RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 001179
(1131 letters)
>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 = 636 bits (1642), Expect = 0.0
Identities = 213/512 (41%), Positives = 275/512 (53%), Gaps = 56/512 (10%)
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 KFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSL 912
KF+SRHGQKGV S++ P DMPF+ G+ PD+I+NPH FPSRMTI LLES+ K G+L
Sbjct: 635 KFASRHGQKGVISKILPQEDMPFT-EDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGAL 693
Query: 913 HGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGVYGTELT 972
GKF DATPF D ++ +++ E+L G NY+G EVLY G G L
Sbjct: 694 LGKFGDATPF-------------DGAE--EEDISELLGEAGLNYYGKEVLYDGRTGEPLE 738
Query: 973 CEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHG 1032
IF+GPVYYQRL+HMV DK RSTG +TRQP+KGR RGGG RFGEMERD+L+AHG
Sbjct: 739 APIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHG 798
Query: 1033 AAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHAC 1092
AAYLL +RL SD VA VC CG +L+A C C
Sbjct: 799 AAYLLQERLTIKSDDVVARVCVKCGIILSANL------------------------CRLC 834
Query: 1093 QTSKGMETVAMPYVFRYLAAELAAMNIKITLQ 1124
+ + V +PY F+ L EL +MNI L+
Sbjct: 835 KKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
Score = 190 bits (485), Expect = 9e-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 = 117 bits (296), 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|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 616 bits (1591), Expect = 0.0
Identities = 285/1217 (23%), Positives = 431/1217 (35%), Gaps = 261/1217 (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 MPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGD 932
MPF G PD+I+NP PSRM I +LE+ K +L G +D F
Sbjct: 854 MPFL-EDGTPPDIILNPLGVPSRMNIGQILETHLGKAAALLGIPVDTPVF---------- 902
Query: 933 TGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDK 992
G E +++ E+L+ GF Y G EVLY G G IF+G +YYQ+L HMV DK
Sbjct: 903 DGAPE-----EDIRELLKEAGFPYSGKEVLYDGRTGEPFDAPIFVGVMYYQKLHHMVDDK 957
Query: 993 FQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSDYHVADV 1052
RSTG +T+QP+ G+ + GG RFGEME +L A+GAAY L +RL SD
Sbjct: 958 IHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTVKSDD----- 1012
Query: 1053 CSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAA 1112
+CG + C + V +P F+ L
Sbjct: 1013 --VCGRIKI-------------------------YECIVKGENIPE--VGIPESFKVLLK 1043
Query: 1113 ELAAMNIKITLQLGDGA 1129
EL ++ I + L+L DG
Sbjct: 1044 ELRSLGIDVRLELEDGK 1060
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 496 bits (1278), Expect = e-157
Identities = 341/1222 (27%), Positives = 525/1222 (42%), Gaps = 243/1222 (19%)
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 QLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANS 925
L P DMPF+ G+ PDLIINPHA PSRMT+ LLES+A K +L G+F+DATPF
Sbjct: 874 MLVPQEDMPFT-EDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF--- 929
Query: 926 VKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRL 985
+EL + L G+ G EV+Y G G ++ IFIG VYYQ+L
Sbjct: 930 ------------YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKL 977
Query: 986 RHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCS 1045
HMV+DK R+ G + +TRQP +GR R GG+RFGEMERD L+ HGAA LL +RL S
Sbjct: 978 HHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSS 1037
Query: 1046 DYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKKVTCHACQTSKGMETVAMPY 1105
