RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3587
(195 letters)
>gnl|CDD|206750 cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras
GTPases. Human HSR1 is localized to the human MHC class
I region and is highly homologous to a putative
GTP-binding protein, MMR1 from mouse. These proteins
represent a new subfamily of GTP-binding proteins that
has only eukaryote members. This subfamily shows a
circular permutation of the GTPase signature motifs so
that the C-terminal strands 5, 6, and 7 (strand 6
contains the G4 box with sequence NKXD) are relocated to
the N-terminus.
Length = 140
Score = 85.4 bits (212), Expect = 1e-21
Identities = 27/35 (77%), Positives = 28/35 (80%)
Query: 42 QVVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFP 76
+ VSVS TPG TKHFQTIFL I LCDCPGLVFP
Sbjct: 106 KKVSVSSTPGKTKHFQTIFLEPGITLCDCPGLVFP 140
Score = 84.6 bits (210), Expect = 3e-21
Identities = 27/34 (79%), Positives = 27/34 (79%)
Query: 1 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFP 34
VSVS TPG TKHFQTIFL I LCDCPGLVFP
Sbjct: 107 KVSVSSTPGKTKHFQTIFLEPGITLCDCPGLVFP 140
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 68.6 bits (168), Expect = 5e-14
Identities = 40/164 (24%), Positives = 65/164 (39%), Gaps = 13/164 (7%)
Query: 43 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKPLQVLMGSFPIAQLREPYSTV 102
V S PG TK Q I L D I L D PG++ P L VL+ P ++++P
Sbjct: 157 VAKTSNRPGTTKGIQWIKLDDGIYLLDTPGIIPPKFDDDEL-VLLKLAPKGEIKDPVLPA 215
Query: 103 QYLAERMDLIKLLHIKH-----------PDDDEYWCAMDICDGWAQKRSYMTAKTGRYDS 151
+AER+ L LL +H + + + A+KR ++ K G D
Sbjct: 216 DEVAERL-LGGLLIDEHYGEKLNITRYESNPIHRTDPEEFLELIAKKRGWLLLKGGEPDL 274
Query: 152 YRAANELLRMATEGRICLCLMPPQYLSKQGVSKHSRPAVRRSTK 195
RAA +L+ G++ + + + V+ +
Sbjct: 275 ERAAETILKDIRNGKLGWFSLEEPEDNIEVVTIRDPEGSVVKAR 318
>gnl|CDD|206753 cd04178, Nucleostemin_like, A circularly permuted subfamily of the
Ras GTPases. Nucleostemin (NS) is a nucleolar protein
that functions as a regulator of cell growth and
proliferation in stem cells and in several types of
cancer cells, but is not expressed in the differentiated
cells of most mammalian adult tissues. NS shuttles
between the nucleolus and nucleoplasm bidirectionally at
a rate that is fast and independent of cell type.
Lowering GTP levels decreases the nucleolar retention of
NS, and expression of NS is abruptly down-regulated
during differentiation prior to terminal cell division.
Found only in eukaryotes, NS consists of an N-terminal
basic domain, a coiled-coil domain, a GTP-binding
domain, an intermediate domain, and a C-terminal acidic
domain. Experimental evidence indicates that NS uses its
GTP-binding property as a molecular switch to control
the transition between the nucleolus and nucleoplasm,
and this process involves interaction between the basic,
GTP-binding, and intermediate domains of the protein.
