RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9283
(242 letters)
>gnl|CDD|202007 pfam01846, FF, FF domain. This domain has been predicted to be
involved in protein-protein interaction. This domain was
recently shown to bind the hyperphosphorylated
C-terminal repeat domain of RNA polymerase II,
confirming its role in protein-protein interactions.
Length = 50
Score = 46.3 bits (111), Expect = 2e-07
Identities = 21/52 (40%), Positives = 34/52 (65%), Gaps = 2/52 (3%)
Query: 76 KKREKFRELLNETSEVTLSSSWKDIRKLIKEDPRYTKFSSSDRRCEREFKDY 127
+ R+ F+ELL E ++T S+W +I+K +++DPRY S R E+ F+DY
Sbjct: 1 EARDAFKELLKEL-KITPYSTWSEIKKKLEKDPRYKALLSPSER-EQLFEDY 50
Score = 32.0 bits (74), Expect = 0.021
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 32 RNSELTWREAKRQLRKDHRWDSADLLDRDEKEKLFNEH 69
TW E K++L KD R+ LL E+E+LF ++
Sbjct: 15 ITPYSTWSEIKKKLEKDPRY--KALLSPSEREQLFEDY 50
Score = 31.3 bits (72), Expect = 0.045
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 11/60 (18%)
Query: 135 AKAEFRELLQETKLISHKSLGLLHENENYLSEIEEILRNDKRFLSLEHIPEERTQIILTY 194
A+ F+ELL+E K I+ S SEI++ L D R+ +L P ER Q+ Y
Sbjct: 2 ARDAFKELLKELK-ITPYST---------WSEIKKKLEKDPRYKAL-LSPSEREQLFEDY 50
>gnl|CDD|128718 smart00441, FF, Contains two conserved F residues. A novel motif
that often accompanies WW domains. Often contains two
conserved Phe (F) residues.
Length = 55
Score = 45.6 bits (109), Expect = 4e-07
Identities = 20/56 (35%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 75 KKKREKFRELLNETSEVTLSSSWKDIRKLIKEDPRYTKFSSSDRRCEREFKDYLKD 130
++ +E F+ELL E +T ++W + RK +K DPRY S R E+ F+D++++
Sbjct: 1 EEAKEAFKELLKEHEVITPDTTWSEARKKLKNDPRYKALLSESER-EQLFEDHIEE 55
Score = 33.7 bits (78), Expect = 0.007
Identities = 17/39 (43%), Positives = 26/39 (66%), Gaps = 2/39 (5%)
Query: 34 SELTWREAKRQLRKDHRWDSADLLDRDEKEKLFNEHIEE 72
+ TW EA+++L+ D R+ LL E+E+LF +HIEE
Sbjct: 19 PDTTWSEARKKLKNDPRY--KALLSESEREQLFEDHIEE 55
Score = 27.9 bits (63), Expect = 0.80
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 10/64 (15%)
Query: 134 TAKAEFRELLQETKLISHKSLGLLHENENYLSEIEEILRNDKRFLSLEHIPEERTQIILT 193
AK F+ELL+E ++I+ + SE + L+ND R+ +L ER Q+
Sbjct: 2 EAKEAFKELLKEHEVITPDTT---------WSEARKKLKNDPRYKALLS-ESEREQLFED 51
Query: 194 YLDE 197
+++E
Sbjct: 52 HIEE 55
>gnl|CDD|148767 pfam07347, CI-B14_5a, NADH:ubiquinone oxidoreductase subunit B14.5a
(Complex I-B14.5a). This family contains the eukaryotic
NADH:ubiquinone oxidoreductase subunit B14.5a (Complex
I-B14.5a) (EC:1.6.5.3). This is approximately 100
residues long, and forms part of a multiprotein complex
that resides on the inner mitochondrial membrane. The
main function of the complex is the transport of
electrons from NADH to ubiquinone, accompanied by
translocation of protons from the mitochondrial matrix
to the intermembrane space.
