RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 045556
(96 letters)
>gnl|CDD|214330 CHL00001, rpoB, RNA polymerase beta subunit.
Length = 1070
Score = 101 bits (253), Expect = 2e-26
Identities = 44/94 (46%), Positives = 57/94 (60%), Gaps = 23/94 (24%)
Query: 26 IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
+D++ NPL VP RMN+G IFEC L RH FDERY+Q+ SRKLV S+LY+A
Sbjct: 848 VDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASRKLVFSELYEA 907
Query: 73 CKQTANP----------CKTLDGQMGNPFKEHVL 96
KQTANP + DG+ G+PF++ V
Sbjct: 908 SKQTANPWVFEPEYPGKSRLFDGRTGDPFEQPVT 941
>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 = 52.2 bits (126), Expect = 2e-09
Identities = 24/85 (28%), Positives = 32/85 (37%), Gaps = 20/85 (23%)
Query: 26 IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
DII NP VP RM IG + E L + FD + + L +A
Sbjct: 255 PDIILNPHGVPSRMTIGQLLESLLGKAAALLGKFIDATPFDGA---SEDVEDIGELLKEA 311
Query: 73 CKQTANPCKTL--DGQMGNPFKEHV 95
K + DG+ G PFK +
Sbjct: 312 GYN--AYGKEVLYDGRTGEPFKAPI 334
>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 = 50.3 bits (121), Expect = 1e-08
Identities = 22/85 (25%), Positives = 30/85 (35%), Gaps = 22/85 (25%)
Query: 26 IDIIFNPLEVPPRMNIGHIFECSL---------RH----FDERYKQKGSRKLVLSKLYKA 72
DII NP P RM IG + E L FD ++ S L + L
Sbjct: 664 PDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLN-- 721
Query: 73 CKQTANPCKTL--DGQMGNPFKEHV 95
K + DG+ G P + +
Sbjct: 722 -----YYGKEVLYDGRTGEPLEAPI 741
>gnl|CDD|214397 CHL00207, rpoB, RNA polymerase beta subunit; Provisional.
Length = 1077
Score = 49.3 bits (118), Expect = 2e-08
Identities = 34/94 (36%), Positives = 43/94 (45%), Gaps = 23/94 (24%)
Query: 26 IDIIFNPLEVPPRMNIGHIFECSL-------------RHFDERYKQKGSRKLVLSKLYKA 72
DII NPL VP RMN+G +FEC L FDE Y + SR L+ +KL +A
Sbjct: 844 PDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMYGSEYSRILINNKLNQA 903
Query: 73 CKQTAN--------PCKTL--DGQMGNPFKEHVL 96
+ P K + DG+ G FK V
Sbjct: 904 SIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVT 937
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 48.2 bits (116), Expect = 5e-08
Identities = 15/24 (62%), Positives = 17/24 (70%)
Query: 26 IDIIFNPLEVPPRMNIGHIFECSL 49
+DI+ NPL VP RMNIG I E L
Sbjct: 914 VDIVLNPLGVPSRMNIGQILETHL 937
>gnl|CDD|223163 COG0085, RpoB, DNA-directed RNA polymerase, beta subunit/140 kD
subunit [Transcription].
