RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12711
(639 letters)
>gnl|CDD|132907 cd07029, RNAP_I_III_AC19, AC19 subunit of Eukaryotic RNA polymerase
(RNAP) I and RNAP III. The eukaryotic AC19 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 AC19
subunit is the equivalent of the RPB11 subunit of RNAP
II. The RPB11 subunit heterodimerizes with the RPB3
subunit, and together with RPB10 and RPB12, anchors the
two largest subunits, RPB1 and RPB2, and stabilizes
their association. The homology of AC19 to RPB11
suggests a similar function. The AC19 subunit is likely
to associate with the RPB3 counterpart, AC40, to form a
heterodimer, which stabilizes the association of the two
largest subunits of RNAP I and RNAP III.
Length = 85
Score = 104 bits (261), Expect = 6e-27
Identities = 37/79 (46%), Positives = 55/79 (69%)
Query: 103 KPNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDI 162
+C TFVF E HT G+ + +++ PEV+F GYS+PHP++ +I +RIQ K G ++D+
Sbjct: 7 DESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGGEPAVDV 66
Query: 163 LKKGIKELESACDRITETF 181
LKKG+++LE CD I TF
Sbjct: 67 LKKGLEDLEQICDHILSTF 85
>gnl|CDD|222292 pfam13656, RNA_pol_L_2, 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. Many of the members of this family carry
only the N-terminal region of Rpb11.
Length = 77
Score = 98.4 bits (246), Expect = 5e-25
Identities = 35/77 (45%), Positives = 51/77 (66%)
Query: 105 NCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILK 164
N TF E E HT G+++ L P+V+FAGYSVPHP + +I +RIQ K G D +D+LK
Sbjct: 1 NEATFEIEGEDHTLGNLLREELLKDPDVEFAGYSVPHPLEDKINLRIQTKSGKDPLDVLK 60
Query: 165 KGIKELESACDRITETF 181
+ +++L S CD + + F
Sbjct: 61 EALEDLISICDELEKEF 77
>gnl|CDD|224675 COG1761, RPB11, DNA-directed RNA polymerase, subunit L
[Transcription].
Length = 99
Score = 75.5 bits (186), Expect = 1e-16
Identities = 30/90 (33%), Positives = 43/90 (47%), Gaps = 4/90 (4%)
Query: 94 ELRDNTLNVKPNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQV 153
E+ + N E E HT G+++ L +V+FA YS+PHP IRI+
Sbjct: 4 EMELRIIKKDDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIRIKT 63
Query: 154 KDGYDSIDILK----KGIKELESACDRITE 179
K G D + LK K +K+LE D+ E
Sbjct: 64 KGGVDPKEALKRAARKILKDLEELLDQFEE 93
>gnl|CDD|132902 cd06926, RNAP_II_RPB11, RPB11 subunit of Eukaryotic RNA polymerase
II. The eukaryotic RPB11 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 RPB11 subunit heterodimerizes with the
RPB3 subunit, and together with RPB10 and RPB12, anchors
the two largest subunits, RPB1 and RPB2, and stabilizes
their association.
Length = 93
Score = 74.6 bits (184), Expect = 2e-16
Identities = 31/78 (39%), Positives = 40/78 (51%)
Query: 104 PNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDIL 163
PN TF KE HT G+++ L P V FAGY VPHP + +I +RIQ + L
Sbjct: 16 PNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSITPKEAL 75
Query: 164 KKGIKELESACDRITETF 181
K I +L S + E F
Sbjct: 76 KNAITDLISELSLLKEEF 93
>gnl|CDD|132905 cd07027, RNAP_RPB11_like, RPB11 subunit of RNA polymerase. The
eukaryotic RPB11 subunit of RNA polymerase (RNAP), as
well as its archaeal (L 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 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 = 83
Score = 71.0 bits (174), Expect = 3e-15
Identities = 26/70 (37%), Positives = 35/70 (50%)
Query: 105 NCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILK 164
N T E E HT G+++ L +VDFA Y + HP +I IRIQ K G D LK
Sbjct: 9 NSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIKHPVIDKIQIRIQTKSGIKPKDALK 68
Query: 165 KGIKELESAC 174
+ + +L
Sbjct: 69 RAVNKLSKLY 78
>gnl|CDD|132903 cd06927, RNAP_L, L subunit of Archaeal RNA polymerase. The
archaeal L subunit of 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 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 = 83
Score = 63.4 bits (155), Expect = 1e-12
Identities = 19/68 (27%), Positives = 30/68 (44%)
Query: 108 TFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKGI 167
E E HT +++ L P V A Y + HP ++I+ G D ++ LK+
Sbjct: 12 ELEIEGEDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKTDGGVDPLEALKEAA 71
Query: 168 KELESACD 175
K L C+
Sbjct: 72 KRLIDLCE 79
>gnl|CDD|234909 PRK01146, PRK01146, DNA-directed RNA polymerase subunit L;
Provisional.
