RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4748
(136 letters)
>gnl|CDD|224510 COG1594, RPB9, DNA-directed RNA polymerase, subunit M/Transcription
elongation factor TFIIS [Transcription].
Length = 113
Score = 59.8 bits (145), Expect = 1e-12
Identities = 31/135 (22%), Positives = 49/135 (36%), Gaps = 41/135 (30%)
Query: 12 EFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFE 71
FC KCG++L + VC+ +E
Sbjct: 3 RFCPKCGSLL-YPKKDDEGGKLVCRKCG------------------------------YE 31
Query: 72 EIKAEYTIHFNTVEKEKQKDKTEIADG----------PIVERKCKRCNNDTMSYATLQLR 121
E + ++ +V++ +K K + P + KC +C N Y LQ R
Sbjct: 32 EEASNKKVYRYSVKEAVEKKKEVVLVVEDETQGAKTLPTAKEKCPKCGNKEAYYWQLQTR 91
Query: 122 SADEGQTIFFTCTKC 136
SADE +T F+ CT+C
Sbjct: 92 SADEPETRFYKCTRC 106
>gnl|CDD|201594 pfam01096, TFIIS_C, Transcription factor S-II (TFIIS).
Length = 39
Score = 54.1 bits (131), Expect = 3e-11
Identities = 16/33 (48%), Positives = 21/33 (63%)
Query: 104 KCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136
KC +C + + LQ RSADE T+F+ CTKC
Sbjct: 2 KCPKCGHREAVFFQLQTRSADEPMTLFYVCTKC 34
>gnl|CDD|128717 smart00440, ZnF_C2C2, C2C2 Zinc finger. Nucleic-acid-binding motif
in transcriptional elongation factor TFIIS and RNA
polymerases.
Length = 40
Score = 48.1 bits (115), Expect = 8e-09
Identities = 16/34 (47%), Positives = 22/34 (64%)
Query: 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136
+C +C N ++ LQ RSADE T+F+ CTKC
Sbjct: 1 AECPKCGNREATFYQLQTRSADEPMTVFYVCTKC 34
>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 = 42.9 bits (101), Expect = 3e-06
Identities = 31/130 (23%), Positives = 43/130 (33%), Gaps = 39/130 (30%)
Query: 12 EFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFE 71
+FC KCG+++ G C C +
Sbjct: 1 KFCPKCGSLM--TPKNGVYVCPSCGYE--------------------------------K 26
Query: 72 EIKAEYTIHFNTVEKEKQKDKTEIADG-----PIVERKCKRCNNDTMSYATLQLRSADEG 126
E K E K K K+ I + P +C +C + Y LQ R ADE
Sbjct: 27 EKKPEDDYKVTEKVKHKIKETIIIREEDSETLPTTRVECPKCGHKEAYYWLLQTRRADEP 86
Query: 127 QTIFFTCTKC 136
+T F+ CTKC
Sbjct: 87 ETRFYKCTKC 96
>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 = 40.2 bits (94), Expect = 1e-04
Identities = 15/33 (45%), Positives = 18/33 (54%)
Query: 104 KCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136
C +C +Y LQ RSADE T F TC +C
Sbjct: 260 TCGKCKQKKCTYYQLQTRSADEPMTTFVTCEEC 292
>gnl|CDD|224559 COG1645, COG1645, Uncharacterized Zn-finger containing protein
[General function prediction only].
Length = 131
Score = 29.0 bits (65), Expect = 0.50
Identities = 13/25 (52%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 11 SEFCSKCGTILPLFDFKGDVKCYVC 35
++ C KCGT PLF G+V C VC
Sbjct: 28 AKHCPKCGT--PLFRKDGEVFCPVC 50
>gnl|CDD|218296 pfam04860, Phage_portal, Phage portal protein. Bacteriophage
portal proteins form a dodecamer and is located at a
five-fold vertex of the viral capsid. The portal complex
forms a channel through which the viral DNA is packaged
into the capsid, and exits during infection. The portal
protein is though to rotate during DNA packaging. Portal
proteins from different phage show little sequence
homology, so this family does not represent all portal
proteins.
