RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 002296
(940 letters)
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 429 bits (1105), Expect = e-134
Identities = 215/1001 (21%), Positives = 335/1001 (33%), Gaps = 212/1001 (21%)
Query: 3 RKKSADFEPLRELVRHHIESFDYMLDEGLSEMFD-------------------------- 36
K +F L LV ++S++ EGL E+F
Sbjct: 15 FGKIPEFLDLPNLVEIQLDSYNAFFLEGLQEVFREIFPIESYNGNTELEYGSYRLGEPPK 74
Query: 37 ----HCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQK 92
CR ++Y+ L + + G + + G P+M +
Sbjct: 75 FYPEECRLRGLTYSAPLYVKLRLVVNETGEEIKEQEVYMGDIPLMTR------------- 121
Query: 93 LVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCV 152
GGYFI+NG ERV S A VI
Sbjct: 122 -----------GGYFIINGTERVIVSQEHRSPGVIF---VEKKDKTGSKVLYVARVIPY- 166
Query: 153 RKDQSSVTL--KLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYD 210
R K + + +PV I+L+AL D EI D
Sbjct: 167 RGSWLEFEFDPKDNLYVRIDRK---------RKIPVTILLRALGLETDEEIIEAF--GGD 215
Query: 211 EKYKKEKGAVGSPLVSERVKIILAEVQDLSLT--TRLQCLQHIGEHFQPVIDGLQSESYY 268
E + E + +L ++ T L+ IG V E Y
Sbjct: 216 ELTD--------LVPPEGEEALLEIYEEAKGEKITARNALELIGSRVFVVKRYDAKEGRY 267
Query: 269 AVAETVIRDYIFVHLNDNNDKFNL--------LIFMLQKLFSLVDHTSVSDNPDSLQNQE 320
A+ V+ + HL + ++++L +I M++ L L D+ D L N+
Sbjct: 268 KRAKYVLDKELLPHLGEAGERYDLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHLGNRR 327
Query: 321 ILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKN------- 373
+ L G L+ + L R ++K+ +EK
Sbjct: 328 LRLVGELLENLFRVGLSRMER-----------------------DVKERLEKADKRDTLV 364
Query: 374 PSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGL 433
P I L TG R+ + ++ N L +S R +
Sbjct: 365 PQDLINAKPIHALITGFFG---------RSQLSQFMDQTNPLSELSHKRRLSALGLSRER 415
Query: 434 RTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSIL 493
VR + P +G +CP+ TP+G GL+ + R+ N F + T
Sbjct: 416 AGFEVRDVHPTHYGRICPIETPEGPNIGLIKSLALYARI--------NEYGFLE--TPYR 465
Query: 494 RVLIGV-GMIPSLPKLVKSGPPAVLSVLLDGRVVGVI--PSSEIEKVVAHLRRLKVSAAS 550
+VL G + ++ V + G+ G + P +E++V RR S
Sbjct: 466 KVLDGSLVVDE-----IEYLSADEEDVYVIGQANGTLDEPGELVEELV-ECRRGGSGEVS 519
Query: 551 VIPDD------------LEVGYVPLSLGGAYPGL-YLFTSPPKFVRPVRNISLPSEESQN 597
V + + VG + L S + +
Sbjct: 520 VADPEGVDYMDVSPKQVVSVGRSLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPLVGTG 579
Query: 598 IELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHPTGMLSVVANLTPYSDHNQSPRNM 657
+E + + I G TH EI P +L + A+L PY +HNQSP N+
Sbjct: 580 MEYLDAEDSGAAVI-AKRPGVV--------THVEISPIVILGIEASLIPYPEHNQSPYNL 630
Query: 658 YQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVL 717
Y+ + Q G + + L R D L P V T E G NA+VA +
Sbjct: 631 YKFARSNQATGINQRPLVKRGDTVEKGLVYADGPSVDT--------GELALGQNALVAFM 682
Query: 718 AYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNKVDRGQKLFRR--NKDAKSL 775
+ GY+ EDA+I+++ SV+R + + + D G + R N ++L
Sbjct: 683 PWNGYNYEDAIIISERSVERDLFTSIHIEEYETEARDTKL----GPEEIRDIPNVSEEAL 738
Query: 776 HSVIDSDGLPYVGQMIHPGEPYCSIYDKTT------------------NSWRTNSRK--G 815
+D DG+ +G + G+ K T R S +
Sbjct: 739 -RNLDEDGIIRIGAEVKGGDILVG---KVTPKGETELTPEERLLRIFGEKVRDTSLRVPH 794
Query: 816 SESVFVDYVAVDMKNSKNLP---QKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDID 872
E VD V V P + + R P IGDK + RHG KGV S++ P D
Sbjct: 795 GEEGIVDDVQV-FTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKGVVSKIVPQED 853
Query: 873 MPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAYM 913
MPF G PD+I+NP PSRM I +LE+ K A +
Sbjct: 854 MPFL-EDGTPPDIILNPLGVPSRMNIGQILETHLGKAAALL 893
>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 = 378 bits (972), Expect = e-117
Identities = 118/304 (38%), Positives = 158/304 (51%), Gaps = 17/304 (5%)
Query: 628 THEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQT 687
TH EI P+ +LSV A+L P+ +HNQSPRN+YQ M KQ +G ++R D KLY L
Sbjct: 396 THIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLY 455
Query: 688 PQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQT 747
PQ P+V T E P G NAIVAV++Y+GY+ EDA+I+NKSSVDRG Y+
Sbjct: 456 PQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKK 515
Query: 748 ETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNS 807
I+L N + + N + +D DG+ G + PG+ +
Sbjct: 516 YEIELRKTKNGPEEITRGDIPNVS-EEKLKNLDEDGIIRPGARVEPGDILVGKITPKGET 574
Query: 808 WRTNSR--------------KGSESVFVDYVAV-DMKNSKNLPQKANIRFRHTRNPIIGD 852
T G E VD V + + + + + R R P IGD
Sbjct: 575 ESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGD 634
Query: 853 KFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAY 912
KF+SRHGQKGV S++ P DMPF+ G+ PD+I+NPH FPSRMTI LLES+ K A