D VC LCG + + +++ K C + V + Y
Sbjct: 1038 DKTTIYVCELCGHIA----WYDRRK--------------NKYVCPIHGDKGNISPVEVSY 1079
Query: 1106 VFRYLAAELAAMNIKITLQLGD 1127
F+ L EL +M I L+LGD
Sbjct: 1080 AFKLLLQELMSMGISPRLKLGD 1101
>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 = 450 bits (1159), Expect = e-149
Identities = 158/391 (40%), Positives = 219/391 (56%), Gaps = 33/391 (8%)
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 CSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFA 923
S++ P DMPF+ G+ PD+I+NPH PSRMTI LLES+ K +L GKF+DATPF
Sbjct: 237 VSKILPQEDMPFT-EDGIPPDIILNPHGVPSRMTIGQLLESLLGKAAALLGKFIDATPF- 294
Query: 924 NSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQ 983
D + V+++GE+L+ G+N +G EVLY G G IF+GP+YYQ
Sbjct: 295 ------------DGASEDVEDIGELLKEAGYNAYGKEVLYDGRTGEPFKAPIFVGPIYYQ 342
Query: 984 RLRHMVSDKFQVRSTGTMDQITRQPIKGRKR 1014
+L+HMV DK RSTG +T+QP+ GR R
Sbjct: 343 KLKHMVDDKIHARSTGPYSLLTQQPLGGRSR 373
>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 = 406 bits (1045), Expect = e-129
Identities = 197/521 (37%), Positives = 272/521 (52%), Gaps = 61/521 (11%)
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 AKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYSGV 966
K +L G+ +D TPF G E +EL + L GF G EV+Y G+
Sbjct: 410 GKVAALEGRRVDGTPF----------EGEPE-----EELRKELLKLGFKPDGKEVMYDGI 454
Query: 967 YGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERD 1026
G +L EIFIG +YYQ+L HMV+DK RS G + +TRQP +GR R GG+RFGEMERD
Sbjct: 455 TGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERD 514
Query: 1027 SLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAPKK 1086
L+ HGAA LL +RL SD +V VC CG + A + +
Sbjct: 515 VLIGHGAAMLLKERLLDESDKYVVYVCENCGHI-----------AWED-------KRKGT 556
Query: 1087 VTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKITLQLGD 1127
C C + + V M Y F+ L EL ++ I L+LGD
Sbjct: 557 AYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLELGD 597
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 404 bits (1040), Expect = e-128
Identities = 195/523 (37%), Positives = 272/523 (52%), Gaps = 65/523 (12%)
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 VAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVLYS 964
+ K GSL G+ +D T F +G DE ++L E L GF + G EV+Y
Sbjct: 414 IGGKVGSLEGRRVDGTAF----------SGEDE-----EDLREALEKLGFEHTGKEVMYD 458
Query: 965 GVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEME 1024
G+ G ++ EIF+G +YYQ+L HMV++K RS G + +TRQP +GR R GG+RFGEME
Sbjct: 459 GITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEME 518
Query: 1025 RDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREIGGLPPARAP 1084
RD L+ HGAA LL +RL SD VC+ CG + A + + R
Sbjct: 519 RDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMI--AIYDKKRNRKY------------ 564
Query: 1085 KKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKITLQLGD 1127
C C + V M Y F+ L EL ++ I L+L D
Sbjct: 565 ----CPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLELED 603
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 146 bits (370), Expect = 2e-35
Identities = 102/378 (26%), Positives = 161/378 (42%), Gaps = 49/378 (12%)
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 SRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAKGGSLHGK 915
RHG KG+ S++ P DMP+ G PD+I+NP PSRM + L E + G K
