RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 018378
(357 letters)
>gnl|CDD|132910 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryotic RNA polymerase
(RNAP) I and RNAP III. The eukaryotic AC40 subunit of
RNA polymerase (RNAP) I and RNAP III is involved in the
assembly of RNAP subunits. RNAP is a large multi-subunit
complex responsible for the synthesis of RNA. It is the
principal enzyme of the transcription process, and is a
final target in many regulatory pathways that control
gene expression in all living cells. At least three
distinct RNAP complexes are found in eukaryotic nuclei:
RNAP I, RNAP II, and RNAP III. RNAP I is responsible for
the synthesis of ribosomal RNA precursor, while RNAP III
functions in the synthesis of 5S and tRNA. The AC40
subunit is the equivalent of the RPB3 subunit of RNAP
II. The RPB3 subunit is similar to the bacterial RNAP
alpha subunit in that it contains two subdomains: one
subdomain is similar the eukaryotic Rpb11/AC19/archaeal
L subunit which is involved in dimerization; and the
other is an inserted beta sheet subdomain. The RPB3
subunit heterodimerizes with the RPB11 subunit, and
together with RPB10 and RPB12, anchors the two largest
subunits, RPB1 and RPB2, and stabilizes their
association. The homology of AC40 to RPB3 suggests a
similar function. The AC40 subunit is likely to
associate with the RPB11 counterpart, AC19, to form a
heterodimer, which stabilizes the association of the two
largest subunits of RNAP I and RNAP III.
Length = 291
Score = 379 bits (976), Expect = e-132
Identities = 152/288 (52%), Positives = 189/288 (65%), Gaps = 44/288 (15%)
Query: 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAH 135
F++E+I L+ +++EFDLIG+DA+IANAFRRIL+AE+PTMAIEKV I NNTSVIQDEVLAH
Sbjct: 1 FKIEIISLSDEELEFDLIGVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAH 60
Query: 136 RLGLIPIIVDPRLFEYMSE-NDTSNEKNTIVFKLHVLCERGGPR-------------LTV 181
RLGLIPI DPRLFEY + +D E+NT+VF+L V C R V
Sbjct: 61 RLGLIPIKADPRLFEYREDSDDEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHKV 120
Query: 182 KTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPML-DITIAR 240
+ +LKW+P GS+ F++NPIRP+ DI IA+
Sbjct: 121 YSGDLKWVPIGSQEKR---------------------------FADNPIRPVHPDILIAK 153
Query: 241 LGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNV 300
L PGQEI+LE H VKGIGK HAK+SPVATA YR+LPEI LL+ + EDAEKL K P V
Sbjct: 154 LRPGQEIDLELHCVKGIGKDHAKFSPVATASYRLLPEITLLKPITGEDAEKLQKCFPPGV 213
Query: 301 FDIEDIGSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFI 348
DIE++ GKK+A VA PR TL RE L EE++ +V + RV+DHFI
Sbjct: 214 IDIEEVK-GKKKAVVANPRKDTLSREVL-RHEEFKDKVELGRVRDHFI 259
>gnl|CDD|214766 smart00662, RPOLD, RNA polymerases D. DNA-directed RNA polymerase
subunit D and bacterial alpha chain.