Sbjct: 635 KFASRHGQKGVISKILPQEDMPFT-EDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGAL 693
Query: 913 MENL 916
+
Sbjct: 694 LGKF 697
Score = 189 bits (483), Expect = 8e-50
Identities = 56/184 (30%), Positives = 88/184 (47%), Gaps = 12/184 (6%)
Query: 289 KFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQ 348
+F LI+M++KL LV D+ D L N+ + L G L+ + L+ R+ K+ +Q
Sbjct: 209 RFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQ 268
Query: 349 DEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQ 408
++ K L N SK I + I+ L TG ++ L QR+G +
Sbjct: 269 KQLSKK-KDLTPQLLIN---------SKPITSGIKEFLATGNWGSKRFL--MQRSGLSQV 316
Query: 409 AERLNFLRFISFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTS 468
+RLN L +S R + F + VR L P WG +CP+ TP+GE CGL+ ++
Sbjct: 317 LDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLAL 376
Query: 469 TCRV 472
R+
Sbjct: 377 MARI 380
Score = 116 bits (294), Expect = 1e-26
Identities = 41/197 (20%), Positives = 72/197 (36%), Gaps = 47/197 (23%)
Query: 15 LVRHHIESFDYMLDEGLSEMFD-------------------------------------- 36
LV+ I+SF+Y L+ GL E+
Sbjct: 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEGGVTRKLT 60
Query: 37 --HCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLV 94
CR ++Y+ L D+ D G + + G+ P+ML+++ C+L G ++L+
Sbjct: 61 PNECRLRDLTYSAPLYVDIRLTVNDKGK-IKEQEVFIGEIPIMLRSKLCNLNGLTPEELI 119
Query: 95 SLKEEAAEMGGYFILNGLERVFRSVILPKQNYP----MSMVRSSFRDRREGYTDKAVVIR 150
L E + GGYFI+NG E+V + N R + Y+
Sbjct: 120 KLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIVEDSKGKRIYTKTSIPSYSPYRGSWL 179
Query: 151 CVRKDQSSVTL--KLYY 165
V+ D+ + ++
Sbjct: 180 EVKSDKKKDRIYVRIDL 196
>gnl|CDD|215994 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6. 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
represents the hybrid binding domain and the wall
domain. The hybrid binding domain binds the nascent RNA
strand / template DNA strand in the Pol II transcription
elongation complex. This domain contains the important
structural motifs, switch 3 and the flap loop and binds
an active site metal ion. This domain is also involved
in binding to Rpb1 and Rpb3. Many of the bacterial
members contain large insertions within this domain, as
region known as dispensable region 2 (DRII).
Length = 373
Score = 320 bits (822), Expect = e-101
Identities = 113/289 (39%), Positives = 157/289 (54%), Gaps = 20/289 (6%)
Query: 639 SVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTY 698
+VA+L P+ DHNQSPR YQC M KQ +G R+DQ Y L PQ P+V+T
Sbjct: 1 GIVASLIPFVDHNQSPRITYQCAMGKQAIGIYTLNKYNRSDQNTYLLCYPQKPLVKTGAV 60
Query: 699 TKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSDDGNK 758
K G E P G NA+VAV++YTGY+ EDA+I+NKSSVDRG+ + I+ K
Sbjct: 61 EKGGFGELPLGQNALVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHIKEYEIEARK--TK 118
Query: 759 VDRGQKLFRR-NKDAKSLHSVIDSDGLPYVGQMIHPGEPY------------CSIYDKTT 805
+ +++ R ++ + +D DG+ VG + PG+ +I+ +
Sbjct: 119 LGPIEEITRDPPNVSEEAYRKLDEDGIVRVGAEVKPGDILVGKITPKGEKLLRAIFGEKA 178
Query: 806 NSWRTNSR--KGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGV 863
+ S K E VD V +D+ +K + R R P +GDKF+SRHGQKGV
Sbjct: 179 RDVKDTSLKVKHGEEGRVDDVKIDLNPGGI--KKVKVYIRQKRKPQVGDKFASRHGQKGV 236
Query: 864 CSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVAY 912
S++ P DMPF+ G+ PD+I+NPH PSRMTI LLES+ K A
Sbjct: 237 VSKILPQEDMPFT-EDGIPPDIILNPHGVPSRMTIGQLLESLLGKAAAL 284
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 318 bits (816), Expect = 6e-93
Identities = 262/1006 (26%), Positives = 418/1006 (41%), Gaps = 210/1006 (20%)
Query: 15 LVRHHIESFDYMLDEGLSEMFD-------------------------------------- 36
LVR H++S++ ++ GL E+ D
Sbjct: 14 LVRQHLDSYNDFIERGLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIKEADGSERPITP 73
Query: 37 -HCRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLVS 95
R ++Y L + ++ G E G P+M+K++ C L G +L+
Sbjct: 74 MEARLRNLTYAAPLY--LTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIE 131
Query: 96 LKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKD 155
+ E+ + GGYFI+NG ER VI+ +++ + V + T A VI
Sbjct: 132 IGEDPKDPGGYFIINGSER----VIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSRAGY 187
Query: 156 QSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKK 215
++ VT++ +G++ + F +P I+++AL D +I
Sbjct: 188 RAQVTVE--RRKDGTIYVSF--PAVPGKIPFVILMRALGLETDRDIVY------------ 231
Query: 216 EKGAVGSPLVSERVKIILAEVQDLS--LTTRLQCLQHIGEHFQPVIDGLQSESYYAVAET 273
AV L E + +L ++ S T L +IG+ G E AE
Sbjct: 232 ---AVS--LDPEIQQELLPSLEQASSIAATVEDALDYIGKRVAI---GQPREYRIERAEQ 283
