RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014847
(417 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 = 270 bits (693), Expect = 9e-83
Identities = 151/507 (29%), Positives = 202/507 (39%), Gaps = 145/507 (28%)
Query: 2 SFLLGLSCGIIP--SHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQ 59
S +L ++ +IP H Q LYQS QA+G P N R+DT L L YPQ
Sbjct: 403 SQILSVAASLIPFPEHNQ----SPRNLYQSNMQK-QAVGTPALNQQYRMDTKLYLLLYPQ 457
Query: 60 RPLFWILISDCLGRP--------------------EDSLVMNQASLECGVFRS---ESYK 96
+PL I + + ED++++N++S++ G FRS + Y+
Sbjct: 458 KPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYE 517
Query: 97 AEVDNK----------DIQVKSRPSDDMLNF-GKI----QSKSGDIVIGKYAEIGA---- 137
E+ DI S L+ G I + + GDI++GK G
Sbjct: 518 IELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETEST 577
Query: 138 -----------DHSIKLKHTERGLVLKVLLSS---NDDGKNFAVVSIRQSVNMVHSACLG 183
D S+K E+G+V V + S ND G V IRQ +G
Sbjct: 578 PIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQ----KRKPQIG 633
Query: 184 DKFSSMHGQKGVLG---------FLEQ-----------------TPAQLLEAALGK-GAC 216
DKF+S HGQKGV+ F E T QLLE+ LGK GA
Sbjct: 634 DKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGAL 693
Query: 217 DGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARN----SGITFIFKHYFLFCLFECP 272
G ATPF + I+E LN G G T E P
Sbjct: 694 LGKFGDATPFDGAEEEDISE---LLGEAGLNYYG--KEVLYDGRTGE--------PLEAP 740
Query: 273 MDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFG 332
IF +YQ+ HM +DK+ R+TG + LT +P+ R R GG FG
Sbjct: 741 -------------IFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFG 787
Query: 333 EMKCDCLIAHGASGNLHERL-------------KCKNVANVIQRVVGGPYCRICNSADDI 379
EM+ D LIAHGA+ L ERL KC + + CR+C +I
Sbjct: 788 EMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILSAN-------LCRLCKKGTNI 840
Query: 380 IKANVPYGAKLLSQELSFSMGITLKFD 406
K +PY KLL QEL SM I +
Sbjct: 841 SKVGIPYAFKLLFQELQ-SMNIDPRLK 866
>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 = 190 bits (484), Expect = 1e-54
Identities = 142/501 (28%), Positives = 208/501 (41%), Gaps = 136/501 (27%)
Query: 2 SFLLGLSCGIIP--SHLQT--MTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFY 57
S +LG+ IP H Q+ TM K Q++G N IR+DT L Y
Sbjct: 124 SAILGIIASTIPYPEHNQSPRNTMGA----AMAK---QSLGLYAANYRIRLDTRGHLLHY 176
Query: 58 PQRPLFWILISDCLG---RP-----------------EDSLVMNQASLECGVFRS----- 92
PQ+PL + + +G RP ED+L+MN+AS+E G+ RS
Sbjct: 177 PQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRT 236
Query: 93 -----------ESYKAEVDNKDI------QVKSRPSDDMLNFGKIQSKSGDIVIGK---- 131
+ + E+ D+ + +D + + +++ K GD++IGK
Sbjct: 237 YEAEERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPP 296
Query: 132 -----YAEIGA------DHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSA 180
E+G D S+ ++H E+G+V KV+++ ++G V +R +
Sbjct: 297 RFLEELRELGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVR----DLRIP 352
Query: 181 CLGDKFSSMHGQKGVLG---------FLEQ-----------------TPAQLLEAALGK- 213
LGDKF+S HGQKGV+G F E T QLLE GK
Sbjct: 353 ELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKV 412
Query: 214 GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPM 273
A +G TPF + + + + L +G + G E
