 EALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVE 1281
EA + ++NEV V+++ G++++ +H+ ++ +M + +
Sbjct: 1532 EAARNAIVNEVNNVFKVYGISVDIRHLSLIADYMTFEGGY-------------------Q 1572
Query: 1282 ELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDG 1341
NR G+ +S S + SF+ T + L +AA+ G+ D L
Sbjct: 1573 PFNR----------------MGMESSS----SPLQKMSFETTCQFLKQAALFGEEDELSS 1612
Query: 1342 FKENVIVGRSIPAGTGA 1358
++VG + GTG+
Sbjct: 1613 PSARLVVGLPVRGGTGS 1629
Score = 31.1 bits (70), Expect = 2.5
Identities = 41/207 (19%), Positives = 74/207 (35%), Gaps = 30/207 (14%)
Query: 20 SVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRM 79
SV + +I LS +I P T + P GL+ + GP+ + +
Sbjct: 15 SVSFGSYTDQEIRKLSVKKITNPITFD-NLGHPIPGGLYDLAL-GPLDNSD--------- 63
Query: 80 KYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPS--RISTLLGMSLR--D 135
+C C + M HI+L PV +P F L + R S L R +
Sbjct: 64 -----VCSTCNQDELNCP---GHMGHIELPVPVYNPLFFDFLYNLLRGSCLFCHHFRCKN 115
Query: 136 VERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIAMMGADAIYELLIALD 195
V+ + F +++ GL E + E E V + + + +
Sbjct: 116 VDVHILFCQLRLLEYGLIE-EAEDL--ESITSETVEDNEDESLNEI---KSCRAQYVTEA 169
Query: 196 LQNLALTLRDQLSKSSSIFRRKKIIKR 222
+ AL + + + +S +KK++
Sbjct: 170 ISE-ALLDKSEPNTKNSTELKKKLVTA 195
>gnl|CDD|147253 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3. RNA
polymerases catalyse 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 = 112 bits (283), Expect = 5e-25
Identities = 55/174 (31%), Positives = 73/174 (41%), Gaps = 36/174 (20%)
Query: 491 NLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKI 550
N+L P +G P+ PSQDMVLGL L+ F D EV L IV H I
Sbjct: 1 NILSPQNGKPIIGPSQDMVLGLYLLT--RRDT------FFDREEVMQLLMYGIVLPHPAI 52
Query: 551 RGRYKSVDKDGNSISKIYDTTPGRMIIGEILPR-----------HHEISFDICNQEMI-- 597
K T R++ EI P+ ++ I N E+I
Sbjct: 53 LKPIKP--------LWTGKQTFSRLLPNEINPKGKPKTNEETLCENDSYVLINNGELISG 104
Query: 598 -------KKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDI 644
K++ +++ IY+ G + TV F D L +LGFRY SG S G DDI
Sbjct: 105 VIDKKLGGKSLGSLIHIIYKEYGPEETVKFLDRLQKLGFRYLTKSGFSIGIDDI 158
>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 = 95.9 bits (239), Expect = 7e-20
Identities = 42/149 (28%), Positives = 69/149 (46%), Gaps = 42/149 (28%)
Query: 1212 PQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYIL 1271
++L G+EA +I E+Q+V +GV+++ +HIE++ M
Sbjct: 50 IHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMT--------------- 94
Query: 1272 GDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASL--QTKSFISAASFQETTKVLTE 1329
+S L+G+T++ S + ASF++TTK L +
Sbjct: 95 -------------------------YSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLLD 129
Query: 1330 AAIAGKVDTLDGFKENVIVGRSIPAGTGA 1358
AA AG+ D L+G EN+I+GR P GTG+
Sbjct: 130 AAAAGEKDELEGVSENIILGRPAPLGTGS 158
Score = 61.7 bits (150), Expect = 2e-09
Identities = 25/34 (73%), Positives = 29/34 (85%), Gaps = 1/34 (2%)
Query: 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMD 942
GEAVGV+AAQSIGEPGTQ+T+RTFH G V M+
Sbjct: 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAG-VASMN 33
>gnl|CDD|147268 pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, domain 4. RNA
polymerases catalyse 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 4, represents the funnel domain. The
funnel contain the binding site for some elongation
factors.