Query: 274 VIRDYIFVHL----NDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLIT 329
++ Y+ HL D K L M KL L D+ D N+ + L G L+
Sbjct: 284 ILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLA 343
Query: 330 IYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLK-- 387
+ K+L++D +K +EK+ ++ + +++
Sbjct: 344 ELFRVAF-------KQLVKD----------------LKYQLEKSYARGRKLDLRAIVRPD 380
Query: 388 --TGRL--ATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTS---VRK 440
T R+ A TG + R G + +R N+L +S R V S R R
Sbjct: 381 IITERIRHALATGNWVGGRTGVSQLLDRTNYLSTLSHLRRVVSPLS----RGQPHFEARD 436
Query: 441 LLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLIGVG 500
L WG +CP TP+G CGL+ ++ +++ D + +L +G
Sbjct: 437 LHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEE-----------EVEEILYELG 485
Query: 501 MIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGY 560
++P + + + V L+GR++G P E++ +R L+ S I D++ V Y
Sbjct: 486 VVPVE-EAREEEYISWSRVYLNGRLIGYHPDG--EELAEKIRELRRSGK--ISDEVNVAY 540
Query: 561 VPLSLGGAYPGLYLFTSPPKFVRPVRNIS--LPSEESQNIELIGPFEQVF--------ME 610
+ +Y+ + RP+ + P +++E + E F +E
Sbjct: 541 IETGEINE---VYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIE 597
Query: 611 IRCPDGGDGGRRNAFPAT----------HEEIHPTGMLSVVANLTPYSDHNQSPRNMYQC 660
+ NA+ A H EI P +L + A++ PY +HNQSPRN YQ
Sbjct: 598 YLDAE----EEENAYVALDPEDLTPEHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQA 653
Query: 661 QMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYT 720
MAKQ++G + R D + + L PQ P+V+T G ++ P G NA+VAVL+YT
Sbjct: 654 AMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYT 713
Query: 721 GYDMEDAMILNKSSVDRGMCHG---QIYQTE----------TIDLSDDGNKVDRGQKLFR 767
GY++EDA+I+NK+S++RG+ + Y+TE I++ + + RG++ +R
Sbjct: 714 GYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYR 773
Query: 768 RNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYD----KT---------------TNSW 808
+ +D DG I E D KT
Sbjct: 774 K----------LDEDG-------IVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGLQER 816
Query: 809 RTNS---RKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCS 865
R S R G + + VD V + N K +R R R P +GDKF+SRHGQKGV
Sbjct: 817 RDTSVTVRHGEKGI-VDTVLITESPEGNKLVK--VRVRDLRIPELGDKFASRHGQKGVIG 873
Query: 866 QLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKVVA 911
L P DMPF+ G+ PDLIINPHA PSRMT+ LLES+A KV A
Sbjct: 874 MLVPQEDMPFT-EDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAA 918
>gnl|CDD|132709 TIGR03670, rpoB_arch, DNA-directed RNA polymerase subunit B. This
model represents the archaeal version of DNA-directed
RNA polymerase subunit B (rpoB) and is observed in all
archaeal genomes.
Length = 599
Score = 231 bits (590), Expect = 2e-65
Identities = 114/305 (37%), Positives = 162/305 (53%), Gaps = 28/305 (9%)
Query: 628 THEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQT 687
TH EI P+ +L ++A+ PY +HNQSPRN MAKQ++G + R D + + L
Sbjct: 117 THLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHY 176
Query: 688 PQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQT 747
PQ P+V+T G D+ P G N +VAV++Y GY++EDA+I+NK+S++RG+ ++T
Sbjct: 177 PQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRT 236
Query: 748 -ETIDLSDDGNKVDRGQKLFRRNKDAKS--LHSVIDSDGLPYVGQMIHPGEPYCSIYDKT 804
E + G + DR + + + + +D DG+ Y + G+ + KT
Sbjct: 237 YEAEERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGD---VLIGKT 293
Query: 805 ---------------TNSWRTNS---RKGSESVFVDYVAVDMKNSKNLPQKANIRFRHTR 846
T R S R G E VD V + N + +R R R
Sbjct: 294 SPPRFLEELRELGLVTERRRDTSVTVRHG-EKGIVDKVIITETEEGN--KLVKVRVRDLR 350
Query: 847 NPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVA 906
P +GDKF+SRHGQKGV + P DMPF+ G+ PDLIINPHA PSRMT+ LLE +A
Sbjct: 351 IPELGDKFASRHGQKGVIGMIVPQEDMPFTE-DGIVPDLIINPHAIPSRMTVGQLLEMIA 409
Query: 907 AKVVA 911
KV A
Sbjct: 410 GKVAA 414
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 224 bits (573), Expect = 4e-63
Identities = 113/305 (37%), Positives = 160/305 (52%), Gaps = 32/305 (10%)
Query: 628 THEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQT 687
TH EI P+ +L + A + PY +HN SPR M KQ++G K R D + + L
Sbjct: 123 THLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHY 182
Query: 688 PQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQT 747
PQ P+V+T T G DE P G N +VAV++Y GY++EDA+I+NK+S++RG+ ++T
Sbjct: 183 PQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRT 242
Query: 748 -ETIDLSDDGNKVDR---GQKLFR--RNKDAKSLHSVIDSDGLPYVGQMIHPG------- 794
E + G + DR K R R ++A + +D DGL + G
