RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8410
(951 letters)
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 353 bits (909), Expect = e-106
Identities = 213/1009 (21%), Positives = 332/1009 (32%), Gaps = 243/1009 (24%)
Query: 47 KNLTDKNFGK---PPDKQNEFLLTLGAPHIASFDFMLDEGLDLAVEDIAPIEFEIYGKTL 103
K +FGK D N L + S++ EGL +I PIE Y
Sbjct: 8 KKRIRDSFGKIPEFLDLPN-----LVEIQLDSYNAFFLEGLQEVFREIFPIE--SYNGNT 60
Query: 104 KLNIVKAAISEPKVPAGPVGIHFNKYYPTEARQTRSVYSGPFNVTVAWSWDGKAGGTFTK 163
+L + EP K+YP E R YS P V + + +
Sbjct: 61 ELEYGSYRLGEPP-----------KFYPEECRLRGLTYSAPLYVKLRLVVNETGEEIKEQ 109
Query: 164 EV--GRVPIMLKSKRCHLRNLTPAQLIERGEHPDEWGGYFIVGGHEKLVRLLINNRRNHP 221
EV G +P+M + GGYFI+ G E+++ +
Sbjct: 110 EVYMGDIPLMTR------------------------GGYFIINGTERVIVSQEHRSPGVI 145
Query: 222 IA---IKRNAWK--------NRG--LLFS---DLGVYIR-SVKRDESAT----------- 253
K + RG L F +Y+R KR T
Sbjct: 146 FVEKKDKTGSKVLYVARVIPYRGSWLEFEFDPKDNLYVRIDRKRKIPVTILLRALGLETD 205
Query: 254 NNVLHFVTNGSARFMFSHRKSMCLLGMMQSLHEEGIHTQHDSKVFFGQIFKEKLQYDLRH 313
++ + LL + + E I ++ + G +YD +
Sbjct: 206 EEIIEAFGGDELTDLVPPEGEEALLEIYEEAKGEKITARN-ALELIGSRVFVVKRYDAK- 263
Query: 314 LNEVEICDYMLTNCILPHL----DDYWDKFLC----LSHMTCKLFHVVQGMVQLDSEDSI 365
+ Y+L +LPHL + Y + + M L + G + D D +
Sbjct: 264 EGRYKRAKYVLDKELLPHLGEAGERYDLSRVGKAKDIIAMIKYLIELRLGKGEEDDIDHL 323
Query: 366 MLQEIMTGGSLYLQLLK----------KEKSGTSAVLKESDIYAAFRASSIESAMTNFLA 415
+ + G L L + KE+ A ++ I + + L
Sbjct: 324 GNRRLRLVGELLENLFRVGLSRMERDVKERL-EKADKRD----TLVPQDLINAKPIHALI 378
Query: 416 TGNVSAGKNSTLQLMQASGFVIMAENINRMRYMSHFRAVHRGSYFQEMRSSEPRQLRTDA 475
TG + S Q M + N + +SH R + +E E R +
Sbjct: 379 TGFFGRSQLS--QFM---------DQTNPLSELSHKRRLSALGLSRERAGFEVRDVHPTH 427
Query: 476 WGFICPVHTPDGTPCGLLNHLTTNCQISEY--IPSKVLAQIPSVLVSLGMLPLTPVIQSI 533
+G ICP+ TP+G GL+ L +I+EY + + + SL + + +
Sbjct: 428 YGRICPIETPEGPNIGLIKSLALYARINEYGFLETPY---RKVLDGSLVVDEIEYLSADE 484
Query: 534 PEQALMVMLDGRIVGYILDQIATSLVPKLRMLKIVGEKIPKSLEIVYLKRPEKGMGLYPG 593
+ V + G+ G + LV +L + G V + PE +
Sbjct: 485 ED----VYVIGQANGTL--DEPGELVEELVECRRGGSG------EVSVADPEGVDYMDVS 532
Query: 594 LYLFTGPGRMLRP----------VMN-----LAAGN-----------IEWIGTFEQVFMD 627
GR L P +M A +E++ +
Sbjct: 533 PKQVVSVGRSLIPFLEHDDANRALMGSNMQRQAVPLLRTEAPLVGTGMEYLDAEDSGAAV 592
Query: 628 ICITMKEAYPGITTHRELSKTDFLSNLANLIPMPDCNQSPRNMYQCQMGKQTMGTPCLNW 687
I PG+ TH E+S L A+LIP P+ NQSP N+Y+ Q G
Sbjct: 593 IAK-----RPGVVTHVEISPIVILGIEASLIPYPEHNQSPYNLYKFARSNQATGINQRPL 647
Query: 688 RYQGVGKLYRLQTPASPFFRPVHYDTLDMDNFPMGTNAIVAVISYTGYDMEDAMILNKSS 747
+G L P D +G NA+VA + + GY+ EDA+I+++ S
Sbjct: 648 VKRGDTVEKGLVYADGPSV--------DTGELALGQNALVAFMPWNGYNYEDAIIISERS 699
Query: 748 YERGFAHGCIFKSMFIELESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDK 807
ER F S+ IE
Sbjct: 700 VERDL-----FTSIHIEEYET--------------------------------------- 715
Query: 808 WQTKDYFG-----RDPANKALE--DKLGPDGLVYVGAKLNERDPMYSYWKESENRYVTC- 859
+ +D RD N + E L DG++ +GA++ D + K +
Sbjct: 716 -EARDTKLGPEEIRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVG--KVTPKGETELT 772
Query: 860 ------------------RYSGKEEMCVEVVRMSSGFTEGGSVTPN-CAYIGYRIQRNPT 900
R EE V+ V++ + E G N + +R P
Sbjct: 773 PEERLLRIFGEKVRDTSLRVPHGEEGIVDDVQVFT--REDGDPGVNKLVKVYVAQKRKPQ 830
Query: 901 VGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPDIVFNPHGFPSRMTIG 949
+GDK A R G KG+ S P ED+PF + G PDI+ NP G PSRM IG
Sbjct: 831 IGDKMAGRHGNKGVVSKIVPQEDMPFLEDGTPPDIILNPLGVPSRMNIG 879
Score = 71.1 bits (175), Expect = 2e-12
Identities = 21/50 (42%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 758 FKSMFIELESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDK 807
+ + E G+ Y G E +Y G G A IF GV++YQ+L HMV DK
Sbjct: 910 IRELLKEA--GFPYSGKEVLYDGRTGEPFDAPIFVGVMYYQKLHHMVDDK 957
>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 = 319 bits (820), Expect = 4e-95
Identities = 115/324 (35%), Positives = 156/324 (48%), Gaps = 52/324 (16%)
