RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 019610
(338 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 = 222 bits (568), Expect = 6e-66
Identities = 123/407 (30%), Positives = 162/407 (39%), Gaps = 118/407 (28%)
Query: 1 MNQASLECGVFRS---ESYKAEVDNK----------DIQVKSRPSDDMLNF-GKI----Q 42
+N++S++ G FRS + Y+ E+ DI S L+ G I +
Sbjct: 498 INKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGAR 557
Query: 43 SKSGDIVIGKYAEIGA---------------DHSIKLKHTERGLVLKVLLSS---NDDGK 84
+ GDI++GK G D S+K E+G+V V + S ND G
Sbjct: 558 VEPGDILVGKITPKGETESTPIFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGN 617
Query: 85 NFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG---------FLEQ------------- 122
V IRQ +GDKF+S HGQKGV+ F E
Sbjct: 618 KLVKVYIRQ----KRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGF 673
Query: 123 ----TPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARN--- 174
T QLLE+ LGK GA G ATPF + I+E LN G
Sbjct: 674 PSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISE---LLGEAGLNYYG--KEVL 728
Query: 175 -SGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSF 233
G T E P IF +YQ+ HM +DK+ R+TG +
Sbjct: 729 YDGRTGE--------PLEAP-------------IFVGPVYYQRLKHMVDDKIHARSTGPY 767
Query: 234 QPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL-------------KCKNVAN 280
LT +P+ R R GG FGEM+ D LIAHGA+ L ERL KC + +
Sbjct: 768 SLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIILS 827
Query: 281 VIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFD 327
CR+C +I K +PY KLL QEL SM I +
Sbjct: 828 AN-------LCRLCKKGTNISKVGIPYAFKLLFQELQ-SMNIDPRLK 866
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 152 bits (386), Expect = 5e-41
Identities = 93/400 (23%), Positives = 153/400 (38%), Gaps = 112/400 (28%)
Query: 1 MNQASLECGVFRS---ESYKAEV-DNK----DIQVKSRPSDDMLNF------GKIQS--K 44
+++ S+E +F S E Y+ E D K +I+ S++ L +I + K
Sbjct: 695 ISERSVERDLFTSIHIEEYETEARDTKLGPEEIRDIPNVSEEALRNLDEDGIIRIGAEVK 754
Query: 45 SGDIVIGKYAEIGA------------------DHSIKLKHTERGLVLKVLLSSNDDGKN- 85
GDI++GK G D S+++ H E G+V V + + +DG
Sbjct: 755 GGDILVGKVTPKGETELTPEERLLRIFGEKVRDTSLRVPHGEEGIVDDVQVFTREDGDPG 814
Query: 86 ---FAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG---------FLEQ----------- 122
V + Q +GDK + HG KGV+ FLE
Sbjct: 815 VNKLVKVYVAQ----KRKPQIGDKMAGRHGNKGVVSKIVPQEDMPFLEDGTPPDIILNPL 870
Query: 123 ------TPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNS 175
Q+LE LGK A G+ F + L
Sbjct: 871 GVPSRMNIGQILETHLGKAAALLGIPVDTPVF-------DGAPEEDIRELLK-------- 915
Query: 176 GITFIFKHYFLFCLFECPMDWIAFICL--------VRSLIFTWITFYQQFIHMSEDKVKF 227
+ F + L + IF + +YQ+ HM +DK+
Sbjct: 916 ------EAGF---------PYSGKEVLYDGRTGEPFDAPIFVGVMYYQKLHHMVDDKIHA 960
Query: 228 RNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVG 287
R+TG + +T +P+ + +FGG FGEM+ L A+GA+ L ERL K ++ + +
Sbjct: 961 RSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTVK--SDDVCGRIK 1018
Query: 288 GPYCRICNSADDIIKANVPYGAKLLSQELSFSMGITLKFD 327
C + +I + +P K+L +EL S+GI ++ +
Sbjct: 1019 IYECIVKGE--NIPEVGIPESFKVLLKELR-SLGIDVRLE 1055
>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 = 150 bits (380), Expect = 1e-40
Identities = 113/399 (28%), Positives = 167/399 (41%), Gaps = 105/399 (26%)
Query: 1 MNQASLECGVFRS----------------ESYKAEVDNKDI------QVKSRPSDDMLNF 38
MN+AS+E G+ RS + + E+ D+ + +D + +
Sbjct: 219 MNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVY 278
Query: 39 GKIQSKSGDIVIGK---------YAEIGA------DHSIKLKHTERGLVLKVLLSSNDDG 83
+++ K GD++IGK E+G D S+ ++H E+G+V KV+++ ++G
Sbjct: 279 PEVEVKGGDVLIGKTSPPRFLEELRELGLVTERRRDTSVTVRHGEKGIVDKVIITETEEG 338
Query: 84 KNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG---------FLEQ------------ 122
V +R + LGDKF+S HGQKGV+G F E
Sbjct: 339 NKLVKVRVR----DLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHA 394
