RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12603
(391 letters)
>gnl|CDD|189046 cd09876, PIN_Nob1, PIN domain of eukaryotic ribosome assembly
factor Nob1 and archaeal UPF0129 protein Ta0041-like
homologs. PIN (PilT N terminus) domain of the
Saccharomyces cerevisiae ribosome assembly factor, Nob1
(Nin one binding) protein, the Thermoplasma acidophilum
DSM 1728, UPF0129 protein Ta0041, and similar eukaryotic
and archaeal homologs are included in this family. The
Nob1 PIN domain binds the single-stranded cleavage site
D at the 3#end of 18S rRNA. Recombinant Nob1 binds as a
tetramer to pre-18S rRNA fragments containing cleavage
site D and believed to cleave at this site. These PIN
domains are homologs of flap endonuclease-1 (FEN1)-like
PIN domains, but lack the extensive arch/clamp region
and the H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region, seen in FEN1-like PIN
domains. PIN domains within this subgroup contain three
highly conserved acidic residues (putative
metal-binding, active site residues).
Length = 109
Score = 132 bits (335), Expect = 4e-38
Identities = 47/92 (51%), Positives = 66/92 (71%)
Query: 1 DIGDNVITIPEVVNEVTSKRQIRRLVVLPYDLQIKEADPDSISFVTEFSKKTGDYPSLSS 60
+ + + T PEVV E+ K+ RRL LP++L+++E P+SI V+EF+KKTGDY SLS+
Sbjct: 16 TLAEELYTTPEVVAEIRDKQARRRLATLPFELKVREPSPESIKAVSEFAKKTGDYASLSA 75
Query: 61 TDIKVIALTYELHKQHIGVDSINTEPISRQIS 92
TDIKVIALTYEL + +G D + EP ++IS
Sbjct: 76 TDIKVIALTYELEAELVGDDHLRNEPGRKKIS 107
>gnl|CDD|192150 pfam08772, NOB1_Zn_bind, Nin one binding (NOB1) Zn-ribbon like.
This domain corresponds to a zinc ribbon and is found on
the RNA binding protein NOB1 (Nin one binding).
Length = 73
Score = 122 bits (308), Expect = 1e-34
Identities = 41/73 (56%), Positives = 52/73 (71%)
Query: 238 LIRELRTFILRCYACYKTTSIMTKVFCPKCGYKTLKRVAVSVDEQGKQKIHINLKRPLTA 297
I++LR +ILRC+AC+KTT MTK FCPKCG TL+RVAVSVDE G+ K+H+
Sbjct: 1 RIKQLRRWILRCHACFKTTPDMTKQFCPKCGNATLRRVAVSVDEDGEIKLHLKKNFQWNT 60
Query: 298 RGKKFSLPTFKGG 310
RG +S+P KGG
Sbjct: 61 RGTIYSIPKPKGG 73
>gnl|CDD|224356 COG1439, COG1439, Predicted nucleic acid-binding protein, consists
of a PIN domain and a Zn-ribbon module [General function
prediction only].
Length = 177
Score = 74.4 bits (183), Expect = 1e-15
Identities = 33/140 (23%), Positives = 61/140 (43%), Gaps = 7/140 (5%)
Query: 148 ESLEELEDHTPEVLQKIDHDEEEHSDDSGNEDDDDGG-EWITPSNLKQAQRTMDARQYEE 206
ES LE K+ E+ + G ++P++++ ++ + +
Sbjct: 43 ESRSLLELLLESGKVKVAEPSTEYVKEVREAAKKTGDLGNLSPTDIEVLALALELGEEVQ 102
Query: 207 KPLVVSCVTTDFAMQNVLKQMGLNVV-ALDGRLIRELRTFILRCYACYKTTSIMTKVFCP 265
V+ T D+++QNV Q+GLNV I+++R + LRC+ C + K FCP
Sbjct: 103 ----VALATDDYSVQNVALQLGLNVRSISYKGKIKKVRKWRLRCHGCKRIFP-EPKDFCP 157
Query: 266 KCGYKTLKRVAVSVDEQGKQ 285
CG ++ S +G+
Sbjct: 158 ICGSPLKRKRVKSRSSKGEF 177
Score = 50.5 bits (121), Expect = 2e-07
Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 6 VITIPEVVNEVTSKRQIRRLVVLPYDLQIKEADPD--SISFVTEFSKKTGDYPSLSSTDI 63
+ T P VV E+ + L +L ++K A+P + V E +KKTGD +LS TDI
Sbjct: 29 LYTTPSVVEEIKDRESRSLLELLLESGKVKVAEPSTEYVKEVREAAKKTGDLGNLSPTDI 88
Query: 64 KVIALTYEL 72
+V+AL EL
Sbjct: 89 EVLALALEL 97
>gnl|CDD|237118 PRK12496, PRK12496, hypothetical protein; Provisional.