Length = 97
Score = 29.8 bits (67), Expect = 0.36
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 192 LTYLDELEKRGPPPPPTASEPNRRLGNNY 220
L Y D + KR PPP P+ +L NY
Sbjct: 20 LRYADGISKRTQPPPKLPDGPSHKLSANY 48
>gnl|CDD|215557 PLN03069, PLN03069, magnesiumprotoporphyrin-IX chelatase subunit H;
Provisional.
Length = 1220
Score = 30.9 bits (70), Expect = 0.70
Identities = 39/124 (31%), Positives = 60/124 (48%), Gaps = 23/124 (18%)
Query: 29 LAVRNSELTWREAKRQL------RKDHRWDS-ADLLDRDEKEKLFNEHIEELTKKKREKF 81
LAV NS +W + K QL RK +DS A +EK +F E F
Sbjct: 1101 LAVENS--SWNDEK-QLQDMYLSRKSFAFDSDAPGAGMEEKRDVF----ESALSTADVTF 1153
Query: 82 RELLNETSEVTLSSSWKDIRKLIKEDPRYTKFSSSDRRCEREFKDYLKDKTSTAKAEFRE 141
+ L ++SE++L+ D+ DP TK S R+ +++ Y+ D T+TA A+ R
Sbjct: 1154 QNL--DSSEISLT----DVSHYFDSDP--TKLVQSLRKDKKKPSSYIAD-TTTANAQVRT 1204
Query: 142 LLQE 145
LL++
Sbjct: 1205 LLRQ 1208
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 30.4 bits (69), Expect = 1.0
Identities = 25/114 (21%), Positives = 42/114 (36%), Gaps = 15/114 (13%)
Query: 66 FNEHIEELTKKKREKFRELLNETSEVT-LSSSWKDIRKLIKEDPRYTKFSSSDRRCEREF 124
NE + +K + R ++ L S K + +K+ S +EF
Sbjct: 15 LNEDVSAFQRKFVNEVRRCDEVERKLRKLESKIKKLGIPLKDTGGKPDVPPS-----KEF 69
Query: 125 KDYLKDKTSTAKAEFRELLQETKLISHKSLGLLHENENYLSEIEEILRNDKRFL 178
D + E +L E K + ++L L + N L E +L +K FL
Sbjct: 70 LDL--------EEEILDLEAEIKEVE-ENLESLEKEINELEEWLNVLDEEKSFL 114
>gnl|CDD|213672 TIGR01990, bPGM, beta-phosphoglucomutase. This model represents
the beta-phosphoglucomutase enzyme which catalyzes the
interconverison of beta-D-glucose-1-phosphate and
beta-D-glucose-6-phosphate. The 6-phosphate is capable
of non-enzymatic anomerization (alpha <-> beta) while
the 1-phosphate is not. A separate enzyme is responsible
for the isomerization of the alpha anomers.
Beta-D-glucose-1-phosphate results from the
phosphorylysis of maltose (2.4.1.8), trehalose
(2.4.1.64) or trehalose-6-phosphate (2.4.1.216).
Alternatively, these reactions can be run in the
synthetic direction to create the disaccharides. All
sequenced genomes which contain a member of this family
also appear to contain at least one putative maltose or
trehalose phosphorylase. Three species, Lactococcus,
Enterococcus and Neisseria appear to contain a pair of
paralogous beta-PGM's. Beta-phosphoglucomutase is a
member of the haloacid dehalogenase superfamily of
hydrolase enzymes. These enzymes are characterized by a
series of three catalytic motifs positioned within an
alpha-beta (Rossman) fold. beta-PGM contains an inserted
alpha helical domain in between the first and second
conserved motifs and thus is a member of subfamily IA of
the superfamily. The third catalytic motif comes in
three variants, the third of which, containing a
conserved DD or ED, is the only one found here as well
as in several other related enzymes (TIGR01509). The
enzyme from L. lactis has been extensively characterized
including a remarkable crystal structure which traps the
pentacoordinate transition state [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 185
Score = 29.2 bits (66), Expect = 1.3
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 39 REAKRQLRKDHRWDSADLLDRDEKEKLFNEHIEELTKKKREKFRELLNETSEVTLSSSWK 98
E L+ R +S + + +K E EEL ++K + + ELL E+T +
Sbjct: 34 EEFNESLKGVSREESLERILDLGGKKYSEEEKEELAERKNDYYVELLK---ELTPADVLP 90
Query: 99 DIRKLIKE 106
I+ L+ +
Sbjct: 91 GIKSLLAD 98
>gnl|CDD|173589 PTZ00398, PTZ00398, phosphoenolpyruvate carboxylase; Provisional.