Length = 108
Score = 84.0 bits (208), Expect = 2e-16
Identities = 36/109 (33%), Positives = 48/109 (44%), Gaps = 21/109 (19%)
Query: 673 ITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGR-----QKKMNSIFMMSHSGA 727
IT E+Y K+ D+WG T ++V E ++ I DP G NSI+MM+ SGA
Sbjct: 1 ITDAERYGKLEDIWGMTLEEVFEALINNILNKARDP-AGNIASKSLDLNNSIYMMADSGA 59
Query: 728 RGSIHQMRQLGGMRGLIAKPSGEI---------------IESPIRSHFK 761
+GSI + Q+ G RG I IESP F
Sbjct: 60 KGSIINISQIAGCRGQQNVEGKRIPFGFSGRTLPHFKKDIESPESRGFV 108
>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 = 69.2 bits (170), Expect = 8e-12
Identities = 24/33 (72%), Positives = 29/33 (87%)
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
SL+ GEAVG++AAQSIGEPGTQ+T+RTFH G
Sbjct: 35 SLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAG 67
Score = 59.6 bits (145), Expect = 6e-09
Identities = 38/151 (25%), Positives = 69/151 (45%), Gaps = 44/151 (29%)
Query: 1212 PQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRH-MLQKVEITDPADTEYI 1270
+I + G+EA + +INE++ +G ++V +RH ML + D
Sbjct: 248 IHEIEEVLGIEAARNAIINEIKRTLEEQG-------LDVDIRHIML----VAD------- 289
Query: 1271 LGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITK--ASLQTKSFISAASFQETTKVLT 1328
++++ ++ I + + + S ++ A+F+ T K L
Sbjct: 290 -----------------------IMTYDGEVRQIGRHGIAGEKPSVLARAAFEVTVKHLL 326
Query: 1329 EAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359
+AA+ G+VD L G EN+IVG+ IP GTG +
Sbjct: 327 DAAVRGEVDELRGVIENIIVGQPIPLGTGDV 357
>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 = 65.7 bits (161), Expect = 8e-11
Identities = 23/33 (69%), Positives = 27/33 (81%)
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
SLV GEAVG++AAQSIGEP TQ+T+ TFH G
Sbjct: 5 SLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAG 37
Score = 44.1 bits (105), Expect = 3e-04
Identities = 39/212 (18%), Positives = 77/212 (36%), Gaps = 52/212 (24%)
Query: 1148 AILAEISGTIR-IKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYIL 1206
A++ EI G R + +GV A + + D ++ +
Sbjct: 145 AVIREIPGITRCFVVEEDKGGKTKYLVITEGVNLAALW---------KFSDILD--VNRI 193
Query: 1207 DGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPAD 1266
N + +L G+EA ++ E+ V+++ G+A++ +H+ ++ +M +
Sbjct: 194 YTNDI-HAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFE-------- 244
Query: 1267 TEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKV 1326
G NR + S SP+ + SF+ T
Sbjct: 245 -----G------GYRPFNRIGMES-----STSPLQK---------------MSFETTLAF 273
Query: 1327 LTEAAIAGKVDTLDGFKENVIVGRSIPAGTGA 1358
L +A + G +D L ++VG+ + GTG
Sbjct: 274 LKKATLNGDIDNLSSPSSRLVVGKPVNGGTGL 305
>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 = 61.5 bits (150), Expect = 2e-09
Identities = 23/33 (69%), Positives = 26/33 (78%)
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
SLV+ GE VG IAAQSIGEP TQ+T+ TFH G
Sbjct: 22 SLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAG 54
Score = 52.2 bits (126), Expect = 9e-07
Identities = 19/42 (45%), Positives = 26/42 (61%)
Query: 1318 ASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359
SF+ET +L EAA G+ D L G EN+++G+ P GTG
Sbjct: 364 CSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGCF 405
>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 = 58.8 bits (143), Expect = 1e-08
Identities = 21/28 (75%), Positives = 24/28 (85%)
Query: 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
G AVG IAAQSIGEPGTQ+T++TFH G
Sbjct: 10 GTAVGAIAAQSIGEPGTQMTLKTFHFAG 37
Score = 58.8 bits (143), Expect = 1e-08
Identities = 40/146 (27%), Positives = 69/146 (47%), Gaps = 38/146 (26%)
Query: 1214 DILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGD 1273
++ ++ G+EA S +INE+Q + G++I+ +HI ++ M K E+ LG
Sbjct: 193 EVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEV---------LG- 242
Query: 1274 NVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIA 1333
+ R GI K +S + ASF++TT L AA+
Sbjct: 243 ---------ITR----------------FGIAKMK---ESVLMLASFEKTTDHLFNAALH 274
Query: 1334 GKVDTLDGFKENVIVGRSIPAGTGAI 1359
G+ D+++G E +I+G+ +P GTG
Sbjct: 275 GRKDSIEGVSECIIMGKPMPIGTGLF 300
>gnl|CDD|147501 pfam05349, GATA-N, GATA-type transcription activator, N-terminal.