Length = 224
Score = 196 bits (500), Expect = 2e-61
Identities = 74/220 (33%), Positives = 95/220 (43%), Gaps = 42/220 (19%)
Query: 88 MEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPR 147
+F L +ANA RR+L++ +P MA+ V I NTS +QDEVLAHRLGL P+ DP
Sbjct: 1 AKFVLEPYGLTLANALRRVLLSSVPGMAVTSVYIEGNTSGVQDEVLAHRLGLKPLASDPD 60
Query: 148 LFEY--MSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNP 205
EY E + EK ++ L V V +LK + PD
Sbjct: 61 GDEYQRDCECEEGCEKCSVTLTLDVKGPG-----EVTAGDLKSDSD---------PDVEI 106
Query: 206 SSKPRTYTSFSSSQDLLPEFSNNPIRPMLDITIARLGPGQEIELEAHAVKGIGKTHAKWS 265
+ DI IA+L GQE+ELEA A KG G HAKWS
Sbjct: 107 VNP--------------------------DIPIAKLREGQELELEARAEKGRGYVHAKWS 140
Query: 266 PVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIED 305
PV+T YR +P I + D CP V +
Sbjct: 141 PVSTVEYRYIPRIPVDASFSPVDRVAYQVECPRVVQRTDC 180
>gnl|CDD|132906 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polymerase. The
eukaryotic RPB3 subunit of RNA polymerase (RNAP), as
well as its archaeal (D subunit) and bacterial (alpha
subunit) counterparts, is involved in the assembly of
RNAP subunits. RNAP is a large multi-subunit complex
responsible for the synthesis of RNA. It is the
principal enzyme of the transcription process, and is a
final target in many regulatory pathways that control
gene expression in all living cells. At least three
distinct RNAP complexes are found in eukaryotic nuclei:
RNAP I, RNAP II, and RNAP III, for the synthesis of
ribosomal RNA precursor, mRNA precursor, and 5S and
tRNA, respectively. A single distinct RNAP complex is
found in prokaryotes and archaea, which may be
responsible for the synthesis of all RNAs. The RPB3
subunit is similar to the bacterial RNAP alpha subunit
in that it contains two subdomains: one subdomain is
similar to the eukaryotic Rpb11/AC19/archaeal L subunit
which is involved in dimerization; and the other is an
inserted beta sheet subdomain. The assembly of the two
largest eukaryotic RNAP subunits that provide most of
the enzyme's catalytic functions depends on the presence
of RPB3/RPB11 heterodimer subunits. This is also true
for the archaeal (D/L subunits) and bacterial (alpha
subunit) counterparts.
Length = 212
Score = 164 bits (416), Expect = 3e-49
Identities = 71/207 (34%), Positives = 102/207 (49%), Gaps = 39/207 (18%)
Query: 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAH 135
+V++ KD+++F L G+D A+ANA RR++IAE+PTMA++ V + NTSV+ DE+LAH
Sbjct: 1 PQVKIREADKDNVDFILSGVDLAMANALRRVMIAEVPTMAVDSVEVETNTSVLADEILAH 60
Query: 136 RLGLIPIIVDPRLFEYMS-----ENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLP 190
RLGLIP+ L Y S E + +K ++V L E V + +L +
Sbjct: 61 RLGLIPLQSMDILQLYRSPEEDCECEDHCDKCSVVLTLQAFAESESTTN-VYSKDLVIVS 119
Query: 191 NGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPML-DITIARLGPGQEIEL 249
N + P++ DI I +L GQEI+L
Sbjct: 120 NLMGRNI--------------------------------GHPIIQDILICKLRKGQEIKL 147
Query: 250 EAHAVKGIGKTHAKWSPVATAWYRMLP 276
A KGIGK HAK+ PVA +R P
Sbjct: 148 TCVAKKGIGKEHAKFGPVAAIEFRYDP 174
>gnl|CDD|234837 PRK00783, PRK00783, DNA-directed RNA polymerase subunit D;
Provisional.
Length = 263
Score = 161 bits (410), Expect = 1e-47
Identities = 86/279 (30%), Positives = 125/279 (44%), Gaps = 59/279 (21%)
Query: 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAH 135
+E++ L F + G+ A ANA RR +IA++PTMAI+ V NTSV+ DE+LAH
Sbjct: 1 MEIEILELDDRSARFVVEGVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDEILAH 60
Query: 136 RLGLIPIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSEL 195
RLGLIP+ D ++ E G P TV L
Sbjct: 61 RLGLIPLTTDLDKYKPPEECTC--------------EGEGCPDCTVT------------L 94
Query: 196 PLETKPDSNPSSKPRT-YTSFSSSQDLLPEFSNNPIRPML-----DITIARLGPGQEIEL 249
LE + P+T Y S DL P + +I I +L GQ++ L
Sbjct: 95 SLEVE-------GPKTVY-----SGDLKSS------DPDVKPVDPNIPIVKLKEGQKLVL 136
Query: 250 EAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSG 309
EA+A G GK HAKW P + Y+ P I + ED ++ EK V+ CP V ++++
Sbjct: 137 EAYARLGRGKEHAKWQPGSACGYKYYPRIEVSEDC--DECEKCVEACPRGVLELKE---- 190
Query: 310 KKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFI 348
+ V C+LC+ C R K + + ++ FI
Sbjct: 191 -GKLVVTDLLNCSLCKLCERACP--GKAIRVSDDENKFI 226
>gnl|CDD|132909 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase
II. The eukaryotic RPB3 subunit of RNA polymerase
(RNAP) II is involved in the assembly of RNAP subunits.