Length = 1060
Score = 46.8 bits (112), Expect = 2e-07
Identities = 16/24 (66%), Positives = 16/24 (66%)
Query: 26 IDIIFNPLEVPPRMNIGHIFECSL 49
DII NPL VP RMNIG I E L
Sbjct: 863 PDIILNPLGVPSRMNIGQILETHL 886
>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 = 46.2 bits (110), Expect = 3e-07
Identities = 26/81 (32%), Positives = 35/81 (43%), Gaps = 11/81 (13%)
Query: 26 IDIIFNPLEVPPRMNIGHIFECSLRHFDERYKQKG-----------SRKLVLSKLYKACK 74
+DI+ NPL VP RMNIG I E L ++ +KG S + + L KA
Sbjct: 871 VDIVLNPLGVPSRMNIGQILETHLGWAGKKLGRKGVPIATPVFDGASEEEIKEYLEKAGL 930
Query: 75 QTANPCKTLDGQMGNPFKEHV 95
+ DG+ G F V
Sbjct: 931 PRDGKVRLYDGRTGEQFDNPV 951
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 39.5 bits (92), Expect = 8e-05
Identities = 16/39 (41%), Positives = 23/39 (58%)
Query: 26 IDIIFNPLEVPPRMNIGHIFECSLRHFDERYKQKGSRKL 64
+DI+ NPL VP RMNIG I E L + + ++ + L
Sbjct: 1122 VDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASML 1160
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 37.7 bits (87), Expect = 4e-04
Identities = 14/21 (66%), Positives = 16/21 (76%)
Query: 26 IDIIFNPLEVPPRMNIGHIFE 46
+DII NPL VP RMN+G I E
Sbjct: 1115 VDIILNPLGVPSRMNVGQILE 1135
>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 = 35.8 bits (83), Expect = 0.001
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 27 DIIFNPLEVPPRMNIGHIFE 46
D+I NP +P RM +G + E
Sbjct: 387 DLIINPHAIPSRMTVGQLLE 406
>gnl|CDD|235972 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 34.9 bits (81), Expect = 0.003
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 27 DIIFNPLEVPPRMNIGHIFE 46
D+I NP +P RM +GH+ E
Sbjct: 393 DLIINPHAIPSRMTVGHVLE 412
>gnl|CDD|236291 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 33.8 bits (78), Expect = 0.006
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 27 DIIFNPLEVPPRMNIGHIFE 46
D+I NP +P RM +G + E
Sbjct: 891 DLIINPHAIPSRMTVGQLLE 910
>gnl|CDD|233775 TIGR02197, heptose_epim,
ADP-L-glycero-D-manno-heptose-6-epimerase. This family
consists of examples of
ADP-L-glycero-D-mannoheptose-6-epimerase, an enzyme
involved in biosynthesis of the inner core of
lipopolysaccharide (LPS) for Gram-negative bacteria.
This enzyme is homologous to UDP-glucose 4-epimerase
(TIGR01179) and belongs to the NAD dependent
epimerase/dehydratase family (pfam01370) [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 314
Score = 29.9 bits (68), Expect = 0.15
Identities = 9/28 (32%), Positives = 11/28 (39%)
Query: 3 LEIAHFEDVELLWPFFTHHRFSNIDIIF 30
L IA + D E F I+ IF
Sbjct: 44 LVIADYIDKEDFLDRLEKGAFGKIEAIF 71
>gnl|CDD|221823 pfam12873, DUF3825, Domain of unknown function (DUF3825).
Potential uncharacterized enzymatic domain associated
with bacterial pfam12872 domains. Has conserved residues
suggestive of an enzymatic role probably related to RNA
metabolism.
Length = 239
Score = 29.2 bits (66), Expect = 0.22
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 27 DIIFNPLEVPPRMNIGHIFECSLR--HFDERYKQKGSRKLVL 66
D+IF+P R+N+ HIFE S + ++ +
Sbjct: 116 DLIFDPDL-DLRLNVDHIFEISENRERLPAKLRELSDSFIRA 156
>gnl|CDD|165277 PHA02973, PHA02973, hypothetical protein; Provisional.
Length = 102
Score = 28.7 bits (64), Expect = 0.24
Identities = 21/56 (37%), Positives = 28/56 (50%)
Query: 1 MLLEIAHFEDVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLRHFDERY 56
ML I F LL FF R + +DI NP++ P + HIF SL H ++Y
Sbjct: 1 MLFLIFFFILFLLLCYFFNFKRTNKMDIGINPIKKIPWSDNDHIFVSSLFHNKDKY 56
>gnl|CDD|213224 cd03257, ABC_NikE_OppD_transporters, ATP-binding cassette domain of
nickel/oligopeptides specific transporters. The ABC
transporter subfamily specific for the transport of
dipeptides, oligopeptides (OppD), and nickel (NikDE).