Query: 640 TTHRELSKTDFLSNLANLIPMPDCNQSPRNMYQCQMGKQTMGTPCLNWRYQGVGKLYRLQ 699
TH E+S + LS A+LIP P+ NQSPRN+YQ M KQ +GTP LN +Y+ KLY L
Sbjct: 395 VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLL 454
Query: 700 TPASPFFRPVHYDTLDMDNFPMGTNAIVAVISYTGYDMEDAMILNKSSYERGFAHGCIFK 759
P P + + P+G NAIVAV+SY+GY+ EDA+I+NKSS +RGF +K
Sbjct: 455 YPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYK 514
Query: 760 SMFIELESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDKWQTKDYFGRDPA 819
IEL +I G + +
Sbjct: 515 KYEIELR---------------KTKNGPEEITRGDIPNVSEEKL---------------- 543
Query: 820 NKALEDKLGPDGLVYVGAKLNERDPMYSY--------------WKESENRYVTCRYSGKE 865
L DG++ GA++ D + K + R + +Y G E
Sbjct: 544 -----KNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGE 598
Query: 866 EMCVEVVRMSSGFTEGGSVTPNCAYIGYRIQRNPTVGDKFASRAGQKGICSVKWPAEDLP 925
+ V+ V++ S G + R +R P +GDKFASR GQKG+ S P ED+P
Sbjct: 599 KGIVDDVKIFSRELNDGG--NKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMP 656
Query: 926 FTDSGLVPDIVFNPHGFPSRMTIG 949
FT+ G+ PDI+ NPHGFPSRMTIG
Sbjct: 657 FTEDGIPPDIILNPHGFPSRMTIG 680
Score = 270 bits (693), Expect = 2e-77
Identities = 120/449 (26%), Positives = 172/449 (38%), Gaps = 81/449 (18%)
Query: 68 LGAPHIASFDFMLDEGLDLAVEDIAPIEFEIYGKTLKLNIVKAAISEPKVPAGPVGIHFN 127
L I SF++ L+ GL V+ I PI LKL + +PKV G V
Sbjct: 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEGGVT---R 57
Query: 128 KYYPTEARQTRSVYSGPFNVTVAWSWDGKAGGTFTKEV--GRVPIMLKSKRCHLRNLTPA 185
K P E R YS P V + + + K G +EV G +PIML+SK C+L LTP
Sbjct: 58 KLTPNECRLRDLTYSAPLYVDIRLTVNDK-GKIKEQEVFIGEIPIMLRSKLCNLNGLTPE 116
Query: 186 QLIERGEHPDEWGGYFIVGGHEKLVRLLINNRRNHPIAIKRNAWKNRGLLFSDLGVYIRS 245
+LI+ GE P + GGYFI+ G EK++ N I + G I +
Sbjct: 117 ELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVII------------VEDSKGKRIYT 164
Query: 246 VKRDESATNNVLHFVTNGSARFMFSHRKSMCLLGMMQSLHEEGIHTQHDSKVFFGQIFKE 305
S + GS + KS + + +
Sbjct: 165 KTSIPSYSPY------RGSWLEV----KSDKKKDRIYVRIDLKRQEEA------------ 202
Query: 306 KLQYDLRHLNEVEICDYMLTNCILPHLDDYWDKFLCLSHMTCKLFHVVQGMVQLDSEDSI 365
L + +F L +M KL +V G +LD D +
Sbjct: 203 --------LKYIG------------------KRFEDLIYMIRKLILLVLGKGKLDDIDHL 236
Query: 366 MLQEIMTGGSLYLQLLK----------KEK-SGTSAVLKESDIYAAFRASSIESAMTNFL 414
+ + G L L + KEK + K+ + I S + FL
Sbjct: 237 GNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFL 296
Query: 415 ATGNVSAGKNSTLQLMQASGFVIMAENINRMRYMSHFRAVHRGSYFQEMRSSEPRQLRTD 474
ATGN S LMQ SG + + +N + +SH R + F+E + E R L
Sbjct: 297 ATGNWG----SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPS 352
Query: 475 AWGFICPVHTPDGTPCGLLNHLTTNCQIS 503
WG ICP+ TP+G CGL+ +L +IS
Sbjct: 353 HWGRICPIETPEGENCGLVKNLALMARIS 381
Score = 88.8 bits (221), Expect = 7e-18
Identities = 30/76 (39%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 741 MILNKSSYERGFAH-GCIFKSM----FIEL--ESGYNYYGTETMYSGVDGSMMQAQIFFG 793
+L K+ G F EL E+G NYYG E +Y G G ++A IF G
Sbjct: 685 SLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVG 744
Query: 794 VVHYQRLRHMVSDKWQ 809
V+YQRL+HMV DK
Sbjct: 745 PVYYQRLKHMVDDKIH 760
>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 = 256 bits (656), Expect = 4e-77
Identities = 110/315 (34%), Positives = 140/315 (44%), Gaps = 65/315 (20%)
Query: 654 LANLIPMPDCNQSPRNMYQCQMGKQTMGTPCLNWRY---QGVGKLYRLQTPASPFFRPVH 710
+A+LIP D NQSPR YQC MGKQ +G LN Q Y L P P +
Sbjct: 3 VASLIPFVDHNQSPRITYQCAMGKQAIGIYTLNKYNRSDQ---NTYLLCYPQKPLVKTGA 59
Query: 711 YDTLDMDNFPMGTNAIVAVISYTGYDMEDAMILNKSSYERGFAHGCIFKSMFIELESGYN 770
+ P+G NA+VAV+SYTGY+ EDA+I+NKSS +RG K IE
Sbjct: 60 VEKGGFGELPLGQNALVAVMSYTGYNQEDAIIINKSSVDRGLFTSIHIKEYEIEARKTKL 119
Query: 771 YYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDKWQTKDYFGRDPANKALE--DKLG 828
E RDP N + E KL
Sbjct: 120 GPIEEIT--------------------------------------RDPPNVSEEAYRKLD 141
Query: 829 PDGLVYVGAKLNERDPMYSYW--------------KESENRYVTCRYSGKEEMCVEVVRM 874
DG+V VGA++ D + K + + + + EE V+ V++