RNAP is a large multi-subunit complex responsible for
the synthesis of RNA. It is the principal enzyme of the
transcription process, and is a final target in many
regulatory pathways that control gene expression in all
living cells. At least three distinct RNAP complexes are
found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP
III. RNAP II is responsible for the synthesis of mRNA
precursor. The RPB3 subunit is similar to the bacterial
RNAP alpha subunit in that it contains two subdomains:
one subdomain is similar the eukaryotic
Rpb11/AC19/archaeal L subunit which is involved in
dimerization, and the other is an inserted beta sheet
subdomain. The RPB3 subunit heterodimerizes with the
RPB11 subunit, and together with RPB10 and RPB12,
anchors the two largest subunits, RPB1 and RPB2, and
stabilizes their association.
Length = 265
Score = 159 bits (405), Expect = 9e-47
Identities = 83/282 (29%), Positives = 116/282 (41%), Gaps = 64/282 (22%)
Query: 77 RVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHR 136
RVE+ LT D ++F L D ++AN+ RR++IAE+PT+AI+ V I NTSV+ DE +AHR
Sbjct: 2 RVEITELTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDLVEIEENTSVLHDEFIAHR 61
Query: 137 LGLIPIIVDP-RLFEYMSENDTSNE---KNTIVFKLHVLCERGGPRLTVKTNELK--WLP 190
LGLIP+ D F Y S + +E K ++ L V C R V + +L
Sbjct: 62 LGLIPLTSDDVDEFLYYSRDCDCDEFCDKCSVELTLDVKCTGDQTRE-VTSRDLVSSGPK 120
Query: 191 NGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLDITIARLGPGQEIELE 250
+P+ + DS + + I I +L GQE++L
Sbjct: 121 VNDVVPVPIRNDSEDNGEED------------------------GILIVKLRKGQELKLR 156
Query: 251 AHAVKGIGKTHAKWSPVATAWYRMLPEIVL----LEDVEDEDAEKLVKTCPVNVFDIEDI 306
A KGIGK HAKWSP A + P+ L +EDED E
Sbjct: 157 CIAKKGIGKEHAKWSPTAAVTFEYDPDNALRHTDYWYLEDEDKEW--------------- 201
Query: 307 GSGKKRATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFI 348
C+ E + I D F
Sbjct: 202 --------------PKSENACIEEPPEKDALFDIDAKPDKFY 229
>gnl|CDD|132908 cd07030, RNAP_D, D subunit of Archaeal RNA polymerase. The D
subunit of archaeal RNA polymerase (RNAP) is involved in
the assembly of RNAP subunits. RNAP is a large
multi-subunit complex responsible for the synthesis of
RNA. It is the principal enzyme of the transcription
process, and is a final target in many regulatory
pathways that control gene expression in all living
cells. A single distinct RNAP complex is found in
archaea, which may be responsible for the synthesis of
all RNAs. The archaeal RNAP harbors homologues of all
eukaryotic RNAP II subunits with two exceptions (RPB8
and RPB9). The 12 archaeal subunits are designated by
letters and can be divided into three functional groups
that are engaged in: (I) catalysis (A'/A", B'/B" or B);
(II) assembly (L, N, D and P); and (III) auxiliary
functions (F, E, H and K). The D subunit is equivalent
to the RPB3 subunit of eukaryotic RNAP II. It contains
two subdomains: one subdomain is similar the eukaryotic
Rpb11/AC19/archaeal L subunit which is involved in
dimerization, and the other is an inserted beta sheet
subdomain. The assembly of the two largest archaeal RNAP
subunits that provide most of the enzyme's catalytic
functions depends on the presence of the archaeal D/L
heterodimer.
