RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 033363
(121 letters)
>gnl|CDD|216088 pfam00730, HhH-GPD, HhH-GPD superfamily base excision DNA repair
protein. This family contains a diverse range of
structurally related DNA repair proteins. The
superfamily is called the HhH-GPD family after its
hallmark Helix-hairpin-helix and Gly/Pro rich loop
followed by a conserved aspartate. This includes
endonuclease III, EC:4.2.99.18 and MutY an A/G-specific
adenine glycosylase, both have a C terminal 4Fe-4S
cluster. The family also includes 8-oxoguanine DNA
glycosylases. The methyl-CPG binding protein MBD4 also
contains a related domain that is a thymine DNA
glycosylase. The family also includes
DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other
members of the AlkA family.
Length = 144
Score = 61.6 bits (150), Expect = 2e-13
Identities = 28/115 (24%), Positives = 48/115 (41%), Gaps = 14/115 (12%)
Query: 18 AGRVISDLFTLC--PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWTHV 75
A ++ LF P + E D EE+ ++I LG +++A IK ++ + V
Sbjct: 14 ANKITKRLFERYGFPTPEDLAEADEEELRELIKGLGFYRRKAKYIKELARILVEGYLGLV 73
Query: 76 ----------TQLHGVGKYAADAFAIFCTGKWDRVRPTDHMLNYYWE--FLVSTK 118
L GVG++ A+A +F G+ D D + + L+ TK
Sbjct: 74 PLDLEELEALLALPGVGRWTAEAVLLFALGRPDVFPAVDTHVRRVAKRLGLIDTK 128
>gnl|CDD|214684 smart00478, ENDO3c, endonuclease III. includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 149
Score = 38.0 bits (89), Expect = 3e-04
Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 7/86 (8%)
Query: 18 AGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ----EYLGE--- 70
+ LF P + D EE+E++I LG +++A + ++ EY GE
Sbjct: 10 VNKATERLFEKFPTPEDLAAADEEELEELIRGLGFYRRKARYLIELARILVEEYGGEVPD 69
Query: 71 SWTHVTQLHGVGKYAADAFAIFCTGK 96
+ +L GVG+ A+A F GK
Sbjct: 70 DREELLKLPGVGRKTANAVLSFALGK 95
>gnl|CDD|238013 cd00056, ENDO3c, endonuclease III; includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 158
Score = 35.3 bits (82), Expect = 0.002
Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 11/77 (14%)
Query: 30 PDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ----EYLGESWTH------VTQLH 79
P + D EE+ ++I +LG +++A +K ++ + G + L
Sbjct: 31 PTPEALAAADEEELRELIRSLGY-RRKAKYLKELARAIVEGFGGLVLDDPDAREELLALP 89
Query: 80 GVGKYAADAFAIFCTGK 96
GVG+ A+ +F G
Sbjct: 90 GVGRKTANVVLLFALGP 106
>gnl|CDD|223255 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA
replication, recombination, and repair].
Length = 211
Score = 35.6 bits (83), Expect = 0.002
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 15/74 (20%)
Query: 25 LFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQ----EYLGESWTHV----- 75
LF P + D EE+E++I ++GL + +A IK ++ ++ GE V
Sbjct: 54 LFKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGE----VPDTRE 109
Query: 76 --TQLHGVGKYAAD 87
L GVG+ A+
Sbjct: 110 ELLSLPGVGRKTAN 123
>gnl|CDD|223200 COG0122, AlkA, 3-methyladenine DNA glycosylase/8-oxoguanine DNA
glycosylase [DNA replication, recombination, and
repair].