GATA transcription factors mediate cell differentiation
in a diverse range of tissues. Mutation are often
associated with certain congenital human disorders. The
six classical vertebrate GATA proteins, GATA-1 to
GATA-6, are highly homologous and have two tandem zinc
fingers. The classical GATA transcription factors
function transcription activators. In lower metazoans
GATA proteins carry a single canonical zinc finger. This
family represents the N-terminal domain of the family of
GATA transcription activators.
Length = 177
Score = 32.9 bits (75), Expect = 0.67
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 488 STNNLLHPASGAPVTVPSQ---DMVLGLCYLST 517
+ LH A+ +PV VP+ M+ L YL
Sbjct: 19 DSGGFLHSAASSPVYVPTTRVPSMLPSLPYLQG 51
>gnl|CDD|35232 KOG0008, KOG0008, KOG0008, Transcription initiation factor TFIID,
subunit TAF1 [Transcription].
Length = 1563
Score = 31.9 bits (72), Expect = 1.2
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 205 DQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPP--DLRPLVA 256
D LSK+ I KRLK F G + +++ LP +LR LV
Sbjct: 719 DDLSKAFPDQSESSIRKRLKECADFKRDGMGKNYWVLKPDFRLPDEEELRSLVT 772
>gnl|CDD|185674 cd00668, Ile_Leu_Val_MetRS_core, catalytic core domain of
isoleucyl, leucyl, valyl and methioninyl tRNA
synthetases. Catalytic core domain of isoleucyl,
leucyl, valyl and methioninyl tRNA synthetases. These
class I enzymes are all monomers. However, in some
species, MetRS functions as a homodimer, as a result of
an additional C-terminal domain. These enzymes
aminoacylate the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding. Enzymes in
this subfamily share an insertion in the core domain,
which is subject to both deletions and rearrangements.
This editing region hydrolyzes mischarged cognate tRNAs
and thus prevents the incorporation of chemically
similar amino acids. MetRS has a significantly shorter
insertion, which lacks the editing function.
Length = 312
Score = 31.2 bits (71), Expect = 2.1
Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 12/95 (12%)
Query: 623 DLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKV 682
D RLG Y S + PE + + ++ Y GLI RG ++
Sbjct: 91 DFRRLGISYDWSDEYITTE-----PEYSKAVELIFSRL-------YEKGLIYRGTHPVRI 138
Query: 683 VDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMN 717
+ W K E+++ ++R + PE + +
Sbjct: 139 TEQWFFDMPKFKEKLLKALRRGKIVPEHVKNRMEA 173
>gnl|CDD|48214 cd03402, Band_7_2, A subgroup of the band 7 domain of flotillin
(reggie) like proteins. This subgroup contains proteins
similar to stomatin, prohibitin, flotillin, HlfK/C and
podicin. Many of these band 7 domain-containing proteins
are lipid raft-associated. Individual proteins of this
band 7 domain family may cluster to form membrane
microdomains which may in turn recruit multiprotein
complexes. Microdomains formed from flotillin proteins
may in addition be dynamic units with their own
regulatory functions. Flotillins have been implicated in
signal transduction, vesicle trafficking, cytoskeleton
rearrangement and are known to interact with a variety of
proteins. Stomatin interacts with and regulates members
of the degenerin/epithelia Na+ channel family in
mechanosensory cells of Caenorhabditis elegans and
vertebrate neurons and participates in trafficking of
Glut1 glucose transporters. Prohibitin may act as a
chaperone for the stabilization of mitochondrial
proteins. Prokaryotic HflK/C plays a role in the
decision between lysogenic and lytic cycle growth during
lambda phage infection. Flotillins have been implicated
in the progression of prion disease, in the pathogenesis
of neurodegenerative diseases such as Parkinson's and
Alzheimer's disease and, in cancer invasion and
metastasis. Mutations in the podicin gene give rise to
autosomal recessive steroid resistant nephritic
syndrome..