Length = 259
Score = 154 bits (392), Expect = 6e-45
Identities = 93/275 (33%), Positives = 128/275 (46%), Gaps = 51/275 (18%)
Query: 76 FRVEVIRLTKDDMEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAH 135
+EV+ L D F L G+ A ANA RR +I+E+PT+AI+ V I NTSV+ DE+LAH
Sbjct: 1 MEIEVLELDDDRARFVLEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAH 60
Query: 136 RLGLIPIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSEL 195
RLGLIP+ D L++Y SE G P TV L
Sbjct: 61 RLGLIPLRTDLDLYKYRSECS--------------CGGAGCPLCTVT------------L 94
Query: 196 PLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLD-ITIARLGPGQEIELEAHAV 254
L + P T S DL + ++P+ D I I +LG GQ++ LEA+A
Sbjct: 95 TLSVE-------GPGTVY----SGDLKSSDPD--VKPVYDNIPIVKLGKGQKLVLEAYAR 141
Query: 255 KGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRAT 314
G GK HAKW P Y+ P I + ED + K V+ CP V ++E+ +
Sbjct: 142 LGRGKEHAKWQPTTACGYKYYPVIEIDEDCDGC--GKCVEECPRGVLELEE-----GKVV 194
Query: 315 VAQPRACTLCRECLR-CGEEWEKRVSIRRVKDHFI 348
V C+LC+ C R C + + +D FI
Sbjct: 195 VEDLEDCSLCKLCERACD---AGAIRVGWDEDRFI 226
>gnl|CDD|223280 COG0202, RpoA, DNA-directed RNA polymerase, alpha subunit/40 kD
subunit [Transcription].
Length = 317
Score = 127 bits (321), Expect = 4e-34
Identities = 59/294 (20%), Positives = 107/294 (36%), Gaps = 44/294 (14%)
Query: 78 VEVIRLTKDD----MEFDLIGIDAAIANAFRRILIAELPTMAIEKVLIA------NNTSV 127
V++ L+ +E G + NA RR+L++ +P A+ V I ++
Sbjct: 7 VKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGVLHEFDSIEG 66
Query: 128 IQDEVLAHRLGLIPIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTV------ 181
+Q++VLAHRL L P+ V +E+ T+ E +TV
Sbjct: 67 VQEDVLAHRLNLKPLAVKL----------DGDEEVTLELDKEGPGEVTASDITVPLDLEV 116
Query: 182 --KTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPM-LDITI 238
+ + L ++L +E + S Y +++ + P+ P+ +D
Sbjct: 117 VNPDHVIATLTEDAKLEMELRVYSG-----DGYVPAEGNRE-----DDPPVGPIAVDAPF 166
Query: 239 ARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEIVLLEDVEDEDAEKLVKTCPV 298
+ + Q I EA +G K H KW P R + + + E E V+ CP
Sbjct: 167 SPVRKVQYIVEEARVGQGTDKDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCPK 226
Query: 299 NV-FDIEDIGSGKKR---ATVAQPRACTLCRECLRCGEEWEKRVSIRRVKDHFI 348
V + E A + + CL+ E E + + + +
Sbjct: 227 AVEIEEEKPEFPILLVLEAPIDELDLSVRSYNCLK-REGIETIGELVQRTEEEL 279
>gnl|CDD|237878 PRK14979, PRK14979, DNA-directed RNA polymerase subunit D;
Provisional.
Length = 195
Score = 93.0 bits (231), Expect = 2e-22
Identities = 61/199 (30%), Positives = 87/199 (43%), Gaps = 58/199 (29%)
Query: 100 ANAFRRILIAELPTMAIEKVLIANNTSVIQDEVLAHRLGLIPIIVDPRLFEYMSENDTSN 159
++A RRI+I+E+PT AIE V N+S + DE+LAHRLGLIPI P
Sbjct: 27 SSALRRIMISEVPTYAIENVYFYENSSSMYDEILAHRLGLIPIKGKPVS----------- 75
Query: 160 EKNTIVFKLHVLCERGGPRLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQ 219
I F L + GP TV +++LK S+
Sbjct: 76 GDEVITFTL----SKEGP-CTVYSSDLK------------------------------SE 100
Query: 220 DLLPEFSNNPIRPMLDITIARLGPGQEIELEAHAVKGIGKTHAKWSPVATAWYRMLPEI- 278
+ F N P I +L GQ++E+E A+ G GK HAKW P A Y+ +
Sbjct: 101 NGEVAFKNIP--------IVKLAEGQKLEIECEALVGTGKIHAKWQP-CNAVYKQISNDE 151
Query: 279 --VLLEDVEDEDAEKLVKT 295
+E DAE ++++
Sbjct: 152 VEFKVESFGQMDAEDILRS 170
>gnl|CDD|110031 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA insert domain.