Length = 285
Score = 32.0 bits (73), Expect = 0.052
Identities = 18/98 (18%), Positives = 34/98 (34%), Gaps = 18/98 (18%)
Query: 24 DLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEYLGESWT---------- 73
+++ P + D E + + GL ++A I ++
Sbjct: 139 EIYHSFPTPEQLAAADEEALRRC----GLSGRKAEYIISLARAAAEGELDLSELKPLSDE 194
Query: 74 ----HVTQLHGVGKYAADAFAIFCTGKWDRVRPTDHML 107
+T L G+G + A+ F +F G+ D D L
Sbjct: 195 EAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGL 232
>gnl|CDD|119433 cd05173, PI3Kc_IA_beta, Phosphoinositide 3-kinase (PI3K), class IA,
beta isoform, catalytic domain; The PI3K catalytic
domain family is part of a larger superfamily that
includes the catalytic domains of other kinases such as
the typical serine/threonine/tyrosine protein kinases
(PKs), aminoglycoside phosphotransferase, choline
kinase, and RIO kinases. PI3Ks catalyze the transfer of
the gamma-phosphoryl group from ATP to the 3-hydroxyl of
the inositol ring of D-myo-phosphatidylinositol (PtdIns)
or its derivatives. PI3Ks can be divided into three main
classes (I, II, and III), defined by their substrate
specificity, regulation, and domain structure. Class I
PI3Ks are the only enzymes capable of converting
PtdIns(4,5)P2 to the critical second messenger
PtdIns(3,4,5)P3. Class I enzymes are heterodimers and
exist in multiple isoforms consisting of one catalytic
subunit (out of four isoforms) and one of several
regulatory subunits. They are further classified into
class IA (alpha, beta and delta) and IB (gamma). Class
IA enzymes contain an N-terminal p85 binding domain, a
Ras binding domain, a lipid binding C2 domain, a PI3K
homology domain of unknown function, and a C-terminal
ATP-binding cataytic domain. They associate with a
regulatory subunit of the p85 family and are activated
by tyrosine kinase receptors. In addition, PI3Kbeta can
also be activated by G-protein-coupled receptors.
Deletion of PI3Kbeta in mice results in early lethality
at around day three of development. PI3Kbeta plays an
important role in regulating sustained integrin
activation and stable platelet agrregation, especially
under conditions of high shear stress.
Length = 362
Score = 31.5 bits (71), Expect = 0.074
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 14 ILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFSQEY---LGE 70
IL K G + LF L A ++I+ + +L L K +K+F Q++ L E
Sbjct: 287 ILRKNGNLFITLFALMLTAGLPELTSVKDIQYLKDSLALGKSEEEALKQFRQKFDEALRE 346
Query: 71 SWT 73
SWT
Sbjct: 347 SWT 349
>gnl|CDD|130155 TIGR01083, nth, endonuclease III. This equivalog model identifes
nth members of the pfam00730 superfamily (HhH-GPD:
Helix-hairpin-helix and Gly/Pro rich loop followed by a
conserved aspartate). The major members of the
superfamily are nth and mutY [DNA metabolism, DNA
replication, recombination, and repair].
Length = 191
Score = 28.5 bits (64), Expect = 0.71
Identities = 25/99 (25%), Positives = 42/99 (42%), Gaps = 19/99 (19%)
Query: 12 IAILLKA-------GRVISDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRAPMIKRFS 64
+A +L A + LF + P + + EE+E+ I ++GL + +A I
Sbjct: 31 VATILSAQATDKSVNKATKKLFEVYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALC 90
Query: 65 Q----EYLGE---SWTHVTQLHGVGKYAAD-----AFAI 91
+ Y GE + +L GVG+ A+ AF I
Sbjct: 91 RILVERYGGEVPEDREELVKLPGVGRKTANVVLNVAFGI 129
>gnl|CDD|221050 pfam11264, ThylakoidFormat, Thylakoid formation protein. THF1 is
localised to the outer plastid membrane and the stroma.
THF1 has a role in sugar signalling. THF1 is also
thought to have a role in chloroplast and leaf
development. THF1 has been shown to play a crucial role
in vesicle-mediated thylakoid membrane biogenesis.
Length = 216
Score = 26.8 bits (60), Expect = 2.9
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 4/37 (10%)
Query: 25 LFTLCPDAKTATEVDAEE----IEKIISTLGLQKKRA 57
LFTL +AK + D E+ ++++ +LGL K+R
Sbjct: 143 LFTLLEEAKGDLDKDEEDLRKILKELSESLGLSKERV 179
>gnl|CDD|237525 PRK13830, PRK13830, conjugal transfer protein TrbE; Provisional.
Length = 818
Score = 26.3 bits (58), Expect = 5.3
Identities = 10/37 (27%), Positives = 24/37 (64%)
Query: 14 ILLKAGRVISDLFTLCPDAKTATEVDAEEIEKIISTL 50
ILLK G +++ + PD++++T+ + E+ + I+ +
Sbjct: 29 ILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAI 65
>gnl|CDD|149273 pfam08123, DOT1, Histone methylation protein DOT1. The DOT1 domain
regulates gene expression by methylating histone H3. H3
methylation by DOT1 has been shown to be required for
the DNA damage checkpoint in yeast.
Length = 205
Score = 25.7 bits (57), Expect = 6.5
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 8 RLKEIAILLKAG-RVISDLFTLCPDAKTATEVDAEEIEKI 46
+LKE+ LK G ++IS L + P + +I I
Sbjct: 140 QLKEMLQDLKDGCKIIS-LKSFVPLNYRINFRNLSDIFNI 178
>gnl|CDD|177698 PLN00068, PLN00068, photosystem II CP47 chlorophyll A apoprotein;
Provisional.