Length = 164
Score = 63.9 bits (156), Expect = 3e-12
Identities = 36/110 (32%), Positives = 52/110 (47%), Gaps = 19/110 (17%)
Query: 2 IGDNVITIPEVVNEVTSKRQIRRLV--VLPY-DLQIKEADPDSISFVTEFSKKTGDYPSL 58
T P VV EV K R ++ + L+I E P+SI V E + KTGD L
Sbjct: 18 EDGEHYTTPSVVEEVKDKE-SRLILESAISAGKLKILEPSPESIEKVEEAAIKTGDLMRL 76
Query: 59 SSTDIKVIALTYELH---------------KQHIGVDSINTEPISRQISY 93
S+TDI+V+AL EL+ K +I ++I T+ I + I +
Sbjct: 77 SNTDIEVLALALELNGTLYTDDYGIQNVAKKLNIKFENIKTKGIKKVIKW 126
Score = 35.4 bits (82), Expect = 0.017
Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 2/64 (3%)
Query: 214 VTTDFAMQNVLKQMGLNVVALDGRLIRELRTFILRCYACYKTTSIMTKV-FCPKCGYKT- 271
T D+ +QNV K++ + + + I+++ + C C K C CG
Sbjct: 95 YTDDYGIQNVAKKLNIKFENIKTKGIKKVIKWRKVCKGCKKKYPEDYPDDVCEICGSPVK 154
Query: 272 LKRV 275
K V
Sbjct: 155 RKMV 158
>gnl|CDD|189033 cd09863, PIN_Smg6-like, PIN domain of human telomerase-binding
protein EST1, Smg6, and ribosome assembly factor, Nob1,
Archaeoglobus fulgidus AF0591 protein and other
eukaryotic, bacterial, and archaeal homologs. PIN (PilT
N terminus) domains of eukaryotic ribonucleases such as
Smg5 and Smg6, essential factors in nonsense-mediated
mRNA decay (NMD), and Nob1, a ribosome assembly factor
critical in pre-rRNA processing, as well as, the
uncharacterized archaeal Archaeoglobus fulgidus AF0591
protein and other eukaryotic, bacterial, and archaeal
homologs are included in this family. Smg5 and Smg6 are
essential factors in NMD, a post-transcriptional
regulatory pathway that recognizes and rapidly degrades
mRNAs containing premature translation termination
codons. In vivo, the Smg6 PIN domain elicits degradation
of bound mRNAs, as well as, metal-ion dependent,
degradation of single-stranded RNA, in vitro. The Nob1
PIN domain binds the single-stranded cleavage site D at
the 3'end of 18S rRNA. Recombinant Nob1 binds as a
tetramer to pre-18S rRNA fragments containing cleavage
site D and believed to cleave at this site. These PIN
domains are structural homologs of flap endonuclease-1
(FEN1)-like PIN domains, but lack the extensive
arch/clamp region and the H3TH (helix-3-turn-helix)
domain, an atypical helix-hairpin-helix-2-like region,
that is seen in FEN1-like PIN domains. PIN domains
within this group typically contain three or four highly
conserved acidic residues (putative metal-binding,
active site residues) which cluster at the C-terminal
end of the beta-sheet and form a negatively charged
pocket near the center of the molecule.
Length = 125
Score = 47.1 bits (112), Expect = 9e-07
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 6/75 (8%)
Query: 5 NVITIPEVVNEVT--SKRQIRRLVVLPYDLQIKE----ADPDSISFVTEFSKKTGDYPSL 58
+ V+ E+ + RQ R+ V L+ E + + + EF + G P L
Sbjct: 27 RLYIPLFVLQELDFLAYRQRRKSVKAREALKFLEELHSSLLEYVEERPEFLEAIGINPLL 86
Query: 59 SSTDIKVIALTYELH 73
DI +++ Y+ H
Sbjct: 87 GRFDILLLSCAYKCH 101
>gnl|CDD|216834 pfam01992, vATP-synt_AC39, ATP synthase (C/AC39) subunit. This
family includes the AC39 subunit from vacuolar ATP
synthase, and the C subunit from archaebacterial ATP
synthase. The family also includes subunit C from the
Sodium transporting ATP synthase from Enterococcus
hirae.