Sbjct: 413 AALEGRRVDGTPF--------EGEPEEELRKELLKLGFKPDGK-------------EVMY 451
Query: 274 DWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGE 333
D I L + IF + +YQ+ HM DK+ R+ G Q LT +P R R GG+ FGE
Sbjct: 452 DGITGEKL-EAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGE 510
Query: 334 MKCDCLIAHGASGNLHERL-------------KCKNVANVIQRVVGGPYCRICNSADDII 380
M+ D LI HGA+ L ERL C ++A + G YC +C DI
Sbjct: 511 MERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIA-WEDKRKGTAYCPVCGETGDIS 569
Query: 381 KANVPYGAKLLSQELSFSMGI 401
+ Y KLL EL S+GI
Sbjct: 570 PVEMSYAFKLLLDELK-SLGI 589
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 181 bits (461), Expect = 5e-50
Identities = 134/464 (28%), Positives = 189/464 (40%), Gaps = 125/464 (26%)
Query: 35 QAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLG---RP----------------- 74
Q++G N IR DT L YPQRPL + +G RP
Sbjct: 658 QSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNI 717
Query: 75 EDSLVMNQASLECGVFRS---ESYKAE-------------VDNKDIQVKSRPS------D 112
ED+++MN+AS+E G+ RS +Y+ E + +++ +
Sbjct: 718 EDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDE 777
Query: 113 DMLNFGKIQSKSGDIVIGK---------YAEIGA------DHSIKLKHTERGLVLKVLLS 157
D + +++ K GD++IGK E+ D S+ ++H E+G+V VL++
Sbjct: 778 DGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLIT 837
Query: 158 SNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG---------FLEQ------- 201
+ +G +V +R V + LGDKF+S HGQKGV+G F E
Sbjct: 838 ESPEG--NKLVKVR--VRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLI 893
Query: 202 ----------TPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIG 250
T QLLE+ GK A +G ATPF E + +LL
Sbjct: 894 INPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF-------YGEPEEELRKELL---- 942
Query: 251 ARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTG 310
K + E D + IF + +YQ+ HM DK+ R G
Sbjct: 943 ----------KLGYKPDGTEVMYDGRTGEKIKAP-IFIGVVYYQKLHHMVADKIHARARG 991
Query: 311 SFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL-------------KCKNV 357
Q LT +P R R GG+ FGEM+ DCLI HGA+ L ERL C ++
Sbjct: 992 PVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHI 1051
Query: 358 ANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGI 401
A R C I +I V Y KLL QEL SMGI
Sbjct: 1052 A-WYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELM-SMGI 1093
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 179 bits (456), Expect = 3e-49
Identities = 110/471 (23%), Positives = 178/471 (37%), Gaps = 135/471 (28%)
Query: 26 LYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISD----CLGRP------- 74
LY+ + S QA G R DT+ + L Y P D LG+
Sbjct: 630 LYKFAR-SNQATGINQRPLVKRGDTVEKGLVYADGP-----SVDTGELALGQNALVAFMP 683
Query: 75 ------EDSLVMNQASLECGVFRS---ESYKAEV-DNK----DIQVKSRPSDDMLNF--- 117
ED++++++ S+E +F S E Y+ E D K +I+ S++ L
Sbjct: 684 WNGYNYEDAIIISERSVERDLFTSIHIEEYETEARDTKLGPEEIRDIPNVSEEALRNLDE 743
Query: 118 ---GKIQS--KSGDIVIGKYAEIGA------------------DHSIKLKHTERGLVLKV 154
+I + K GDI++GK G D S+++ H E G+V V
Sbjct: 744 DGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRIFGEKVRDTSLRVPHGEEGIVDDV 803
Query: 155 LLSSNDDGKN----FAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG---------FLEQ 201