Length = 85
Score = 61.0 bits (149), Expect = 9e-12
Identities = 19/67 (28%), Positives = 31/67 (46%)
Query: 109 FVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKGIK 168
E E HT +++ L P V+ A Y + HP ++I+ G D ++ LK+ K
Sbjct: 15 LEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGIDPLEALKEAAK 74
Query: 169 ELESACD 175
+ CD
Sbjct: 75 RIIDLCD 81
>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 = 60.3 bits (147), Expect = 2e-11
Identities = 24/87 (27%), Positives = 35/87 (40%), Gaps = 19/87 (21%)
Query: 108 TFVFEKEGHTFGSVITHILQSY-PEVDFAGYSVPHPADFQ------------------IF 148
F+ E E HT G+ + +L S P V AG +PHPA F +
Sbjct: 2 EFLLEGEDHTLGNALRRVLLSDVPGVAIAGVKIPHPAKFSPVKKVNYRVVGVGTDYDKLI 61
Query: 149 IRIQVKDGYDSIDILKKGIKELESACD 175
+RI+ + LK+ +K L D
Sbjct: 62 LRIETDGSITPEEALKEALKILIEKLD 88
>gnl|CDD|132901 cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits of RNA
polymerase. The eukaryotic RPB11 and RPB3 subunits of
RNA polymerase (RNAP), as well as their archaeal (L and
D subunits) and bacterial (alpha subunit) counterparts,
are involved in the assembly of RNAP, 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 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 = 86
Score = 57.8 bits (140), Expect = 1e-10
Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 105 NCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQ------IFIRIQVKDGYD 158
N FV E E HT G+ + IL V+FA Y V HP Q +RI+
Sbjct: 9 NYVDFVLENEDHTLGNSLRRILLK-SPVEFAAYYVEHPVKLQRTDEDKFILRIETVGSIP 67
Query: 159 SIDILKKGIKEL 170
+ L++ ++ L
Sbjct: 68 PEEALRRAVEIL 79
>gnl|CDD|222311 pfam13676, TIR_2, TIR domain. This is a family of bacterial
Toll-like receptors.
Length = 102
Score = 39.9 bits (94), Expect = 4e-04
Identities = 18/92 (19%), Positives = 33/92 (35%), Gaps = 9/92 (9%)
Query: 392 YDEADFDLAKQFNTQLNKMGFTV-CDKDNSFLTGQFEHSAFIQVMDRCTCVIVLMSTHFM 450
Y AD + A+ L G V D D G+ + + V+VL+S ++
Sbjct: 5 YASADREWAEWLADALEAAGIRVWLDWD--IPPGEDWRDEIEEALRSADVVLVLLSPAYL 62
Query: 451 NNSLLHSLTQYAEAKHIDHTIHSKIIPILCSD 482
+ + A + ++IP+ D
Sbjct: 63 ASPWCRAEWGAALERGK------RLIPVRLED 88
>gnl|CDD|176728 cd08312, Death_MyD88, Death domain of Myeloid Differentation
primary response protein MyD88. Death Domain (DD) of
Myeloid Differentiation primary response protein 88
(MyD88). MyD88 is an adaptor protein involved in
interleukin-1 receptor (IL-1R)- and Toll-like receptor
(TLR)-induced activation of nuclear factor-kappaB
(NF-kB) and mitogen activated protein kinase pathways
that lead to the induction of proinflammatory cytokines.
