RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 046830
(518 letters)
>gnl|CDD|191028 pfam04563, RNA_pol_Rpb2_1, RNA polymerase beta subunit. 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
forms one of the two distinctive lobes of the Rpb2
structure. This domain is also known as the protrusion
domain. The other lobe (pfam04561) is nested within this
domain.
Length = 394
Score = 419 bits (1080), Expect = e-144
Identities = 164/402 (40%), Positives = 211/402 (52%), Gaps = 18/402 (4%)
Query: 33 GLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGE 92
GLV QQLDSF+ F +QE +DE IE E P +I L+KP + ESDG+
Sbjct: 1 GLVEQQLDSFNWFLDEGLQEEIDEFPPIEDEDE---EPEFSLKVGQIKLAKPKIKESDGK 57
Query: 93 TATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEE------VPIMLRSSYCTLYQNSQ 146
T ++ + ARLRNLTYS+PLYV V +E +P+MLRS+ C L S+
Sbjct: 58 TREIYPREARLRNLTYSSPLYVPAELTVNNTEEIEKEKVFIGKIPLMLRSNACILNGASE 117
Query: 147 KALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAES 206
L +LGECP D GGYFI+NGSEKV+I Q + S N YVFKK + Y A + S
Sbjct: 118 SELVKLGECPLDPGGYFIVNGSEKVIINQIQRSPNIYYVFKKDKNGIRIYSASIISNRGR 177
Query: 207 QNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHIC 266
R T + +R ++ + L EI + +L + +DI +
Sbjct: 178 SLRLEITSKGKIYARINSGAKLIMFVLLLALGLNLVEIILNLLVPEVDLEIQDDIGINDE 237
Query: 267 YDFQDTQMMELLRPSLEEAFFIQNQQ----YIGKRGATVGVTREKMIKYAKEILQKEMLP 322
D T +P LEE F IQ Q YIG RG+ G RE+ I A IL +LP
Sbjct: 238 EDEFLTD-----KPELEEQFVIQTQDEALDYIGGRGSAKGFPRERRILGAVGILDLNLLP 292
Query: 323 HVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFR 382
H+G + T KA G++IHRLLL ALGR DD DH GNKRL LAG LL FR L
Sbjct: 293 HLGVSENTRTLKAQDIGYMIHRLLLLALGRGPLDDIDHLGNKRLRLAGELLQSQFRILLN 352
Query: 383 KLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATG 424
+L DVR +QKC+ D LQ + +K IT G++Y L TG
Sbjct: 353 RLERDVRERIQKCLKKKFDFTLQNLVNSKPITSGIRYFLGTG 394
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 427 bits (1099), Expect = e-138
Identities = 205/515 (39%), Positives = 288/515 (55%), Gaps = 44/515 (8%)
Query: 22 WAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYL 81
W V+ AYF+EKGLVRQ LDS+++F + +QEIVDE +I+ PG + +I +
Sbjct: 2 WTVVEAYFKEKGLVRQHLDSYNDFIERGLQEIVDEFGEIKT-----EIPGLKIVLGKIRV 56
Query: 82 SKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEV-----PIMLRS 136
+P + E+DG + ARLRNLTY+APLY+ + ++ EEV PIM++S
Sbjct: 57 GEPEIKEADGSERPITPMEARLRNLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKS 116
Query: 137 SYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAY 196
C L S L E+GE P D GGYFIINGSE+V+++QE ++ N V V K + +
Sbjct: 117 KICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVLVDKGEAGSSITH 176
Query: 197 VAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFT 256
A+V S + + V K G+ I+ + P + +IP +IL RALG
Sbjct: 177 TAKVISSRAGYR---AQVTVERR-----KDGT----IYVSFPAVPGKIPFVILMRALGLE 224
Query: 257 ADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQ-----YIGKRGATVGVTREKMIKY 311
D DI+ + D ++ + L PSLE+A I YIGKR A +G RE I+
Sbjct: 225 TDRDIVYAV---SLDPEIQQELLPSLEQASSIAATVEDALDYIGKRVA-IGQPREYRIER 280
Query: 312 AKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGP 371
A++IL K +LPH+GT KKAY+ G + +LL LGRR DD+DHY NKRL LAG
Sbjct: 281 AEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGD 340
Query: 372 LLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNA 431
LL LFR F++L D++ ++K G+ ++L+ ++ IT ++++LATGNW G
Sbjct: 341 LLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGG-- 398
Query: 432 AGTRAGVSQVLNCLTYASTFTYY------LSWKLA--KPRQLHNSQWGMMCPAETPEGQA 483
R GVSQ+L+ Y ST ++ LS + R LH +QWG +CP ETPEG
Sbjct: 399 ---RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPN 455
Query: 484 CGLVKNLALMVYITIGSAAYPILEFLEEWGTENFE 518
CGLVKNLALM I++G + E L E G E
Sbjct: 456 CGLVKNLALMAQISVGVDEEEVEEILYELGVVPVE 490
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B'';
Validated.