Length = 508
Score = 26.0 bits (57), Expect = 6.7
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 74 HVTQLHGVGKYAADAFAIFCTGKWDRVRPT 103
HVT L+G G + +D + + TGK V P
Sbjct: 157 HVTGLYGPGIWVSDPYGL--TGKVQPVNPA 184
>gnl|CDD|240086 cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN
binding domain, group 4. Each monomer of OYE contains
FMN as a non-covalently bound cofactor, uses NADPH as a
reducing agent with oxygens, quinones, and
alpha,beta-unsaturated aldehydes and ketones, and can
act as electron acceptors in the catalytic reaction.
Other members of OYE family include trimethylamine
dehydrogenase, 2,4-dienoyl-CoA reductase, enoate
reductase, pentaerythriol tetranitrate reductase,
xenobiotic reductase, and morphinone reductase.
Length = 353
Score = 25.6 bits (57), Expect = 7.7
Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 2/57 (3%)
Query: 3 QIYSIRLKEIAILLKAGRVI--SDLFTLCPDAKTATEVDAEEIEKIISTLGLQKKRA 57
QI+ L+ G V+ S + P A T E+ EEIE II G +RA
Sbjct: 97 QIFHAGRMANPALVPGGDVVSPSAIAAFRPGAHTPRELTHEEIEDIIDAFGEATRRA 153
>gnl|CDD|216067 pfam00696, AA_kinase, Amino acid kinase family. This family
includes kinases that phosphorylate a variety of amino
acid substrates, as well as uridylate kinase and
carbamate kinase. This family includes: Aspartokinase
EC:2.7.2.4, Acetylglutamate kinase EC:2.7.2.8, Glutamate
5-kinase EC:2.7.2.11, Uridylate kinase EC:2.7.4.-,
Carbamate kinase EC:2.7.2.2.
Length = 230
Score = 25.5 bits (56), Expect = 7.8
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 9/45 (20%)
Query: 12 IAILLKAGRVI--SD---LFT----LCPDAKTATEVDAEEIEKII 47
+A L A ++I +D ++T PDAK E+ +E E+++
Sbjct: 155 LAEALGADKLIILTDVDGVYTADPRKNPDAKLIPELSYDEAEELL 199
>gnl|CDD|130815 TIGR01754, flav_RNR, ribonucleotide reductase-associated
flavodoxin, putative. This model represents a family of
proteins found immediately downstream of ribonucleotide
reductase genes in Xyella fastidiosa and some
Gram-positive bacteria. It appears to be a highly
divergent flavodoxin of the short chain type, more like
the flavodoxins of the sulfate-reducing genus
Desulfovibrio than like the NifF flavodoxins associated
with nitrogen fixation.
Length = 140
Score = 25.2 bits (55), Expect = 8.6
Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 7/67 (10%)
Query: 59 MIKRFSQEYLGESWTHVTQLHGVGKYAADA-----FAIFCTGKW--DRVRPTDHMLNYYW 111
+ Q+YL + V LH +G A + + G W +R R D M ++
Sbjct: 16 EVAFMIQDYLQKDGHEVDILHRIGTLADAPLDPENYDLVFLGTWTWERGRTPDEMKDFIA 75
Query: 112 EFLVSTK 118
E
Sbjct: 76 ELGYKPS 82
>gnl|CDD|218270 pfam04795, PAPA-1, PAPA-1-like conserved region. Family of
proteins with a conserved region found in PAPA-1, a
PAP-1 binding protein.
Length = 89
Score = 24.6 bits (54), Expect = 8.9
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 32 AKTATEVDAEEIEKIISTLGLQKKRAPMIKR 62
K A E E I K++ +KKR IK+
Sbjct: 18 EKRAEEEKMETINKLLKKQARRKKREDKIKK 48
>gnl|CDD|177290 PHA00619, PHA00619, CRISPR-associated Cas4-like protein.
Length = 201
Score = 25.2 bits (55), Expect = 9.2
Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 96 KWDRVRPTDHM--LNYYWEFLVSTKGNL 121
D+ R +++ LNYY E + G L
Sbjct: 113 DLDKGRLNNYLRQLNYYIEMANAMAGYL 140
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 0.136 0.412
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,231,869
Number of extensions: 542550
Number of successful extensions: 594
Number of sequences better than 10.0: 1
Number of HSP's gapped: 591
Number of HSP's successfully gapped: 27
Length of query: 121
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 37
Effective length of database: 7,211,866
Effective search space: 266839042
Effective search space used: 266839042
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 (24.1 bits)