RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8689
(72 letters)
>gnl|CDD|224510 COG1594, RPB9, DNA-directed RNA polymerase, subunit M/Transcription
elongation factor TFIIS [Transcription].
Length = 113
Score = 68.3 bits (167), Expect = 6e-17
Identities = 29/47 (61%), Positives = 36/47 (76%), Gaps = 2/47 (4%)
Query: 26 VDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
+ T +EKCPKC + AY+ Q+QTRSADEP T FYKC +CG+RWRE
Sbjct: 68 LPTAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKCT--RCGYRWRE 112
>gnl|CDD|201594 pfam01096, TFIIS_C, Transcription factor S-II (TFIIS).
Length = 39
Score = 66.1 bits (162), Expect = 8e-17
Identities = 27/40 (67%), Positives = 28/40 (70%), Gaps = 2/40 (5%)
Query: 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
KCPKC H A F Q+QTRSADEPMT FY C CG RWR
Sbjct: 2 KCPKCGHREAVFFQLQTRSADEPMTLFYVCTK--CGHRWR 39
>gnl|CDD|128717 smart00440, ZnF_C2C2, C2C2 Zinc finger. Nucleic-acid-binding
motif in transcriptional elongation factor TFIIS and
RNA polymerases.
Length = 40
Score = 60.4 bits (147), Expect = 1e-14
Identities = 26/41 (63%), Positives = 29/41 (70%), Gaps = 2/41 (4%)
Query: 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
+CPKC + A F Q+QTRSADEPMT FY C KCG WRE
Sbjct: 2 ECPKCGNREATFYQLQTRSADEPMTVFYVC--TKCGHHWRE 40
>gnl|CDD|130451 TIGR01384, TFS_arch, transcription factor S, archaeal. This model
describes archaeal transcription factor S, a protein
related in size and sequence to certain eukaryotic RNA
polymerase small subunits, and in sequence and function
to the much larger eukaryotic transcription factor IIS
(TFIIS). Although originally suggested to be a subunit
of the archaeal RNA polymerase, it elutes separately
from active polymerase in gel filtration experiments and
acts, like TFIIs, as an induction factor for RNA
cleavage by RNA polymerase. There has been an apparent
duplication event in the Halobacteriaceae lineage
(Haloarcula, Haloferax, Haloquadratum, Halobacterium and
Natromonas). There appears to be a separate duplication
in Methanosphaera stadtmanae [Transcription,
Transcription factors].
Length = 104
Score = 55.2 bits (133), Expect = 8e-12
Identities = 28/49 (57%), Positives = 33/49 (67%), Gaps = 2/49 (4%)
Query: 24 ENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
E + TT +CPKC H AY+ +QTR ADEP T FYKC KCG+ WRE
Sbjct: 56 ETLPTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKC--TKCGYVWRE 102
>gnl|CDD|233390 TIGR01385, TFSII, transcription elongation factor S-II. This model
represents eukaryotic transcription elongation factor
S-II. This protein allows stalled RNA transcription
complexes to perform a cleavage of the nascent RNA and
restart at the newly generated 3-prime end.
Length = 299
Score = 53.3 bits (128), Expect = 4e-10
Identities = 25/67 (37%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 5 RLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI 64
R +I + + G + T C KC+ + + Q+QTRSADEPMTTF C
Sbjct: 235 REEITKENLFEAQGAKI--QKAVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEE- 291
Query: 65 KCGFRWR 71
CG RW+
Sbjct: 292 -CGNRWK 297
>gnl|CDD|222958 PHA02998, PHA02998, RNA polymerase subunit; Provisional.
Length = 195
Score = 36.3 bits (84), Expect = 4e-04
Identities = 15/38 (39%), Positives = 20/38 (52%)
Query: 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69
CP C+ M IQTR+ADEP + C + K F+
Sbjct: 145 PCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK 182
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 27.5 bits (62), Expect = 0.51
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 14/53 (26%)
Query: 2 RCGRLKIKPKEIDHVMG--------GAAAWENVD------TTEEKCPKCEHPR 40
CGRLK+ +EI+ + G+ A + + CP C +
Sbjct: 103 ECGRLKLTEEEIEEYLEKLERLKEWGSLADDLIKEVKKEAAKRMVCPHCGEKQ 155
>gnl|CDD|132431 TIGR03390, ascorbOXfungal, L-ascorbate oxidase, fungal type. This
model describes a family of fungal ascorbate oxidases,
within a larger family of multicopper oxidases that also
includes plant ascorbate oxidases (TIGR03388), plant
laccases and laccase-like proteins (TIGR03389), and
related proteins. The member from Acremonium sp. HI-25
is characterized.