Length = 494
Score = 366 bits (943), Expect = e-122
Identities = 191/520 (36%), Positives = 291/520 (55%), Gaps = 51/520 (9%)
Query: 17 TQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDF 76
E+ + AYF+E LVR +DS+++F N +Q+I+DE IE + G +
Sbjct: 1 MMEDRRVLSDAYFKEHRLVRHHIDSYNDFVDNGLQKIIDEQGPIET----EIEDGVYVEL 56
Query: 77 AEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGE-------E 129
+I + KP++ E+DG ++ ARLRNLTYSAPLY++++ ++ G + E E
Sbjct: 57 GKIRVGKPVVKEADGSEREIYPMEARLRNLTYSAPLYLEMS--PVEGGEEEEPEEVYIGE 114
Query: 130 VPIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKR 189
+P+M+ S C LY S++ L E+GE P D GGYFI+NGSE+VL+ E ++ N + V K
Sbjct: 115 LPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLEDLAPNKILVEKDE 174
Query: 190 QPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIIL 249
+ VA+V S R T+ R + G + + P + IP +IL
Sbjct: 175 RYGDRIEVAKVFSQ-RRGYRALVTV-----ERN--RDG----LLEVSFPSVPGSIPFVIL 222
Query: 250 FRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQQ----YIGKRGATVGVTR 305
RALG DE+I+E + D + +++ + +LEEA + Q+ YIGKR A G T+
Sbjct: 223 MRALGLETDEEIVEAVSDDPE---IVKFMLENLEEAE-VDTQEEALEYIGKRVAP-GQTK 277
Query: 306 EKMIKYAKEILQKEMLPHVGTGDFCETKKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKR 365
E IK A+ ++ + +LPH+G KA+Y G + ALGRR EDD+DHY NKR
Sbjct: 278 EYRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKR 337
Query: 366 LDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITGGLKYSLATGN 425
L LAG L+ LFR F +L DV+ +++ ++++++ A+++ +T L++++ATGN
Sbjct: 338 LKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGN 397
Query: 426 WGQGNAAGTRAGVSQVLNCLTYASTFTYY------LSWKLAKP----RQLHNSQWGMMCP 475
W G R GVSQ+L+ Y +T ++ LS ++P R LH +QWG +CP
Sbjct: 398 W-----VGGRTGVSQLLDRTDYMATLSHLRRVVSPLS--RSQPHFEARDLHPTQWGRICP 450
Query: 476 AETPEGQACGLVKNLALMVYITIGSAAYPILEFLEEWGTE 515
+ETPEG CGLVKN A MV I+ G + E L+E G E
Sbjct: 451 SETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVE 490
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 346 bits (889), Expect = e-108
Identities = 147/537 (27%), Positives = 220/537 (40%), Gaps = 103/537 (19%)
Query: 17 TQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDF 76
+++ I + + LV QLDS++ F +QE+ E I P +N + ++
Sbjct: 10 RIRDSFGKIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFRE-----IFPIESYNGNTELEY 64
Query: 77 AEIYLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGE-------- 128
L +P + + RLR LTYSAPLYV + V+ + +
Sbjct: 65 GSYRLGEP---------PKFYPEECRLRGLTYSAPLYVKLRL-VVNETGEEIKEQEVYMG 114
Query: 129 EVPIMLRSSYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKK 188
++P+M R GGYFIING+E+V+++QE S ++V KK
Sbjct: 115 DIPLMTR------------------------GGYFIINGTERVIVSQEHRSPGVIFVEKK 150
Query: 189 RQP-NKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPII 247
+ +K YVA V S K + + +IP+
Sbjct: 151 DKTGSKVLYVARVIPYRGSWL----------EFEFDPKDNLYVR------IDRKRKIPVT 194
Query: 248 ILFRALGFTADEDILEHIC----YDFQDTQMMELLRPSLEEA--FFIQNQ---QYIGKRG 298
IL RALG DE+I+E D + E L EEA I + + IG R
Sbjct: 195 ILLRALGLETDEEIIEAFGGDELTDLVPPEGEEALLEIYEEAKGEKITARNALELIGSRV 254
Query: 299 ATVGVT--REKMIKYAKEILQKEMLPHVGTG----DFCETKKAYYFGHIIHRLLLCALGR 352
V +E K AK +L KE+LPH+G D KA +I L+ LG+
Sbjct: 255 FVVKRYDAKEGRYKRAKYVLDKELLPHLGEAGERYDLSRVGKAKDIIAMIKYLIELRLGK 314