Length = 974
Score = 29.7 bits (67), Expect = 1.6
Identities = 11/42 (26%), Positives = 27/42 (64%), Gaps = 4/42 (9%)
Query: 72 ELTKKKREKFRELLNETSEVTLSSSWKDIRKLIKEDPRYTKF 113
++++REL++E SE+++ K+ RK+++E+P + +
Sbjct: 729 ADPIPVKQEWRELMDEMSEISM----KEYRKVVRENPDFVPY 766
>gnl|CDD|227435 COG5104, PRP40, Splicing factor [RNA processing and modification].
Length = 590
Score = 29.3 bits (65), Expect = 2.0
Identities = 26/127 (20%), Positives = 49/127 (38%), Gaps = 7/127 (5%)
Query: 55 DLLDRDEKEKLFNEHIEELTKKKREKFRELLNE---TSEVTLSSSWKDIRKLIKEDPRYT 111
+LL E+ K + R++FR LL + ++ WK+ LIK+DPR+
Sbjct: 343 ELLSAIEERKAAAAQNA---RHHRDEFRTLLRKLYSEGKIYYRMKWKNAYPLIKDDPRFL 399
Query: 112 K-FSSSDRRCEREFKDYLKDKTSTAKAEFRELLQETKLISHKSLGLLHENENYLSEIEEI 170
+ F D++ D + R +ET+ +E + + E+
Sbjct: 400 NLLGRTGSSPLDLFFDFIVDLENMYGFARRSYERETRTGQISPTDRRAVDEIFEAIAEKK 459
Query: 171 LRNDKRF 177
+ +F
Sbjct: 460 EEGEIKF 466
Score = 27.4 bits (60), Expect = 9.2
Identities = 32/156 (20%), Positives = 58/156 (37%), Gaps = 21/156 (13%)
Query: 10 KKARQEASLREREKEVQRTLAVRNSELTW---------REAKRQLRKDHRWDSADLLDR- 59
K A + E EKE L + TW R+ + + DL +
Sbjct: 137 KDAVYRLTKEEAEKEFITMLKENQVDSTWPIFRAIEELRDPRYWMVDTDPLWRKDLFKKY 196
Query: 60 -DEKEKLFNEHIEELTKKKREKFRELLNETSEVTLSSSWKDIRKLIKEDPRYTKFSS--S 116
+ +EK E E +K +F ++L S + + W + + + P Y+ + +
Sbjct: 197 FENQEKDQREEEENKQRKYINEFCKMLAGNSHIKYYTDWFTFKSIFSKHPYYSSVVNEKT 256
Query: 117 DRRCEREFKDYL--------KDKTSTAKAEFRELLQ 144
R+ +++KD L K TA E+L+
Sbjct: 257 KRQTFQKYKDKLGCYEKYVGKHMGGTALGRLEEVLR 292
>gnl|CDD|227480 COG5151, SSL1, RNA polymerase II transcription
initiation/nucleotide excision repair factor TFIIH,
subunit SSL1 [Transcription / DNA replication,
recombination, and repair].
Length = 421
Score = 28.8 bits (64), Expect = 2.6
Identities = 22/85 (25%), Positives = 28/85 (32%), Gaps = 10/85 (11%)
Query: 1 MNETDK--DADKKARQEASLREREKEVQRTLAVRNSELTWR-EAKRQLRKDHRWDSADLL 57
MNE K D+DK ++ R K R N +W E KR WD +
Sbjct: 1 MNENQKSFDSDKSESEDEQKNGRVKVRSRKTDDMNKGYSWEQEYKRS------WDDVNDD 54
Query: 58 DRDEKEKLFNEHIEELTKKKREKFR 82
+ E E TK R
Sbjct: 55 KEGSLVGVVAEFNLE-TKAPYSNNR 78
>gnl|CDD|232933 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR
family. This gene is part of the type I restriction and
modification system which is composed of three
polypeptides R (restriction endonuclease), M
(modification) and S (specificity). This group of
enzymes recognize specific short DNA sequences and have
an absolute requirement for ATP (or dATP) and
S-adenosyl-L-methionine. They also catalyse the
reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar
site specificity.(J. Mol. Biol. 271 (3), 342-348
(1997)). Members of this family are assumed to differ
from each other in DNA site specificity [DNA metabolism,
Restriction/modification].