Length = 348
Score = 29.2 bits (66), Expect = 0.55
Identities = 19/54 (35%), Positives = 22/54 (40%), Gaps = 8/54 (14%)
Query: 36 KTSYGTQEQQPLL-----LGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTV 84
K +Y EQQ L L P LKR + N L EE +A Y FN
Sbjct: 265 KATYSNIEQQNLAFVTNTLLP---LLKRIEQELNRKLLTPEERRAGYYFEFNVE 315
>gnl|CDD|219003 pfam06381, DUF1073, Protein of unknown function (DUF1073). This
family consists of several hypothetical bacterial
proteins. The function of this family is unknown.
Length = 361
Score = 27.3 bits (61), Expect = 2.4
Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 8/57 (14%)
Query: 40 GTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTVEKEKQKDKTEIA 96
G QE + L P + L L L+ + + FN + + +K+K EI
Sbjct: 300 GIQENE---LRPLLERLIEL-----LVLSELGSRPPDISYEFNPLWQLSEKEKAEIF 348
>gnl|CDD|238912 cd01937, ribokinase_group_D, Ribokinase-like subgroup D. Found in
bacteria and archaea, this subgroup is part of the
ribokinase/pfkB superfamily. Its oligomerization state
is unknown at this time.
Length = 254
Score = 26.6 bits (59), Expect = 3.9
Identities = 10/39 (25%), Positives = 15/39 (38%), Gaps = 2/39 (5%)
Query: 69 VFEEIKAEYT-IHFNTVEKEKQKDKTEIADGPIVERKCK 106
+ I + + + VE E TE+A I E K
Sbjct: 148 IKCVILKLHDVLKLSRVEAEVISTPTELARL-IKETGVK 185
>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'. All proteins in this
family for which functions are known are components of
the primosome which is involved in replication, repair,
and recombination.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 505
Score = 27.0 bits (60), Expect = 3.9
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 4/34 (11%)
Query: 42 QEQQPLLLGPDILF----LKRFKGHFNLFLAVFE 71
+ L+L P+I ++RFK F +AV
Sbjct: 24 LGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLH 57
>gnl|CDD|117706 pfam09151, DUF1936, Domain of unknown function (DUF1936). This
domain is found in a set of hypothetical Archaeal
proteins. Its exact function has not, as yet, been
defined. It possesses a zinc ribbon fold.
Length = 36
Score = 24.2 bits (52), Expect = 6.0
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 13 FCSKCGT--ILPLFDFKGDVKCYVC 35
C KCG + P++D KG++K + C
Sbjct: 3 LCPKCGVGVLEPVYDEKGEIKVFRC 27
>gnl|CDD|153274 cd07590, BAR_Bin3, The Bin/Amphiphysin/Rvs (BAR) domain of Bridging
integrator 3. BAR domains are dimerization, lipid
binding and curvature sensing modules found in many
different proteins with diverse functions. Bridging
integrator 3 (Bin3) is widely expressed in many tissues
except in the brain. It plays roles in regulating
filamentous actin localization and in cell division. In
humans, the Bin3 gene is located in chromosome 8p21.3, a
region that is implicated in cancer suppression.
Homozygous inactivation of the Bin3 gene in mice led to
the development of cataracts and an increased likelihood
of lymphomas during aging, suggesting a role for Bin3 in
lens development and cancer suppression. BAR domains
form dimers that bind to membranes, induce membrane
bending and curvature, and may also be involved in
protein-protein interactions.
Length = 225
Score = 25.8 bits (57), Expect = 7.7
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 56 LKRFKGHF---NLFLAVFEEIKAEYTIHFNTVEKEKQKDKT 93
LKR + F N + E+ EY VEK +K+KT
Sbjct: 100 LKRLRSVFPSVNAAIKRREQSLQEYERLQAKVEKLAEKEKT 140
>gnl|CDD|115340 pfam06677, Auto_anti-p27, Sjogren's syndrome/scleroderma
autoantigen 1 (Autoantigen p27). This family consists
of several Sjogren's syndrome/scleroderma autoantigen 1
(Autoantigen p27) sequences. It is thought that the
potential association of anti-p27 with anti-centromere
antibodies suggests that autoantigen p27 might play a
role in mitosis.