Sbjct: 142 EDGIVRVGAEVKPGDILVGKITPKGEKLLRAIFGEKARDVKDTSLKVKHGEEGRVDDVKI 201
Query: 875 SSGFTEGGSVTPNCAYIGYRIQRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPD 934
V YI R +R P VGDKFASR GQKG+ S P ED+PFT+ G+ PD
Sbjct: 202 DLNPGGIKKV---KVYI--RQKRKPQVGDKFASRHGQKGVVSKILPQEDMPFTEDGIPPD 256
Query: 935 IVFNPHGFPSRMTIG 949
I+ NPHG PSRMTIG
Sbjct: 257 IILNPHGVPSRMTIG 271
Score = 78.7 bits (195), Expect = 2e-15
Identities = 22/44 (50%), Positives = 29/44 (65%)
Query: 766 ESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDKWQ 809
E+GYN YG E +Y G G +A IF G ++YQ+L+HMV DK
Sbjct: 310 EAGYNAYGKEVLYDGRTGEPFKAPIFVGPIYYQKLKHMVDDKIH 353
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 257 bits (659), Expect = 1e-71
Identities = 196/692 (28%), Positives = 302/692 (43%), Gaps = 128/692 (18%)
Query: 322 YMLTNCILPHL----DDYWDKFLCLSHMTCKLFHVVQGMVQLDSEDSIMLQEIMTGGSL- 376
+L +LPHL +D K L M KL + G + D +D + + G L
Sbjct: 283 QILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLL 342
Query: 377 -------YLQLLKKEKSG---TSAVLKESDIYAAFRASSIESAMTNFLATGNVSAGKNST 426
+ QL+K K + A ++ D+ A R I + + LATGN G+
Sbjct: 343 AELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGRTGV 402
Query: 427 LQLMQASGFVIMAENINRMRYMSHFRAV----HRG-SYFQEMRSSEPRQLRTDAWGFICP 481
QL+ + N + +SH R V RG +F E R L WG ICP
Sbjct: 403 SQLL---------DRTNYLSTLSHLRRVVSPLSRGQPHF------EARDLHGTQWGRICP 447
Query: 482 VHTPDGTPCGLLNHLTTNCQISEYIPSKVLAQIPSVLVSLGMLPLTPVIQSIPEQALMVM 541
TP+G CGL+ +L QIS + + + +I L LG++P+ + V
Sbjct: 448 FETPEGPNCGLVKNLALMAQISVGVDEEEVEEI---LYELGVVPVEEAREEEYISWSRVY 504
Query: 542 LDGRIVGYILDQIATSLVPKLRMLKIVGEKIPKSLEIVYLKRPEKGMGLYPGLYLFTGPG 601
L+GR++GY D L K+R L+ G KI + + Y++ E +Y+ G
Sbjct: 505 LNGRLIGYHPDGEE--LAEKIRELRRSG-KISDEVNVAYIETGEIN-----EVYVNCDSG 556
Query: 602 RMLRPVMNLAAGN--------------------------IEWIGTFEQVFMDICITMKEA 635
R+ RP++ + G IE++ E+ + + ++
Sbjct: 557 RVRRPLIVVENGKPKLTREHVEKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL 616
Query: 636 YPGITTHRELSKTDFLSNLANLIPMPDCNQSPRNMYQCQMGKQTMGTPCLNWRYQGVGKL 695
P TH E+ L A++IP P+ NQSPRN YQ M KQ++G N+R + +
Sbjct: 617 TPE-HTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRG 675
Query: 696 YRLQTPASPFFRPVHYDTLDMDNFPMGTNAIVAVISYTGYDMEDAMILNKSSYERGFAHG 755
+ L P P + + + ++ P G NA+VAV+SYTGY++EDA+I+NK+S ERG A
Sbjct: 676 HLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLA-- 733
Query: 756 CIFKSMFIELESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDKWQTKDYFG 815
+S F Y E Y G Q + + + + Y G
Sbjct: 734 ---RSTFFRT-----YETEERKYPGG----------------QEDKIEIPEP-NVRGYRG 768
Query: 816 RDPANKALEDKLGPDGLVYVGAK----------------LNERDPMYSYWKESENRYVTC 859
+ KL DG+V + L E + + +E + VT
Sbjct: 769 ----EEYYR-KLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGLQERRDTSVTV 823
Query: 860 RYSGKEEMCVEVVRMSSGFTEGGSVTPNCAYIGYRIQRNPTVGDKFASRAGQKGICSVKW 919
R+ E+ V+ V ++ + G+ + R R P +GDKFASR GQKG+ +
Sbjct: 824 RHG--EKGIVDTVLITE--SPEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLV 876
Query: 920 PAEDLPFTDSGLVPDIVFNPHGFPSRMTIGFL 951
P ED+PFT+ G+VPD++ NPH PSRMT+G L
Sbjct: 877 PQEDMPFTEDGIVPDLIINPHAIPSRMTVGQL 908
Score = 96.6 bits (241), Expect = 3e-20
Identities = 46/139 (33%), Positives = 74/139 (53%), Gaps = 4/139 (2%)
Query: 72 HIASFDFMLDEGLDLAVEDIAPIEFEIYGKTLKLNIVKAAISEPKVPAGPVGIHFNKYYP 131
H+ S++ ++ GL V++ I+ EI G LK+ + K + EP++ P
Sbjct: 18 HLDSYNDFIERGLQEIVDEFGEIKTEIPG--LKIVLGKIRVGEPEIKEADGSE--RPITP 73
Query: 132 TEARQTRSVYSGPFNVTVAWSWDGKAGGTFTKEVGRVPIMLKSKRCHLRNLTPAQLIERG 191
EAR Y+ P +T+ +G ++G +PIM+KSK C L L+P +LIE G
Sbjct: 74 MEARLRNLTYAAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIG 133
Query: 192 EHPDEWGGYFIVGGHEKLV 210
E P + GGYFI+ G E+++
Sbjct: 134 EDPKDPGGYFIINGSERVI 152
Score = 70.8 bits (174), Expect = 3e-12
Identities = 24/43 (55%), Positives = 30/43 (69%)
Query: 765 LESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDK 807
L+ GY GTE MY G G ++A IF GVV+YQ+L HMV+DK