Sbjct: 243 YEGEERRYPGGQEDRFEIPDKDVRGYRGEEA---YRHLDEDGLVNPETEVKEGDVLIGKT 299
Query: 795 -------EPYCSIYDKTTNSWRTNS---RKGSESVFVDYVAVDMKNSKNLPQKANIRFRH 844
EP + + R S R G E VD V + ++ + +R R
Sbjct: 300 SPPRFLEEP--DDFGISPEKRRETSVTMRSG-EEGIVD--TVILTETEEGSRLVKVRVRD 354
Query: 845 TRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLES 904
R P +GDKF+SRHGQKGV + P DMPF+ +G+ PDLIINPHA PSRMT+ +LE
Sbjct: 355 LRIPELGDKFASRHGQKGVIGLIVPQEDMPFT-ESGVVPDLIINPHAIPSRMTVGHVLEM 413
Query: 905 VAAKV 909
+ KV
Sbjct: 414 IGGKV 418
>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 = 122 bits (307), Expect = 1e-29
Identities = 96/426 (22%), Positives = 152/426 (35%), Gaps = 82/426 (19%)
Query: 14 ELVRHHIESFDYMLDEGLSE-MFDH----------------------------------- 37
LV ++SF++ LDEGL E + +
Sbjct: 1 GLVEQQLDSFNWFLDEGLQEEIDEFPPIEDEDEEPEFSLKVGQIKLAKPKIKESDGKTRE 60
Query: 38 -----CRQAKISYTGKLMADVEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQK 92
R ++Y+ L E + + +E+ G+ P+ML++ C L GA +
Sbjct: 61 IYPREARLRNLTYSSPLYVPAELTVNNTEE-IEKEKVFIGKIPLMLRSNACILNGASESE 119
Query: 93 LVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCV 152
LV L E + GGYFI+NG E+V + I N + R + + R +
Sbjct: 120 LVKLGECPLDPGGYFIVNGSEKVIINQIQRSPNIYYVFKKDKNGIRIYSASIISNRGRSL 179
Query: 153 RKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEK 212
R + +S + +G+ + F L L V I+L LV DLEI + + DE+
Sbjct: 180 RLEITSKGKIYARINSGAKLIMFVLLLALGLNLVEIILNLLVPEVDLEIQDDI-GINDEE 238
Query: 213 YKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAVAE 272
+ E + + + QD +L G F + AV
Sbjct: 239 DEFLTDKP------ELEEQFVIQTQDEALDYIGGRGSAKG--FPR-----ERRILGAVG- 284
Query: 273 TVIRDYIF-----VHLNDNNDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHL 327
I D V N K + +M+ +L L D+ D L N+ + L G L
Sbjct: 285 --ILDLNLLPHLGVSENTRTLKAQDIGYMIHRLLLLALGRGPLDDIDHLGNKRLRLAGEL 342
Query: 328 IT----IYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIE 383
+ I L D + +K ++ KKFDF + SK I + I
Sbjct: 343 LQSQFRILLNRLERDVRERIQKCLK-------KKFDFTLQNLVN-------SKPITSGIR 388
Query: 384 TMLKTG 389
L TG
Sbjct: 389 YFLGTG 394
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B'';
Validated.
Length = 494
Score = 101 bits (254), Expect = 2e-22
Identities = 126/545 (23%), Positives = 209/545 (38%), Gaps = 146/545 (26%)
Query: 15 LVRHHIESFDYMLDEGLSEMFDHCRQAKISY---------TGKLM--------AD----- 52
LVRHHI+S++ +D GL ++ D Q I GK+ AD
Sbjct: 18 LVRHHIDSYNDFVDNGLQKIID--EQGPIETEIEDGVYVELGKIRVGKPVVKEADGSERE 75
Query: 53 ------------------VEFQYLDAGSPVVRERFNFGQFPVMLKTRRCHLQGADSQKLV 94
+E ++ G E G+ PVM+ ++ C+L G ++L+
Sbjct: 76 IYPMEARLRNLTYSAPLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELI 135
Query: 95 SLKEEAAEMGGYFILNGLERVFRS--------VILPKQN-YPMSMVRSSFRDRREGYTDK 145
+ E+ + GGYFI+NG ERV + +++ K Y + + +R GY +
Sbjct: 136 EVGEDPLDPGGYFIVNGSERVLMTLEDLAPNKILVEKDERYGDRIEVAKVFSQRRGY--R 193
Query: 146 AVVIRCVRKDQSSVTLKLYYLLNGSVRLGF-WLQGKEYLLPVGIVLKALVDTNDLEIFNH 204
A+V R +G + + F + G +P I+++AL D EI
Sbjct: 194 ALVT-VERNR------------DGLLEVSFPSVPGS---IPFVILMRALGLETDEEIVE- 236
Query: 205 LTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQS 264
AV E VK +L +++ + T+ + L++IG + V G Q+
Sbjct: 237 --------------AVSDD--PEIVKFMLENLEEAEVDTQEEALEYIG---KRVAPG-QT 276
Query: 265 ESY-YAVAETVIRDYIFVHLNDNNDKFNL----LIFMLQKLFSLVDHTSVSDNPDSLQNQ 319
+ Y AE VI Y+ HL + L M + F L D+ D N+
Sbjct: 277 KEYRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANK 336
Query: 320 EILLPGHLITIYLKEKLEDWLRKG-KKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQI 378
+ L G L +ED R +L +D +K +E+ +
Sbjct: 337 RLKLAGDL--------MEDLFRVAFNRLARD----------------VKYQLERANMRNR 372
Query: 379 GTSIETMLK----TGRL--ATQTGLDLQQRAGYTVQAERLNFLRFISFFRAV-------- 424
SI+T ++ T RL A TG + R G + +R +++ +S R V
Sbjct: 373 ELSIKTAVRSDVLTERLEHAMATGNWVGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQ 432
Query: 425 -HRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIR 483
H A R L P WG +CP TP+G CGL+ + +++ D
Sbjct: 433 PHFEA----------RDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKE 482
Query: 484 DFSKM 488
++
Sbjct: 483 ILKEL 487
>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 = 90.4 bits (225), Expect = 4e-22
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 409 AERLNFLRFISFFRAVHR-GASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMT 467
++ N+L +S R V+R G +T VR L P +G +CP+ TP+G CGL+N +
Sbjct: 3 LDQTNWLSELSHKRRVNRLGGLSKERKTFEVRDLHPSQYGRICPIETPEGANCGLVNSLA 62
Query: 468 STCRV 472
R+
Sbjct: 63 LYARI 67
>gnl|CDD|219216 pfam06883, RNA_pol_Rpa2_4, RNA polymerase I, Rpa2 specific domain.