Length = 538
Score = 27.1 bits (60), Expect = 0.70
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 2/52 (3%)
Query: 9 KPKEIDHVMGGAAAWENV--DTTEEKCPKCEHPRAYFMQIQTRSADEPMTTF 58
KP +IDH+ G +V E R YF+Q +TR + +
Sbjct: 242 KPAKIDHLQLGGGQRYSVLFKAKTEDELCGGDKRQYFIQFETRDRPKVYRGY 293
>gnl|CDD|222907 PHA02611, 51, baseplate hub assembly protein; Provisional.
Length = 249
Score = 27.0 bits (60), Expect = 0.75
Identities = 9/42 (21%), Positives = 17/42 (40%), Gaps = 5/42 (11%)
Query: 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYK-CCNIKCGFRWRE 72
CPKC+ + ++ E + N+K F++ E
Sbjct: 84 TCPKCKKEKTVLFNLK----QEELKNPVLEVANLKLKFKFPE 121
>gnl|CDD|238528 cd01095, Nitrilotriacetate_monoxgenase, nitrilotriacetate
monoxygenase oxidizes nitrilotriacetate utilizing
reduced flavin mononucleotide (FMNH2) and oxygen. The
FMNH2 is provided by an NADH:flavin mononucleotide (FMN)
oxidorductase that uses NADH to reduce FMN to FMNH2.
Length = 358
Score = 26.9 bits (60), Expect = 0.75
Identities = 9/17 (52%), Positives = 12/17 (70%), Gaps = 1/17 (5%)
Query: 13 IDHVMGGAAAWENVDTT 29
+DH+ GG A W NV T+
Sbjct: 106 LDHISGGRAGW-NVVTS 121
>gnl|CDD|152228 pfam11792, Baculo_LEF5_C, Baculoviridae late expression factor 5
C-terminal domain. This C-terminal domain is likely to
be a zinc-binding domain.
Length = 43
Score = 25.3 bits (56), Expect = 0.93
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 36 CEHPRAYFMQIQTRSADEPMTTFYKCCNIKCG 67
C+H ++ Q R+ DE +F K C +KCG
Sbjct: 13 CKH-EFVTVEKQLRAGDE-AVSFIKYC-VKCG 41
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 26.4 bits (59), Expect = 1.4
Identities = 10/16 (62%), Positives = 10/16 (62%)
Query: 27 DTTEEKCPKCEHPRAY 42
D T KCP CE P AY
Sbjct: 53 DATIRKCPDCEEPEAY 68
>gnl|CDD|179529 PRK03057, PRK03057, hypothetical protein; Provisional.
Length = 180
Score = 25.6 bits (56), Expect = 1.9
Identities = 15/36 (41%), Positives = 17/36 (47%), Gaps = 5/36 (13%)
Query: 24 ENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFY 59
ENV TE E RA + I T +DEP FY
Sbjct: 39 ENVHFTET-----EQKRARTLIISTAQSDEPGFVFY 69
>gnl|CDD|184161 PRK13580, PRK13580, serine hydroxymethyltransferase; Provisional.
Length = 493
Score = 25.8 bits (57), Expect = 2.0
Identities = 9/23 (39%), Positives = 12/23 (52%), Gaps = 2/23 (8%)
Query: 21 AAWENVDTTEEKCPKCEHPRAYF 43
A +NVDT E + EH + F
Sbjct: 88 AGCQNVDTVEWEA--AEHAKELF 108
>gnl|CDD|235516 PRK05582, PRK05582, DNA topoisomerase I; Validated.
Length = 650
Score = 25.5 bits (57), Expect = 2.6
Identities = 12/41 (29%), Positives = 12/41 (29%), Gaps = 9/41 (21%)
Query: 29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI-KCGF 68
E CPKC P M R F C N C
Sbjct: 570 AGEDCPKCGSPMVIKM---GRYGK-----FIACSNFPDCRN 602
>gnl|CDD|224508 COG1592, COG1592, Rubrerythrin [Energy production and conversion].
Length = 166
Score = 25.0 bits (55), Expect = 3.0
Identities = 6/17 (35%), Positives = 7/17 (41%)
Query: 27 DTTEEKCPKCEHPRAYF 43
E CP C P+ F
Sbjct: 146 GEAPEVCPICGAPKEKF 162
>gnl|CDD|203053 pfam04606, Ogr_Delta, Ogr/Delta-like zinc finger. This is a
viral family of phage zinc-binding transcriptional
activators, which also contains cryptic members in some
bacterial genomes. The P4 phage delta protein contains
two such domains attached covalently, while the P2
phage Ogr proteins possess one domain but function as
dimers. All the members of this family have the
following consensus sequence:
C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F. This
family also includes zinc fingers in recombinase
proteins.