Length = 335
Score = 45.8 bits (109), Expect = 2e-05
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 123 YLEGLCRGFKNGILKQTDYLNLVQCESLEEL 153
Y R ++ +LK+ DY L++ ESLE L
Sbjct: 1 YPNARVRAMRSRLLKEEDYRELLEMESLEIL 31
>gnl|CDD|185695 cd01081, Aldose_epim, aldose 1-epimerase superfamily. Aldose
1-epimerases or mutarotases are key enzymes of
carbohydrate metabolism; they catalyze the
interconversion of the alpha- and beta-anomers of hexose
sugars such as glucose and galactose. This
interconversion is an important step that allows anomer
specific metabolic conversion of sugars. Studies of the
catalytic mechanism of the best known member of the
family, galactose mutarotase, have shown a glutamate and
a histidine residue to be critical for catalysis; the
glutamate serves as the active site base to initiate the
reaction by removing the proton from the C-1 hydroxyl
group of the sugar substrate and the histidine as the
active site acid to protonate the C-5 ring oxygen.
Length = 284
Score = 34.0 bits (78), Expect = 0.11
Identities = 10/53 (18%), Positives = 22/53 (41%), Gaps = 5/53 (9%)
Query: 28 LPYDLQIKEADPDSISFVTEFSKKTGDYPSLSSTDIKVIALTYELHKQHIGVD 80
LP+ + + + S++ + + G YP ++ V TY L + +
Sbjct: 82 LPWRVVATDEEEASVTLSYDLNDGPGGYP--FPLELTV---TYTLDADTLTIT 129
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 32.3 bits (74), Expect = 0.40
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 165 DHDEEEHSDDSGNEDDDDGGEWIT 188
D DEEE + +ED DD GEWI
Sbjct: 97 DDDEEEEWEVEEDEDSDDEGEWID 120
>gnl|CDD|226908 COG4531, ZnuA, ABC-type Zn2+ transport system, periplasmic
component/surface adhesin [Inorganic ion transport and
metabolism].
Length = 318
Score = 32.0 bits (73), Expect = 0.50
Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 13/73 (17%)
Query: 149 SLEELEDHTPEVLQKIDHDEEE--------HSDDSGNEDDDDGGE-----WITPSNLKQA 195
+L +L P + ++ EEE +D G+ D GE W++P+ K
Sbjct: 104 TLADLPGVKPLLFREAHDHEEEHDHGHDHAGADHKGDHDHHHEGEYDMHLWLSPAIAKAV 163
Query: 196 QRTMDARQYEEKP 208
+ + E P
Sbjct: 164 AAAIAKKLAELDP 176
>gnl|CDD|216695 pfam01780, Ribosomal_L37ae, Ribosomal L37ae protein family. This
ribosomal protein is found in archaebacteria and
eukaryotes. It contains four conserved cysteine residues
that may bind to zinc.
Length = 90
Score = 29.9 bits (68), Expect = 0.52
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 261 KVFCPKCGYKTLKRVAV 277
K CP CG +KR AV
Sbjct: 35 KYTCPFCGKDAVKRKAV 51
>gnl|CDD|117775 pfam09224, DUF1961, Domain of unknown function (DUF1961). Members
of this family are found in a set of hypothetical
bacterial proteins. Their exact function has not, as
yet, been determined.
Length = 218
Score = 31.4 bits (71), Expect = 0.67
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 44 FVTEFSKKTGDYPSLSSTDIKVIALTYELHKQH 76
F + + +TG YP S DI + L+Y HK
Sbjct: 94 FDADLAPRTGYYPQYHSGDINALHLSYFRHKHA 126
>gnl|CDD|217752 pfam03833, PolC_DP2, DNA polymerase II large subunit DP2.