This domain is found between domain 3 (pfam04565) and
domain 5 (pfam04565), but shows no homology to domain 4
of Rpb2. The external domains in multisubunit RNA
polymerase (those most distant from the active site) are
known to demonstrate more sequence variability.
Length = 58
Score = 71.8 bits (177), Expect = 1e-15
Identities = 26/58 (44%), Positives = 34/58 (58%)
Query: 526 VGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVR 583
+G + V LR LKV +P LE+GYVP S GG YPGLYLF++P + +R
Sbjct: 1 LGYLSPKLAPTVADTLRYLKVEGEHSVPPTLEIGYVPPSNGGQYPGLYLFSTPARMMR 58
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 78.2 bits (193), Expect = 1e-14
Identities = 54/228 (23%), Positives = 94/228 (41%), Gaps = 35/228 (15%)
Query: 705 EYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQTETIDLSD-DGNKVDRGQ 763
E G N +VA + + GY+ EDA+++NK V + ++ + I+ + + + G
Sbjct: 643 ELALGQNVLVAYMPWEGYNFEDAILINKRLV-----YEDLFTSIHIEKYEIELRQTKLGS 697
Query: 764 KLFRRNKDAKSLHSV--IDSDGLPYVGQMIHPGEPYC-------------------SIYD 802
+ RN S +S+ +D +G+ +G + G+ +I+
Sbjct: 698 EEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFG 757
Query: 803 KTTNSWRTNS---RKGSESVFVDYVAVDMKNSKNLPQKANIRFR----HTRNPIIGDKFS 855
+ + S G + L ++ R R +GDK +
Sbjct: 758 EKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLA 817
Query: 856 SRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLE 903
RHG KG+ S++ P DMP+ G PD+I+NP PSRM + L E
Sbjct: 818 GRHGNKGIISRILPRQDMPYLP-DGTPPDIILNPLGVPSRMNVGQLFE 864
Score = 56.3 bits (136), Expect = 7e-08
Identities = 87/398 (21%), Positives = 151/398 (37%), Gaps = 91/398 (22%)
Query: 105 GYFILNGLERVFRSVILPKQNYPMSMVRSSFRDRREG-YTDKAVVIRCVRKDQSSVTLKL 163
G FI+NGLERV S I +RS G Y K + K S+
Sbjct: 106 GTFIINGLERVIVSQI----------IRSP------GIYFKKEI------KKNSNKIYSA 143
Query: 164 YYLLNGSVRLGFWLQGKEYL---------LPVGIVLKALVDTNDLEIFNHLTCCYDEKYK 214
+ N + F L + + P+ I LKAL D +I++ LT K
Sbjct: 144 TLIPNRGSWIKFELDKNKEIWIRIDKNRKKPLIIFLKAL-GLTDQDIYSRLTKSEFLKKL 202
Query: 215 KEKGAVGSPLVSERVKI----ILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQSESYYAV 270
K + +E + + L+ ++ ++ Q L F P Y +
Sbjct: 203 KPILLNSNSYTNEEILLEIYKNLSPIEPATVNDANQNL--FSRFFDP--------KNYDL 252
Query: 271 AETVIRDYIF-VHLNDNNDKFNL----LIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPG 325
+ ++LN NL ++ ++ KL +L + D+ D L+N+ + G
Sbjct: 253 GKVGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVG 312
Query: 326 ----HLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDF----FNLANIKKVMEKNPSKQ 377
+ I LK +LE LR ++ +I++ KF+ +A I++ + Q
Sbjct: 313 ELLQNQFRIGLK-RLERILRN--RMTICDIDSL-SKFNLINPKPLIALIREFFGSSQLSQ 368
Query: 378 IGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTTS 437
M +T L+ +L + R++ L + SFA
Sbjct: 369 Y------MDQTNPLS-----ELTHK-------RRISILGPGGLDKD---RISFA------ 401
Query: 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASY 475
VR + P +G +CP+ TP+G CGL+ + + R+ +
Sbjct: 402 VRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKF 439
>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 = 61.6 bits (150), Expect = 8e-11
Identities = 37/188 (19%), Positives = 67/188 (35%), Gaps = 23/188 (12%)
Query: 144 DKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFN 203
DK + S L L + K+ +P+ I LKAL +D EI +
Sbjct: 12 DKNGIGATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREILD 71
Query: 204 HLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRLQCLQHIGEHFQPVIDGLQ 263
L CYD + + + ++ T+ + L +IG+ F + G +
Sbjct: 72 RL--CYDFNDPQML-----------ELLKPELEEAENIYTQEEALDYIGKGF-ALRRGEE 117
Query: 264 SESYYA---VAETVIRDYIFVHLNDNND------KFNLLIFMLQKLFSLVDHTSVSDNPD 314
A + + + HL N K +++M+ +L +L D+ D
Sbjct: 118 PRLQRAREILYSRDPKYNLNKHLGLNEPFENERLKAQDILYMIDRLLNLKLGRRKPDDID 177
Query: 315 SLQNQEIL 322
L N+ +
Sbjct: 178 HLGNKRVR 185
>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 = 62.0 bits (151), Expect = 1e-09