The NikABCDE system of E. coli belongs to this family
and is composed of the periplasmic binding protein NikA,
two integral membrane components (NikB and NikC), and
two ATPase (NikD and NikE). The NikABCDE transporter is
synthesized under anaerobic conditions to meet the
increased demand for nickel resulting from hydrogenase
synthesis. The molecular mechanism of nickel uptake in
many bacteria and most archaea is not known. Many other
members of this ABC family are also involved in the
uptake of dipeptides and oligopeptides. The oligopeptide
transport system (Opp) is a five-component ABC transport
composed of a membrane-anchored substrate binding
proteins (SRP), OppA, two transmembrane proteins, OppB
and OppC, and two ATP-binding domains, OppD and OppF.
Length = 228
Score = 26.7 bits (60), Expect = 2.0
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 22 RFSNIDIIF-NPLE-VPPRMNIGHIFECSLR-HFDERYKQKGSRKLVL 66
R I ++F +P+ + PRM IG LR H K+ ++L
Sbjct: 80 RRKEIQMVFQDPMSSLNPRMTIGEQIAEPLRIHGKLSKKEARKEAVLL 127
>gnl|CDD|132595 TIGR03556, photolyase_8HDF, deoxyribodipyrimidine photo-lyase,
8-HDF type. This model describes a narrow clade of
cyanobacterial deoxyribodipyrimidine photo-lyase. This
group, in contrast to several closely related proteins,
uses a chromophore that, in other lineages is modified
further to become coenzyme F420. This chromophore is
called 8-HDF in most articles on the DNA photolyase and
FO in most literature on coenzyme F420 [DNA metabolism,
DNA replication, recombination, and repair].
Length = 471
Score = 26.0 bits (57), Expect = 3.7
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 48 SLRHFDERYKQKGSRKLVLS 67
L+ +RY+Q GS+ L+L
Sbjct: 56 CLQELQQRYQQAGSQLLILQ 75
>gnl|CDD|218019 pfam04307, DUF457, Predicted membrane-bound metal-dependent
hydrolase (DUF457). Family of predicted membrane-bound
metal-dependent hydrolases, based on CA_C0507. May act
as phospholipases.
Length = 157
Score = 25.4 bits (56), Expect = 4.2
Identities = 10/31 (32%), Positives = 13/31 (41%)
Query: 11 VELLWPFFTHHRFSNIDIIFNPLEVPPRMNI 41
V LLWPF + I +PL P +
Sbjct: 110 VPLLWPFSDKRFALPLIFIIDPLFTLPLLAG 140
>gnl|CDD|100814 PRK01207, PRK01207, methionine synthase; Provisional.
Length = 343
Score = 25.3 bits (55), Expect = 5.6
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 37 PRMNI-GHIFECSLRHFDERYKQKGS 61
P I G IF +R FD RY +KGS
Sbjct: 69 PAERIKGIIFYGMVRSFDNRYYRKGS 94
>gnl|CDD|178130 PLN02515, PLN02515, naringenin,2-oxoglutarate 3-dioxygenase.
Length = 358
Score = 25.3 bits (55), Expect = 5.8
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 52 FDERYKQKGSRKLVLSKLYKACKQ 75
F E Y++K SR L L++L K K+
Sbjct: 319 FAEMYRRKMSRDLELARLKKLAKE 342
>gnl|CDD|182651 PRK10692, PRK10692, hypothetical protein; Provisional.
Length = 92
Score = 24.6 bits (54), Expect = 5.9
Identities = 5/15 (33%), Positives = 12/15 (80%)
Query: 49 LRHFDERYKQKGSRK 63
+RH+D+R ++ +R+
Sbjct: 76 VRHYDKRCRRSDNRR 90
>gnl|CDD|206621 pfam14455, Metal_CEHH, Predicted metal binding domain. A predicted
metal-binding domain that is found in gene-neighborhood
associations with genes encoding components of the
bacterial homologs of the ubiquitin modification pathway
including the E1, E2, JAB metallopeptidase and ubiquitin
proteins. The domain is characterized by a conserved
motif with a CxxxxxEYHxxxxH signature.