Length = 171
Score = 39.5 bits (93), Expect = 3e-04
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 1 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPG 30
+V TPG TK Q + L +++L D PG
Sbjct: 141 ACNVGATPGVTKSMQEVHLDKHVKLLDSPG 170
Score = 39.5 bits (93), Expect = 3e-04
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 43 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPG 72
+V TPG TK Q + L +++L D PG
Sbjct: 141 ACNVGATPGVTKSMQEVHLDKHVKLLDSPG 170
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 39.4 bits (93), Expect = 3e-04
Identities = 22/87 (25%), Positives = 34/87 (39%), Gaps = 17/87 (19%)
Query: 46 VSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPKPLQVLMGSFPIAQLREPYSTVQYL 105
S+TPG T+ + D RL D PG + +KV K ++ G +YL
Sbjct: 28 TSKTPGRTQLINFFNVGDKFRLVDLPGYGY-AKVSKEVREKWGKL----------IEEYL 76
Query: 106 AERMDLIKLLH---IKHP---DDDEYW 126
R +L ++ +H D E
Sbjct: 77 ENRENLKGVVLLIDARHGPTPIDLEML 103
Score = 34.0 bits (79), Expect = 0.019
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 4 VSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPK 39
S+TPG T+ + D RL D PG + +KV K
Sbjct: 28 TSKTPGRTQLINFFNVGDKFRLVDLPGYGY-AKVSK 62
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related
GTPases. These proteins are found in bacteria,
eukaryotes, and archaea. They all exhibit a circular
permutation of the GTPase signature motifs so that the
order of the conserved G box motifs is G4-G5-G1-G2-G3,
with G4 and G5 being permuted from the C-terminal region
of proteins in the Ras superfamily to the N-terminus of
YlqF-related GTPases.
Length = 146
Score = 36.6 bits (85), Expect = 0.003
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 2 VSVSRTPGHTKHFQTIFLTDNIRLCDCPGL 31
+ V PG TK Q + L I L D PG+
Sbjct: 117 LKVGSIPGTTKLQQDVKLDKEIYLYDTPGI 146
Score = 36.6 bits (85), Expect = 0.003
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 44 VSVSRTPGHTKHFQTIFLTDNIRLCDCPGL 73
+ V PG TK Q + L I L D PG+
Sbjct: 117 LKVGSIPGTTKLQQDVKLDKEIYLYDTPGI 146
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 37.1 bits (87), Expect = 0.003
Identities = 37/148 (25%), Positives = 52/148 (35%), Gaps = 36/148 (24%)
Query: 43 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKVPK------------------PLQ 84
+ PG TK Q I L + L D PG + K+ L+
Sbjct: 146 IAKTGNRPGVTKAQQWIKLGKGLELLDTPG-ILWPKLEDQEVGLKLALTGAIKDEALDLE 204
Query: 85 VLMGSFPIAQLREPYSTVQYLAERMDLIKLLHIKHPDDDEYWCAMDICDGWAQKRSYMTA 144
+ F + L + Y L ER L +L P+D ++ A+KR
Sbjct: 205 -EVAIFALEYLSKHYPER--LKERYKLDEL-----PEDILEL--LEA---IARKRG-ALR 250
Query: 145 KTGRYDSYRAANELL---RMATEGRICL 169
K G D RA+ LL R G+I L
Sbjct: 251 KGGEIDYERASELLLNEFRNGKLGKITL 278
Score = 33.2 bits (77), Expect = 0.056
Identities = 12/37 (32%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 1 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKV 37
+ PG TK Q I L + L D PG + K+
Sbjct: 146 IAKTGNRPGVTKAQQWIKLGKGLELLDTPG-ILWPKL 181
>gnl|CDD|206751 cd01858, NGP_1, A novel nucleolar GTP-binding protein, circularly
permuted subfamily of the Ras GTPases. Autoantigen
NGP-1 (Nucleolar G-protein gene 1) has been shown to
localize in the nucleolus and nucleolar organizers in
all cell types analyzed, which is indicative of a
function in ribosomal assembly. NGP-1 and its homologs
show a circular permutation of the GTPase signature
motifs so that the C-terminal strands 5, 6, and 7
(strand 6 contains the G4 box with NKXD motif) are
relocated to the N terminus.
Length = 157
Score = 33.4 bits (77), Expect = 0.028
Identities = 15/31 (48%), Positives = 18/31 (58%)
Query: 42 QVVSVSRTPGHTKHFQTIFLTDNIRLCDCPG 72
+V V+ PG TK +Q I L I L DCPG
Sbjct: 126 KVCKVAPIPGETKVWQYITLMKRIYLIDCPG 156
Score = 32.7 bits (75), Expect = 0.057
Identities = 15/30 (50%), Positives = 17/30 (56%)
Query: 1 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPG 30
V V+ PG TK +Q I L I L DCPG
Sbjct: 127 VCKVAPIPGETKVWQYITLMKRIYLIDCPG 156
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The
full-length GTPase protein is required for the complete
activity of the protein of interacting with the 50S
ribosome and binding of both adenine and guanine
nucleotides, with a preference for guanine nucleotide.