Identities = 66/270 (24%), Positives = 103/270 (38%), Gaps = 51/270 (18%)
Query: 689 QTPIVRTNTYTKYG---IDEYPT-------GTNAIVAVLAYTGYDMEDAMILNKSSVDRG 738
Q PIV G D T G N +VA + + GY+ EDA+++++ V
Sbjct: 644 QRPIVSVGDRVVAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDD 703
Query: 739 M---CHGQIYQTETIDLSDDGNKVDRGQKLFRR---NKDAKSLHSVIDSDGLPYVGQMIH 792
+ H + Y+ E D G + R N +L + +D +G+ +G +
Sbjct: 704 VFTSIHIEEYEVEARDTK-------LGPEEITRDIPNVSEDALRN-LDENGIVRIGAEVK 755
Query: 793 PGEPYC-------------------SIYDKTTNSWRTNSRK---GSESVFVDYVAVDMKN 830
G+ +I+ + R S + G E +D K
Sbjct: 756 AGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRKE 815
Query: 831 SKNLPQKANIRFRH----TRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLI 886
LP N + R +GDK + RHG KGV S++ P DMPF G D++
Sbjct: 816 GDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLE-DGTPVDIV 874
Query: 887 INPHAFPSRMTIAMLLESVAAKVVAYMENL 916
+NP PSRM I +LE+ +
Sbjct: 875 LNPLGVPSRMNIGQILETHLGWAGKKLGRK 904
Score = 33.5 bits (77), Expect = 0.61
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASY 475
VR + P +G +CP+ TP+G GL+N +++ RV Y
Sbjct: 423 VRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNDY 460
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 58.0 bits (140), Expect = 2e-08
Identities = 24/54 (44%), Positives = 34/54 (62%), Gaps = 1/54 (1%)
Query: 850 IGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLE 903
+GDK + RHG KG+ S + P DMP++ G D+++NP PSRM I +LE
Sbjct: 1090 VGDKMAGRHGNKGIVSNIVPVADMPYTA-DGEPVDIVLNPLGVPSRMNIGQILE 1142
Score = 38.0 bits (88), Expect = 0.028
Identities = 65/257 (25%), Positives = 101/257 (39%), Gaps = 42/257 (16%)
Query: 311 DNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFF---NLANIK 367
D+ D L N+ I G L L +L L K +K I+D++ FD +L N
Sbjct: 455 DDRDHLGNRRIRAVGEL----LANELHSGLVKMQKTIKDKLTTMSGAFDSLMPHDLVN-- 508
Query: 368 KVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRG 427
SK I ++I + G L Q T + R +S A+ G
Sbjct: 509 -------SKMITSTI--------MEFFMGGQLSQFMDQTNPLSEVTHKRRLS---ALGEG 550
Query: 428 ASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRV-------ASYYD-SR 479
R + P +G +CP+ TP+G+ GL+N +++ RV A Y
Sbjct: 551 GLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVD 610
Query: 480 GNIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVV- 538
G + + T+I + P+ + + G +L L++ RV G I +E KV
Sbjct: 611 GKVVGETIYLTAIQED--SHIIAPASTPIDEEG--NILGDLIETRVEGEIVLNEKSKVTL 666
Query: 539 --AHLRRLKVSAASVIP 553
L AAS+IP
Sbjct: 667 MDLSSSMLVGVAASLIP 683
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 56.6 bits (136), Expect = 7e-08
Identities = 32/78 (41%), Positives = 44/78 (56%), Gaps = 9/78 (11%)
Query: 833 NLPQ------KANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLI 886
+LPQ K I +H+ P GDK + RHG KGV S++ P DMP+ G D+I
Sbjct: 1062 DLPQGVSMSVKVFIAVKHSLQP--GDKMAGRHGNKGVISRVVPVEDMPYLE-DGTPVDII 1118
Query: 887 INPHAFPSRMTIAMLLES 904
+NP PSRM + +LE+
Sbjct: 1119 LNPLGVPSRMNVGQILET 1136
Score = 37.7 bits (87), Expect = 0.036
Identities = 14/38 (36%), Positives = 23/38 (60%)
Query: 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASY 475
VR + P +G +CP+ TP+G+ GL+N + R+ Y
Sbjct: 568 VRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKY 605
Score = 32.7 bits (74), Expect = 1.2
Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 20/81 (24%)
Query: 679 DQKLYHLQT----------PQTPIVRTNTYTKYG--IDEYPT--------GTNAIVAVLA 718
D +YHL+ Q P+V Y K G I + P G N +VA ++
Sbjct: 767 DVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMS 826
Query: 719 YTGYDMEDAMILNKSSVDRGM 739
+ GY+ ED++I++ V + +
Sbjct: 827 WQGYNFEDSIIISSEVVKKDL 847
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 54.3 bits (132), Expect = 3e-07
Identities = 28/66 (42%), Positives = 39/66 (59%), Gaps = 12/66 (18%)
Query: 850 IGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGM---RP-DLIINPHAFPSRMTIAMLLESV 905
+GDK + RHG KGV S++ P DMP+ + P D+++NP PSRM I +LE+