Length = 667
Score = 28.9 bits (65), Expect = 2.6
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 13/90 (14%)
Query: 54 ADLLDRDEKEKLFNEHIEELTKKKREKFRELLNE---------TSEVTLSSSWKDIRKLI 104
D LD+ + + F+E E L ++ RE +E L E +E L S KDI +
Sbjct: 447 EDHLDKKKLDAFFDEIFELLPERIREITKESLKEKLQKTKKILFNEDRLESIAKDIAEHY 506
Query: 105 KEDPRYTKFS----SSDRRCEREFKDYLKD 130
+ KF + R E K+ L +
Sbjct: 507 AKFKELFKFKAMVVAISRYACVEEKNALDE 536
>gnl|CDD|212042 cd10334, SLC6sbd_u1, uncharacterized bacterial and archaeal solute
carrier 6 subfamily; solute-binding domain. SLC6
proteins (also called the sodium- and chloride-dependent
neurotransmitter transporter family or Na+/Cl--dependent
transporter family) include neurotransmitter
transporters (NTTs): these are sodium- and
chloride-dependent plasma membrane transporters for the
monoamine neurotransmitters serotonin
(5-hydroxytryptamine), dopamine, and norepinephrine, and
the amino acid neurotransmitters GABA and glycine. These
NTTs are widely expressed in the mammalian brain,
involved in regulating neurotransmitter signaling and
homeostasis, and the target of a range of therapeutic
drugs for the treatment of psychiatric diseases.
Bacterial members of the SLC6 family include the LeuT
amino acid transporter.
Length = 480
Score = 29.0 bits (66), Expect = 2.7
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 77 KREKFRELLNETSEVTLSSSWK 98
EK RE LN S+ + W
Sbjct: 405 GAEKLREHLNAVSDFKVGKWWD 426
>gnl|CDD|233221 TIGR00985, 3a0801s04tom, mitochondrial import receptor subunit
translocase of outer membrane 20 kDa subunit.
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 148
Score = 28.0 bits (62), Expect = 2.9
Identities = 17/67 (25%), Positives = 24/67 (35%), Gaps = 5/67 (7%)
Query: 5 DKDADKKARQEASLREREKEVQRTLAVRNSELTWREAKRQLRKDHRWDSADLLDRDEKEK 64
D D KK R+ + ++ LA R A L K D D EKE
Sbjct: 34 DPDFRKKLRRRRKKQAGAEKQYGGLAKEKQRQRIRPAAAGLAKA-----PDPTDPSEKEA 88
Query: 65 LFNEHIE 71
F + ++
Sbjct: 89 FFLQEVQ 95
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 157
Score = 27.6 bits (62), Expect = 3.5
Identities = 24/100 (24%), Positives = 51/100 (51%), Gaps = 7/100 (7%)
Query: 7 DADKKARQEASLREREKEVQRTLAVRNSELTWREAKRQLRKDHRWDSADLLDRDEKEKLF 66
A K A+++ L + K++Q L + EL ++ +++L+K S + R K++
Sbjct: 31 PAGKAAQKQ--LEKEFKKLQAELQKKEKEL--QKEEQKLQKQAATLSEE--ARKAKQQEL 84
Query: 67 NEHIEELTKKKREKFRELLNETSEVTLSSSWKDIRKLIKE 106
+ +EL ++K++ ++ L + + L + I K IKE
Sbjct: 85 QQKQQEL-QQKQQAAQQELQQKQQELLQPIYDKIDKAIKE 123
>gnl|CDD|235366 PRK05218, PRK05218, heat shock protein 90; Provisional.