Sbjct: 942 LKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADK 984
>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 = 209 bits (533), Expect = 1e-57
Identities = 131/453 (28%), Positives = 199/453 (43%), Gaps = 94/453 (20%)
Query: 540 VMLDGRIVGYILDQIATSLVPKLRMLKIVGEKIPKSLEIVYLKRPEKGMGLYPGLYLFTG 599
V L+GR++GY D LV ++R L+ G K+ + + + Y + + +Y+
Sbjct: 1 VYLNGRLIGYHDDPEE--LVEEVRKLRRSG-KLSQEVNVAYYEETNE-------VYINCD 50
Query: 600 PGRMLRPVM---------------NLAAGNIEW-----IGTFEQVFMD------ICITMK 633
GR+ RP++ L G + W G E ++D I +
Sbjct: 51 AGRIRRPLIVVENGKPKLTREHVEKLKEGELTWDDLVKQGVIE--YLDAEEEENAYIALD 108
Query: 634 EAYPGIT---THRELSKTDFLSNLANLIPMPDCNQSPRNMYQCQMGKQTMGTPCLNWRYQ 690
+T TH E+ + L +A+ IP P+ NQSPRN M KQ++G N+R +
Sbjct: 109 PE--ELTPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIR 166
Query: 691 GVGKLYRLQTPASPFFRPVHYDTLDMDNFPMGTNAIVAVISYTGYDMEDAMILNKSSYER 750
+ + L P P + + + D+ P G N +VAV+SY GY++EDA+I+NK+S ER
Sbjct: 167 LDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIER 226
Query: 751 GFAHGCIFKSMFIELESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDKWQT 810
G A +S F Y E Y G G D+++
Sbjct: 227 GLA-----RSTFFRT-----YEAEERRYPG--GQ--------------------EDRFEI 254
Query: 811 KDYFGRDPANKALEDKLGPDGLVYVGAKLNERDPMYSYWKESENRYVTCRYSGKEEMCVE 870
+ R + L DG+VY ++ D + K S R++ +E V
Sbjct: 255 PEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIG--KTSPPRFLE---ELRELGLVT 309
Query: 871 VVRMSSGFT----EGGSV-------TPN---CAYIGYRIQRNPTVGDKFASRAGQKGICS 916
R + T E G V T + R R P +GDKFASR GQKG+
Sbjct: 310 ERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIG 369
Query: 917 VKWPAEDLPFTDSGLVPDIVFNPHGFPSRMTIG 949
+ P ED+PFT+ G+VPD++ NPH PSRMT+G
Sbjct: 370 MIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVG 402
Score = 64.7 bits (158), Expect = 1e-10
Identities = 21/43 (48%), Positives = 31/43 (72%)
Query: 765 LESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDK 807
L+ G+ G E MY G+ G ++A+IF GV++YQ+L HMV+DK
Sbjct: 438 LKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADK 480
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 193 bits (492), Expect = 4e-52
Identities = 140/457 (30%), Positives = 203/457 (44%), Gaps = 102/457 (22%)
Query: 540 VMLDGRIVGYILDQIATSLVPKLRMLKIVGEKIPKSLEIVYLKRPEKGMGLYPGLYLFTG 599
V ++G+++G D LV ++R + GE I + + + Y + + + + T
Sbjct: 7 VYVNGKLIGTHDD--PEELVEEIREARRSGE-ISEEVNVSYKEETNE-------VIINTD 56
Query: 600 PGRMLRP---VMN------------LAAGNIEWIGTFEQVFM---------DICITMKEA 635
GR RP V N L G + + +Q + + I + E
Sbjct: 57 AGRARRPLIVVENGEPLLTEEHIEKLKNGELTFDDLVKQGVIEYLDAEEEENAYIAVYEE 116
Query: 636 YPGIT---THRELSKTDFLSNLANLIPMPDCNQSPRNMYQCQMGKQTMGTPCLN--WRYQ 690
+T TH E+ + L A +IP P+ N SPR M KQ++G P N R
Sbjct: 117 --DLTEEHTHLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPD 174
Query: 691 GVGKLYRLQTPASPFFRPVHYDTLDMDNFPMGTNAIVAVISYTGYDMEDAMILNKSSYER 750
G L L P P + + + D P G N +VAV+SY GY++EDA+I+NK+S ER
Sbjct: 175 TRGHL--LHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIER 232
Query: 751 GFAHGCIFKSMFIELESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDKWQT 810
G F++ Y G E Y G G Q R + DK
Sbjct: 233 GLGRSHFFRT----------YEGEERRYPG--G--------------QEDRFEIPDK-DV 265
Query: 811 KDYFGRDPANKALEDKLGPDGLVYVGAKLNERDPMYSYWKESENRY-------------- 856
+ Y G + A + L++ DGLV ++ E D + K S R+
Sbjct: 266 RGYRGEE-AYRHLDE----DGLVNPETEVKEGDVLIG--KTSPPRFLEEPDDFGISPEKR 318
Query: 857 ----VTCRYSGKEEMCVEVVRMSSGFTEGGSVTPNCAYIGYRIQRNPTVGDKFASRAGQK 912
VT R SG EE V+ V ++ TE GS + R R P +GDKFASR GQK
Sbjct: 319 RETSVTMR-SG-EEGIVDTVILTE--TEEGS---RLVKVRVRDLRIPELGDKFASRHGQK 371
Query: 913 GICSVKWPAEDLPFTDSGLVPDIVFNPHGFPSRMTIG 949
G+ + P ED+PFT+SG+VPD++ NPH PSRMT+G
Sbjct: 372 GVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVG 408
Score = 63.1 bits (154), Expect = 5e-10
Identities = 19/43 (44%), Positives = 31/43 (72%)
Query: 765 LESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDK 807