Query: 353 RAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKT 412
EDD DH GN+RL L G LL LFR ++ DV+ ++K +
Sbjct: 315 GEEDDIDHLGNRRLRLVGELLENLFRVGLSRMERDVKERLEKAD------KRDTLVPQDL 368
Query: 413 ITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYY-------LS--WKLAKPR 463
I ++L TG +G R+ +SQ ++ S ++ LS + R
Sbjct: 369 INAKPIHALITGFFG-------RSQLSQFMDQTNPLSELSHKRRLSALGLSRERAGFEVR 421
Query: 464 QLHNSQWGMMCPAETPEGQACGLVKNLALMVYITI-GSAAYPILEFL-EEWGTENFE 518
+H + +G +CP ETPEG GL+K+LAL I G P + L + E
Sbjct: 422 DVHPTHYGRICPIETPEGPNIGLIKSLALYARINEYGFLETPYRKVLDGSLVVDEIE 478
>gnl|CDD|238353 cd00653, RNA_pol_B_RPB2, RNA polymerase beta subunit. RNA
polymerases catalyse the DNA dependent polymerization of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Each RNA
polymerase complex contains two related members of this
family, in each case they are the two largest
subunits.The clamp is a mobile structure that grips DNA
during elongation.
Length = 866
Score = 215 bits (550), Expect = 3e-61
Identities = 75/174 (43%), Positives = 101/174 (58%), Gaps = 9/174 (5%)
Query: 333 KKAYYFGHIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYV 392
K+ ++I +L+L LG+ DD DH GNKR+ LAG LL LFR+ ++L +V+ +
Sbjct: 208 KRFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKL 267
Query: 393 QKCVDNGKDVNLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFT 452
QK + KD+ Q I +K IT G+K LATGNWG R+G+SQVL+ L S +
Sbjct: 268 QKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQRSGLSQVLDRLNPLSELS 327
Query: 453 ---------YYLSWKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT 497
+ K + R LH S WG +CP ETPEG+ CGLVKNLALM I+
Sbjct: 328 HKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
Score = 191 bits (488), Expect = 8e-53
Identities = 82/234 (35%), Positives = 110/234 (47%), Gaps = 25/234 (10%)
Query: 34 LVRQQLDSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGET 93
LV+QQ+DSF+ F +QEIV I + + F +IYL KP + E G T
Sbjct: 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTD---DDGRLKLKFGDIYLGKPKVEE-GGVT 56
Query: 94 ATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGE------EVPIMLRSSYCTLYQNSQK 147
L RLR+LTYSAPLYVD+ V KG E E+PIMLRS C L + +
Sbjct: 57 RKLTPNECRLRDLTYSAPLYVDIRLTVNDKGKIKEQEVFIGEIPIMLRSKLCNLNGLTPE 116
Query: 148 ALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQ 207
L +LGECP D GGYFIING+EKV+I QE+ S N + V +K + S+
Sbjct: 117 ELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVE----DSKGKRIYTKTSIPSYS 172
Query: 208 NRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIIL---FRALGFTAD 258
S + V + I+ + R E + + F L +
Sbjct: 173 PYRGSWLEVKSDKKK--------DRIYVRIDLKRQEEALKYIGKRFEDLIYMIR 218
>gnl|CDD|218151 pfam04561, RNA_pol_Rpb2_2, RNA polymerase Rpb2, 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). Rpb2 is the
second largest subunit of the RNA polymerase. This
domain forms one of the two distinctive lobes of the
Rpb2 structure. This domain is also known as the lobe
domain. DNA has been demonstrated to bind to the concave
surface of the lobe domain, and plays a role in
maintaining the transcription bubble. Many of the
bacterial members contain large insertions within this
domain, as region known as dispensable region 1 (DRI).