Length = 613
Score = 28.5 bits (65), Expect = 3.5
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 54 ADLLDRDEKEKLFNEHIEELTKKKREKFRELLNE-TSEVTLSS 95
DL DE+EK E EE K E+ +E L + +V LS
Sbjct: 474 LDLGKEDEEEKEEKEEAEEEFKPLLERLKEALGDKVKDVRLSH 516
>gnl|CDD|165538 PHA03281, PHA03281, envelope glycoprotein E; Provisional.
Length = 642
Score = 28.5 bits (63), Expect = 3.6
Identities = 11/39 (28%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 194 YLDELEKRGPPP----PPTASEPNRRLGNNYVNTFGAYP 228
+++ +E+ G PP PP S+P N+ ++ G +P
Sbjct: 514 FVNAIEEHGFPPEAGNPPAPSKPKEIANNDVISEPGTFP 552
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 28.2 bits (64), Expect = 3.8
Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 1/82 (1%)
Query: 121 EREFKDYLKDKTSTAKAEFRELLQETKLISHKSLGLLHENENYLSEIEEILRNDKRFL-S 179
++E + K+ AK E +L E + + L + E L + EE L L
Sbjct: 48 KKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEK 107
Query: 180 LEHIPEERTQIILTYLDELEKR 201
E E++ + + ELEK+
Sbjct: 108 REEELEKKEKELEQKQQELEKK 129
>gnl|CDD|211382 cd11010, S1-P1_nuclease, S1/P1 nucleases and related enzymes. This
family summarizes both S1 and P1 nucleases (EC:3.1.30.1)
which cleave RNA and single stranded DNA with no base
specificity. S1 nuclease is more active on DNA than RNA.
Its reaction products are oligonucleotides or single
nucleotides with 5' phosphoryl groups. Although its
primary substrate is single-stranded, it may also
introduce single-stranded breaks in double-stranded DNA
or RNA, or DNA-RNA hybrids. It is used as a reagent in
nuclease protection assays and in removing single
stranded tails from DNA molecules to create blunt ended
molecules and opening hairpin loops generated during
synthesis of double stranded cDNA. P1 nuclease cleaves
its substrate at every position yielding nucleoside 5'
monophosphates, and it does not recognize or act on
double-stranded DNA. It is useful at removing single
stranded strands hanging off the end of double stranded
DNA and at completely cleaving melted DNA for simple DNA
composition analysis.
Length = 249
Score = 28.1 bits (63), Expect = 4.3
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 71 EELTKKKREKFRELLNETSEVTL--SSSWKDIRKLIKEDPRYTKFSS 115
+ LT K R+ LL S +L +++W D I+ DP Y +
Sbjct: 15 QYLTPKARKAVDRLLGGLSGESLAEAATWADD---IRSDPAYKWTAP 58
>gnl|CDD|204665 pfam11494, Ta0938, Ta0938. Ta0938 is a protein of unknown function
however the structure has been determined. The protein
has a novel fold and a putative Zn-binding motif. The
structure has two different parts, one region contains a
beta sheet flanked by two alpha helices and the other
contains a bundle of loops which contain all cysteines
in the protein.
Length = 106
Score = 26.7 bits (59), Expect = 4.5
Identities = 13/61 (21%), Positives = 23/61 (37%)
Query: 82 RELLNETSEVTLSSSWKDIRKLIKEDPRYTKFSSSDRRCEREFKDYLKDKTSTAKAEFRE 141
E +N +EV + W + +LI Y + + +E K Y+K F+
Sbjct: 45 LEFVNMLNEVKKRTGWHKVDELIINGNYYLGRNCLAKSGGKELKFYVKFGEDAGIETFKI 104
Query: 142 L 142
Sbjct: 105 T 105
>gnl|CDD|217888 pfam04091, Sec15, Exocyst complex subunit Sec15-like.