Length = 852
Score = 31.7 bits (72), Expect = 0.76
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 9/57 (15%)
Query: 264 CPKCGYKTLKRV-------AVSVDEQGKQKIHIN--LKRPLTARGKKFSLPTFKGGK 311
CP CG ++ + +D GK+KI ++ L+R L G + L KG K
Sbjct: 632 CPSCGKESPESTCPKCGSRERKLDGYGKRKIDLSDLLRRALENLGIRKDLDELKGVK 688
>gnl|CDD|236558 PRK09545, znuA, high-affinity zinc transporter periplasmic
component; Reviewed.
Length = 311
Score = 31.1 bits (71), Expect = 0.79
Identities = 6/36 (16%), Positives = 14/36 (38%)
Query: 149 SLEELEDHTPEVLQKIDHDEEEHSDDSGNEDDDDGG 184
++ +L D P +++ D + D + D
Sbjct: 102 TIAQLPDVKPLLMKGAHDDHHDDDHDHAGHEKSDED 137
>gnl|CDD|224297 COG1379, COG1379, PHP family phosphoesterase with a Zn ribbon
[General function prediction only].
Length = 403
Score = 31.3 bits (71), Expect = 0.91
Identities = 24/76 (31%), Positives = 32/76 (42%), Gaps = 4/76 (5%)
Query: 223 VLKQMGLNVVA---LDGRLIRELRTFILRCYACYKTT-SIMTKVFCPKCGYKTLKRVAVS 278
+ + G +VA LD RL + T RCY Y + + CPKCG K K V+
Sbjct: 223 IKGKDGCKIVANYGLDPRLGKYHLTACSRCYTRYSLEEAKSLRWRCPKCGGKIKKGVSDR 282
Query: 279 VDEQGKQKIHINLKRP 294
V E + RP
Sbjct: 283 VLELADTEPEHPKHRP 298
>gnl|CDD|234747 PRK00398, rpoP, DNA-directed RNA polymerase subunit P; Provisional.
Length = 46
Score = 27.9 bits (63), Expect = 0.92
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 248 RCYACYKTTSI---MTKVFCPKCGYKTL 272
+C C + + T V CP CGY+ L
Sbjct: 5 KCARCGREVELDEYGTGVRCPYCGYRIL 32
>gnl|CDD|115196 pfam06524, NOA36, NOA36 protein. This family consists of several
NOA36 proteins which contain 29 highly conserved
cysteine residues. The function of this protein is
unknown.
Length = 314
Score = 31.1 bits (70), Expect = 1.0
Identities = 13/34 (38%), Positives = 14/34 (41%), Gaps = 9/34 (26%)
Query: 247 LRCYACYKTTSIMTKVF---------CPKCGYKT 271
LRC C + K F CPKCGY T
Sbjct: 186 LRCKVCCCNDHVRRKGFKYDKDKNLPCPKCGYPT 219
>gnl|CDD|173867 cd08502, PBP2_NikA_DppA_OppA_like_16, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 472
Score = 31.0 bits (71), Expect = 1.1
Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 9/61 (14%)
Query: 179 DDDDGGEWITPSNLKQAQRTMDARQYEEKPLVVSCVTTDFA--------MQNVLKQMGLN 230
+ G E +L++A++ + Y+ +P+V+ TD+A LK G N
Sbjct: 304 YSEAGKEGYNKPDLEKAKKLLKEAGYDGEPIVI-LTPTDYAYLYNAALVAAQQLKAAGFN 362
Query: 231 V 231
V
Sbjct: 363 V 363
>gnl|CDD|224444 COG1527, NtpC, Archaeal/vacuolar-type H+-ATPase subunit C [Energy
production and conversion].
Length = 346
Score = 30.8 bits (70), Expect = 1.1
Identities = 10/32 (31%), Positives = 14/32 (43%)
Query: 122 GYLEGLCRGFKNGILKQTDYLNLVQCESLEEL 153
Y R + +L Y L++ ESLEE
Sbjct: 10 AYPNARIRVMEARLLTDEQYSELLEAESLEEF 41
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 31.0 bits (71), Expect = 1.2
Identities = 12/34 (35%), Positives = 24/34 (70%)
Query: 154 EDHTPEVLQKIDHDEEEHSDDSGNEDDDDGGEWI 187
+D+ E L++++ ++++ DD +EDDD+G E I
Sbjct: 354 DDYHREQLEEVEEEDDDDWDDDWDEDDDEGVEVI 387
>gnl|CDD|235189 PRK03988, PRK03988, translation initiation factor IF-2 subunit
beta; Validated.