Length = 177
Score = 24.9 bits (54), Expect = 6.3
Identities = 16/80 (20%), Positives = 26/80 (32%), Gaps = 6/80 (7%)
Query: 17 FFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLRHFDER-----YKQKGSRKLVLSKLYK 71
F F +IF +V PR+ IG ++D R + +R+ V K
Sbjct: 30 FLIEANFPTAFVIFAHPKVAPRI-IGAAVRLDFTNYDLRPPSVVFVDPFTRRPVARKDLL 88
Query: 72 ACKQTANPCKTLDGQMGNPF 91
P +M +
Sbjct: 89 LSMLRRPPLPGAPPEMISVL 108
>gnl|CDD|107367 cd06372, PBP1_GC_G_like, Ligand-binding domain of membrane guanylyl
cyclase G. This group includes the ligand-binding
domain of membrane guanylyl cyclase G (GC-G) which is a
sperm surface receptor and might function, similar to
its sea urchin counterpart, in the early signaling event
that regulates the Ca2+ influx/efflux and subsequent
motility response in sperm. GC-G appears to be a
pseudogene in human. Furthermore, in contrast to the
other orphan receptor GCs, GC-G has a broad tissue
distribution in rat, including lung, intestine, kidney,
and skeletal muscle.
Length = 391
Score = 25.2 bits (55), Expect = 6.8
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 35 VPPRMNIGHIFECSLRHF 52
VPP+ IG + + SL+HF
Sbjct: 118 VPPKQKIGEVLQKSLQHF 135
>gnl|CDD|185037 PRK15079, PRK15079, oligopeptide ABC transporter ATP-binding
protein OppF; Provisional.
Length = 331
Score = 25.1 bits (55), Expect = 7.2
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 24 SNIDIIF-NPL-EVPPRMNIGHIFECSLRHF 52
S+I +IF +PL + PRM IG I LR +
Sbjct: 98 SDIQMIFQDPLASLNPRMTIGEIIAEPLRTY 128
>gnl|CDD|193591 cd09977, LOTUS_1_Limkain_b1, The first LOTUS domain on Limkain
b1(LKAP). The first LOTUS domain on Limkain b1(LKAP):
Limkain b1 is a novel human autoantigen, localized to
a subset of ABCD3 and PXF marked peroxisomes. Limkain
b1 may be a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. The protein contains multiple copies of
LOTUS domains and a conserved RNA recognition motif.
The exact molecular function of LOTUS domain remains to
be identified. Its occurrence in proteins associated
with RNA metabolism suggests that it might be involved
in RNA binding function. The presence of several basic
residues and RNA fold recognition motifs support this
hypothesis. The RNA binding function might be the first
step of regulating mRNA translation or localization.
Length = 62
Score = 24.1 bits (52), Expect = 7.4
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 49 LRHFDERYKQKGSRKLVLSKLYK 71
L F E Y++K KL +S LY+
Sbjct: 22 LFKFTEIYEKKFGHKLAVSDLYR 44
>gnl|CDD|218709 pfam05707, Zot, Zonular occludens toxin (Zot). This family
consists of bacterial and viral proteins which are very
similar to the Zonular occludens toxin (Zot). Zot is
elaborated by bacteriophages present in toxigenic
strains of Vibrio cholerae. Zot is a single polypeptide
chain of 44.8 kDa, with the ability to reversibly alter
intestinal epithelial tight junctions, allowing the
passage of macromolecules through mucosal barriers.
Length = 183
Score = 24.6 bits (54), Expect = 8.0
Identities = 6/14 (42%), Positives = 7/14 (50%)
Query: 17 FFTHHRFSNIDIIF 30
F+ HR DII
Sbjct: 98 AFSTHRHLGWDIIL 111
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
0.327 0.142 0.457
Gapped
Lambda K H
0.267 0.0570 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,942,480
Number of extensions: 397877
Number of successful extensions: 392
Number of sequences better than 10.0: 1
Number of HSP's gapped: 391
Number of HSP's successfully gapped: 27
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.5 bits)