Length = 311
Score = 28.0 bits (63), Expect = 4.7
Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 12/75 (16%)
Query: 99 DIRKLIKEDPRYTKFSSSDRRCEREFKDYLKDKTSTAKAEFRELLQETKLISHKSLGLLH 158
IR I ++ KF + E + ++ LL +++ L L
Sbjct: 39 QIRSFIN---QFYKFLDDLYQEPTEINEIVRKS-------LDRLL--IDVVNDCLLERLD 86
Query: 159 ENENYLSEIEEILRN 173
L +I +IL N
Sbjct: 87 STSLNLEQIVQILIN 101
>gnl|CDD|178867 PRK00106, PRK00106, hypothetical protein; Provisional.
Length = 535
Score = 28.3 bits (63), Expect = 4.8
Identities = 26/94 (27%), Positives = 48/94 (51%), Gaps = 7/94 (7%)
Query: 10 KKARQEASLR----EREKEVQRTLAVRNSELTWREAKRQLRKDHRWDSADLLDRDEKEKL 65
K A++ A L E+E R A R++E + AKR+ K + + LL+ E+ +
Sbjct: 27 KSAKEAAELTLLNAEQEAVNLRGKAERDAEHIKKTAKRE-SKALKKEL--LLEAKEEARK 83
Query: 66 FNEHIEELTKKKREKFRELLNETSEVTLSSSWKD 99
+ E IE+ K +R++ +++ + +E S KD
Sbjct: 84 YREEIEQEFKSERQELKQIESRLTERATSLDRKD 117
>gnl|CDD|213919 TIGR04306, salvage_TenA, thiaminase II. The TenA protein of
Bacillus subtilis and Staphylococcus aurues, and the
C-terminal region of trifunctional protein Thi20p from
Saccharomyces cerevisiae, perform cleavages on thiamine
and related compounds to produce
4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), a
substrate a salvage pathway for thiamine biosynthesis.
The gene symbol tenA, for Transcription ENhancement A,
reflects a misleading early characterization as a
regulatory protein. This family is related to PqqC from
the PQQ biosynthesis system (see TIGR02111), heme
oxygenase (pfam01126), and CADD (Chlamydia protein
Associating with Death Domains), a putative folate
metabolism enzyme (see TIGR04305).
Length = 208
Score = 27.5 bits (61), Expect = 5.1
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 60 DEKEKLFNEHIEELTKKKREKFRELLNETSE 90
+E E L N E + ++ EK +E+ E+ E
Sbjct: 166 NEGENLLNHLAETSSPEELEKLKEIFAESCE 196
>gnl|CDD|224375 COG1458, COG1458, Predicted DNA-binding protein containing PIN
domain [General function prediction only].
Length = 221
Score = 27.8 bits (62), Expect = 5.3
Identities = 11/45 (24%), Positives = 26/45 (57%)
Query: 43 RQLRKDHRWDSADLLDRDEKEKLFNEHIEELTKKKREKFRELLNE 87
++ ++ +++ EKE++ E + ++ +K REK+RE L +
Sbjct: 112 LRVAEEAIREASIECYELEKEEIIREVVGKIIRKLREKYREALRK 156
>gnl|CDD|215114 PLN02170, PLN02170, probable pectinesterase/pectinesterase
inhibitor.
Length = 529
Score = 27.6 bits (61), Expect = 6.0
Identities = 24/99 (24%), Positives = 42/99 (42%), Gaps = 14/99 (14%)
Query: 34 SELTWREAKRQLRKD-HRWDSADLLDRD------EKEKLFNEHIEELTKKKREKFRELLN 86
S + + +D H W SA L +++ +++ +H + R LL
Sbjct: 117 SRIVVIKHADHDEEDVHTWLSAALTNQETCEQSLQEKSSSYKHGLAMDFVAR-NLTGLLT 175
Query: 87 ETSEVTLS------SSWKDIRKLIKEDPRYTKFSSSDRR 119
+ ++ +S SS K RKL+ E T SSS+R+
Sbjct: 176 NSLDLFVSVKSKHSSSSKGGRKLLSEQDFPTWVSSSERK 214
>gnl|CDD|217890 pfam04097, Nic96, Nup93/Nic96. Nup93/Nic96 is a component of the
nuclear pore complex. It is required for the correct
assembly of the nuclear pore complex. In Saccharomyces
cerevisiae, Nic96 has been shown to be involved in the
distribution and cellular concentration of the GTPase
Gsp1. The structure of Nic96 has revealed a mostly alpha
helical structure.