Sbjct: 882 VGDKMAGRHGNKGVVSRILPVEDMPY-----LEDGTPVDIVLNPLGVPSRMNIGQILETH 936
Query: 906 ---AAK 908
AAK
Sbjct: 937 LGWAAK 942
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 49.9 bits (120), Expect = 7e-06
Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 7/57 (12%)
Query: 850 IGDKFSSRHGQKGVCSQLWPDIDMPF--SGVTGMRP-DLIINPHAFPSRMTIAMLLE 903
+GDK + RHG KG+ S++ P DMP+ G P D+++NP PSRM + + E
Sbjct: 816 VGDKVAGRHGNKGIISKILPRQDMPYLQDG----TPVDMVLNPLGVPSRMNVGQIFE 868
>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 34.7 bits (80), Expect = 0.20
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 8/47 (17%)
Query: 447 GFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSIL 493
G LC PDGEPCG TC A + ++GN D+ +R L
Sbjct: 44 GLLCETPQPDGEPCG-------TC-AACNWFAQGNHPDYRIVRPEAL 82
>gnl|CDD|191029 pfam04567, RNA_pol_Rpb2_5, RNA polymerase Rpb2, 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). Domain 5,
is also known as the external 2 domain.
Length = 46
Score = 30.2 bits (69), Expect = 0.35
Identities = 10/37 (27%), Positives = 12/37 (32%)
Query: 598 IELIGPFEQVFMEIRCPDGGDGGRRNAFPATHEEIHP 634
IE + E+ I TH EIHP
Sbjct: 10 IEYLDAEEEETAMIAMSPEDLRLEDITKTTTHCEIHP 46
>gnl|CDD|225142 COG2233, UraA, Xanthine/uracil permeases [Nucleotide transport and
metabolism].
Length = 451
Score = 33.0 bits (76), Expect = 0.71
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 484 DFSKMRTSILRVLIGVGMIPSL-PKLVKSGPPAVLSVLLDGRVVGVI 529
D S+ I+ V +G+G+ P++ P + +L G +G +
Sbjct: 378 DRSRRNLLIVAVSLGLGIGVGAVPEVFLQLPAWLRPLLSSGIALGTL 424
>gnl|CDD|227602 COG5277, COG5277, Actin and related proteins [Cytoskeleton].
Length = 444
Score = 31.6 bits (72), Expect = 2.0
Identities = 13/70 (18%), Positives = 25/70 (35%), Gaps = 11/70 (15%)
Query: 305 DHTSVS------DNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKK-LIQDEIENNGKK 357
T V P +++ I + G IT YLK+ L + + ++ E+
Sbjct: 166 SVTHVIPVVDGIVLPKAVKR--IDIGGRDITDYLKKLLREKYPPSRGYNLKSELVEY--S 221
Query: 358 FDFFNLANIK 367
+ N +
Sbjct: 222 SEIVNEIKEE 231
>gnl|CDD|220261 pfam09484, Cas_TM1802, CRISPR-associated protein TM1802
(cas_TM1802). Clusters of short DNA repeats with
non-homologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This minor cas protein is
found in at least five prokaryotic genomes:
Methanosarcina mazei, Sulfurihydrogenibium azorense,
Thermotoga maritima, Carboxydothermus hydrogenoformans,
and Dictyoglomus thermophilum, the first of which is
archaeal while the rest are bacterial.
Length = 584
Score = 31.2 bits (71), Expect = 3.2
Identities = 27/118 (22%), Positives = 46/118 (38%), Gaps = 9/118 (7%)
Query: 279 IFVHLNDNNDKFNLLI---FMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEK 335
+ + + ++ ++I F + + + + N +S Q P + IT +E
Sbjct: 40 LKIDFDTEENEIEIVIGEEFDKKTARKYL-YKGQAGNGNSSQ---WYSPTNKITYDPEET 95
Query: 336 LEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLAT 393
L L+ K + K F +IKKV+EKN K I I+ G L T
Sbjct: 96 LNKKLKSIFKKFYKDKGEINKYRYFLK--DIKKVLEKNFEKIIKDLIDLKKNEGVLYT 151
>gnl|CDD|216097 pfam00750, tRNA-synt_1d, tRNA synthetases class I (R). Other tRNA
synthetase sub-families are too dissimilar to be
included. This family includes only arginyl tRNA
synthetase.
Length = 345
Score = 30.9 bits (70), Expect = 3.6
Identities = 22/139 (15%), Positives = 46/139 (33%), Gaps = 18/139 (12%)
Query: 250 HIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLNDNNDKFNLLIFMLQKLFSLVDHTSV 309
H+G +I S + V+R+ ++ D +F +LI L+ + +V
Sbjct: 35 HVGHLRSTIIGDALSRLLEFLGYDVVREN---YVGDWGTQFGMLIASLEAAAK--EELTV 89
Query: 310 SDNPDSLQN------------QEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKK 357
L++ + + L+ E++ LI D I+ + K
Sbjct: 90 PMPIQDLEDGYRGIKKDYIAEEIFAKEARNAVVLLQSGDEEFREMWVLLIFDHIKQSLNK 149
Query: 358 F-DFFNLANIKKVMEKNPS 375
D F++ +
Sbjct: 150 IYDDFDVTLHEGESVYKGR 168
>gnl|CDD|237607 PRK14091, PRK14091, RNA-binding protein Hfq; Provisional.