Length = 117
Score = 32.7 bits (75), Expect = 0.040
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 1 VVSVSRTPGHTKHFQTIFLTDN--IRLCDCPGLVFPSKVPKPLQVVS 45
V VS PG T+ L I L D PGL+ + K ++ +
Sbjct: 24 VAIVSDYPGTTRDPILGVLGLGRQIILVDTPGLIEGASEGKGVEGFN 70
Score = 32.3 bits (74), Expect = 0.047
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 4/57 (7%)
Query: 43 VVSVSRTPGHTKHFQTIFLTDN--IRLCDCPGLVFPSKVPKPLQVLMGSFPIAQLRE 97
V VS PG T+ L I L D PGL+ + + V + + +RE
Sbjct: 24 VAIVSDYPGTTRDPILGVLGLGRQIILVDTPGLIEGA--SEGKGVEGFNRFLEAIRE 78
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members commonly
are called EngB based on homology to EngA, one of
several other GTPases of ribosome biogenesis. Cutoffs as
set find essentially all bacterial members, but also
identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about 80
percent of bacterial genomes [Protein synthesis, Other].
Length = 178
Score = 32.4 bits (75), Expect = 0.076
Identities = 26/87 (29%), Positives = 38/87 (43%), Gaps = 22/87 (25%)
Query: 46 VSRTPGHTKHFQTI---FLTDNIRLCDCPGLVFPSKVPKPLQVLMGSFPIAQLREPYSTV 102
S+TPG T Q I + D RL D PG + +KV K + I
Sbjct: 47 TSKTPGRT---QLINFFEVNDGFRLVDLPGYGY-AKVSKEEKEKWQKL-IE--------- 92
Query: 103 QYLAERMDL---IKLLHIKHP--DDDE 124
+YL +R +L + L+ I+HP + D
Sbjct: 93 EYLEKRENLKGVVLLMDIRHPLKELDL 119
Score = 30.1 bits (69), Expect = 0.47
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 7/39 (17%)
Query: 4 VSRTPGHTKHFQTI---FLTDNIRLCDCPGLVFPSKVPK 39
S+TPG T Q I + D RL D PG + +KV K
Sbjct: 47 TSKTPGRT---QLINFFEVNDGFRLVDLPGYGY-AKVSK 81
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 32.1 bits (74), Expect = 0.12
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 1 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFP 34
V V PG TK Q I L+D + L D PG+++P
Sbjct: 143 VAKVGNRPGVTKGQQWIKLSDGLELLDTPGILWP 176
Score = 32.1 bits (74), Expect = 0.12
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 43 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFP 76
V V PG TK Q I L+D + L D PG+++P
Sbjct: 143 VAKVGNRPGVTKGQQWIKLSDGLELLDTPGILWP 176
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 32.0 bits (74), Expect = 0.13
Identities = 26/91 (28%), Positives = 38/91 (41%), Gaps = 30/91 (32%)
Query: 46 VSRTPGHTKHFQTI--F-LTDNIRLCDCPGLVFPSKVPKPL----QVLMGSFPIAQLREP 98
S+TPG T Q I F + D +RL D PG + +KV K Q L+
Sbjct: 53 TSKTPGRT---QLINFFEVNDKLRLVDLPGYGY-AKVSKEEKEKWQKLIE---------- 98
Query: 99 YSTVQYLAERMDLIKLLH---IKHP--DDDE 124
+YL R +L ++ +HP + D
Sbjct: 99 ----EYLRTRENLKGVVLLIDSRHPLKELDL 125
Score = 29.3 bits (67), Expect = 0.88
Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 7/39 (17%)
Query: 4 VSRTPGHTKHFQTI--F-LTDNIRLCDCPGLVFPSKVPK 39
S+TPG T Q I F + D +RL D PG + +KV K
Sbjct: 53 TSKTPGRT---QLINFFEVNDKLRLVDLPGYGY-AKVSK 87
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily
of the Ras GTPases. This family represents archaeal
GTPase typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 29.6 bits (67), Expect = 0.68
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 8 PGHTKHFQTIFLTDNIRLCDCPG 30
PG+TK Q + + I L D PG
Sbjct: 134 PGYTKGIQLVRIDSKIYLIDTPG 156
Score = 29.6 bits (67), Expect = 0.68
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 50 PGHTKHFQTIFLTDNIRLCDCPG 72
PG+TK Q + + I L D PG
Sbjct: 134 PGYTKGIQLVRIDSKIYLIDTPG 156
>gnl|CDD|238425 cd00829, SCP-x_thiolase, Thiolase domain associated with sterol
carrier protein (SCP)-x isoform and related proteins;
SCP-2 has multiple roles in intracellular lipid
circulation and metabolism. The N-terminal presequence
in the SCP-x isoform represents a peroxisomal
3-ketacyl-Coa thiolase specific for branched-chain acyl
CoAs, which is proteolytically cleaved from the sterol
carrier protein.