Members of this family include: alpha subunit from
eubacteria alpha subunits from chloroplasts Rpb3
subunits from eukaryotes RpoD subunits from archaeal.
Length = 117
Score = 54.9 bits (133), Expect = 1e-09
Identities = 39/131 (29%), Positives = 51/131 (38%), Gaps = 37/131 (28%)
Query: 133 LAHRLGLIPIIVDPRLFEYMSENDTSNEKNTIVFKLHVLCERGGPRLTVKTNELKWLPNG 192
+AH GLIP + + L + N K +V K+ CE LT+
Sbjct: 6 VAHEFGLIPGVSEDVLEIIL------NLKE-LVCKIEG-CEECSVTLTLD---------- 47
Query: 193 SELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLDITIARLGPGQEIELEAH 252
P T+ DL + + P DI IA L GQE+ELEA+
Sbjct: 48 -------------VKGPGEVTA----GDLESDPDVEIVNP--DILIATLRKGQELELEAY 88
Query: 253 AVKGIGKTHAK 263
A KG G HAK
Sbjct: 89 AKKGRGYVHAK 99
>gnl|CDD|216354 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerisation
domain. The two eukaryotic subunits Rpb3 and Rpb11
dimerise to from a platform onto which the other
subunits of the RNA polymerase assemble (D/L in
archaea). The prokaryotic equivalent of the Rpb3/Rpb11
platform is the alpha-alpha dimer. The dimerisation
domain of the alpha subunit/Rpb3 is interrupted by an
insert domain (pfam01000). Some of the alpha subunits
also contain iron-sulphur binding domains (pfam00037).
Rpb11 is found as a continuous domain. Members of this
family include: alpha subunit from eubacteria, alpha
subunits from chloroplasts, Rpb3 subunits from
eukaryotes, Rpb11 subunits from eukaryotes, RpoD
subunits from archaeal spp, and RpoL subunits from
archaeal spp.
Length = 88
Score = 51.1 bits (123), Expect = 2e-08
Identities = 15/34 (44%), Positives = 23/34 (67%)
Query: 88 MEFDLIGIDAAIANAFRRILIAELPTMAIEKVLI 121
+EF L G D + NA RR+L++++P +AI V I
Sbjct: 1 IEFLLEGEDHTLGNALRRVLLSDVPGVAIAGVKI 34
>gnl|CDD|221801 pfam12838, Fer4_7, 4Fe-4S dicluster domain. Superfamily includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. Structure of the
domain is an alpha-antiparallel beta sandwich. Domain
contains two 4Fe4S clusters.
Length = 48
Score = 32.1 bits (73), Expect = 0.035
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 293 VKTCPVNVFDIEDIGSGKKRATVAQPRACTLCREC 327
V+ CP +++ G K + P CT C C
Sbjct: 8 VRACPYGAITLDEEGGKKGTVEI-DPDKCTGCGAC 41
>gnl|CDD|132062 TIGR03017, EpsF, chain length determinant protein EpsF. Sequences
in this family of proteins are members of the chain
length determinant family (pfam02706) which includes the
wzc protein from E.coli. This family of proteins are
homologous to the EpsF protein of the methanolan
biosynthesis operon of Methylobacillus species strain
12S. The distribution of this protein appears to be
restricted to a subset of exopolysaccharide operons
containing a syntenic grouping of genes including a
variant of the EpsH exosortase protein. Exosortase has
been proposed to be involved in the targetting and
processing of proteins containing the PEP-CTERM domain
to the exopolysaccharide layer.