+ G+ + G E MY G+ G ++A+IF GV++YQ+L HMV++K
Sbjct: 444 EKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANK 486
>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 = 158 bits (401), Expect = 5e-42
Identities = 88/399 (22%), Positives = 155/399 (38%), Gaps = 55/399 (13%)
Query: 68 LGAPHIASFDFMLDEGLDLAVEDIAPIEFEIYGKTLKLNIVKAAISEPKVPAGPVGIHFN 127
L + SF++ LDEGL +++ PIE E L + + +++PK+
Sbjct: 2 LVEQQLDSFNWFLDEGLQEEIDEFPPIEDEDEEPEFSLKVGQIKLAKPKIKESDGKTR-- 59
Query: 128 KYYPTEARQTRSVYSGPFNVTVAWSWDGKAGGTFTK-EVGRVPIMLKSKRCHLRNLTPAQ 186
+ YP EAR YS P V + + K +G++P+ML+S C L + ++
Sbjct: 60 EIYPREARLRNLTYSSPLYVPAELTVNNTEEIEKEKVFIGKIPLMLRSNACILNGASESE 119
Query: 187 LIERGEHPDEWGGYFIVGGHEKLVRLLINNRRNHPIAIKRNAWKNRGLLFSDLGVYIRSV 246
L++ GE P + GGYFIV G EK++ I N K++ R S + RS+
Sbjct: 120 LVKLGECPLDPGGYFIVNGSEKVIINQIQRSPNIYYVFKKDKNGIRIYSASIISNRGRSL 179
Query: 247 KRDESATNNVLHFVTNGSARFMFSHRKSMCLL------------GMMQSLHEEGIHTQHD 294
+ + ++ + + +G+ MF ++ L ++ + GI+ + D
Sbjct: 180 RLEITSKGKIYARINSGAKLIMFVLLLALGLNLVEIILNLLVPEVDLEIQDDIGINDEED 239
Query: 295 SKVFFGQIFKEKLQY---------------------DLRHLNEVEICDYMLTNCILPHLD 333
+ +E+ + R L V I L +LPHL
Sbjct: 240 EFLTDKPELEEQFVIQTQDEALDYIGGRGSAKGFPRERRILGAVGI----LDLNLLPHLG 295
Query: 334 ----DYWDKFLCLSHMTCKLFHVVQGMVQLDSEDSIMLQEIMTGGSL-------YLQLLK 382
K + +M +L + G LD D + + + G L L L+
Sbjct: 296 VSENTRTLKAQDIGYMIHRLLLLALGRGPLDDIDHLGNKRLRLAGELLQSQFRILLNRLE 355
Query: 383 KE-KSGTSAVLKESDIY---AAFRASSIESAMTNFLATG 417
++ + LK+ + + I S + FL TG
Sbjct: 356 RDVRERIQKCLKKKFDFTLQNLVNSKPITSGIRYFLGTG 394
>gnl|CDD|236587 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B'';
Validated.
Length = 494
Score = 132 bits (334), Expect = 2e-32
Identities = 129/530 (24%), Positives = 206/530 (38%), Gaps = 126/530 (23%)
Query: 68 LGAPHIASFDFMLDEGLDLAVEDIAPIEFEIYGKTLKLNIVKAAISEPKV--PAGPVGIH 125
L HI S++ +D GL +++ PIE EI + + + K + +P V G
Sbjct: 18 LVRHHIDSYNDFVDNGLQKIIDEQGPIETEI-EDGVYVELGKIRVGKPVVKEADGSE--- 73
Query: 126 FNKYYPTEARQTRSVYSGPFNVTVAWSWDGKAGGTFTKEVGRVPIMLKSKRCHLRNLTPA 185
+ YP EAR YS P + ++ G+ +G +P+M+ SK C+L L+
Sbjct: 74 -REIYPMEARLRNLTYSAPLYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEE 132
Query: 186 QLIERGEHPDEWGGYFIVGGHEK-LVRL--LINNR------------------------R 218
+LIE GE P + GGYFIV G E+ L+ L L N+
Sbjct: 133 ELIEVGEDPLDPGGYFIVNGSERVLMTLEDLAPNKILVEKDERYGDRIEVAKVFSQRRGY 192
Query: 219 NHPIAIKRNAWKNRGLL---FSDLGVYIRSV--------KRDESATNNVLHFVTNGSARF 267
+ ++RN GLL F + I V + DE ++ V++
Sbjct: 193 RALVTVERN---RDGLLEVSFPSVPGSIPFVILMRALGLETDE----EIVEAVSDDPEIV 245
Query: 268 MFSHRKSMCLLGMMQSLHEEGIHTQHDSKVFFGQIF--KEKLQYDLRHLNEVEICDYMLT 325
F M+++L E + TQ ++ + G+ + +Y ++ V I Y+
Sbjct: 246 KF----------MLENLEEAEVDTQEEALEYIGKRVAPGQTKEYRIKRAEYV-IDRYL-- 292
Query: 326 NCILPHL----DDYWDKFLCLSHMTCKLFHVVQGMVQLDSEDSIMLQEIMTGGSL----- 376
LPHL + K L M F + G + D +D + + G L
Sbjct: 293 ---LPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLF 349
Query: 377 ---YLQLLKK-----EKSGTSAVLKESDIYAAFRA----SSIESAMTNFLATGNVSAGKN 424
+ +L + E++ + +E I A R+ +E AM ATGN G+
Sbjct: 350 RVAFNRLARDVKYQLERA--NMRNRELSIKTAVRSDVLTERLEHAM----ATGNWVGGRT 403
Query: 425 STLQLMQASGFVIMAENINRMRYMSHFRAVHRGSYFQEMRSS--------EPRQLRTDAW 476
QL+ + + M +SH R V S E R L W
Sbjct: 404 GVSQLL---------DRTDYMATLSHLRRV---------VSPLSRSQPHFEARDLHPTQW 445
Query: 477 GFICPVHTPDGTPCGLLNHLTTNCQISEYIPSKVLAQIPSVLVSLGMLPL 526
G ICP TP+G CGL+ + +IS + + +I L LG+ P
Sbjct: 446 GRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEI---LKELGVEPE 492
>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 = 96.5 bits (241), Expect = 3e-24
Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 437 IMAENINRMRYMSHFRAVHR-GSYFQEMRSSEPRQLRTDAWGFICPVHTPDGTPCGLLNH 495
+ + N + +SH R V+R G +E ++ E R L +G ICP+ TP+G CGL+N
Sbjct: 1 QVLDQTNWLSELSHKRRVNRLGGLSKERKTFEVRDLHPSQYGRICPIETPEGANCGLVNS 60
Query: 496 LTTNCQIS 503
L +I+