Length = 375
Score = 29.9 bits (68), Expect = 0.68
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 13/46 (28%)
Query: 91 PIAQLREPYSTVQYLAERM--DLIKLLHIKHPDDDEYWCAMDICDG 134
P AQ R+P + L RM D ++LL C + DG
Sbjct: 173 PYAQFRKPITVEDVLNSRMIADPLRLLD----------CCP-VSDG 207
>gnl|CDD|233770 TIGR02188, Ac_CoA_lig_AcsA, acetate--CoA ligase. This model
describes acetate-CoA ligase (EC 6.2.1.1), also called
acetyl-CoA synthetase and acetyl-activating enzyme. It
catalyzes the reaction ATP + acetate + CoA = AMP +
diphosphate + acetyl-CoA and belongs to the family of
AMP-binding enzymes described by pfam00501.
Length = 625
Score = 29.1 bits (66), Expect = 1.4
Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 2/22 (9%)
Query: 121 DDDEYWCAMDICDGWAQKRSYM 142
D D +WC D+ GW SY+
Sbjct: 277 DGDIFWCTADV--GWITGHSYI 296
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 28.3 bits (64), Expect = 2.0
Identities = 13/30 (43%), Positives = 15/30 (50%)
Query: 1 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPG 30
V V PG T+ Q I + NI L D PG
Sbjct: 140 VAKVGNKPGVTRGQQWIRIGPNIELLDTPG 169
Score = 28.3 bits (64), Expect = 2.0
Identities = 13/30 (43%), Positives = 15/30 (50%)
Query: 43 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPG 72
V V PG T+ Q I + NI L D PG
Sbjct: 140 VAKVGNKPGVTRGQQWIRIGPNIELLDTPG 169
>gnl|CDD|234677 PRK00174, PRK00174, acetyl-CoA synthetase; Provisional.
Length = 637
Score = 28.6 bits (65), Expect = 2.1
Identities = 10/23 (43%), Positives = 12/23 (52%), Gaps = 2/23 (8%)
Query: 121 DDDEYWCAMDICDGWAQKRSYMT 143
D D YWC D+ GW SY+
Sbjct: 286 DGDVYWCTADV--GWVTGHSYIV 306
>gnl|CDD|213313 cd05966, ACS, Acetyl-CoA synthetase (also known as acetate-CoA
ligase and acetyl-activating enzyme). Acetyl-CoA
synthetase (ACS) catalyzes the formation of acetyl-CoA
from acetate, CoA, and ATP. Synthesis of acetyl-CoA is
carried out in a two-step reaction. In the first step,
the enzyme catalyzes the synthesis of acetyl-AMP
intermediate from acetate and ATP. In the second step,
acetyl-AMP reacts with CoA to produce acetyl-CoA. This
enzyme is widely present in all living organisms. The
activity of this enzyme is crucial for maintaining the
required levels of acetyl-CoA, a key intermediate in
many important biosynthetic and catabolic processes.
Acetyl-CoA is used in the biosynthesis of glucose, fatty
acids, and cholesterol. It can also be used in the
production of energy in the citric acid cycle.
Eukaryotes typically have two isoforms of acetyl-CoA
synthetase, a cytosolic form involved in biosynthetic
processes and a mitochondrial form primarily involved in
energy generation.