Length = 185
Score = 179 bits (457), Expect = 6e-54
Identities = 67/203 (33%), Positives = 95/203 (46%), Gaps = 32/203 (15%)
Query: 179 STNHVYVFKKRQPNKYAYVAEVCSMAESQNRPPSTIFVPMLSRTSA---KGGSSGQYIHA 235
+N +YV K+ N + L K G+ +
Sbjct: 1 RSNGIYVEKELDKNGIG-----------------ATYTSSLISNRGSWLKLEIDGKTLIW 43
Query: 236 TLPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQMMELLRPSLEEAFFIQNQ---- 291
+ P + +IPI+I +ALG +D +IL+ +CYDF D QM+ELL+P LEEA I Q
Sbjct: 44 SRPSKKRKIPIVIFLKALGLVSDREILDRLCYDFNDPQMLELLKPELEEAENIYTQEEAL 103
Query: 292 QYIGKRGATVGVTREKMIKYAKEILQK-----EMLPHVGTGDFCETK--KAYYFGHIIHR 344
YIGK A + E ++ A+EIL + H+G + E + KA ++I R
Sbjct: 104 DYIGKGFA-LRRGEEPRLQRAREILYSRDPKYNLNKHLGLNEPFENERLKAQDILYMIDR 162
Query: 345 LLLCALGRRAEDDRDHYGNKRLD 367
LL LGRR DD DH GNKR+
Sbjct: 163 LLNLKLGRRKPDDIDHLGNKRVR 185
>gnl|CDD|146955 pfam04565, RNA_pol_Rpb2_3, RNA polymerase Rpb2, 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). Domain 3, s
also known as the fork domain and is proximal to
catalytic site.
Length = 68
Score = 76.9 bits (190), Expect = 1e-17
Identities = 22/40 (55%), Positives = 26/40 (65%)
Query: 458 KLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYIT 497
K + R LH SQ+G +CP ETPEG CGLV +LAL I
Sbjct: 29 KTFEVRDLHPSQYGRICPIETPEGANCGLVNSLALYARIN 68
>gnl|CDD|233685 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit. This
model describes orthologs of the beta subunit of
Bacterial RNA polymerase. The core enzyme consists of
two alpha chains, one beta chain, and one beta' subunit
[Transcription, DNA-dependent RNA polymerase].
Length = 1065
Score = 68.6 bits (168), Expect = 5e-12
Identities = 115/520 (22%), Positives = 190/520 (36%), Gaps = 131/520 (25%)
Query: 25 ISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIE-----IRPESQHNPGQQSDFAEI 79
I E L+ QLDS+D F Q + +E I P + + ++
Sbjct: 11 IPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNMELEYLSY 70
Query: 80 YLSKPMMTESDGETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYC 139
L +P ++ + R LTYS PL V + ++ E I + Y
Sbjct: 71 ELGEPKYD----------VEECKERGLTYSVPLKVKLRLINKEEDGTKE---IKEQEVY- 116
Query: 140 TLYQNSQKALTELGECPY-DEGGYFIINGSEKVLIAQEKMSTNHVYVFKKR--QPNKYAY 196
+G+ P + G FIING+E+V+++Q S + +K + K Y
Sbjct: 117 ------------MGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDTHKNGKVLY 164
Query: 197 VAEVC----SMAESQNRPPSTIFVPMLSRTSAKGGSSGQYIHATLPYI--RTEIPIIILF 250
A + S E + ++V I + ++P +L
Sbjct: 165 SARIIPYRGSWLEFETDKKDLVYV----------------------RIDRKRKLPATVLL 202
Query: 251 RALGFTADEDILEHI----------------CYDFQDTQMMELLRPS----LEEA-FFIQ 289
RALG+T D L + D ++ +LRP +E A ++
Sbjct: 203 RALGYTIDTLKLNRVGSYEYISNTLRKDPTNSRDEALLEIYRVLRPGEPPTVEAARSLLE 262
Query: 290 NQQYIGKRGATVGVTREKMIKYAKEILQKEMLPHVGT---GDFCETKKAYYFGHIIHRLL 346
N + KR V R KM K L ++ +G D T K Y + +
Sbjct: 263 NLFFDPKRYDLGRVGRYKMNKK----LGLDVPEDIGVLTKEDIIATIK--YLIKLRN--- 313
Query: 347 LCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNL-- 404
G+ DD DH GN+R+ G LL FR ++ VR + +D +
Sbjct: 314 ----GKGEVDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERM-----TTQDTDTLT 364
Query: 405 -QFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYY--------- 454