Sbjct: 818 GRHGNKGIISRILPRQDMPYLP-DGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNK 876
Query: 916 FMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCG-----FN-YH-GVEVLYSGVYG 968
PF G++ S+ L++ FN YH G VL G G
Sbjct: 877 RFKILPFDEM-------YGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTG 929
Query: 969 TELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSL 1028
+ + +G Y +L H+V DK R+TG +T+QP+ G+ + GG RFGEME +L
Sbjct: 930 YKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWAL 989
Query: 1029 LAHGAAYLLHDRLHTCSD 1046
A GAAY L + L SD
Sbjct: 990 EAFGAAYTLKELLTIKSD 1007
Score = 58.9 bits (143), Expect = 1e-08
Identities = 90/399 (22%), Positives = 152/399 (38%), Gaps = 93/399 (23%)
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 AETVIRDYIFVHLNDN-NDKFNLLIFM-----LQKLFSLVDHTSVSDNPDSLQNQEILLP 324
+ V R I LN N ++ L + + KL +L + D+ D L+N+ +
Sbjct: 253 GK-VGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSV 311
Query: 325 G----HLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDF----FNLANIKKVMEKNPSK 376
G + I LK +LE LR ++ +I++ KF+ +A I++ +
Sbjct: 312 GELLQNQFRIGLK-RLERILRN--RMTICDIDSL-SKFNLINPKPLIALIREFFGSSQLS 367
Query: 377 QIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFFRAVHRGASFAGLRTT 436
Q M +T L+ +L + R++ L + SFA
Sbjct: 368 QY------MDQTNPLS-----ELTHK-------RRISILGPGGLDKD---RISFA----- 401
Query: 437 SVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASY 475
VR + P +G +CP+ TP+G CGL+ + + R+ +
Sbjct: 402 -VRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKF 439
>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 = 135 bits (343), Expect = 3e-32
Identities = 114/400 (28%), Positives = 169/400 (42%), Gaps = 63/400 (15%)
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 INPHAFPSRMTIAMLLESVAAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELG 946
+NP PSRM I +LE+ G G+ P A V +G + +E+
Sbjct: 875 LNPLGVPSRMNIGQILETHLGWAGKKLGRKG--VPIATPV--FDGAS--------EEEIK 922
Query: 947 EMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMDQITR 1006
E L G G LY G G + + +G +Y +L H+V DK RSTG +T+
Sbjct: 923 EYLEKAGLPRDGKVRLYDGRTGEQFDNPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQ 982
Query: 1007 QPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSD 1046
QP+ G+ + GG RFGEME +L A+GAAY L + L SD
Sbjct: 983 QPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1022
Score = 33.5 bits (77), Expect = 0.73
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|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 = 124 bits (313), Expect = 3e-30
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|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 112 bits (282), Expect = 6e-25
Identities = 78/200 (39%), Positives = 103/200 (51%), Gaps = 40/200 (20%)
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 ---AAKGGSLHGKFMDATPFANSVKKTNGDTGTDESKSLVDELGEMLRTCGFNYHGVEVL 962
AAKG L KF ATP + K+ +E+ E+L G G L
Sbjct: 937 LGWAAKG--LGIKF--ATPVFDGAKE--------------EEIKELLEEAGLPEDGKTTL 978
Query: 963 YSGVYGTELTCEIFIGPV-----YYQRLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGG 1017
Y G T E F PV Y +L H+V DK RSTG +T+QP+ G+ + GG
Sbjct: 979 YDG-----RTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGG 1033
Query: 1018 IRFGEMERDSLLAHGAAYLL 1037
RFGEME +L A+GAAY L
Sbjct: 1034 QRFGEMEVWALEAYGAAYTL 1053
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B'';
Validated.