+ + +DG V + Q +GDK + HG KGV+ FLE
Sbjct: 804 QVFTREDGDPGVNKLVKVYVAQ----KRKPQIGDKMAGRHGNKGVVSKIVPQEDMPFLED 859
Query: 202 -----------------TPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVS 243
Q+LE LGK A G+ F +
Sbjct: 860 GTPPDIILNPLGVPSRMNIGQILETHLGKAAALLGIPVDTPVF-------DGAPEEDIRE 912
Query: 244 QLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFICL--------VRSLIFTWITFYQQ 295
L + F + L + IF + +YQ+
Sbjct: 913 LLK--------------EAGF---------PYSGKEVLYDGRTGEPFDAPIFVGVMYYQK 949
Query: 296 FIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCK 355
HM +DK+ R+TG + +T +P+ + +FGG FGEM+ L A+GA+ L ERL K
Sbjct: 950 LHHMVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTVK 1009
Query: 356 NVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFD 406
++ + + C + +I + +P K+L +EL S+GI ++ +
Sbjct: 1010 --SDDVCGRIKIYECIVKGE--NIPEVGIPESFKVLLKELR-SLGIDVRLE 1055
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 170 bits (432), Expect = 4e-47
Identities = 139/516 (26%), Positives = 201/516 (38%), Gaps = 166/516 (32%)
Query: 2 SFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSP----------QAIGFPTTNPNIRVDTL 51
S +LG+ G+IP Y SP Q++G P N +R DT
Sbjct: 130 SLILGIGAGMIP-------------YPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTR 176
Query: 52 LQQLFYPQRPLFWILISDCLG---RP-----------------EDSLVMNQASLECGVFR 91
L YPQ PL + +G RP ED+L+MN+AS+E G+ R
Sbjct: 177 GHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGR 236
Query: 92 S---ESYKA-------------EVDNKDIQVKSRPS-------DDMLNFGKIQSKSGDIV 128
S +Y+ E+ +KD++ R +D L + + K GD++
Sbjct: 237 SHFFRTYEGEERRYPGGQEDRFEIPDKDVR-GYRGEEAYRHLDEDGLVNPETEVKEGDVL 295
Query: 129 IGK---------YAEIGA------DHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQS 173
IGK + G + S+ ++ E G+V V+L+ ++G V +R
Sbjct: 296 IGKTSPPRFLEEPDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVR-- 353
Query: 174 VNMVHSACLGDKFSSMHGQKGVLG---------FLEQ-----------------TPAQLL 207
+ LGDKF+S HGQKGV+G F E T +L
Sbjct: 354 --DLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVL 411
Query: 208 EAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIF------ 260
E GK G+ +G T F +G E + L G ++G ++
Sbjct: 412 EMIGGKVGSLEGRRVDGTAF---SG----EDEEDLREALEKL-GFEHTGKEVMYDGITGE 463
Query: 261 KHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPV 320
K E IF + +YQ+ HM +K+ R+ G Q LT +P
Sbjct: 464 K-------IEAE-------------IFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPT 503
Query: 321 ADRKRFGGIEFGEMKCDCLIAHGASGNLHERL-------------KCKNVA--NVIQRVV 365
R R GG+ FGEM+ D LI HGA+ L ERL KC +A + +
Sbjct: 504 EGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCGMIAIYDKKRNRK 563
Query: 366 GGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGI 401
YC IC DI + Y KLL EL S+GI
Sbjct: 564 ---YCPICGEETDIYPVEMSYAFKLLLDELK-SLGI 595
>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 = 164 bits (418), Expect = 6e-47
Identities = 100/387 (25%), Positives = 136/387 (35%), Gaps = 117/387 (30%)
Query: 25 VLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLFWILISDCLGRP---------- 74
+ YQ QAIG T N R D L YPQ+PL + G
Sbjct: 18 ITYQCA-MGKQAIGIYTLNKYNRSDQNTYLLCYPQKPLVKTGAVEKGGFGELPLGQNALV 76