It is a key component in the signaling pathway of
pathogen recognition in the innate immune system. MyD88
contains an N-terminal DD and a C-terminal Toll/IL-1
Receptor (TIR) homology domain that mediates interaction
with TLRs and IL-1R. In general, DDs are protein-protein
interaction domains found in a variety of domain
architectures. Their common feature is that they form
homodimers by self-association or heterodimers by
associating with other members of the DD superfamily
including CARD (Caspase activation and recruitment
domain), DED (Death Effector Domain), and PYRIN. They
serve as adaptors in signaling pathways and can recruit
other proteins into signaling complexes.
Length = 79
Score = 35.4 bits (82), Expect = 0.007
Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 17/70 (24%)
Query: 275 DYRGLADLMD--------IKAPPNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLEC 326
D+ LA+ M + P+P +K+ EDW +V N+ L LE
Sbjct: 18 DWTALAEEMGFEYLEIRNFETKPSP-----TEKVLEDWETRP-DGATVGNL---LELLEK 68
Query: 327 IDRFDVYDDC 336
++R DV +
Sbjct: 69 LERRDVLHEL 78
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 35.9 bits (83), Expect = 0.065
Identities = 17/71 (23%), Positives = 23/71 (32%), Gaps = 9/71 (12%)
Query: 553 QAIQFQTTPTSMPVAPPDYTLSQQAVAPPDYTLPQQATNSQSITNNMSEEKKDSMKKPML 612
A Q TP ++ V PP P T PQ +Q E+K K L
Sbjct: 416 SATQPAGTPPTVSVDPPA-----AVPVNPPSTAPQAVRPAQFK----EEKKIPVSKVSSL 466
Query: 613 MLTLQNGIRNT 623
+ I+
Sbjct: 467 GPSTLRPIQEK 477
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 33.9 bits (77), Expect = 0.35
Identities = 25/69 (36%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 551 QKQAIQFQTTPTSMPVAP-PDYTLSQQAVAP-PDYTLPQQATNS----QSITNNMSEEKK 604
Q A Q Q PVAP P Y QQ VAP P Y PQQ Q ++ + +
Sbjct: 783 QPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQ 842
Query: 605 DSMKKPMLM 613
D++ P+LM
Sbjct: 843 DTLLHPLLM 851
>gnl|CDD|178496 PLN02908, PLN02908, threonyl-tRNA synthetase.
Length = 686
Score = 31.7 bits (72), Expect = 1.5
Identities = 33/128 (25%), Positives = 54/128 (42%), Gaps = 31/128 (24%)
Query: 3 IEYLDSKILKKYRFQLFHSERQDNTSSTSTSIHRSKVQVQLLYMTEEQQLKPGLEQWCFC 62
I + D K+LK+Y+ ++ ++++D HR Q Q L+ E L PG C
Sbjct: 271 ISFPDKKLLKEYKHRIEEAKKRD---------HRLLGQKQELFFFHE--LSPG-----SC 314
Query: 63 FSIPTSTSSVNTSLCINYMESKQLENS-----SP------VWELRDNTLNVKPNCRTFVF 111
F +P N ++++ + E +P +WE + + K N FVF
Sbjct: 315 FFLPHGARIYNK--LMDFIREQYWERGYDEVITPNIYNMDLWETSGHAAHYKEN--MFVF 370
Query: 112 EKEGHTFG 119
E E FG
Sbjct: 371 EIEKQEFG 378
>gnl|CDD|234383 TIGR03895, protease_PatA, cyanobactin maturation protease,
PatA/PatG family. This model describes a protease
domain associated with the maturation of various members
of the cyanobactin family of ribosomally produced,
heavily modified bioactive metabolites. Members include
the PatA protein and C-terminal domain of the PatG
protein of Prochloron didemni, TenA and a region of TenG
from Nostoc spongiaeforme var. tenue, etc.
Length = 602
Score = 30.1 bits (68), Expect = 4.0
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 535 FWDRLYYSLKGVGKGSQKQAIQFQTT 560
F +R+YY L+ +G+ SQ +A+ F T
Sbjct: 498 FLNRVYYDLRNLGQTSQDRALNFAAT 523
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
0.320 0.134 0.403
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,494,513
Number of extensions: 3003655
Number of successful extensions: 2410
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2399
Number of HSP's successfully gapped: 23
Length of query: 639
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 536
Effective length of database: 6,369,140
Effective search space: 3413859040
Effective search space used: 3413859040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (27.5 bits)