Length = 494
Score = 102 bits (257), Expect = 1e-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 = 90.8 bits (226), 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|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 99 bits (250), Expect = 4e-21
Identities = 73/218 (33%), Positives = 100/218 (45%), Gaps = 43/218 (19%)
Query: 850 IGDKFSSRHGQKGVCSQLWPDIDMPF--SGVTGMRP-DLIINPHAFPSRMTIAMLLESVA 906
+GDK + RHG KG+ S++ P DMP+ G P D+++NP PSRM + + E +
Sbjct: 816 VGDKVAGRHGNKGIISKILPRQDMPYLQDG----TPVDMVLNPLGVPSRMNVGQIFECLL 871
Query: 907 AKGGSLHGKFMDATPFANSVKKTNGDTGTDE------SKSLV-DELGEMLRTCG----F- 954
G L + PF DE S+ LV EL E + F
Sbjct: 872 GLAGDLLNRHYRIAPF-------------DERYEQEASRKLVFSELYEASKQTANPWVFE 918
Query: 955 -NYHGVEVLYSGVYGTELTCEIF-----IGPVYYQRLRHMVSDKFQVRSTGTMDQITRQP 1008
Y G L+ G G + F IG Y +L H V DK RS+G +T+QP
Sbjct: 919 PEYPGKSRLFDGRTG-----DPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQP 973
Query: 1009 IKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSD 1046
++GR + GG R GEME +L G AY+L + L SD
Sbjct: 974 LRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 99.6 bits (248), Expect = 7e-21
Identities = 70/243 (28%), Positives = 101/243 (41%), Gaps = 50/243 (20%)
Query: 850 IGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLE------ 903
+GDK + RHG KG+ S + P DMP++ G D+++NP PSRM I +LE
Sbjct: 1090 VGDKMAGRHGNKGIVSNIVPVADMPYTA-DGEPVDIVLNPLGVPSRMNIGQILEMHLGLV 1148
Query: 904 ------------SVAAKG--GSLHGKFMDATPFANSVKK------TNGDT------GTDE 937
K L K ++ N N D
Sbjct: 1149 GKEFGKQIASMLEDKTKDFAKELRAKMLEIANAINEKDPLTIHALENCSDEELLEYAKDW 1208
Query: 938 SKSL--------------VDELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQ 983
SK + +L E+ + G LY G G ++ + +G +Y
Sbjct: 1209 SKGVKMAIPVFEGISQEKFYKLFELAK---IAMDGKMDLYDGRTGEKMRERVNVGYMYMI 1265
Query: 984 RLRHMVSDKFQVRSTGTMDQITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHT 1043
+L H+V +K RSTG +T QP+ G+ GG RFGEME +L A+GAA+ L + L
Sbjct: 1266 KLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTI 1325
Query: 1044 CSD 1046
SD
Sbjct: 1326 KSD 1328
Score = 38.4 bits (89), 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|146952 pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, domain 7. 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 comprised of
the structural domains anchor and clamp. The clamp region
(C-terminal) contains a zinc-binding motif. The clamp
region is named due to its interaction with the clamp
domain found in Rpb1. The domain also contains a region
termed "switch 4". The switches within the polymerase are
thought to signal different stages of transcription.
Length = 78
Score = 77.1 bits (191), Expect = 3e-17
Identities = 35/108 (32%), Positives = 45/108 (41%), Gaps = 33/108 (30%)
Query: 1016 GGIRFGEMERDSLLAHGAAYLLHDRLHTCSDYHVADVCSLCGSVLTATFIHPQKRAIREI 1075
GG RFGEME +L A+GAAY L +RL SD DVC CG A I
Sbjct: 1 GGQRFGEMEVWALEAYGAAYTLQERLTIKSD----DVCGRCG-------------AYAAI 43
Query: 1076 GGLPPARAPKKVTCHACQTSKGMETVAMPYVFRYLAAELAAMNIKITL 1123
C+ +E +P F+ L EL ++ + I L
Sbjct: 44 ----------------CKGKTIIEPGDIPESFKLLLQELRSLGLDIRL 75
>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|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 75.4 bits (185), Expect = 2e-13
Identities = 38/104 (36%), Positives = 58/104 (55%)
Query: 943 DELGEMLRTCGFNYHGVEVLYSGVYGTELTCEIFIGPVYYQRLRHMVSDKFQVRSTGTMD 1002
+++ ++ G + G VLY G G + ++ +G +Y +L H+V K RS G
Sbjct: 1283 EQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYS 1342
Query: 1003 QITRQPIKGRKRGGGIRFGEMERDSLLAHGAAYLLHDRLHTCSD 1046
+T+QP+ G+ GG RFGEME +L A+GAAY L + L SD
Sbjct: 1343 LVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSD 1386
Score = 56.9 bits (137), 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 = 0.041
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 = 33.1 bits (75), Expect = 1.3
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|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 = 62.7 bits (153), Expect = 5e-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|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 34.7 bits (80), Expect = 0.27
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 = 30.6 bits (70), Expect = 0.37
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 = 0.96
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 = 32.0 bits (73), Expect = 1.8
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 = 31.9 bits (73), Expect = 2.3
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|128594 smart00299, CLH, Clathrin heavy chain repeat homology.