Sbjct: 61 LALYARIN 68
>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 = 66.8 bits (164), Expect = 5e-14
Identities = 27/60 (45%), Positives = 39/60 (65%), Gaps = 3/60 (5%)
Query: 547 VGYILDQIATSLVPKLRMLKIVGEK-IPKSLEIVYLKRPEKGMGLYPGLYLFTGPGRMLR 605
+GY+ ++A ++ LR LK+ GE +P +LEI Y+ P G YPGLYLF+ P RM+R
Sbjct: 1 LGYLSPKLAPTVADTLRYLKVEGEHSVPPTLEIGYV--PPSNGGQYPGLYLFSTPARMMR 58
>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 = 68.2 bits (167), Expect = 1e-11
Identities = 31/60 (51%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 890 YIGYRIQRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPDIVFNPHGFPSRMTIG 949
YI + R VGDK A R G KG+ S P ED+PF + G DIV NP G PSRM IG
Sbjct: 830 YIAQK--RKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIG 887
Score = 34.3 bits (79), Expect = 0.34
Identities = 13/30 (43%), Positives = 22/30 (73%)
Query: 476 WGFICPVHTPDGTPCGLLNHLTTNCQISEY 505
+G ICP+ TP+G GL+N L+T ++++Y
Sbjct: 431 YGRICPIETPEGPNIGLINSLSTYARVNDY 460
Score = 30.4 bits (69), Expect = 6.1
Identities = 11/42 (26%), Positives = 19/42 (45%)
Query: 766 ESGYNYYGTETMYSGVDGSMMQAQIFFGVVHYQRLRHMVSDK 807
++G G +Y G G + G ++ +L H+V DK
Sbjct: 927 KAGLPRDGKVRLYDGRTGEQFDNPVTVGYMYMLKLHHLVDDK 968
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 67.4 bits (165), Expect = 3e-11
Identities = 29/68 (42%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 886 PNCAYIGYRI----QRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPDIVFNPHG 941
Y+ R+ R VGDK A R G KGI S P +D+P+ G PDI+ NP G
Sbjct: 793 KFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLG 852
Query: 942 FPSRMTIG 949
PSRM +G
Sbjct: 853 VPSRMNVG 860
Score = 43.5 bits (103), Expect = 6e-04
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 469 RQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQISEY 505
R + +G ICP+ TP+G CGL+ L TN +I+++
Sbjct: 403 RDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKF 439
Score = 33.1 bits (76), Expect = 0.81
Identities = 15/36 (41%), Positives = 24/36 (66%), Gaps = 2/36 (5%)
Query: 712 DTLDMDN--FPMGTNAIVAVISYTGYDMEDAMILNK 745
D D+DN +G N +VA + + GY+ EDA+++NK
Sbjct: 635 DGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINK 670
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 64.4 bits (158), Expect = 2e-10
Identities = 29/56 (51%), Positives = 34/56 (60%), Gaps = 4/56 (7%)
Query: 894 RIQRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPDIVFNPHGFPSRMTIG 949
+IQ VGDK A R G KG+ S P ED+P+ + G DIV NP G PSRM IG
Sbjct: 879 KIQ----VGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIG 930
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 61.5 bits (149), Expect = 2e-09
Identities = 29/54 (53%), Positives = 32/54 (59%)
Query: 896 QRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPDIVFNPHGFPSRMTIG 949
+R VGDK A R G KGI S P D+P+T G DIV NP G PSRM IG
Sbjct: 1085 KRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIG 1138
Score = 41.8 bits (98), Expect = 0.002
Identities = 55/240 (22%), Positives = 93/240 (38%), Gaps = 57/240 (23%)
Query: 291 TQHDSKVFFGQIFKEKLQYDL--------RHLNEVEICDYMLTNCILPHLDDYWDKFLCL 342
T +K F ++F + +YDL H + + DY+ T L H D +
Sbjct: 389 TTEVAKQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITT---LTHED-----IIT- 439
Query: 343 SHMTCK-LFHVVQGMVQLDSEDSIMLQEIMTGGSL-----YLQLLKKEK---------SG 387
T K L + ++D D + + I G L + L+K +K SG
Sbjct: 440 ---TVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSG 496
Query: 388 TSAVLKESDIYAAFRASSIESAMTNFLATGNVSAGKNSTLQLMQASGFVIMAENINRMRY 447
L D+ + I S + F G +S Q M + N +
Sbjct: 497 AFDSLMPHDL---VNSKMITSTIMEFFMGGQLS-------QFM---------DQTNPLSE 537
Query: 448 MSHFR---AVHRGSYFQEMRSSEPRQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQISE 504
++H R A+ G ++ E R + +G ICP+ TP+G GL+N L+T ++++
Sbjct: 538 VTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVND 597
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 59.9 bits (146), Expect = 6e-09