Q I AK I+ +K + +SQ ++ + T+
Sbjct: 365 PQDLINAKPISAAIKEFFGSSQ------------LSQFMDQTNPLAELTHKRRLSALGPG 412
Query: 455 -LSWKLA--KPRQLHNSQWGMMCPAETPEGQACGLVKNLA 491
L+ + A + R +H + +G +CP ETPEG GL+ +L+
Sbjct: 413 GLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLS 452
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 60.1 bits (146), Expect = 2e-09
Identities = 85/378 (22%), Positives = 138/378 (36%), Gaps = 80/378 (21%)
Query: 152 LGECP-YDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVCSMAESQNRP 210
+G P + G FIING E+V+++Q + + +Y FKK N+
Sbjct: 96 IGNLPKMTQRGTFIINGLERVIVSQ-IIRSPGIY-FKKEIKKNS-------------NKI 140
Query: 211 PSTIFVPMLSRTSAKGGSSGQYIHATLPYIRTEIPIIILFRALGFTADEDILEHICYDFQ 270
S +P + I + R + P+II +ALG T D+DI +
Sbjct: 141 YSATLIPNRGSWIKFELDKNKEIWIRIDKNR-KKPLIIFLKALGLT-DQDIYSRLTKSEF 198
Query: 271 -------------------DTQMMELLRPSLEEAFFIQNQQYIGKRGATVGVTREKMIKY 311
++ + L P +E A Q + R K
Sbjct: 199 LKKLKPILLNSNSYTNEEILLEIYKNLSP-IEPATVNDANQNLFSR-----FFDPKNYDL 252
Query: 312 AKEILQKEMLPHVGTGDFCETKKAYY--FGHIIHRLLLCALGRRAEDDRDHYGNKRLDLA 369
K + + ++ + + Y II +L+ + + DD DH N+R+
Sbjct: 253 GK-VGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSV 311
Query: 370 GPLLGGLFRTLFRKLTGDVRSYVQKCV-DNGKDVNLQFAIKAKTITGGLKYSLATGNWGQ 428
G LL FR ++L +R+ + C D+ NL I K + ++
Sbjct: 312 GELLQNQFRIGLKRLERILRNRMTICDIDSLSKFNL---INPKPLIALIREFF------- 361
Query: 429 GNAAGTRAGVSQV---------LNCLTYASTFTYYLSWKLAKP------RQLHNSQWGMM 473
G SQ+ L+ LT+ + L K R +H S +G +
Sbjct: 362 --------GSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRI 413
Query: 474 CPAETPEGQACGLVKNLA 491
CP ETPEG CGL+ +LA
Sbjct: 414 CPIETPEGPNCGLIGSLA 431
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 57.0 bits (139), Expect = 2e-08
Identities = 64/247 (25%), Positives = 95/247 (38%), Gaps = 83/247 (33%)
Query: 38 QLDSFDEFNQNT-------MQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESD 90
QLDSFD F Q ++E+ I P N +F L +P
Sbjct: 31 QLDSFDWFLQLDVPPEDEGLEEVFRS-----IFPIEDFNGNLSLEFVSYELGEPKYDV-- 83
Query: 91 GETATLFLKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVPIMLRSSYCTLYQNSQKALT 150
+ + R LTYSAPL V + R+I K + E+ Q+
Sbjct: 84 --------EECKERGLTYSAPLRVKL--RLINK--ETGEI-------------KEQEVY- 117
Query: 151 ELGECPY-DEGGYFIINGSEKVLIAQEKMSTNHVYVFK----KRQPNKYAYVAEVCSMAE 205
+G+ P E G FIING+E+V+++Q S VY F K K Y A +
Sbjct: 118 -MGDIPLMTENGTFIINGTERVIVSQLHRSPG-VY-FDHDKDKTSSGKLLYSARI----- 169
Query: 206 SQNRPPSTIFVPMLSR-------TSAKGGSSGQYIHATLPYI--RTEIPIIILFRALGFT 256
+P R K ++ I R ++P+ +L RALG++
Sbjct: 170 ----------IP--YRGSWLEFEFDPKD-----ILYV---RIDRRRKLPVTVLLRALGYS 209
Query: 257 ADEDILE 263
DE+IL+
Sbjct: 210 -DEEILD 215
Score = 41.6 bits (99), Expect = 0.001
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 463 RQLHNSQWGMMCPAETPEGQACGLVKNLA 491
R +H + +G +CP ETPEG GL+ +LA
Sbjct: 469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
Score = 30.1 bits (69), Expect = 3.7
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 351 GRRAEDDRDHYGNKRLDLAGPLLGGLFRT 379
G+ DD DH GN+R+ G LL FR
Sbjct: 359 GKGEVDDIDHLGNRRVRSVGELLQNQFRI 387
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase
subunit beta/beta'; Provisional.