Length = 47
Score = 24.2 bits (53), Expect = 3.1
Identities = 10/42 (23%), Positives = 18/42 (42%), Gaps = 6/42 (14%)
Query: 32 KCPKCEHPRAYFMQIQTRSADEPMTT--FYKCCNIKCGFRWR 71
+CP C +I+T + +Y+C N +CG +
Sbjct: 1 RCPHCGAK----ARIRTSRRLSALVRELYYQCTNPECGHTFV 38
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 25.0 bits (55), Expect = 3.7
Identities = 7/12 (58%), Positives = 7/12 (58%)
Query: 32 KCPKCEHPRAYF 43
KCPKC P Y
Sbjct: 83 KCPKCPRPTCYQ 94
>gnl|CDD|236831 PRK11052, malQ, 4-alpha-glucanotransferase; Provisional.
Length = 695
Score = 24.8 bits (55), Expect = 4.3
Identities = 9/19 (47%), Positives = 11/19 (57%), Gaps = 6/19 (31%)
Query: 1 MR-CGRLKIKPKEIDHVMG 18
M+ CG L+I DHVM
Sbjct: 441 MQHCGALRI-----DHVMS 454
>gnl|CDD|173680 cd05589, STKc_PKN, Catalytic domain of the Protein Serine/Threonine
Kinase, Protein Kinase N. Serine/Threonine Kinases
(STKs), Protein Kinase N (PKN) subfamily, catalytic (c)
domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The PKN subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. PKN has a
C-terminal catalytic domain that is highly homologous to
PKCs. Its unique N-terminal regulatory region contains
antiparallel coiled-coil (ACC) domains. In mammals,
there are three PKN isoforms from different genes
(designated PKN-alpha, beta, and gamma), which show
different enzymatic properties, tissue distribution, and
varied functions. PKN can be activated by the small
GTPase Rho, and by fatty acids such as arachidonic and
linoleic acids. It is involved in many biological
processes including cytokeletal regulation, cell
adhesion, vesicle transport, glucose transport,
regulation of meiotic maturation and embryonic cell
cycles, signaling to the nucleus, and tumorigenesis.
Length = 324
Score = 24.6 bits (54), Expect = 4.9
Identities = 8/19 (42%), Positives = 8/19 (42%)
Query: 44 MQIQTRSADEPMTTFYKCC 62
M I T EP FY C
Sbjct: 91 MHIHTDVFSEPRAVFYAAC 109
>gnl|CDD|238371 cd00729, rubredoxin_SM, Rubredoxin, Small Modular nonheme iron
binding domain containing a [Fe(SCys)4] center, present
in rubrerythrin and nigerythrin and detected either N-
or C-terminal to such proteins as flavin reductase,
NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin
reductase. In rubredoxin, the iron atom is coordinated
by four cysteine residues (Fe(S-Cys)4), and believed
to be involved in electron transfer. Rubrerythrins and
nigerythrins are small homodimeric proteins, generally
consisting of 2 domains: a rubredoxin domain C-terminal
to a non-sulfur, oxo-bridged diiron site in the
N-terminal rubrerythrin domain. Rubrerythrins and
nigerythrins have putative peroxide activity.
Length = 34
Score = 22.9 bits (50), Expect = 5.4
Identities = 7/13 (53%), Positives = 8/13 (61%)
Query: 31 EKCPKCEHPRAYF 43
EKCP C P+ F
Sbjct: 19 EKCPICGAPKEKF 31
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'.
This family consists of the archaeal A' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein.
Length = 867
Score = 24.7 bits (54), Expect = 5.8
Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 15/54 (27%)
Query: 3 CGRLKIKPKEIDHVM---------GGAAAWENVD------TTEEKCPKCEHPRA 41
CGR+ + +EI+ + GG A ++ KCP C +
Sbjct: 99 CGRITLTEEEIEQYLEKINKLKEEGGDLASTLIEKIVKEAAKRMKCPHCGEEQK 152
>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 24.6 bits (54), Expect = 6.0
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 9/46 (19%)
Query: 25 NVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCC-NIKCGFR 69
+ T+EKCP+C P ++ + CC N KC +
Sbjct: 728 KITVTDEKCPECGLP-----LLRVKGGFGD---ELGCCNNPKCNYT 765
>gnl|CDD|137468 PRK09678, PRK09678, DNA-binding transcriptional regulator;
Provisional.
Length = 72
Score = 23.4 bits (50), Expect = 9.8
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 2/35 (5%)
Query: 33 CPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCG 67
CP C+H A + D +++C N+ C
Sbjct: 4 CPLCQH--AAHARTSRYITDTTKERYHQCQNVNCS 36
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
0.324 0.136 0.473
Gapped
Lambda K H
0.267 0.0658 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,477,117
Number of extensions: 228780
Number of successful extensions: 336
Number of sequences better than 10.0: 1
Number of HSP's gapped: 332
Number of HSP's successfully gapped: 29
Length of query: 72
Length of database: 10,937,602
Length adjustment: 42
Effective length of query: 30
Effective length of database: 9,074,734
Effective search space: 272242020
Effective search space used: 272242020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.3 bits)