Length = 41
Score = 23.8 bits (52), Expect = 7.8
Identities = 14/26 (53%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 11 SEFCSKCGTILPLFDFK-GDVKCYVC 35
E C KCGT PLF K G V C C
Sbjct: 17 DEHCPKCGT--PLFRLKDGKVFCPSC 40
>gnl|CDD|234127 TIGR03158, cas3_cyano, CRISPR-associated helicase Cas3, subtype
CYANO. CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) is a widespread family of
prokaryotic direct repeats with spacers of unique
sequence between consecutive repeats. This protein
family is a CRISPR-associated (Cas) family strictly
associated with the Cyano subtype of CRISPR/Cas locus,
found in several species of Cyanobacteria and several
archaeal species. It contains helicase motifs and
appears to represent the Cas3 protein of the Cyano
subtype of CRISPR/Cas system [Mobile and
extrachromosomal element functions, Other].
Length = 357
Score = 26.0 bits (57), Expect = 7.8
Identities = 11/52 (21%), Positives = 17/52 (32%), Gaps = 4/52 (7%)
Query: 27 KGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYT 78
KG+ + + GT LL PDI ++ + YT
Sbjct: 97 KGEKLYNLLRNPIGTSTPIILLTNPDIFVY----LTRFAYIDRGDIAAGFYT 144
>gnl|CDD|187841 cd09710, Cas3_I-D, CRISPR/Cas system-associated protein Cas3;
Distinct diverged subfamily of Cas3 helicase domain.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Diverged DNA helicase Cas3'; signature gene for Type I
and subtype I-D.
Length = 353
Score = 26.0 bits (57), Expect = 8.3
Identities = 11/52 (21%), Positives = 17/52 (32%), Gaps = 4/52 (7%)
Query: 27 KGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYT 78
KG+ + + GT LL PDI ++ + YT
Sbjct: 93 KGEKLYNLLRNDIGTSTPIILLTNPDIFVY----LTRFAYIDRGDIAAGFYT 140
>gnl|CDD|201484 pfam00874, PRD, PRD domain. The PRD domain (for PTS Regulation
Domain), is the phosphorylatable regulatory domain
found in bacterial transcriptional antiterminator such
as BglG, SacY and LicT, as well as in activators such
as MtlR and LevR. The PRD is phosphorylated on one or
two conserved histidine residues. PRD-containing
proteins are involved in the regulation of catabolic
operons in Gram+ and Gram- bacteria and are often
characterized by a short N-terminal effector domain
that binds to either RNA (CAT-RBD for antiterminators
pfam03123) or DNA (for activators), and a duplicated
PRD module which is phosphorylated by the sugar
phosphotransferase system (PTS) in response to the
availability of carbon source. The phosphorylations
modify the conformation and stability of the dimeric
proteins and thereby the RNA- or DNA-binding activity
of the effector domain. The structure of the LicT PRD
domains has been solved in both the active (pdb:1h99)
and inactive state (pdb:1tlv), revealing massive
structural rearrangements upon activation.
Length = 90
Score = 24.9 bits (55), Expect = 8.5
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 54 LFLKRFKGHFNLFLAVFEEIKAEYTIHFNTVEK 86
++R K + + EEIK +Y + +K
Sbjct: 30 FAIERIKYGITIDNPLLEEIKEKYPKEYEIAKK 62
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
0.323 0.138 0.425
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,570,103
Number of extensions: 559099
Number of successful extensions: 528
Number of sequences better than 10.0: 1
Number of HSP's gapped: 528
Number of HSP's successfully gapped: 28
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
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: 54 (24.6 bits)