Length = 2836
Score = 49.6 bits (118), Expect = 4e-06
Identities = 45/169 (26%), Positives = 71/169 (42%), Gaps = 28/169 (16%)
Query: 341 IIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGK 400
I+ +++L G+ + DD DH GN+R+ G + FRT KL R+ V +
Sbjct: 449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLE---RAVVDSMSTSSL 505
Query: 401 D-VNLQFAIKAKTITGGLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKL 459
D V+ I K +T L+ + +SQ ++ S T+
Sbjct: 506 DKVSPSDFINPKVLTNVLRDFFNSSQ------------LSQFMDQTNPLSEITHKRRLSA 553
Query: 460 AKP------------RQLHNSQWGMMCPAETPEGQACGLVKNLALMVYI 496
P R +H + +G +CP ETPEGQ GL+ +LA+ I
Sbjct: 554 LGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARI 602
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase
subunit beta/beta'; Reviewed.
Length = 2890
Score = 45.3 bits (107), Expect = 7e-05
Identities = 35/142 (24%), Positives = 57/142 (40%), Gaps = 12/142 (8%)
Query: 356 DDRDHYGNKRLDLAGPLLGGLFRTLFRKLTGDVRSYVQKCVDNGKDVNLQFAIKAKTITG 415
DDRDH GN+R+ G LL + K+ ++ + + + +K IT
Sbjct: 455 DDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITS 514
Query: 416 GLKYSLATGNWGQGNAAGTRAGVSQVLNCLTYASTFTYYLSWKLAK------PRQLHNSQ 469
+ G Q + L+ +T+ + L K R +H +
Sbjct: 515 TIMEFFMGGQLSQ------FMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTH 568
Query: 470 WGMMCPAETPEGQACGLVKNLA 491
+G +CP ETPEGQ GL+ L+
Sbjct: 569 YGRICPIETPEGQNIGLINTLS 590
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 44.1 bits (105), Expect = 2e-04
Identities = 63/257 (24%), Positives = 93/257 (36%), Gaps = 92/257 (35%)
Query: 33 GLVRQQLDSFDEF-NQNTMQEIVD----ESADIEIRPESQHNPGQQSDFAEIY-LSKPMM 86
G + Q + F F +Q +E+ E D EI + F E Y L +P++
Sbjct: 14 GFNQIQFEGFCRFIDQGLTEELSKFPKIEDTDQEIEFQL---------FVETYQLVEPLI 64
Query: 87 TESDGETATLFLKAARLRNLTYSAPLYVDV-----TKRVIKK-----GHDGEEVPIMLRS 136
E D A +LTYS+ LYV R +++ G +P+M
Sbjct: 65 KERD----------AVYESLTYSSELYVPAGLIWKKSRDMQEQTVFIG----NIPLM--- 107
Query: 137 SYCTLYQNSQKALTELGECPYDEGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAY 196
NS G FIING +V+I Q R P Y Y
Sbjct: 108 -------NSL--------------GTFIINGIYRVVINQ-----------ILRSPGIY-Y 134
Query: 197 VAEVCSMAESQNRPPSTIFVPMLSRTSAKGGSS------GQYIHATLPYIRTEIPIIILF 250
+E+ N I V + S GG I A + + +I I++L
Sbjct: 135 RSEL-----DHNG----ISVYTGTIISDWGGRLELEIDRKARIWARVSRKQ-KISILVLL 184
Query: 251 RALGFTADEDILEHICY 267
A+G E IL+++CY
Sbjct: 185 SAMGLNLRE-ILDNVCY 200
Score = 39.5 bits (93), Expect = 0.004
Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 463 RQLHNSQWGMMCPAETPEGQACGLVKNLALMVYI----TIGSAAYPILEFLEE 511
R +H S +G +CP +T EG GL+ +LA+ I ++ S Y I E +E
Sbjct: 411 RDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKE 463
>gnl|CDD|212088 cd11519, SLC5sbd_SMCT1, Na(+)/monocarboxylate cotransporter SMCT1
and related proteins; solute-binding domain. SMCT1 is a
high-affinity transporter of various monocarboxylates
including lactate and pyruvate, short-chain fatty acids,
ketone bodies, nicotinate and its structural analogs,
pyroglutamate, benzoate and its derivatives, and iodide.