Length = 138
Score = 29.5 bits (67), Expect = 1.4
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 233 ALDGRLIRELRTFILRCYAC 252
+ D +LI+E R ++L+C AC
Sbjct: 110 SPDTKLIKEGRIWVLKCEAC 129
>gnl|CDD|218126 pfam04520, Senescence_reg, Senescence regulator. This protein
regulates the expression of proteins associated with
leaf senescence in plants.
Length = 146
Score = 29.7 bits (67), Expect = 1.5
Identities = 6/22 (27%), Positives = 9/22 (40%)
Query: 168 EEEHSDDSGNEDDDDGGEWITP 189
D +E+D DG + P
Sbjct: 83 RSIEDSDDDDEEDGDGAMMVPP 104
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 30.4 bits (69), Expect = 1.6
Identities = 15/39 (38%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 246 ILRCYACYKTTSIMTKVFCPKCGYKT-LKRVAVSVDEQG 283
I +C CY+ T+ CP CG +T L R VD G
Sbjct: 57 IYKCPECYRPECYTTEPKCPNCGAETELVRRVSFVDAPG 95
>gnl|CDD|238501 cd01019, ZnuA, Zinc binding protein ZnuA. These proteins have been
shown to function as initial receptors in the ABC uptake
of Zn2+. They belong to the TroA superfamily of
periplasmic metal binding proteins that share a distinct
fold and ligand binding mechanism. They are comprised
of two globular subdomains connected by a single helix
and bind their specific ligands in the cleft between
these domains. A typical TroA protein is comprised of
two globular subdomains connected by a single helix and
can bind the metal ion in the cleft between these
domains. In addition, these proteins sometimes have a
low complexity region containing a metal-binding
histidine-rich motif (repetitive HDH sequence).
Length = 286
Score = 30.4 bits (69), Expect = 1.7
Identities = 15/60 (25%), Positives = 23/60 (38%)
Query: 135 ILKQTDYLNLVQCESLEELEDHTPEVLQKIDHDEEEHSDDSGNEDDDDGGEWITPSNLKQ 194
K+ L L + L+ LED + DH+ D E D W++P N +
Sbjct: 73 GRKKGKVLTLAKLIDLKTLEDGASHGDHEHDHEHAHGEHDGHEEGGLDPHLWLSPENAAE 132
>gnl|CDD|217385 pfam03140, DUF247, Plant protein of unknown function. The function
of the plant proteins constituting this family is
unknown.
Length = 387
Score = 30.3 bits (69), Expect = 1.9
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 100 TDKEVLAGFYSPSRGCTFNVDGGYLEGLCRG 130
+D+EV F RG F+VD YL G+
Sbjct: 317 SDEEVAKFFNRLCRGVVFDVDDSYLSGVFED 347
>gnl|CDD|224908 COG1997, RPL43A, Ribosomal protein L37AE/L43A [Translation,
ribosomal structure and biogenesis].
Length = 89
Score = 28.1 bits (63), Expect = 2.1
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 264 CPKCGYKTLKRVAVSV 279
CP CG T+KR+A +
Sbjct: 38 CPFCGRTTVKRIATGI 53
>gnl|CDD|235183 PRK03976, rpl37ae, 50S ribosomal protein L37Ae; Reviewed.
Length = 90
Score = 28.0 bits (63), Expect = 2.6
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 264 CPKCGYKTLKRVAVSV 279
CP CG +KRV +
Sbjct: 39 CPVCGRPKVKRVGTGI 54
>gnl|CDD|222046 pfam13324, GCIP, Grap2 and cyclin-D-interacting. GCIP, or Grap2
and cyclin-D-interacting protein, is found in
eukaryotes, and in the human protein CCNDBP1, residues
149-190 constitute a helix-loop-helix domain, residues
190-240 an acidic region, and 240-261 a leucine zipper
domain. GCIP interacts with full-length Grap2 protein
and with the COOH-terminal unique and SH3 domains
(designated QC domain) of Grap2. It is potentially
involved in the regulation of cell differentiation and
proliferation through Grap2 and cyclin D-mediated
signalling pathways. In mice, it is involved in
G1/S-phase progression of hepatocytes, which in older
animals is associated with the development of liver
tumours. In vitro it acts as an inhibitory HLH protein,
for example, blocking transcription of the HNF-4
promoter. In its function as a cyclin D1-binding protein
it is able to reduce CDK4-mediated phosphorylation of
the retinoblastoma protein and to inhibit E2F-mediated
transcriptional activity. GCIP has also been shown to
have interact physically with Rad (Ras associated with
diabetes), Rad being important in regulating cellular
senescence.