Length = 602
Score = 28.7 bits (65), Expect = 2.1
Identities = 11/21 (52%), Positives = 11/21 (52%), Gaps = 2/21 (9%)
Query: 121 DDDEYWCAMDICDGWAQKRSY 141
DD YWC DI GW SY
Sbjct: 266 PDDVYWCTADI--GWITGHSY 284
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 28.4 bits (64), Expect = 2.8
Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 9/70 (12%)
Query: 1 VVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSK-----VPKPLQVVS----VSRTPG 51
V++ S PG T I L D L D PG++ + K L+ ++ +
Sbjct: 184 VITTSPFPGTTLDLIEIPLDDGHSLYDTPGIINSHQMAHYLDKKDLKYITPKKEIKPKTY 243
Query: 52 HTKHFQTIFL 61
QT+FL
Sbjct: 244 QLNPNQTLFL 253
Score = 26.4 bits (59), Expect = 9.3
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 42 QVVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVF 75
V++ S PG T I L D L D PG++
Sbjct: 183 DVITTSPFPGTTLDLIEIPLDDGHSLYDTPGIIN 216
>gnl|CDD|115849 pfam07220, DUF1420, Protein of unknown function (DUF1420). This
family consists of several hypothetical putative
lipoproteins which seem to be found specifically in the
bacterium Leptospira interrogans. Members of this family
are typically around 670 resides in length and their
function is unknown.
Length = 672
Score = 28.0 bits (62), Expect = 3.5
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 65 IRLCDCPGLVFPSKVPKP--LQVLMGSFPIAQLREPYSTVQYLAERMDLIKLLHI 117
I P LVF PKP LQ+ M SF I L E +S + ++ L+ I
Sbjct: 270 IAFLSSPVLVFLVSSPKPQLLQIGMTSFAITLLLEIFSKAKTDKNKLFAFILICI 324
>gnl|CDD|107334 cd06339, PBP1_YraM_LppC_lipoprotein_like, Periplasmic binding
component of lipoprotein LppC, an immunodominant
antigen. This subgroup includes periplasmic binding
component of lipoprotein LppC, an immunodominant
antigen, whose molecular function is not characterized.
Members of this subgroup are predicted to be involved in
transport of lipid compounds, and they are sequence
similar to the family of ABC-type hydrophobic amino acid
transporters (HAAT).
Length = 336
Score = 28.0 bits (63), Expect = 3.6
Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 10/53 (18%)
Query: 136 AQKRSYMTAKTGR-----YDSYRAANELLRMATEGRICLCLMPPQYLSKQGVS 183
+ +Y R YD+Y A L ++ G+ L P GV+
Sbjct: 271 RYRAAYGWPPLSRLAALGYDAYALAAALAQL---GQGDAALTPGAGF--SGVT 318
>gnl|CDD|236462 PRK09303, PRK09303, adaptive-response sensory kinase; Validated.
Length = 380
Score = 27.6 bits (62), Expect = 4.9
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 13/57 (22%)
Query: 41 LQVVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPSKV-PKPLQVLMGSFPIAQLR 96
LQ++ P + F RL P L+ K+ P+P QVL GS QL+
Sbjct: 49 LQIIDPGEQPELLELF---------RLVATPALI---KISPEPRQVLAGSNIFQQLK 93
>gnl|CDD|198173 cd00173, SH2, Src homology 2 (SH2) domain. In general, SH2
domains are involved in signal transduction; they bind
pTyr-containing polypeptide ligands via two surface
pockets, a pTyr and hydrophobic binding pocket,
allowing proteins with SH2 domains to localize to
tyrosine phosphorylated sites. They are present in a
wide array of proteins including: adaptor proteins
(Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1),
kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1,
Shp-2), transcription factors (STAT1), Ras signaling
molecules (Ras-Gap), ubiquitination factors (c-Cbl),
cytoskeleton regulators (Tensin), signal regulators
(SAP), and phospholipid second messengers (PLCgamma),
amongst others.