Query: 123 -----TPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSG 176
T QLLE GK A +G TPF + + + + L +G + G
Sbjct: 395 IPSRMTVGQLLEMIAGKVAALEGRRVDGTPF--------EGEPEEELRKELLKLGFKPDG 446
Query: 177 ITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPL 236
E D I L + IF + +YQ+ HM DK+ R+ G Q L
Sbjct: 447 K-------------EVMYDGITGEKL-EAEIFIGVIYYQKLHHMVADKIHARSRGPVQVL 492
Query: 237 TGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL-------------KCKNVANVIQ 283
T +P R R GG+ FGEM+ D LI HGA+ L ERL C ++A
Sbjct: 493 TRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVCENCGHIA-WED 551
Query: 284 RVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGI 322
+ G YC +C DI + Y KLL EL S+GI
Sbjct: 552 KRKGTAYCPVCGETGDISPVEMSYAFKLLLDELK-SLGI 589
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 147 bits (374), Expect = 2e-39
Identities = 115/399 (28%), Positives = 163/399 (40%), Gaps = 105/399 (26%)
Query: 1 MNQASLECGVFRS---ESYKAE-------------VDNKDIQVKSRPS------DDMLNF 38
MN+AS+E G+ RS +Y+ E + +++ +D +
Sbjct: 723 MNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVS 782
Query: 39 GKIQSKSGDIVIGK---------YAEIGA------DHSIKLKHTERGLVLKVLLSSNDDG 83
+++ K GD++IGK E+ D S+ ++H E+G+V VL++ + +G
Sbjct: 783 PEVEVKGGDVLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESPEG 842
Query: 84 KNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG---------FLEQ------------ 122
+V +R V + LGDKF+S HGQKGV+G F E
Sbjct: 843 --NKLVKVR--VRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHA 898
Query: 123 -----TPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSG 176
T QLLE+ GK A +G ATPF E + +LL
Sbjct: 899 IPSRMTVGQLLESIAGKVAALEGRFVDATPF-------YGEPEEELRKELL--------- 942
Query: 177 ITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPL 236
K + E D + IF + +YQ+ HM DK+ R G Q L
Sbjct: 943 -----KLGYKPDGTEVMYDGRTGEKIKAP-IFIGVVYYQKLHHMVADKIHARARGPVQIL 996
Query: 237 TGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL-------------KCKNVANVIQ 283
T +P R R GG+ FGEM+ DCLI HGA+ L ERL C ++A
Sbjct: 997 TRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCELCGHIA-WYD 1055
Query: 284 RVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGI 322
R C I +I V Y KLL QEL SMGI
Sbjct: 1056 RRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELM-SMGI 1093
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 132 bits (334), Expect = 2e-34
Identities = 111/408 (27%), Positives = 163/408 (39%), Gaps = 123/408 (30%)
Query: 1 MNQASLECGVFRS---ESYKA-------------EVDNKDIQVKSRPS-------DDMLN 37
MN+AS+E G+ RS +Y+ E+ +KD++ R +D L
Sbjct: 225 MNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKDVR-GYRGEEAYRHLDEDGLV 283
Query: 38 FGKIQSKSGDIVIGK---------YAEIGA------DHSIKLKHTERGLVLKVLLSSNDD 82
+ + K GD++IGK + G + S+ ++ E G+V V+L+ ++
Sbjct: 284 NPETEVKEGDVLIGKTSPPRFLEEPDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEE 343
Query: 83 GKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG---------FLEQ----------- 122
G V +R + LGDKF+S HGQKGV+G F E
Sbjct: 344 GSRLVKVRVR----DLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPH 399
Query: 123 ------TPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNS 175
T +LE GK G+ +G T F +G E + L G ++
Sbjct: 400 AIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAF---SG----EDEEDLREALEKL-GFEHT 451
Query: 176 GITFIF------KHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRN 229
G ++ K E IF + +YQ+ HM +K+ R+
Sbjct: 452 GKEVMYDGITGEK-------IEAE-------------IFVGVIYYQKLHHMVANKLHARS 491
Query: 230 TGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERL-------------KCK 276
G Q LT +P R R GG+ FGEM+ D LI HGA+ L ERL KC
Sbjct: 492 RGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEIYVCAKCG 551
Query: 277 NVA--NVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQELSFSMGI 322