Length = 271
Score = 29.3 bits (66), Expect = 3.2
Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 150 LEELEDHTPEVLQKIDHDEEEHSDDSGNEDDDDGGE 185
L E+++ D E+ SD ++DD +G +
Sbjct: 139 LREMKEAKEG--CSNDDSEDPFSDGHHDDDDVEGDD 172
>gnl|CDD|232904 TIGR00280, L37a, ribosomal protein L37a. This model finds
eukaryotic ribosomal protein L37a and its archaeal
orthologs. The nomeclature is tricky because eukaryotes
have proteins called both L37 and L37a [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 92
Score = 27.5 bits (61), Expect = 3.4
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 2/42 (4%)
Query: 261 KVFCPKCGYKTLKRVAVSVDEQGK--QKIHINLKRPLTARGK 300
K CP CG KT+KR + + K K P+T GK
Sbjct: 36 KYVCPFCGKKTVKRGSTGIWTCRKCGAKFAGGAYTPVTPAGK 77
>gnl|CDD|224072 COG1150, HdrC, Heterodisulfide reductase, subunit C [Energy
production and conversion].
Length = 195
Score = 28.1 bits (63), Expect = 5.4
Identities = 15/88 (17%), Positives = 26/88 (29%), Gaps = 14/88 (15%)
Query: 246 ILRCYACYKTTSIMTKVFCPKCGYKTLKRVAVSVDEQGKQKIHINLKRPLTARGKKFSLP 305
+ C CY T + K L+ +AV ++G + P+ ++
Sbjct: 82 LWACVTCYTCTERCPRGVKIVEVVKALRNIAV---KEGLIE-------PMLKAHREVLET 131
Query: 306 TFKGGKHA----NNPIVAEDQPVPDQRP 329
G HA D+ P
Sbjct: 132 VITTGNHAVPINKELRAKRKALGLDELP 159
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 28.8 bits (64), Expect = 5.5
Identities = 16/65 (24%), Positives = 22/65 (33%), Gaps = 8/65 (12%)
Query: 144 LVQCESLEELEDHTPEVLQKIDHDEEEHSDDS--GNEDDDDGGEWITPSNLKQAQRTMDA 201
L E EE+ D T DEE+ DD NE ++ G Q +
Sbjct: 194 LRSMELAEEMGDDTE------SEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEAT 247
Query: 202 RQYEE 206
+ E
Sbjct: 248 DRESE 252
>gnl|CDD|216321 pfam01136, Peptidase_U32, Peptidase family U32.
Length = 232
Score = 28.4 bits (64), Expect = 5.5
Identities = 23/81 (28%), Positives = 31/81 (38%), Gaps = 11/81 (13%)
Query: 58 LSSTDIKVIALTYELHKQHIGVDSINTEPISRQISYINHSVLTDKEVLAGFYSPSRGCTF 117
LS D+ +I EL + GVDS+ E + Y+ V +E L +
Sbjct: 151 LSPKDLCLIEELPELLE--AGVDSLKIEGRMKSPEYVAEVVRAYREALDAYLEGKD---- 204
Query: 118 NVDGGYLEGLC----RGFKNG 134
V E L RGF NG
Sbjct: 205 -VAEELKEELKKLFNRGFTNG 224
>gnl|CDD|221173 pfam11702, DUF3295, Protein of unknown function (DUF3295). This
family is conserved in fungi but the function is not
known.
Length = 509
Score = 28.8 bits (64), Expect = 5.8
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 167 DEEEHSDDSGNEDDDDGGEW 186
EE+ D+S EDDDD +W
Sbjct: 293 TEEDDVDESAIEDDDDDSDW 312
>gnl|CDD|218291 pfam04850, Baculo_E66, Baculovirus E66 occlusion-derived virus
envelope protein.