Length = 165
Score = 29.8 bits (67), Expect = 4.0
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 118 SVILPKQNYPMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGFWL 177
S I+P +S S ++ + V + VR VT+ +L+NG + L
Sbjct: 66 STIMPAHPLDLSRFSKSLDANKKSRLLQDVFLSAVRDSGEPVTM---FLVNGVM-----L 117
Query: 178 QGK 180
QG+
Sbjct: 118 QGE 120
>gnl|CDD|128594 smart00299, CLH, Clathrin heavy chain repeat homology.
Length = 140
Score = 29.2 bits (66), Expect = 4.5
Identities = 21/87 (24%), Positives = 32/87 (36%), Gaps = 24/87 (27%)
Query: 287 NDKFNLLIFMLQKLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKL 346
+ LI L+ L S+NP LQ + LI +Y K
Sbjct: 20 RNLLEELIPYLESALKLN-----SENPA-LQTK-------LIELYAKYDP---------- 56
Query: 347 IQDEIENNGKKFDFFNLANIKKVMEKN 373
Q EIE K + +++ + K+ EK
Sbjct: 57 -QKEIERLDNKSNHYDIEKVGKLCEKA 82
>gnl|CDD|224524 COG1608, COG1608, Predicted archaeal kinase [General function
prediction only].
Length = 252
Score = 30.0 bits (68), Expect = 4.9
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 516 VLSVLLDG--RVVGVIPSSEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYP 570
V+ LLD R V V+P S R+ + I D LE G+VP+ G P
Sbjct: 86 VVDALLDAGVRAVSVVPIS----FSTFNGRILYTYLEAIKDALEKGFVPVLYGDVVP 138
>gnl|CDD|149395 pfam08321, PPP5, PPP5 TPR repeat region. This region is specific
to the PPP5 subfamily of serine/threonine phosphatases
and contains TPR repeats.
Length = 95
Score = 28.5 bits (64), Expect = 5.4
Identities = 11/48 (22%), Positives = 23/48 (47%), Gaps = 8/48 (16%)
Query: 328 ITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFNLANIKKVMEKNPS 375
+T+ + + + + KKL KK + L +K++++K PS
Sbjct: 52 VTLEFVKDMMERFKDQKKL--------HKKCAYQILLQVKELLKKLPS 91
>gnl|CDD|180426 PRK06148, PRK06148, hypothetical protein; Provisional.
Length = 1013
Score = 30.4 bits (69), Expect = 5.4
Identities = 11/42 (26%), Positives = 16/42 (38%), Gaps = 2/42 (4%)
Query: 771 DAKSLHSVIDSDGLPYVGQMIH--PGEPYCSIYDKTTNSWRT 810
SL S D DG P + +++ PG P +T
Sbjct: 92 SGASLASAQDPDGEPRLLRLLSWLPGTPLAEAAPRTEALLDN 133
>gnl|CDD|234126 TIGR03157, cas_Csc2, CRISPR type I-D/CYANO-associated protein Csc2.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) is a widespread family of
prokaryotic direct repeats with spacers of unique
sequence between consecutive repeats. This protein
family is a CRISPR-associated (Cas) family strictly
associated with the Cyano subtype of CRISPR/Cas locus,
found in several species of Cyanobacteria and several
archaeal species. This family is designated Csc2 for
CRISPR/Cas Subtype Cyano protein 2, as it is often the
second gene upstream of the core cas genes,
cas3-cas4-cas1-cas2 [Mobile and extrachromosomal element
functions, Other].
Length = 282
Score = 29.8 bits (67), Expect = 6.4
Identities = 24/90 (26%), Positives = 33/90 (36%), Gaps = 8/90 (8%)
Query: 420 FFRAVHRGA---SFAGLRTTSVRK--LLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVAS 474
A SF G RT+S+ + + F C V D P L + + R A
Sbjct: 131 TQNAPGEDGTKTSFIGTRTSSINEPDFIKPGTLFPCVVTLKDVTPAEFLYVVNNIARTAR 190
Query: 475 YYDSRGNIRDFSKMRTSILRVLIGVGMIPS 504
Y N F ++R IL V + PS
Sbjct: 191 Y---GANTTRFGRVRNRILGVFLSPYEGPS 217
>gnl|CDD|224249 COG1330, RecC, Exonuclease V gamma subunit [DNA replication,
recombination, and repair].
Length = 1078
Score = 30.0 bits (68), Expect = 7.7
Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 2/76 (2%)
Query: 317 QNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFFN--LANIKKVMEKNP 374
NQ + LP +L+ + +D + KKL+ N K + + L + + + K
Sbjct: 997 MNQPLPLPPKSALAWLEARYDDEEKALKKLLDLYEGNLLSKGEGDDRYLQRVLRPLTKEL 1056
Query: 375 SKQIGTSIETMLKTGR 390
+ +E++L
Sbjct: 1057 LASLVEQLESLLLAPL 1072
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
0.321 0.137 0.405
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 48,379,059
Number of extensions: 4850155
Number of successful extensions: 4132
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4094
Number of HSP's successfully gapped: 58
Length of query: 940
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 834
Effective length of database: 6,236,078
Effective search space: 5200889052
Effective search space used: 5200889052
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 (28.4 bits)