+A + + YC IC DI + Y KLL EL S+GI
Sbjct: 552 MIAIYDKKRNRK---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 = 120 bits (304), Expect = 3e-31
Identities = 81/312 (25%), Positives = 111/312 (35%), Gaps = 96/312 (30%)
Query: 1 MNQASLECGVFRSESYK-------------AEVDNKDIQVKSRPSDDMLNFGKI-----Q 42
+N++S++ G+F S K E +D S + L+ I +
Sbjct: 92 INKSSVDRGLFTSIHIKEYEIEARKTKLGPIEEITRDPPNVSEEAYRKLDEDGIVRVGAE 151
Query: 43 SKSGDIVIGKYAEIGA---------------DHSIKLKHTERGLVLKVLLSSNDDGKNFA 87
K GDI++GK G D S+K+KH E G V V + N G
Sbjct: 152 VKPGDILVGKITPKGEKLLRAIFGEKARDVKDTSLKVKHGEEGRVDDVKIDLNPGGIKKV 211
Query: 88 VVSIRQSVNMVHSACLGDKFSSMHGQKGVLG---------FLE----------------- 121
V IRQ +GDKF+S HGQKGV+ F E
Sbjct: 212 KVYIRQ----KRKPQVGDKFASRHGQKGVVSKILPQEDMPFTEDGIPPDIILNPHGVPSR 267
Query: 122 QTPAQLLEAALGK-GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARN------ 174
T QLLE+ LGK A G ATPF +E + L
Sbjct: 268 MTIGQLLESLLGKAAALLGKFIDATPF-----DGASEDVEDIGELLKEAGYNAYGKEVLY 322
Query: 175 SGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQ 234
G T P + IF +YQ+ HM +DK+ R+TG +
Sbjct: 323 DGRT------------GEPFK---------APIFVGPIYYQKLKHMVDDKIHARSTGPYS 361
Query: 235 PLTGRPVADRKR 246
LT +P+ R R
Sbjct: 362 LLTQQPLGGRSR 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 = 70.2 bits (173), Expect = 2e-15
Identities = 28/90 (31%), Positives = 38/90 (42%), Gaps = 22/90 (24%)
Query: 248 GGIEFGEMKCDCLIAHGASGNLHERL---------KCKNVANVIQRVVGGPYCRICNSAD 298
GG FGEM+ L A+GA+ L ERL +C A IC
Sbjct: 1 GGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRCGAYAA------------ICKGKT 48
Query: 299 DIIKANVPYGAKLLSQELSFSMGITLKFDT 328
I ++P KLL QEL S+G+ ++
Sbjct: 49 IIEPGDIPESFKLLLQEL-RSLGLDIRLFL 77
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 65.5 bits (160), Expect = 1e-11
Identities = 74/300 (24%), Positives = 116/300 (38%), Gaps = 64/300 (21%)
Query: 20 VDNKDI---QVKSRPSDDMLNFGKIQSKSGDIVIGKYAEIGADHSIKLKHTERGLVLKVL 76
V DI ++ + D L GK+ + G+ A+ D S+++ + G V+KV
Sbjct: 727 VLAGDILVGKITPKGESDQLPEGKLLR----AIFGEKAKDVKDTSLRMPNGGYGRVIKVE 782
Query: 77 L---SSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG---------FL-EQT 123
+ S D+ K + IR + + +GDK + HG KG++ +L + T
Sbjct: 783 IFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGT 842
Query: 124 P----------------AQLLEAALGKGACDGLMS--YATPFATSTGGVITEQHQSFVSQ 165
P QL E LG A D L PF G +E + ++
Sbjct: 843 PPDIILNPLGVPSRMNVGQLFECLLGL-AGDNLNKRFKILPFDEMYG---SEYSRILINN 898
Query: 166 LLNCIG-ARNSGITFIFKHYFLFCL--------FECPMDWIAFICLVRSLIFTWITFYQQ 216
LN N F H L F+ P + I + +
Sbjct: 899 KLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNP-------------VTVGIAYMLK 945
Query: 217 FIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCK 276
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 = 58.9 bits (143), Expect = 2e-09
Identities = 71/304 (23%), Positives = 112/304 (36%), Gaps = 80/304 (26%)
Query: 18 AEVDNKDIQV---------KSRPSDDMLN--FGKIQSKSGDIVIGKYAEIGADHSIKLKH 66
AEV DI V + P + +L FG+ K+ D+ D S+++
Sbjct: 752 AEVKAGDILVGKVTPKGETELTPEEKLLRAIFGE---KARDVR---------DTSLRVPP 799
Query: 67 TERGLVLKVLLSSNDDG---KNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLG----- 118
G V+ V + S +G ++ + +GDK + HG KGV+
Sbjct: 800 GVEGTVIDVKVFSRKEGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPI 859
Query: 119 ----FLEQ-TP----------------AQLLEAALGKGACDGLMSYATPFATS-TGGVIT 156
FLE TP Q+LE LG A L P AT G
Sbjct: 860 EDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGW-AGKKLGRKGVPIATPVFDGASE 918
Query: 157 EQHQSFVSQLLNCIGARNSGITFIFK----HYFLFCLFECPMDWIAFICLVRSLIFTWIT 212
E+ + + L G G ++ F + +
Sbjct: 919 EE----IKEYLEKAGLPRDGKVRLYDGRTGEQF------------------DNPVTVGYM 956
Query: 213 FYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHER 272
+ + H+ +DK+ R+TG + +T +P+ + +FGG FGEM+ L A+GA+ L E