Length = 389
Score = 28.4 bits (64), Expect = 6.6
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 11/71 (15%)
Query: 24 RLVVLPYDLQIKEADP----DSISFVTEFSKKTG------DYPSLSSTDIKVIALTYELH 73
R VVL D + DP D+ S T ++ T +YPSL + ++ + E
Sbjct: 202 RCVVLTRDTNVNTNDPSWSADNSSNGTTYNGVTARHHNITNYPSLPNFTVRTLD-NVETV 260
Query: 74 KQHIGVDSINT 84
+Q I DSIN
Sbjct: 261 EQIISADSINN 271
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 28.5 bits (64), Expect = 7.1
Identities = 24/94 (25%), Positives = 36/94 (38%), Gaps = 3/94 (3%)
Query: 100 TDKEVLAGFYSPSRGCTFNVDGGYLEGLCRGF---KNGILKQTDYLNLVQCESLEELEDH 156
T E ++G R T ++ GG L G I K T + + L+EL D
Sbjct: 220 TGDEEVSGHRDLERVETNSLRGGMCLVLAEGIALKAPKIQKYTRKMKEEGWDWLQELIDG 279
Query: 157 TPEVLQKIDHDEEEHSDDSGNEDDDDGGEWITPS 190
T E + EE + ++ + G I PS
Sbjct: 280 TIEGKSDAGEEGEEEELSTDADEYEKGPPRIAPS 313
>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation
factor RRN3. This family consists of several eukaryotic
proteins which are homologous to the yeast RRN3 protein.
RRN3 is one of the RRN genes specifically required for
the transcription of rDNA by RNA polymerase I (Pol I) in
Saccharomyces cerevisiae.
Length = 554
Score = 28.4 bits (64), Expect = 7.1
Identities = 13/55 (23%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 149 SLEELEDH-TPEVLQKIDHDEEEHS-DDSGNEDDDDGGEWITPSNLKQAQRTMDA 201
L++++D VL D D+E+ D +++++ E S +K+ +DA
Sbjct: 221 ELDDIDDEEEERVLADEDDDDEDDMFDMDDDDEEESDPEVERTSTIKEVSEKLDA 275
>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen;
Provisional.
Length = 1136
Score = 28.6 bits (63), Expect = 7.7
Identities = 25/95 (26%), Positives = 43/95 (45%), Gaps = 7/95 (7%)
Query: 137 KQTDYLNLVQCESLEELE-----DHTPEVLQKIDHDEEEHSDDSGNEDDDDGGEWITPSN 191
K D L+ + ES+E+ E D E L +H EE ++DDSG + DD E +
Sbjct: 423 KYMDMLDGSEDESVEDNEEEHSGDANEEELSVDEHVEEHNADDSGEQQSDD--ESGEHQS 480
Query: 192 LKQAQRTMDARQYEEKPLVVSCVTTDFAMQNVLKQ 226
+ + ++ E+P V V + ++V +
Sbjct: 481 VNEIVEEQSVNEHVEEPTVADIVEQETVDEHVEEP 515
>gnl|CDD|219366 pfam07295, DUF1451, Protein of unknown function (DUF1451). This
family consists of several hypothetical bacterial
proteins of around 160 residues in length. Members of
this family contain four highly conserved cysteine
resides toward the C-terminal region of the protein. The
function of this family is unknown.
Length = 148
Score = 27.2 bits (61), Expect = 8.8
Identities = 9/34 (26%), Positives = 11/34 (32%), Gaps = 3/34 (8%)
Query: 246 ILRCYACYKTTSIMTKVF---CPKCGYKTLKRVA 276
L C C + CPKCG+ R
Sbjct: 114 TLVCENCGHMLTFYHPSVIPPCPKCGHTEFTRQP 147
>gnl|CDD|216161 pfam00865, Osteopontin, Osteopontin.
Length = 293
Score = 27.8 bits (61), Expect = 9.1
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 149 SLEELEDHTPEVLQKIDHDEEEHSDDSGNEDDDD 182
S EE +D E L ++ EH DD ++DDDD
Sbjct: 43 SSEETDDLKQETLPSKSNESHEHMDDDDDDDDDD 76
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
0.316 0.134 0.392
Gapped
Lambda K H
0.267 0.0563 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,924,289
Number of extensions: 1918106
Number of successful extensions: 2323
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2289
Number of HSP's successfully gapped: 51
Length of query: 391
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 292
Effective length of database: 6,546,556
Effective search space: 1911594352
Effective search space used: 1911594352
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 60 (27.3 bits)