Length = 219
Score = 30.2 bits (68), Expect = 4.2
Identities = 36/181 (19%), Positives = 69/181 (38%), Gaps = 36/181 (19%)
Query: 1206 LDGNPVPQDILRIKGVE--ALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITD 1263
+GNP+ + + V A A + +++ +E ++ E +RH+ + D
Sbjct: 57 ANGNPIEIAAVIVWRVVDTAKAVFNVDDYEEFVHIQ--------SESALRHVASQYPYDD 108
Query: 1264 PADTEYILGDNVDRI---EVEELNRSLAQQGKKLVS-------FSPILQGITKASLQTKS 1313
P + E L N D + EL LA G ++V ++P + Q +
Sbjct: 109 PVNKETSLRGNSDEVSDELARELQERLAVAGVEVVEARITHLAYAPEIAQAMLQRQQASA 168
Query: 1314 FISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAMNRDQM 1373
I+A + + E A+ L +E IV L ++R+ AM + +
Sbjct: 169 IIAA------RRKIVEGAVGMVEMALTRLEEREIVE----------LDDERKAAMVSNLL 212
Query: 1374 I 1374
+
Sbjct: 213 V 213
>gnl|CDD|36223 KOG1005, KOG1005, KOG1005, Telomerase catalytic subunit/reverse
transcriptase TERT [Replication, recombination and
repair, Chromatin structure and dynamics].
Length = 888
Score = 29.9 bits (67), Expect = 4.4
Identities = 39/234 (16%), Positives = 72/234 (30%), Gaps = 34/234 (14%)
Query: 23 ISIASPAKIASLSYGEIKKPETINYR------TFKPERDGLFCARIFGPIKDYECICGKY 76
I S + A KK ET+ + ++ ER G+ I Y +
Sbjct: 452 IINMSKLRGARKRRNTKKKEETMQLKRLNSILSYLRERSGVLGNSILIHDDIYRKLDFLK 511
Query: 77 KRMKYKGIICEKCGVEVTLSSVRRDRMAHI----------DLASPVAHPWFLKSLPSRIS 126
KR + + + K V ++ +D + I D + + S I
Sbjct: 512 KRSRNQKLYFVKADVSKCFDTIPQDELISIIRDRLFVQRKDAYTVAGKGRVRGNFVSLIF 571
Query: 127 TLLGMSL---RDVERVLYFESYVVVDPG----LSSLEKYQILTEEEYVEAVSQFGQDQFI 179
+ + +V++ LSS + + ++ V + G ++
Sbjct: 572 CSADVEPNAHVVNALKMETSDVLVIENVSREMLSSSDLFSVIRNMLSTNYV-KIGGKSYV 630
Query: 180 AMMG---ADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFI 230
G + LL L +L K S + I L+ VD F+
Sbjct: 631 QKKGIPQGSILSSLLCHLYYGDL-------EDKYFSFEKEDGSIVLLRYVDDFL 677
>gnl|CDD|133077 cd03866, M14_CPM, Peptidase M14 Carboxypeptidase (CP) M (CPM) belongs
to the N/E subfamily of the M14 family of
metallocarboxypeptidases (MCPs).The M14 family are
zinc-binding CPs which hydrolyze single, C-terminal amino
acids from polypeptide chains, and have a recognition
site for the free C-terminal carboxyl group, which is a
key determinant of specificity. CPM is an extracellular
glycoprotein, bound to cell membranes via a
glycosyl-phosphatidylinositol on the C-terminus of the
protein. It specifically removes C-terminal basic
residues such as lysine and arginine from peptides and
proteins. The highest levels of CPM have been found in
human lung and placenta, but significant amounts are
present in kidney, blood vessels, intestine, brain, and
peripheral nerves. CPM has also been found in soluble
form in various body fluids, including amniotic fluid,
seminal plasma and urine. Due to its wide distribution in
a variety of tissues, it is believed that it plays an
important role in the control of peptide hormones and
growth factor activity on the cell surface and in the
membrane-localized degradation of extracellular proteins,
for example it hydrolyses the C-terminal arginine of
epidermal growth factor (EGF) resulting in des-Arg-EGF
which binds to the EGF receptor (EGFR) with an equal or
greater affinity than native EGF. CPM is a required
processing enzyme that generates specific agonists for
the B1 receptor.