Length = 140
Score = 30.3 bits (69), Expect = 2.5
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|237607 PRK14091, PRK14091, RNA-binding protein Hfq; Provisional.
Length = 165
Score = 30.2 bits (68), Expect = 3.8
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|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 = 3.9
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|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 = 28.8 bits (65), Expect = 4.8
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|224524 COG1608, COG1608, Predicted archaeal kinase [General function
prediction only].
Length = 252
Score = 30.0 bits (68), Expect = 7.0
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|224249 COG1330, RecC, Exonuclease V gamma subunit [DNA replication,
recombination, and repair].
Length = 1078
Score = 30.4 bits (69), Expect = 7.0
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
>gnl|CDD|180426 PRK06148, PRK06148, hypothetical protein; Provisional.
Length = 1013
Score = 30.4 bits (69), Expect = 7.4
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|143561 cd07452, CRD_sizzled, Cysteine-rich domain of the sizzled protein.
The cysteine-rich domain (CRD) is an essential part of
the sizzled protein, which regulates bone morphogenetic
protein (Bmp) signaling by stabilizing chordin, and plays
a critical role in the patterning of vertebrate and
invertebrate embryos. Sizzled also functions in the
ventral region as a Wnt inhibitor and modulates canonical
Wnt signaling. Sizzled proteins belong to the secreted
frizzled-related protein family (SFRP), and have be
identified in the genomes of birds, fishes and frogs, but
not mammals.
Length = 141
Score = 28.7 bits (64), Expect = 8.6
Identities = 27/115 (23%), Positives = 43/115 (37%), Gaps = 21/115 (18%)
Query: 1018 IRFGEMERDSLLAHG--------AAYLLHDRLHT-CSDYHVADVCSLCGSVLTATFIHPQ 1068
+ + EM +LL H +A LHT C + +CSL V TFI P
Sbjct: 22 VGYSEMRLPNLLGHTSMAEVVPKSADWQT-LLHTGCHPHARTFLCSLFAPVCLDTFIQPC 80
Query: 1069 KR---AIREIGGLPPARA------PKKVTCHACQTSKGMETVAMPYVFRYLAAEL 1114
+ A+R+ P A P+ + C + M ++ ++Y E
Sbjct: 81 RSMCVAVRD--SCAPVLACHGHSWPESLDCDRFPAGEDMCLASLSKEYQYFYKEF 133
>gnl|CDD|221454 pfam12175, WSS_VP, White spot syndrome virus structural envelope
protein VP. This family of proteins is found in viruses.
Proteins in this family are approximately 210 amino acids
in length. There is a conserved NNT sequence motif. These
proteins are structural envelope proteins in viruses.
This is the beta barrel C terminal domain. There is a
protruding N terminal domain which completes the
proteins. Three of four envelope proteins in white spot
syndrome virus share sequence homology with each other
and are present in this family - VP24, VP26 and VP28.
VP19 is the other major envelope protein but shares no
sequence homology with the other proteins. These proteins
are essential for entry into cells of the crustacean
host.
Length = 206
Score = 29.5 bits (66), Expect = 8.7
Identities = 9/27 (33%), Positives = 11/27 (40%)
Query: 1001 MDQITRQPIKGRKRGGGIRFGEMERDS 1027
D+I R PI G RG F +
Sbjct: 48 EDEIIRLPINGVARGNHFNFVNGSLQT 74
>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 = 29.5 bits (66), Expect = 9.0
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
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 0.407
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: 58,103,707
Number of extensions: 5824636
Number of successful extensions: 4956
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4901
Number of HSP's successfully gapped: 63
Length of query: 1131
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 1024
Effective length of database: 6,191,724
Effective search space: 6340325376
Effective search space used: 6340325376
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)