Sbjct: 957 YMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 1016
Query: 273 LKCK 276
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 = 6e-07
Identities = 22/59 (37%), Positives = 35/59 (59%)
Query: 219 HMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKN 277
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 = 49.5 bits (118), Expect = 2e-06
Identities = 24/59 (40%), Positives = 36/59 (61%)
Query: 219 HMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKN 277
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 = 3e-05
Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 10/61 (16%)
Query: 218 IHMSEDKVKFRNTGSF-----QPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHER 272
H+ +DK+ R+TG + QPL G+ A +FGG FGEM+ L A+GA+ L E
Sbjct: 1002 HHLVDDKIHARSTGPYSLVTQQPLGGK--A---QFGGQRFGEMEVWALEAYGAAYTLQEM 1056
Query: 273 L 273
L
Sbjct: 1057 L 1057
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 35.3 bits (82), Expect = 0.050
Identities = 20/59 (33%), Positives = 31/59 (52%)
Query: 218 IHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCK 276
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 = 0.20
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 6/53 (11%)
Query: 168 NCIGARNSGITFIFKHYFLFCLFECPMDWIAFICLVRSLIFTWITFYQQFIHM 220
NCIG RN K++ LF L+ + + L++ F +
Sbjct: 77 NCIGRRN------HKYFLLFLLYLTLYLILLLVLSFYYLVYLIRNIELFFFLI 123
>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 = 29.2 bits (66), Expect = 3.1
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 47 DIVIGKYA-EIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVV 89
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 = 28.8 bits (65), Expect = 3.8
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 148 ATSTGGVITEQHQSFVSQLLNCIGARNSGITFI 180
A++T I +Q + LL G N+G +
Sbjct: 82 ASTTSRTIVDQQDDLDALLLAATGLSNTGTDVL 114
>gnl|CDD|182445 PRK10420, PRK10420, L-lactate permease; Provisional.
Length = 551
Score = 29.0 bits (65), Expect = 4.5
Identities = 34/148 (22%), Positives = 55/148 (37%), Gaps = 17/148 (11%)
Query: 70 GLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPAQLLE 129
G+VL SN G +S ++ + H+ FS G GV T + L
Sbjct: 413 GMVLAFAFISNYSG-----LSSTLALALAHTGHAFTFFSPFLGWLGVFLTGSDTSSNALF 467
Query: 130 AALGK------GACDGLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKH 183
AAL G D L+ A TG +I+ Q + + +G + F KH
Sbjct: 468 AALQATAAQQIGVSDVLLVAANTTGGVTGKMISPQSIAIACAAVGLVGKESDLFRFTVKH 527
Query: 184 YFLFCLFECPMDWIAFICLVRSLIFTWI 211
+F + I +++ + TW+
Sbjct: 528 SLIFTCM------VGVITTLQAYVLTWM 549
>gnl|CDD|185429 PTZ00074, PTZ00074, 60S ribosomal protein L34; Provisional.
Length = 135
Score = 27.0 bits (60), Expect = 8.3
Identities = 12/39 (30%), Positives = 16/39 (41%)
Query: 276 KNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQ 314
+ V ++ GP C C IKA P K LS+
Sbjct: 29 RLVVQKRKKKSSGPKCGDCGKVLAGIKALRPTEYKQLSR 67
>gnl|CDD|221000 pfam11145, DUF2921, Protein of unknown function (DUF2921). This
eukaryotic family of proteins has no known function.
Length = 871
Score = 27.9 bits (62), Expect = 9.9
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 290 YCRICNS---ADDIIKANVPYGAKLLSQELSFSMG 321
Y C+S +K P + S++LSF G
Sbjct: 1 YSDHCSSIVPESSELKDEDPTRPLVRSRQLSFFDG 35
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 0.137 0.412
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: 16,591,701
Number of extensions: 1569141
Number of successful extensions: 1099
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1072
Number of HSP's successfully gapped: 32
Length of query: 338
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 240
Effective length of database: 6,590,910
Effective search space: 1581818400
Effective search space used: 1581818400
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: 59 (26.5 bits)