Length = 607
Score = 27.6 bits (62), Expect = 6.5
Identities = 28/101 (27%), Positives = 42/101 (41%), Gaps = 12/101 (11%)
Query: 109 RYTK-FSSSDRRCEREFKDYL------KDKTSTAKAEFRELLQETKLISHKSLGLLHENE 161
+YT+ F +SD R E YL KDKT + E L+E L + + LL +
Sbjct: 327 QYTRSFEASDPR---EALQYLYLIALFKDKTGRSL--CHEALRELVLETREFDLLLGDIN 381
Query: 162 NYLSEIEEILRNDKRFLSLEHIPEERTQIILTYLDELEKRG 202
S I ++ + + LE E I +E + RG
Sbjct: 382 PDGSRIPGLIERRLKLIKLEDEEEFLRTITEQAAEEADDRG 422
>gnl|CDD|216953 pfam02265, S1-P1_nuclease, S1/P1 Nuclease. This family contains
both S1 and P1 nucleases (EC:3.1.30.1) which cleave RNA
and single stranded DNA with no base specificity.
Length = 251
Score = 27.2 bits (61), Expect = 7.1
Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 6/45 (13%)
Query: 73 LTKKKREKFRELLNETSEVTLS--SSWKDIRKLIKEDPRYTKFSS 115
L+ K R+ + LL L+ ++W D I+ D +Y S
Sbjct: 17 LSPKARKAVQRLLPGLDG-DLAQVATWAD---DIRSDGKYRWTSP 57
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 27.8 bits (62), Expect = 7.2
Identities = 39/195 (20%), Positives = 76/195 (38%), Gaps = 10/195 (5%)
Query: 8 ADKKARQEASLREREKEVQRTLAVRNSELTWREAKRQLRKDHRWDSADLLDR-DEKEKLF 66
++ + L ER +E++ + EL RE + + + + + +EK
Sbjct: 311 LEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLLAELEEAKEELEEKLSAL 370
Query: 67 NEHIEELTKKKREKFRELLNETSEVTLSSSWKDIRKLIKEDPRYTKFSSSDRRCEREFKD 126
E +EEL + RE+ EL E +E+ ++ +L +E + E +
Sbjct: 371 LEELEELFEALREELAELEAELAEIR-----NELEELKRE----IESLEERLERLSERLE 421
Query: 127 YLKDKTSTAKAEFRELLQETKLISHKSLGLLHENENYLSEIEEILRNDKRFLSLEHIPEE 186
LK++ +AE EL E + ++ + L + E ++E+ R E+
Sbjct: 422 DLKEELKELEAELEELQTELEELNEELEELEEQLEELRDRLKELERELAELQEELQRLEK 481
Query: 187 RTQIILTYLDELEKR 201
+ LD LE
Sbjct: 482 ELSSLEARLDRLEAE 496
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 27.4 bits (61), Expect = 7.8
Identities = 21/96 (21%), Positives = 37/96 (38%), Gaps = 7/96 (7%)
Query: 3 ETDKDADKKARQEASLREREKEVQRTLAVRNS--ELTWREAKRQLRKDHRWDSAD----- 55
E +A +E LRER ++ Q R R +++ + D R + D
Sbjct: 47 EEKLEAALLEAKELLLRERNQQRQEARREREELQREEERLVQKEEQLDARAEKLDNLENQ 106
Query: 56 LLDRDEKEKLFNEHIEELTKKKREKFRELLNETSEV 91
L +R++ +EEL K+ + + T E
Sbjct: 107 LEEREKALSARELELEELEKQLDNELYRVAGLTPEQ 142
>gnl|CDD|225914 COG3379, COG3379, Uncharacterized conserved protein [Function
unknown].