Identities = 27/56 (48%), Positives = 32/56 (57%), Gaps = 4/56 (7%)
Query: 894 RIQRNPTVGDKFASRAGQKGICSVKWPAEDLPFTDSGLVPDIVFNPHGFPSRMTIG 949
IQ VGDK A R G KGI S P +D+P+ G D+V NP G PSRM +G
Sbjct: 813 EIQ----VGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVG 864
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 56.9 bits (137), Expect = 5e-08
Identities = 24/48 (50%), Positives = 30/48 (62%)
Query: 902 GDKFASRAGQKGICSVKWPAEDLPFTDSGLVPDIVFNPHGFPSRMTIG 949
GDK A R G KG+ S P ED+P+ + G DI+ NP G PSRM +G
Sbjct: 1084 GDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVG 1131
Score = 39.6 bits (92), Expect = 0.011
Identities = 21/75 (28%), Positives = 36/75 (48%)
Query: 431 QASGFVIMAENINRMRYMSHFRAVHRGSYFQEMRSSEPRQLRTDAWGFICPVHTPDGTPC 490
Q S F+ ++ + + A+ G +E E R + +G ICP+ TP+G
Sbjct: 531 QLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNI 590
Query: 491 GLLNHLTTNCQISEY 505
GL+N L +I++Y
Sbjct: 591 GLINSLAIYARINKY 605
Score = 30.4 bits (68), Expect = 7.4
Identities = 14/44 (31%), Positives = 27/44 (61%), Gaps = 5/44 (11%)
Query: 721 MGTNAIVAVISYTGYDMEDAMILNKSSYERGFAHGCIFKSMFIE 764
+G N +VA +S+ GY+ ED++I++ ++ +F S+ IE
Sbjct: 816 LGQNLLVAFMSWQGYNFEDSIIISSEVVKKD-----LFTSIHIE 854
>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 = 41.0 bits (97), Expect = 6e-05
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 4/44 (9%)
Query: 606 PVMNLAAGNIEWIGTFEQVFMDICIT----MKEAYPGITTHREL 645
V L G IE++ E+ I ++ E TTH E+
Sbjct: 1 FVDLLKEGVIEYLDAEEEETAMIAMSPEDLRLEDITKTTTHCEI 44
>gnl|CDD|183446 PRK12331, PRK12331, oxaloacetate decarboxylase; Provisional.
Length = 448
Score = 35.4 bits (82), Expect = 0.12
Identities = 28/96 (29%), Positives = 40/96 (41%), Gaps = 12/96 (12%)
Query: 458 SYFQEMRSS-------EPRQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQISEYIPSKV 510
YF +R P+ + I V P G LL+ L +Y +V
Sbjct: 268 EYFNPIRDHYREEGILNPKVKDVEPKTLIYQV--PGGMLSNLLSQLKEQGAEDKY--EEV 323
Query: 511 LAQIPSVLVSLGMLPL-TPVIQSIPEQALMVMLDGR 545
L ++P V LG PL TP+ Q + QALM ++ G
Sbjct: 324 LKEVPKVRADLGYPPLVTPLSQMVGTQALMNVISGE 359
>gnl|CDD|237209 PRK12796, spaP, type III secretion system protein SpaP;
Provisional.
Length = 221
Score = 32.6 bits (75), Expect = 0.69
Identities = 17/42 (40%), Positives = 28/42 (66%), Gaps = 2/42 (4%)
Query: 505 YIPSKVLAQ-IPSVLVSLGMLPLTPVIQSIP-EQALMVMLDG 544
Y+P V+ + SVL++LGM+ ++PV S+P + L V +DG
Sbjct: 163 YLPFVVVDLVVSSVLLALGMMMMSPVTISVPIKLILFVAMDG 204
>gnl|CDD|236593 PRK09617, PRK09617, type III secretion system protein; Reviewed.
Length = 243
Score = 32.4 bits (74), Expect = 0.84
Identities = 16/42 (38%), Positives = 30/42 (71%), Gaps = 2/42 (4%)
Query: 505 YIPSKVLAQIPS-VLVSLGMLPLTPVIQSIPEQALM-VMLDG 544
Y+P V+ + + VL+++GM+ L+P+ S+P + L+ VM+DG
Sbjct: 189 YLPFFVIDLVTANVLLAMGMMMLSPLSISLPLKLLLVVMVDG 230
>gnl|CDD|237592 PRK14040, PRK14040, oxaloacetate decarboxylase; Provisional.
Length = 593
Score = 32.6 bits (75), Expect = 1.0
Identities = 17/37 (45%), Positives = 24/37 (64%), Gaps = 1/37 (2%)
Query: 509 KVLAQIPSVLVSLGMLPL-TPVIQSIPEQALMVMLDG 544
+VLA+IP V LG +PL TP Q + QA++ +L G
Sbjct: 320 EVLAEIPRVREDLGFIPLVTPTSQIVGTQAVLNVLTG 356
>gnl|CDD|144419 pfam00813, FliP, FliP family.
Length = 194
Score = 31.3 bits (72), Expect = 1.6
Identities = 14/32 (43%), Positives = 23/32 (71%), Gaps = 1/32 (3%)
Query: 514 IPSVLVSLGMLPLTPVIQSIP-EQALMVMLDG 544
+ SVL+++GM+ L PV S+P + L V++DG
Sbjct: 154 VASVLMAMGMMMLPPVTISLPFKLLLFVLVDG 185
>gnl|CDD|211625 TIGR01103, fliP, flagellar biosynthetic protein FliP. This model
describes bacterial flagellar biogenesis protein fliP,
which is one of the genes in motility locus on the
bacterial chromosome that is involved in structure and
function of bacterial flagellum. It was demonstrated
that mutants in fliP locus were non-flagellated and
non-motile, while revertants were flagellated and motile
[Cellular processes, Chemotaxis and motility].