Query: 75 ----------EDSLVMNQASLECGVFRSESYK-------------AEVDNKDIQVKSRPS 111
ED++++N++S++ G+F S K E +D S +
Sbjct: 77 AVMSYTGYNQEDAIIINKSSVDRGLFTSIHIKEYEIEARKTKLGPIEEITRDPPNVSEEA 136
Query: 112 DDMLNFGKI-----QSKSGDIVIGKYAEIGA---------------DHSIKLKHTERGLV 151
L+ I + K GDI++GK G D S+K+KH E G V
Sbjct: 137 YRKLDEDGIVRVGAEVKPGDILVGKITPKGEKLLRAIFGEKARDVKDTSLKVKHGEEGRV 196
Query: 152 LKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG---------FLE-- 200
V + N G V IRQ +GDKF+S HGQKGV+ F E
Sbjct: 197 DDVKIDLNPGGIKKVKVYIRQ----KRKPQVGDKFASRHGQKGVVSKILPQEDMPFTEDG 252
Query: 201 ---------------QTPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQ 244
T QLLE+ LGK A G ATPF +E +
Sbjct: 253 IPPDIILNPHGVPSRMTIGQLLESLLGKAAALLGKFIDATPF-----DGASEDVEDIGEL 307
Query: 245 LLNCIGARN------SGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIH 298
L G T P + IF +YQ+ H
Sbjct: 308 LKEAGYNAYGKEVLYDGRT------------GEPFK---------APIFVGPIYYQKLKH 346
Query: 299 MSEDKVKFRNTGSFQPLTGRPVADRKR 325
M +DK+ R+TG + LT +P+ R R
Sbjct: 347 MVDDKIHARSTGPYSLLTQQPLGGRSR 373
>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 = 70.6 bits (174), Expect = 2e-15
Identities = 28/90 (31%), Positives = 38/90 (42%), Gaps = 22/90 (24%)
Query: 327 GGIEFGEMKCDCLIAHGASGNLHERL---------KCKNVANVIQRVVGGPYCRICNSAD 377
GG FGEM+ L A+GA+ L ERL +C A IC
Sbjct: 1 GGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRCGAYAA------------ICKGKT 48
Query: 378 DIIKANVPYGAKLLSQELSFSMGITLKFDT 407
I ++P KLL QEL S+G+ ++
Sbjct: 49 IIEPGDIPESFKLLLQEL-RSLGLDIRLFL 77
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 65.9 bits (161), Expect = 2e-11
Identities = 74/300 (24%), Positives = 116/300 (38%), Gaps = 64/300 (21%)
Query: 99 VDNKDI---QVKSRPSDDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVL 155
V DI ++ + D L GK+ + G+ A+ D S+++ + G V+KV
Sbjct: 727 VLAGDILVGKITPKGESDQLPEGKLLR----AIFGEKAKDVKDTSLRMPNGGYGRVIKVE 782
Query: 156 L---SSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG---------FL-EQT 202
+ S D+ K + IR + + +GDK + HG KG++ +L + T
Sbjct: 783 IFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGT 842
Query: 203 P----------------AQLLEAALGKGACDGLMS--YATPFATSTGGVITEQHQSFVSQ 244
P QL E LG A D L PF G +E + ++
Sbjct: 843 PPDIILNPLGVPSRMNVGQLFECLLGL-AGDNLNKRFKILPFDEMYG---SEYSRILINN 898
Query: 245 LLNCIG-ARNSGITFIFKHYFLFCL--------FECPMDWIAFICLVRSLIFTWITFYQQ 295
LN N F H L F+ P + I + +
Sbjct: 899 KLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNP-------------VTVGIAYMLK 945
Query: 296 FIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCK 355
IH+ +DK+ R TG + +T +P+ + + GG FGEM+ L A GA+ L E L K
Sbjct: 946 LIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIK 1005
>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 = 59.3 bits (144), Expect = 2e-09
Identities = 71/304 (23%), Positives = 112/304 (36%), Gaps = 80/304 (26%)
Query: 97 AEVDNKDIQV---------KSRPSDDMLN--FGKIQSKSGDIVIGKYAEIGADHSIKLKH 145
AEV DI V + P + +L FG+ K+ D+ D S+++
Sbjct: 752 AEVKAGDILVGKVTPKGETELTPEEKLLRAIFGE---KARDVR---------DTSLRVPP 799
Query: 146 TERGLVLKVLLSSNDDG---KNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG----- 197
G V+ V + S +G ++ + +GDK + HG KGV+