Length = 471
Score = 27.5 bits (61), Expect = 8.4
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 39 REAKRQ-LRKDHRWDSADLLDRDEKEKLFNEHIEELTKKKREKFRELLNE 87
E K + D+ DE + +F E + E T+ ++E +E L+
Sbjct: 140 PELKDEIENTTGNEYVFDVEYHDEDKDIFIEDLWENTESRKEVVKEYLSP 189
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 27.3 bits (61), Expect = 8.9
Identities = 31/165 (18%), Positives = 52/165 (31%), Gaps = 17/165 (10%)
Query: 20 EREKEVQRTLAVRNSELTWREAKRQLRKDHRWDSADLLDRD---EKEKLFNEHIEELTKK 76
E E + Q E +AK +L++ + +L D K IEEL
Sbjct: 727 EGELDNQLAQLSAAIEAARTQAKARLKELKKQYDRELASLDVDPNTVKELKRQIEELETT 786
Query: 77 --KREKFRELLNETSEVTLSSSWKDIRKLIKEDPRYTKFSSSDRRCEREFKDYLKDKTST 134
+ R + E + +W L +E P E + L
Sbjct: 787 IERIAVRRPEVREY-RAFMQETWLHRDSLREERPNLAIQLRELESSAEELQQELTRLIKD 845
Query: 135 AKAEFRELLQETKLISHKSLGLLHENENYLSEIEEILRNDKRFLS 179
K ++L QE E L +++E+LR + +
Sbjct: 846 TKLRRKKLEQE-----------RKALEKQLDQLDELLRGLRDEMR 879
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 27.2 bits (61), Expect = 9.3
Identities = 25/95 (26%), Positives = 50/95 (52%), Gaps = 15/95 (15%)
Query: 1 MNETDKDADKK----ARQEASLREREKEVQRTLAVRNSEL------TWREAKRQLRKDHR 50
+++ +++ +KK + +E +L E+E+E++ +A + EL T EAK L ++
Sbjct: 99 LDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREELERISGLTQEEAKEILLEEVE 158
Query: 51 WDSADLLDRDEKEKLFNEHIEELTKKKREKFRELL 85
++ R E KL E EE ++ +K +E+L
Sbjct: 159 EEA-----RHEAAKLIKEIEEEAKEEADKKAKEIL 188
>gnl|CDD|239791 cd04258, AAK_AKiii-LysC-EC, AAK_AKiii-LysC-EC: Amino Acid Kinase
Superfamily (AAK), AKiii-LysC-EC: this CD includes the
N-terminal catalytic aspartokinase (AK) domain of the
lysine-sensitive aspartokinase isoenzyme AKIII. AKIII is
a monofunctional class enzyme (LysC) found in some
bacteria such as E. coli. Aspartokinase is the first
enzyme in the aspartate metabolic pathway and catalyzes
the conversion of aspartate and ATP to aspartylphosphate
and ADP. In E. coli, LysC is reported to be a homodimer
of 50 kD subunits.
Length = 292
Score = 26.9 bits (60), Expect = 9.3
Identities = 9/32 (28%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 81 FRELLNETSEVTLSSSWKDIRKLIKEDPRYTK 112
F E L E + + W D+R +++ D R+ +
Sbjct: 128 FSEALREQG---VPAEWFDVRTVLRTDSRFGR 156
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 27.3 bits (61), Expect = 9.6
Identities = 29/106 (27%), Positives = 46/106 (43%), Gaps = 11/106 (10%)
Query: 2 NETDKDADKKARQEASLREREKEVQRTLAVRNSELTWREAKRQLRKDHRWDSADLLDRDE 61
E K ++ +R EA LRE E+++ R E + E + Q ++ +D E
Sbjct: 798 AELSKLEEEVSRIEARLREIEQKLNR----LTLEKEYLEKEIQELQE------QRIDLKE 847
Query: 62 KEKLFNEHIEELTKKKREKFRELLNETSEV-TLSSSWKDIRKLIKE 106
+ K + IE L KK E EL + + L S D++K E
Sbjct: 848 QIKSIEKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDE 893
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
0.311 0.130 0.366
Gapped
Lambda K H
0.267 0.0865 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,692,666
Number of extensions: 1248053
Number of successful extensions: 2068
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2027
Number of HSP's successfully gapped: 237
Length of query: 242
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 148
Effective length of database: 6,768,326
Effective search space: 1001712248
Effective search space used: 1001712248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 58 (25.9 bits)