Length = 197
Score = 31.2 bits (71), Expect = 1.8
Identities = 22/61 (36%), Positives = 37/61 (60%), Gaps = 4/61 (6%)
Query: 488 TPCGLLNHLTTNCQIS--EYIPSKVLAQI-PSVLVSLGMLPLTPVIQSIP-EQALMVMLD 543
P +L+ L T QI +IP ++ + SVL+++GM+ L PV+ S+P + L V++D
Sbjct: 125 VPAFMLSELKTAFQIGFLIFIPFLIIDLVVASVLMAMGMMMLPPVMISLPFKLMLFVLVD 184
Query: 544 G 544
G
Sbjct: 185 G 185
>gnl|CDD|79056 PRK12581, PRK12581, oxaloacetate decarboxylase; Provisional.
Length = 468
Score = 31.6 bits (71), Expect = 2.2
Identities = 35/149 (23%), Positives = 62/149 (41%), Gaps = 18/149 (12%)
Query: 403 ASSIESAMTNFLATGNVSAGKNSTLQLMQASGFVIMAENINRMRYMSHFRAVHR-----G 457
A I++A++ F + G S ++ +G+ I + + +H R + G
Sbjct: 232 ADRIDTALSPF-SEGTSQPATESMYLALKEAGYDITLDETLLEQAANHLRQARQKYLADG 290
Query: 458 SYFQEMRSSEPRQLRTDAWGFICPVHTPDGTPCGLLNHLTTNCQISEYIPSKVLAQIPSV 517
+ +PR L+ P G +L+ L S+ +VLA++P V
Sbjct: 291 ILDPSLLFPDPRTLQ---------YQVPGGMLSNMLSQLKQANAESKL--EEVLAEVPRV 339
Query: 518 LVSLGMLPL-TPVIQSIPEQALMVMLDGR 545
LG PL TP+ Q + QA M ++ G+
Sbjct: 340 RKDLGYPPLVTPLSQMVGTQAAMNVILGK 368
>gnl|CDD|235566 PRK05699, fliP, flagellar biosynthesis protein FliP; Reviewed.
Length = 245
Score = 30.9 bits (71), Expect = 2.8
Identities = 16/30 (53%), Positives = 23/30 (76%), Gaps = 1/30 (3%)
Query: 516 SVLVSLGMLPLTPVIQSIP-EQALMVMLDG 544
SVL+S+GM+ L PVI S+P + L V++DG
Sbjct: 202 SVLMSMGMMMLPPVIISLPFKLLLFVLVDG 231
>gnl|CDD|224257 COG1338, FliP, Flagellar biosynthesis pathway, component FliP [Cell
motility and secretion / Intracellular trafficking and
secretion].
Length = 248
Score = 30.7 bits (70), Expect = 2.9
Identities = 14/30 (46%), Positives = 24/30 (80%), Gaps = 1/30 (3%)
Query: 516 SVLVSLGMLPLTPVIQSIPEQALM-VMLDG 544
SVL+++GM+ L PV+ S+P + L+ V++DG
Sbjct: 206 SVLMAMGMMMLPPVMISLPFKLLLFVLVDG 235
>gnl|CDD|220110 pfam09095, DUF1926, Domain of unknown function (DUF1926). Members
of this family, which are found in a set of prokaryotic
transferases, adopt a beta-sandwich fold, in which two
layers of anti-parallel beta-sheets are arranged in a
nearly parallel fashion. The exact function of this
family is, as yet, unknown, however it has been proposed
that they may play a role in transglycosylation
reactions.
Length = 275
Score = 30.5 bits (69), Expect = 4.1
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 271 HRKSMCLLGMMQSLHEEGIHTQHDSKVFFGQIFKEKLQYD 310
H K + S EGI + H+ F + +++L YD
Sbjct: 53 HDK----IQGESSSEGEGIASIHELVKFKPEGLRKELYYD 88
>gnl|CDD|220422 pfam09818, ABC_ATPase, Predicted ATPase of the ABC class. Members
of this family include various bacterial predicted ABC
class ATPases.
Length = 447
Score = 30.6 bits (70), Expect = 4.2
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 3/34 (8%)
Query: 571 KIPKSLEIVYL---KRPEKGMGLYPGLYLFTGPG 601
+ P+SLE+ GMG+ G+ L G G
Sbjct: 219 ESPESLEVEIELPNGGTVSGMGIPKGITLIVGGG 252
>gnl|CDD|233273 TIGR01108, oadA, oxaloacetate decarboxylase alpha subunit. This
model describes the bacterial oxaloacetate decarboxylase
alpha subunit and its equivalents in archaea. The
oxaloacetate decarboxylase Na+ pump is the paradigm of
the family of Na+ transport decarboxylases that present
in bacteria and archaea. It a multi subunit enzyme
consisting of a peripheral alpha-subunit and integral
membrane subunits beta and gamma. The energy released by
the decarboxylation reaction of oxaloacetate is coupled
to Na+ ion pumping across the membrane [Transport and
binding proteins, Cations and iron carrying compounds,
Energy metabolism, Other].
Length = 582
Score = 30.2 bits (68), Expect = 7.1
Identities = 16/37 (43%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 509 KVLAQIPSVLVSLGMLPL-TPVIQSIPEQALMVMLDG 544
+VL +IP V LG PL TP Q + QA++ +L G
Sbjct: 314 EVLEEIPRVREDLGYPPLVTPTSQIVGTQAVLNVLTG 350
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
0.322 0.138 0.424
Gapped
Lambda K H
0.267 0.0750 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 48,925,682
Number of extensions: 4840951
Number of successful extensions: 3500
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3471
Number of HSP's successfully gapped: 64
Length of query: 951
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 845
Effective length of database: 6,236,078
Effective search space: 5269485910
Effective search space used: 5269485910
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 (21.9 bits)
S2: 64 (28.4 bits)