Length = 444
Score = 33.6 bits (77), Expect = 0.14
Identities = 22/64 (34%), Positives = 27/64 (42%), Gaps = 6/64 (9%)
Query: 178 RLTVKTNELKWLPNGSELPLETKPDSNPSSKPRTYTSFSSSQDLLPEFSNNPIRPMLDIT 237
RL V+ L L ++L + SSK SS +D LPE NPI L
Sbjct: 209 RLDVERARLNEL--SAQLVAAQAQVMDASSKEG----GSSGKDALPEVIANPIIQNLKTD 262
Query: 238 IARL 241
IAR
Sbjct: 263 IARA 266
>gnl|CDD|185346 PRK15449, PRK15449, ferredoxin-like protein FixX; Provisional.
Length = 95
Score = 30.7 bits (69), Expect = 0.30
Identities = 22/65 (33%), Positives = 29/65 (44%), Gaps = 10/65 (15%)
Query: 276 PEIVLLEDVEDEDAEKLVKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLRCG---- 331
P IV+ D + + E LVK CP ++ +D GS R A C C C G
Sbjct: 23 PHIVVKADADKQALELLVKACPAGLYKKQDDGS--VRFDYA---GCLECGTCRILGLGSA 77
Query: 332 -EEWE 335
E+WE
Sbjct: 78 LEQWE 82
>gnl|CDD|224069 COG1146, COG1146, Ferredoxin [Energy production and conversion].
Length = 68
Score = 29.7 bits (67), Expect = 0.33
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 293 VKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR 329
V+ CP VFD+ + + VA+P C C C
Sbjct: 17 VEVCPAGVFDLGE--DEGGKPVVARPEECIDCGLCEL 51
>gnl|CDD|197863 smart00760, Bac_DnaA_C, Bacterial dnaA protein helix-turn-helix
domain. Could be involved in DNA-binding.
Length = 69
Score = 29.0 bits (66), Expect = 0.70
Identities = 8/27 (29%), Positives = 12/27 (44%), Gaps = 2/27 (7%)
Query: 302 DIEDIGSGKKRATVAQPR--ACTLCRE 326
ED+ S ++ + R A L RE
Sbjct: 16 KPEDLKSKSRKREIVLARQIAMYLARE 42
>gnl|CDD|220981 pfam11104, Competence_A, Competence protein A. Competence protein
A is responsible for the export of a
competence-stimulating peptide from the cell, which is
thought to induce competence when a critical
extracellular concentration is reached.
Length = 340
Score = 30.2 bits (69), Expect = 1.7
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 116 IEKVLIANNTSVIQ--DEVLAHRLGLIPIIVDPRLFEYMSENDTSNEK 161
++ +++A + + DE+L RLG+ + +P F MS + N K
Sbjct: 275 VDYIVLAGGCASLPGLDELLQQRLGIPTTVANP--FANMSLSSRVNAK 320
>gnl|CDD|224068 COG1145, NapF, Ferredoxin [Energy production and conversion].
Length = 99
Score = 28.3 bits (62), Expect = 2.4
Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 293 VKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR 329
VK CP ++ + G + P C LC CL+
Sbjct: 38 VKVCPTGAIELIEEGLLLPEVVID-PDLCVLCGACLK 73
>gnl|CDD|132904 cd06928, RNAP_alpha_NTD, N-terminal domain of the Alpha subunit of
Bacterial RNA polymerase. The bacterial alpha subunit
of RNA polymerase (RNAP) consists of two independently
folded domains: an amino-terminal domain (alphaNTD) and
a carboxy-terminal domain (alphaCTD). AlphaCTD is not
required for RNAP assembly but interacts with
transcription activators. AlphaNTD is essential in vivo
and in vitro for RNAP assembly and basal transcription.
It is similar to the eukaryotic RPB3/AC40/archaeal D
subunit, and contains two subdomains: one subdomain is
similar the eukaryotic Rpb11/AC19/archaeal L subunit
which is involved in dimerization; and the other is an
inserted beta sheet subdomain. The alphaNTDs of plant
plastid RNAP (PEP) are also included in this subfamily.
PEP is largely responsible for the transcription of
photosynthetic genes and is closely related to the
multi-subunit bacterial RNAP, which is a large
multi-subunit complex responsible for the synthesis of
all bacterial RNAs. The bacterial RNAP core enzyme
consists of four subunits (beta', beta, alpha and
omega). All residues in the alpha subunit that is
involved in dimerization or in the interaction with
other subunits are located within alphaNTD.