Length = 79
Score = 25.9 bits (57), Expect = 5.9
Identities = 14/47 (29%), Positives = 16/47 (34%)
Query: 31 LVFPSKVPKPLQVVSVSRTPGHTKHFQTIFLTDNIRLCDCPGLVFPS 77
LV S V+SV G KH+ L G FPS
Sbjct: 25 LVRESSSEPGDYVLSVRSGDGKVKHYLIERNEGGYYLLGGSGRTFPS 71
>gnl|CDD|239941 cd04495, BRCA2DBD_OB3, BRCA2DBD_OB3: A subfamily of OB folds
corresponding to the third OB fold (OB3) of the
800-amino acid C-terminal ssDNA binding domain (DBD) of
BRCA2 (breast cancer susceptibility gene 2) protein,
called BRCA2DBD. BRCA2 participates in homologous
recombination-mediated repair of double-strand DNA
breaks. It stimulates the displacement of Replication
protein A (RPA), the most abundant eukaryotic ssDNA
binding protein. It also facilitates filament
formation. Mutations that map throughout the BRCA2
protein are associated with breast cancer
susceptibility. BRCA2 is a large nuclear protein and
its most conserved region is the C-terminal BRCA2DBD.
BRCA2DBD binds ssDNA in vitro, and is composed of five
structural domains, three of which are OB folds (OB1,
OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in
tandem, and their mode of binding can be considered
qualitatively similar to two OB folds of RPA1, DBD-A
and DBD-B (the major DBDs of RPA).
Length = 100
Score = 25.8 bits (57), Expect = 6.6
Identities = 6/21 (28%), Positives = 10/21 (47%), Gaps = 2/21 (9%)
Query: 1 VVSVSRTPGHTKHFQTIFLTD 21
V+SV + F ++L D
Sbjct: 6 VISVGKPI--EGKFPAVYLAD 24
Score = 25.8 bits (57), Expect = 6.6
Identities = 6/21 (28%), Positives = 10/21 (47%), Gaps = 2/21 (9%)
Query: 43 VVSVSRTPGHTKHFQTIFLTD 63
V+SV + F ++L D
Sbjct: 6 VISVGKPI--EGKFPAVYLAD 24
>gnl|CDD|239615 cd03542, Rieske_RO_Alpha_HBDO, Rieske non-heme iron oxygenase (RO)
family, 2-Halobenzoate 1,2-dioxygenase (HBDO) subfamily,
N-terminal Rieske domain of the oxygenase alpha subunit;
ROs comprise a large class of aromatic
ring-hydroxylating dioxygenases that enable
microorganisms to tolerate and utilize aromatic
compounds for growth. The oxygenase alpha subunit
contains an N-terminal Rieske domain with an [2Fe-2S]
cluster and a C-terminal catalytic domain with a
mononuclear Fe(II) binding site. The Rieske [2Fe-2S]
cluster accepts electrons from a reductase or ferredoxin
component and transfers them to the mononuclear iron for
catalysis. HBDO catalyzes the double hydroxylation of
2-halobenzoates with concomitant release of halogenide
and carbon dioxide, yielding catechol.
Length = 123
Score = 26.3 bits (58), Expect = 7.1
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 6/41 (14%)
Query: 113 KLLHIKHPDDDEYWCAMDICDGWAQKRSYMTAKTGRYDSYR 153
KLL +K P Y + CDG S+ K R++SYR
Sbjct: 75 KLLKVKDPKTAGYPEGFN-CDG-----SHDLTKVARFESYR 109
>gnl|CDD|237340 PRK13300, PRK13300, tRNA CCA-pyrophosphorylase; Provisional.
Length = 447
Score = 26.8 bits (60), Expect = 9.3
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 8/37 (21%)
Query: 36 KVPKPLQVVS-VSRTPGHTKHFQTIFLTDNI--RLCD 69
KV +++S V RTP HTK ++ + + +L D
Sbjct: 122 KVESGEEIISAVDRTPFHTK-----YVKERLKGKLED 153
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 0.138 0.439
Gapped
Lambda K H
0.267 0.0592 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,670,849
Number of extensions: 852197
Number of successful extensions: 818
Number of sequences better than 10.0: 1
Number of HSP's gapped: 816
Number of HSP's successfully gapped: 40
Length of query: 195
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 103
Effective length of database: 6,857,034
Effective search space: 706274502
Effective search space used: 706274502
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: 56 (25.6 bits)