Sbjct: 800 GVEGTVIDVKVFSRKEGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPI 859
Query: 198 ----FLEQ-TP----------------AQLLEAALGKGACDGLMSYATPFATS-TGGVIT 235
FLE TP Q+LE LG A L P AT G
Sbjct: 860 EDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGW-AGKKLGRKGVPIATPVFDGASE 918
Query: 236 EQHQSFVSQLLNCIGARNSGITFIFK----HYFLFCLFECPMDWIAFICLVRSLIFTWIT 291
E+ + + L G G ++ F + +
Sbjct: 919 EE----IKEYLEKAGLPRDGKVRLYDGRTGEQF------------------DNPVTVGYM 956
Query: 292 FYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHER 351
+ + H+ +DK+ R+TG + +T +P+ + +FGG FGEM+ L A+GA+ L E
Sbjct: 957 YMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 1016
Query: 352 LKCK 355
L K
Sbjct: 1017 LTVK 1020
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 51.2 bits (122), Expect = 8e-07
Identities = 22/59 (37%), Positives = 35/59 (59%)
Query: 298 HMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKN 356
H+ + K+ R+ G + +T +P+ + FGG FGEM+C L A+GA+ L E L K+
Sbjct: 1327 HLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKS 1385
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 49.9 bits (119), Expect = 2e-06
Identities = 24/59 (40%), Positives = 36/59 (61%)
Query: 298 HMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKN 356
H+ ++KV R+TG + +T +PV + FGG FGEM+ L A+GA+ L E L K+
Sbjct: 1269 HLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKS 1327
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 45.5 bits (109), Expect = 4e-05
Identities = 35/110 (31%), Positives = 54/110 (49%), Gaps = 26/110 (23%)
Query: 297 IHMSEDKVKFRNTGSF-----QPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHER 351
H+ +DK+ R+TG + QPL G+ A +FGG FGEM+ L A+GA+ L E
Sbjct: 1002 HHLVDDKIHARSTGPYSLVTQQPLGGK--A---QFGGQRFGEMEVWALEAYGAAYTLQEM 1056
Query: 352 LKCKNVANVIQRV------VGGPYCRICNSADDIIKANVPYGAKLLSQEL 395
L K+ +V+ R V G ++I + +P +L +EL
Sbjct: 1057 LTVKS-DDVVGRTKVYEAIVKG---------ENIPEPGIPESFNVLVKEL 1096
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 35.3 bits (82), Expect = 0.074
Identities = 20/59 (33%), Positives = 31/59 (52%)
Query: 297 IHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCK 355
IH +DK+ R++G + +T +P+ R + GG GEM+ L G + L E L K
Sbjct: 951 IHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYK 1009
>gnl|CDD|216554 pfam01529, zf-DHHC, DHHC palmitoyltransferase. This family
includes the well known DHHC zinc binding domain as well
as three of the four conserved transmembrane regions
found in this family of palmitoyltransferase enzymes.
Length = 167
Score = 32.1 bits (73), Expect = 0.30
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 6/53 (11%)
Query: 247 NCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHM 299
NCIG RN K++ LF L+ + + L++ F +
Sbjct: 77 NCIGRRN------HKYFLLFLLYLTLYLILLLVLSFYYLVYLIRNIELFFFLI 123
>gnl|CDD|234611 PRK00071, nadD, nicotinic acid mononucleotide adenylyltransferase;
Provisional.
Length = 203
Score = 29.8 bits (68), Expect = 1.8
Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 48 VDTL--LQQLFYPQRPLFWILISDCL 71
+DTL L+ YP L +I+ +D L
Sbjct: 88 IDTLRELRAR-YPDVELVFIIGADAL 112
>gnl|CDD|224179 COG1259, COG1259, Uncharacterized conserved protein [Function
unknown].