Length = 215
Score = 29.0 bits (66), Expect = 3.2
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 99 IANAFRRILIAELPTMAIEKVLIAN 123
+ NA RR+L++ LP AI V I
Sbjct: 26 LGNALRRVLLSSLPGAAITAVKIEG 50
>gnl|CDD|205417 pfam13237, Fer4_10, 4Fe-4S dicluster domain. This family includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. The structure of
the domain is an alpha-antiparallel beta sandwich.
Length = 51
Score = 26.6 bits (58), Expect = 3.3
Identities = 9/35 (25%), Positives = 9/35 (25%), Gaps = 2/35 (5%)
Query: 293 VKTCPVNVFDIEDIGSGKKRATVAQPRACTLCREC 327
V CP V G P C C C
Sbjct: 14 VAACPARVGAGAIRDEGGAVEID--PDRCIGCGAC 46
>gnl|CDD|119330 cd06571, Bac_DnaA_C, C-terminal domain of bacterial DnaA proteins.
The DNA-binding C-terminal domain of DnaA contains a
helix-turn-helix motif that specifically interacts with
the DnaA box, a 9-mer motif that occurs repetitively in
the replication origin oriC. Multiple copies of DnaA,
which is an ATPase, bind to 9-mers at the origin and
form an initial complex in which the DNA strands are
being separated in an ATP-dependent step.
Length = 90
Score = 27.5 bits (62), Expect = 3.8
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 2/31 (6%)
Query: 302 DIEDIGSGKKRATVAQPR--ACTLCRECLRC 330
+ED+ S ++ +A R A L RE
Sbjct: 15 SVEDLRSKSRKKEIALARQIAMYLARELTGL 45
>gnl|CDD|221963 pfam13183, Fer4_8, 4Fe-4S dicluster domain. Superfamily includes
proteins containing domains which bind to iron-sulfur
clusters. Members include bacterial ferredoxins, various
dehydrogenases, and various reductases. Structure of the
domain is an alpha-antiparallel beta sandwich. Domain
contains two 4Fe4S clusters.
Length = 54
Score = 26.0 bits (57), Expect = 5.1
Identities = 11/36 (30%), Positives = 14/36 (38%), Gaps = 1/36 (2%)
Query: 296 CPVNVFDIEDIGSGKKRATVAQPRACTLCREC-LRC 330
CPV G + A A+ +CT C C C
Sbjct: 15 CPVYRALGRFSGDPRGGALAAELWSCTSCGACTEVC 50
>gnl|CDD|237510 PRK13795, PRK13795, hypothetical protein; Provisional.
Length = 636
Score = 28.4 bits (64), Expect = 6.6
Identities = 10/37 (27%), Positives = 11/37 (29%), Gaps = 4/37 (10%)
Query: 293 VKTCPVNVFDIEDIGSGKKRATVAQPRACTLCRECLR 329
V CP IE KR C C +C
Sbjct: 590 VGACPTGAIRIE----EGKRKISVDEEKCIHCGKCTE 622
>gnl|CDD|233711 TIGR02076, pyrH_arch, uridylate kinase, putative. This family
consists of the archaeal and spirochete proteins most
closely related to bacterial uridylate kinases
(TIGR02075), an enzyme involved in pyrimidine
biosynthesis. Members are likely, but not known, to be
functionally equivalent to their bacterial counterparts.
However, substantial sequence differences suggest that
regulatory mechanisms may be different; the bacterial
form is allosterically regulated by GTP [Purines,
pyrimidines, nucleosides, and nucleotides, Nucleotide
and nucleoside interconversions].
Length = 221
Score = 27.7 bits (62), Expect = 9.4
Identities = 15/31 (48%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 89 EFDLIGIDAAIANAFRRILIAELPTMAIEKV 119
D IGIDA NA +LIA L A KV
Sbjct: 61 FLDEIGIDATRLNA--MLLIAALGDDAYPKV 89
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
0.319 0.135 0.405
Gapped
Lambda K H
0.267 0.0848 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,431,121
Number of extensions: 1791441
Number of successful extensions: 1650
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1634
Number of HSP's successfully gapped: 37
Length of query: 357
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 259
Effective length of database: 6,590,910
Effective search space: 1707045690
Effective search space used: 1707045690
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 (21.7 bits)
S2: 60 (26.7 bits)