Human SMCT1 (hSMCT1, also called AIT) is encoded by the
tumor suppressor gene SLC5A8. Its expression is under
the control of the C/EBP transcription factor. Its
tumor-suppressive role is related to uptake of butyrate,
propionate, and pyruvate, these latter are inhibitors of
histone deacetylases. SMCT1 is expressed in the colon,
small intestine, kidney, thyroid gland, retina, and
brain. SMCT1 may contribute to the intestinal/colonic
and oral absorption of monocarboxylate drugs. SMCT1 also
mediates iodide transport from thyrocyte into the
colloid lumen in thyroid gland and through transporting
l-lactate and ketone bodies helps maintain the energy
status and the function of neurons. In the kidney its
expression is limited to the S3 segment of the proximal
convoluted tubule (in contrast to the low-affinity
monocarboxylate transporter SMCT2, belonging to a
different family, which is expressed along the entire
length of the tubule). In the retina, SMCT1 and SMCT2
may play a differential role in monocarboxylate
transport in a cell type-specific manner, SMCT1 is
expressed predominantly in retinal neurons and in
retinal pigmented epithelial (RPE) cells. This subgroup
belongs to the solute carrier 5 (SLC5) transporter
family.
Length = 541
Score = 32.0 bits (73), Expect = 0.90
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 471 GMMCPAETPEGQACGLVKNLALMVYITIGSAAYP 504
G++ P G GLV A+ +++ IG+ YP
Sbjct: 425 GILFPFANSIGALVGLVSGFAISLWVGIGAQIYP 458
>gnl|CDD|212074 cd11505, SLC5sbd_SMCT, Na(+)/monocarboxylate cotransporters SMCT1
and 2 and related proteins; solute-binding domain.
SMCT1 is a high-affinity transporter of various
monocarboxylates including lactate and pyruvate,
short-chain fatty acids, ketone bodies, nicotinate and
its structural analogs, pyroglutamate, benzoate and its
derivatives, and iodide. Human SMCT1 (hSMCT1, also
called AIT) is encoded by the tumor suppressor gene
SLC5A8. SMCT1 is expressed in the colon, small
intestine, kidney, thyroid gland, retina, and brain.
SMCT1 may contribute to the intestinal/colonic and oral
absorption of monocarboxylate drugs. It also mediates
iodide transport from thyrocyte into the colloid lumen
in thyroid gland and, through transporting L-lactate and
ketone bodies, helps maintain the energy status and the
function of neurons. SMCT2 is a low-affinity transporter
for short-chain fatty acids, lactate, pyruvate, and
nicotinate. hSMCT2 is encoded by the SLC5A12 gene. SMCT2
is expressed in the kidney, small intestine, skeletal
muscle, and retina. In the kidney, SMCT2 may initiate
lactate absorption in the early parts of the tubule,
SMCT1 in the latter parts of the tubule. In the retina,
SMCT1 and SMCT2 may play a differential role in
monocarboxylate transport in a cell type-specific
manner. This subgroup belongs to the solute carrier 5
(SLC5) transporter family.
Length = 536
Score = 31.2 bits (71), Expect = 1.3
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 471 GMMCPAETPEGQACGLVKNLALMVYITIGSAAYP 504
G++ P +G GL+ A+ +++ IG+ YP
Sbjct: 425 GILFPFANSKGALSGLLTGFAISLWVGIGAQIYP 458
>gnl|CDD|217829 pfam03985, Paf1, Paf1. Members of this family are components of
the RNA polymerase II associated Paf1 complex. The Paf1
complex functions during the elongation phase of
transcription in conjunction with Spt4-Spt5 and
Spt16-Pob3i.
Length = 431
Score = 30.9 bits (70), Expect = 1.9
Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 10/73 (13%)
Query: 3 MEEERLEEDEEEETTQEEAWAVISAYFEEKGLVRQQLDSFDEFNQNTMQEIVDESADIEI 62
++ E ++EDE+EE Q ++ + DS +E +Q+ + S+D+
Sbjct: 365 IDFEEVDEDEDEEEEQR----------SDEHEEEEGEDSEEEGSQSREDGSSESSSDVGS 414
Query: 63 RPESQHNPGQQSD 75
ES+ + SD
Sbjct: 415 DSESKADKESASD 427
>gnl|CDD|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subfamily
corresponds to the RRM2 of GRSF-1, a cytoplasmic
poly(A)+ mRNA binding protein which interacts with RNA
in a G-rich element-dependent manner. It may function in
RNA packaging, stabilization of RNA secondary structure,
or other macromolecular interactions. GRSF-1 contains
three potential RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 28.2 bits (63), Expect = 2.1
Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 7/65 (10%)
Query: 237 LPYIRTEIPIIILFRALGFTADEDILEHICYDFQDTQ----MMELLRPSLEEAFFIQNQQ 292
LPY TE II FR L D + I + + + ++ P + +++++
Sbjct: 9 LPYSCTEDDIIDFFRGLDIVDDGVV---IVLNRRGRKTGEAYVQFATPEMANKALLKHRE 65
Query: 293 YIGKR 297
IG R
Sbjct: 66 EIGNR 70
>gnl|CDD|222925 PHA02743, PHA02743, Viral ankyrin protein; Provisional.
