RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7584
(67 letters)
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 91.9 bits (229), Expect = 7e-24
Identities = 32/57 (56%), Positives = 43/57 (75%)
Query: 10 FSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
+RD S +R+ E GIVD V++T + +G K K+RVR +RIP++GDKFASRHGQKG
Sbjct: 814 QERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRDLRIPELGDKFASRHGQKG 870
>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 = 91.5 bits (228), Expect = 9e-24
Identities = 32/64 (50%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 7 TKRFSKRDGSTFLRNSETGIVDQVMLT---LNVDGYKFCKIRVRSVRIPQIGDKFASRHG 63
K RD S E GIVD V + LN G K K+ +R R PQIGDKFASRHG
Sbjct: 582 EKARDVRDTSLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHG 641
Query: 64 QKGT 67
QKG
Sbjct: 642 QKGV 645
>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 = 89.7 bits (223), Expect = 4e-23
Identities = 32/55 (58%), Positives = 43/55 (78%)
Query: 12 KRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
+RD S +R+ E GIVD+V++T +G K K+RVR +RIP++GDKFASRHGQKG
Sbjct: 312 RRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKG 366
>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 = 86.4 bits (215), Expect = 4e-22
Identities = 29/61 (47%), Positives = 37/61 (60%)
Query: 7 TKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
K +D S +++ E G VD V + LN G K K+ +R R PQ+GDKFASRHGQKG
Sbjct: 176 EKARDVKDTSLKVKHGEEGRVDDVKIDLNPGGIKKVKVYIRQKRKPQVGDKFASRHGQKG 235
Query: 67 T 67
Sbjct: 236 V 236
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 86.2 bits (214), Expect = 8e-22
Identities = 31/55 (56%), Positives = 42/55 (76%)
Query: 12 KRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRHGQKG 66
+R+ S +R+ E GIVD V+LT +G + K+RVR +RIP++GDKFASRHGQKG
Sbjct: 318 RRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKG 372
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 79.5 bits (197), Expect = 2e-19
Identities = 27/61 (44%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 11 SKRDGSTFLRNSETGIVDQVMLTLNVDG----YKFCKIRVRSVRIPQIGDKFASRHGQKG 66
RD S + + E GIVD V + DG K K+ V R PQIGDK A RHG KG
Sbjct: 784 KVRDTSLRVPHGEEGIVDDVQVFTREDGDPGVNKLVKVYVAQKRKPQIGDKMAGRHGNKG 843
Query: 67 T 67
Sbjct: 844 V 844
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 34.7 bits (80), Expect = 0.001
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 13 RDGSTFLRNSETG-IVDQVMLTLNV-DGYKF-----CKIRVRSVRIPQIGDKFASRHGQK 65
+D S + N G ++ + + + D KF ++ + +R Q+GDK A RHG K
Sbjct: 764 KDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNK 823
Query: 66 GT 67
G
Sbjct: 824 GI 825
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 30.7 bits (69), Expect = 0.029
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 40 KFCKIRVRSVRIPQIGDKFASRHGQKG 66
K K+ + + R ++GDK A RHG KG
Sbjct: 1076 KKVKLYIATKRKLKVGDKMAGRHGNKG 1102
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 30.3 bits (69), Expect = 0.041
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 53 QIGDKFASRHGQKG 66
Q+GDK A RHG KG
Sbjct: 815 QVGDKVAGRHGNKG 828
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 30.1 bits (69), Expect = 0.045
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 53 QIGDKFASRHGQKG 66
Q+GDK A RHG KG
Sbjct: 881 QVGDKMAGRHGNKG 894
>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 = 29.3 bits (66), Expect = 0.11
Identities = 20/61 (32%), Positives = 26/61 (42%), Gaps = 7/61 (11%)
Query: 13 RDGSTFLRNSETGIVDQVMLTLNVDG-------YKFCKIRVRSVRIPQIGDKFASRHGQK 65
RD S + G V V + +G K K+ + R Q+GDK A RHG K
Sbjct: 791 RDTSLRVPPGVEGTVIDVKVFSRKEGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNK 850
Query: 66 G 66
G
Sbjct: 851 G 851
>gnl|CDD|205675 pfam13497, DUF4121, Domain of unknown function (DUF4121). Based
on Bacteroides thetaiotaomicron gene BT_2588, a
putative uncharacterized protein. As seen in gene
expression experiments
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2
231), it appears to be upregulated in the presence of
host or vs when in culture.
Length = 262
Score = 26.6 bits (59), Expect = 0.76
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 45 RVRSVRIPQIGDK--FASRHG 63
+ RS PQ GD+ + SRHG
Sbjct: 41 QTRSEVTPQAGDRLEYVSRHG 61
>gnl|CDD|236235 PRK08314, PRK08314, long-chain-fatty-acid--CoA ligase; Validated.
Length = 546
Score = 25.7 bits (57), Expect = 2.0
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 9/46 (19%)
Query: 4 EGTTKRFSKRDGSTFLRNSETG---------IVDQVMLTLNVDGYK 40
E T + F + DG F R + G I D++ +N G+K
Sbjct: 403 EATAEAFIEIDGKRFFRTGDLGRMDEEGYFFITDRLKRMINASGFK 448
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 25.7 bits (56), Expect = 2.2
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 53 QIGDKFASRHGQKG 66
Q GDK A RHG KG
Sbjct: 1082 QPGDKMAGRHGNKG 1095
>gnl|CDD|147863 pfam05941, Chordopox_A20R, Chordopoxvirus A20R protein. This
family consists of several Chordopoxvirus A20R proteins.
The A20R protein is required for DNA replication, is
associated with the processive form of the viral DNA
polymerase, and directly interacts with the viral
proteins encoded by the D4R, D5R, and H5R open reading
frames. A20R may contribute to the assembly or stability
of the multiprotein DNA replication complex.
Length = 334
Score = 25.3 bits (56), Expect = 2.2
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 36 VDGYKFCKIRVRSVRIPQIGD 56
+D +K + V+S+ + +IGD
Sbjct: 212 IDFFKRGYVCVKSIELEKIGD 232
>gnl|CDD|235564 PRK05691, PRK05691, peptide synthase; Validated.
Length = 4334
Score = 25.5 bits (56), Expect = 2.2
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 4 EGTTKRFSKRDGSTFLRNSETG 25
E + K F + DG T+LR + G
Sbjct: 416 EASAKTFVEHDGRTWLRTGDLG 437
>gnl|CDD|223087 COG0008, GlnS, Glutamyl- and glutaminyl-tRNA synthetases
[Translation, ribosomal structure and biogenesis].
Length = 472
Score = 25.0 bits (55), Expect = 3.2
Identities = 7/31 (22%), Positives = 12/31 (38%), Gaps = 1/31 (3%)
Query: 5 GTTKRFSKRDGSTFLRNS-ETGIVDQVMLTL 34
K+ SKR G+ + G + + L
Sbjct: 246 EDGKKLSKRKGAVSIGEYRVEGWLPPALPNL 276
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 0.137 0.398
Gapped
Lambda K H
0.267 0.0670 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,212,344
Number of extensions: 223184
Number of successful extensions: 171
Number of sequences better than 10.0: 1
Number of HSP's gapped: 169
Number of HSP's successfully gapped: 17
Length of query: 67
Length of database: 10,937,602
Length adjustment: 38
Effective length of query: 29
Effective length of database: 9,252,150
Effective search space: 268312350
Effective search space used: 268312350
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: 53 (24.3 bits)