Length = 151
Score = 29.6 bits (67), Expect = 1.9
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 58 PQRPLFWILISDCLGRPE---DSLVMNQASLECGVFRSESYKAEVDNKDIQVKSRPSD 112
P RPL L+ + + +V++ L + + + D+ IQ+ +RPSD
Sbjct: 55 PPRPLTHDLLVEIFEELGARVEKVVID--DLIDNTYYATLILEQ-DDGKIQIDARPSD 109
>gnl|CDD|216240 pfam01008, IF-2B, Initiation factor 2 subunit family. This family
includes initiation factor 2B alpha, beta and delta
subunits from eukaryotes, initiation factor 2B subunits
1 and 2 from archaebacteria and some proteins of unknown
function from prokaryotes. Initiation factor 2 binds to
Met-tRNA, GTP and the small ribosomal subunit. Members
of this family have also been characterized as
5-methylthioribose- 1-phosphate isomerases, an enzyme of
the methionine salvage pathway. The crystal structure of
Ypr118w, a non-essential, low-copy number gene product
from Saccharomyces cerevisiae, reveals a dimeric protein
with two domains and a putative active site cleft.
Length = 281
Score = 29.6 bits (67), Expect = 3.3
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 126 DIVIGKYA-EIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVV 168
IG A E+ D L H G VL VL +++ +GK F V+
Sbjct: 94 RRKIGAIAAELIKDGDTILTHCNSGTVLGVLRAAHKEGKRFRVI 137
>gnl|CDD|221291 pfam11887, DUF3407, Protein of unknown function (DUF3407). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 360 to 454 amino acids in
length. This protein is found associated with pfam02470.
Length = 270
Score = 28.4 bits (64), Expect = 6.8
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 227 ATSTGGVITEQHQSFVSQLLNCIGARNSGITFI 259
A++T I +Q + LL G N+G +
Sbjct: 82 ASTTSRTIVDQQDDLDALLLAATGLSNTGTDVL 114
>gnl|CDD|182445 PRK10420, PRK10420, L-lactate permease; Provisional.
Length = 551
Score = 28.3 bits (63), Expect = 8.7
Identities = 34/148 (22%), Positives = 55/148 (37%), Gaps = 17/148 (11%)
Query: 149 GLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLE 208
G+VL SN G +S ++ + H+ FS G GV T + L
Sbjct: 413 GMVLAFAFISNYSG-----LSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALF 467
Query: 209 AALGK------GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKH 262
AAL G D L+ A TG +I+ Q + + +G + F KH
Sbjct: 468 AALQATAAQQIGVSDVLLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKH 527
Query: 263 YFLFCLFECPMDWIAFICLVRSLIFTWI 290
+F + I +++ + TW+
Sbjct: 528 SLIFTCM------VGVITTLQAYVLTWM 549
>gnl|CDD|236280 PRK08515, flgA, flagellar basal body P-ring biosynthesis protein
FlgA; Reviewed.
Length = 222
Score = 27.7 bits (62), Expect = 9.0
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 7/73 (9%)
Query: 96 KAEVDNKDIQVKSR-PSDDMLNFGKIQSKS----GDIVIGKYAEIGADHSIKLKHTERGL 150
+ ++DN + KS P +L K ++ DI+ G E G I LK + G
Sbjct: 137 EDDIDN--LSAKSFIPPGTILTADKFKALILVRKNDIINGVLKEGGVSIEISLKALQDGN 194
Query: 151 VLKVLLSSNDDGK 163
+ ++ + N K
Sbjct: 195 LGDIIQAKNKSNK 207
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
0.323 0.138 0.420
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: 20,699,626
Number of extensions: 1972125
Number of successful extensions: 1387
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1352
Number of HSP's successfully gapped: 34
Length of query: 417
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 318
Effective length of database: 6,546,556
Effective search space: 2081804808
Effective search space used: 2081804808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 60 (26.8 bits)