Length = 166
Score = 29.4 bits (66), Expect = 2.9
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 264 HICYDFQDTQMMELLR 279
HI Y +D +MME+LR
Sbjct: 133 HIAYKMRDRRMMEILR 148
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 27.3 bits (61), Expect = 6.6
Identities = 15/26 (57%), Positives = 19/26 (73%)
Query: 4 EEERLEEDEEEETTQEEAWAVISAYF 29
EEE EE+EEEE ++EEA A + A F
Sbjct: 79 EEEEEEEEEEEEESEEEAMAGLGALF 104
>gnl|CDD|180393 PRK06087, PRK06087, short chain acyl-CoA synthetase; Reviewed.
Length = 547
Score = 28.9 bits (65), Expect = 7.2
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 12/81 (14%)
Query: 114 VDVTKRVIKKGHDGEEV---PIMLRSSYCTLYQNSQKALTELGE------CPYDEGGYFI 164
VD ++ + G +GEE P + Y + + +AL E G C DE GY
Sbjct: 369 VDEARKTLPPGCEGEEASRGPNVF-MGYLDEPELTARALDEEGWYYSGDLCRMDEAGYIK 427
Query: 165 INGSEKVLIAQ--EKMSTNHV 183
I G +K +I + E +S+ V
Sbjct: 428 ITGRKKDIIVRGGENISSREV 448
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is functionally
equivalent to L7/L12 in bacteria and the P1 and P2
proteins in eukaryotes. L12p is homologous to P1 and P2
but is not homologous to bacterial L7/L12. It is located
in the L12 stalk, with proteins L10, L11, and 23S rRNA.
L12p is the only protein in the ribosome to occur as
multimers, always appearing as sets of dimers. Recent
data indicate that most archaeal species contain six
copies of L12p (three homodimers), while eukaryotes have
four copies (two heterodimers), and bacteria may have
four or six copies (two or three homodimers), depending
on the species. The organization of proteins within the
stalk has been characterized primarily in bacteria,
where L7/L12 forms either two or three homodimers and
each homodimer binds to the extended C-terminal helix of
L10. L7/L12 is attached to the ribosome through L10 and
is the only ribosomal protein that does not directly
interact with rRNA. Archaeal L12p is believed to
function in a similar fashion. However, hybrid ribosomes
containing the large subunit from E. coli with an
archaeal stalk are able to bind archaeal and eukaryotic
elongation factors but not bacterial elongation factors.
In several mesophilic and thermophilic archaeal species,
the binding of 23S rRNA to protein L11 and to the
L10/L12p pentameric complex was found to be
temperature-dependent and cooperative.
Length = 106
Score = 27.1 bits (60), Expect = 8.7
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 4 EEERLEEDEEEETTQEEAWAVISAYF 29
+EE +++EE+E +EEA A + A F
Sbjct: 81 KEEEKKKEEEKEEEEEEALAGLGALF 106
>gnl|CDD|215443 PLN02829, PLN02829, Probable galacturonosyltransferase.
Length = 639
Score = 28.7 bits (64), Expect = 9.0
Identities = 13/67 (19%), Positives = 31/67 (46%), Gaps = 6/67 (8%)
Query: 40 DSFDEFNQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFLK 99
D D+ +N+ + ++ +E +S + + +P++T++D +T +
Sbjct: 128 DDSDQQEKNSQSQSASQAESLEHVQQSAQTSEKVDE------KEPLLTKTDKQTDQTVMP 181
Query: 100 AARLRNL 106
AR+R L
Sbjct: 182 DARVRQL 188
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
0.318 0.134 0.396
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,695,059
Number of extensions: 2617358
Number of successful extensions: 2638
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2581
Number of HSP's successfully gapped: 50
Length of query: 518
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 417
Effective length of database: 6,457,848
Effective search space: 2692922616
Effective search space used: 2692922616
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (27.2 bits)