Length = 376
Score = 29.8 bits (67), Expect = 5.2
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 1206 LDGNPVPQDILRIKGVEALASYLINEVQEVYRL 1238
+GNP+P I+ +KG + + Y N E + L
Sbjct: 304 SNGNPIPNAIVEVKGRKHICPYRTNVNGEYFLL 336
>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 = 29.7 bits (67), Expect = 5.2
Identities = 16/54 (29%), Positives = 25/54 (46%)
Query: 1305 TKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGA 1358
+ SL+ + + A F K +AA G D+L G + G+ P GTG+
Sbjct: 322 QRRSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGS 375
>gnl|CDD|34338 COG4722, COG4722, Phage-related protein [Function unknown].
Length = 239
Score = 29.5 bits (66), Expect = 6.1
Identities = 21/119 (17%), Positives = 40/119 (33%), Gaps = 12/119 (10%)
Query: 1202 GDYILDGNPV-PQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVE 1260
+I +G +++ E L+ + EVY GV + + + +
Sbjct: 3 PMFIFNGIKSSENEVVNGFDRELLSPREVTLN-EVYGRNGVVFEDDTYKPIELTI--PLN 59
Query: 1261 ITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAAS 1319
++ D+ R + E+N L K + FS I A ++ I S
Sbjct: 60 LSSK--------DHSLRDVLREINGWLNVSEPKPLIFSDEPDYIYLALFISEVLIEEVS 110
>gnl|CDD|37022 KOG1811, KOG1811, KOG1811, Predicted Zn2+-binding protein, contains
FYVE domain [General function prediction only].
Length = 1141
Score = 29.4 bits (65), Expect = 6.7
Identities = 18/96 (18%), Positives = 39/96 (40%), Gaps = 9/96 (9%)
Query: 765 CGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKG----LTIT 820
CG + + C KG + ++ + L D+ ++ + +K L +
Sbjct: 470 CGHQLAEHCCRKLKGTTE---SLNNNEEDAGDLDDIMKDAGFSAKGMFSKAEPSDDLALC 526
Query: 821 HI-VDSGQVVYSL-GSRVLGRTALDDIINPLTNECI 854
I + ++ L + + +LDDI +P +EC+
Sbjct: 527 DIWIGKADLLNILLAAAIRHVPSLDDIADPAASECL 562
>gnl|CDD|37725 KOG2514, KOG2514, KOG2514, Uncharacterized conserved protein
[Function unknown].
Length = 861
Score = 29.5 bits (66), Expect = 7.1
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 1280 VEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTE------AAIA 1333
V + R +A + + ++ ILQGI K ++ T +FI A + +++ E
Sbjct: 638 VTQKRRPVAARAVDIGAWYGILQGIGKLAVITNAFIIAFTSDFIPRLVYEFKYSKSQPRM 697
Query: 1334 GKVDTLDGFKENV 1346
TL G+ +
Sbjct: 698 RSFGTLLGYVNHT 710
>gnl|CDD|143853 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac,
Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
pfam00063. As regards Rab GTPases, these are important
regulators of vesicle formation, motility and fusion.
They share a fold in common with all Ras GTPases: this
is a six-stranded beta-sheet surrounded by five
alpha-helices.
Length = 162
Score = 29.4 bits (67), Expect = 8.2
Identities = 10/24 (41%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 973 GRNTTLQILDMSGQEQY-SHRIMY 995
G+ LQI D +GQE++ + R +Y
Sbjct: 45 GKTVKLQIWDTAGQERFRALRPLY 68
>gnl|CDD|30472 COG0123, AcuC, Deacetylases, including yeast histone deacetylase
and acetoin utilization protein [Chromatin structure and
dynamics / Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 340
Score = 29.2 bits (65), Expect = 8.2
Identities = 16/75 (21%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 111 PVAHPWFLKSLPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAV 170
P HP P R+ +L + +E +S +V+P ++LE+ ++ +YVE +
Sbjct: 18 PPGHPE----NPDRLRLILEL----LESSGLPDSLELVEPRPATLEELLLVHSPDYVEFL 69
Query: 171 SQFGQDQFIAMMGAD 185
+++ + D
Sbjct: 70 ESLSEEEGYGNLDGD 84
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.320 0.137 0.395
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 16,670,815
Number of extensions: 923801
Number of successful extensions: 2269
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2229
Number of HSP's successfully gapped: 66
Length of query: 1398
Length of database: 6,263,737
Length adjustment: 106
Effective length of query: 1292
Effective length of database: 3,973,183
Effective search space: 5133352436
Effective search space used: 5133352436
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: 64 (28.6 bits)