RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8312
(145 letters)
>gnl|CDD|241334 cd13180, RanBD_RanBP3, Ran-binding protein 3 Ran-binding domain.
RanBP3, a Ran-interacting nuclear protein, unlike the
related proteins RanBP1 and RanBP2, which promote
disassembly of the export complex in the cytosol, acts
as a CRM1 cofactor, enhancing nuclear export signal
(NES) export by stabilizing the export complex in the
nucleus. CRM1/Exportin1 is responsible for exporting
many proteins and ribonucleoproteins from the nucleus to
the cytosol. RanBP3 also alters the cargo selectivity of
CRM1, promoting recognition of the NES of HIV-1 Rev and
of other cargos while deterring recognition of the
import adaptor protein Snurportin1. RanBP3 contains a
N-terminal nuclear localization signal (NLS), 2 FxFG
motifs, and a single RanBD. RabBD shares structural
similarity to the PH domain, but lacks detectable
sequence similarity.
Length = 113
Score = 128 bits (325), Expect = 1e-39
Identities = 48/93 (51%), Positives = 67/93 (72%), Gaps = 6/93 (6%)
Query: 58 EEVNILQINCKLFLYDSVK-TWIELGRGQLRLNDINNSL----SRIVIRVVGSLRVILNT 112
E N+LQINCKLF +D K +W+E GRG LRLND + SR+V+R G+LRVILNT
Sbjct: 1 GERNVLQINCKLFAFDKSKQSWVERGRGTLRLNDKASEDGPFQSRLVMRTQGTLRVILNT 60
Query: 113 KIWAEMVVQKPSDNSVRLTAI-ENGQAKVYLVK 144
KIW M V++ S+ S+R+TA+ +G+ KV+L++
Sbjct: 61 KIWPGMTVERASEKSLRITAMDPDGEVKVFLIQ 93
>gnl|CDD|197549 smart00160, RanBD, Ran-binding domain. Domain of apporximately 150
residues that stabilises the GTP-bound form of Ran (the
Ras-like nuclear small GTPase).
Length = 130
Score = 62.0 bits (151), Expect = 3e-13
Identities = 29/92 (31%), Positives = 45/92 (48%), Gaps = 5/92 (5%)
Query: 50 VAVVTGEEEEVNILQINCKLFLYDS-VKTWIELGRGQLRLN--DINNSLSRIVIRVVGSL 106
V V TGEE+E I KL+ + + K W E G G L++ N RIV+R G L
Sbjct: 10 VEVKTGEEDEEVIFSARAKLYRFANDKKEWKERGVGDLKILKSKDNGGKVRIVMRRDGVL 69
Query: 107 RVILNTKIWAEMVVQ--KPSDNSVRLTAIENG 136
+V N I+ M ++ S+ +++ T +
Sbjct: 70 KVCANHPIFKSMTLKPLAGSNRALKWTPEDFA 101
>gnl|CDD|241232 cd00835, RanBD_family, Ran-binding domain. The RanBD is present in
RanBD1, RanBD2, RanBD3, Nuc2, and Nuc50. Most of these
proteins have a single RanBD, with the exception of
RanBD2 which has 4 RanBDs. Ran is a Ras-like nuclear
small GTPase, which regulates receptor-mediated
transport between the nucleus and the cytoplasm. RanGTP
hydrolysis is stimulated by RanGAP together with the
Ran-binding domain containing acessory proteins RanBP1
and RanBP2. These accessory proteins stabilize the
active GTP-bound form of Ran. The Ran-binding domain is
found in multiple copies in Nuclear pore complex
proteins. RabBD shares structural similarity to the PH
domain, but lacks detectable sequence similarity. The
RanBD proteins of the nuclear pore complex (NPC):
nucleoporin 1 (NUP1), NUP2, NUP61, and Nuclear Pore
complex Protein 9 (npp-9) are present in the parent, but
specific models were not made due to lineage. To date
there been no reports of inositol phosphate or
phosphoinositide binding by Ran-binding proteins.
Length = 111
Score = 60.0 bits (146), Expect = 1e-12
Identities = 25/95 (26%), Positives = 42/95 (44%), Gaps = 8/95 (8%)
Query: 59 EVNILQINCKLFLYDS-VKTWIELGRGQLRLN-DINNSLSRIVIRVVGSLRVILNTKIWA 116
E + KL+ +D K W E G G L++ RI++R +V LN I
Sbjct: 1 EEVLFSERAKLYRFDKDTKEWKERGVGDLKILKHKETGKYRILMRREQVGKVCLNHLITP 60
Query: 117 EMVVQK--PSDNSVRLTAI----ENGQAKVYLVKV 145
EM ++ SD +V TA+ G+ + + ++
Sbjct: 61 EMKLKPTAGSDKAVVWTAVDDSDGEGKPETFALRF 95
>gnl|CDD|241323 cd13169, RanBD_NUP50_plant, Ran-binding protein 2, repeat 1.
RanBP2 (also called E3 SUMO-protein ligase RanBP2, 358
kDa nucleoporin, and nuclear pore complex (NPC) protein
Nup358) is a giant nucleoporin that localizes to the
cytosolic face of the NPC. RanBP2 contains a
leucine-rich region, 8 zinc-finger motifs, a cyclophilin
A homologous domain, and 4 RanBDs. Ran is a Ras-like
nuclear small GTPase, which regulates receptor-mediated
transport between the nucleus and the cytoplasm. RanGTP
hydrolysis is stimulated by RanGAP together with the
Ran-binding domain containing acessory proteins RanBP1
and RanBP2. These accessory proteins stabilize the
active GTP-bound form of Ran. All eukaryotic cells
contain RanBP1, but in vertebrates however, the main
RanBP seems to be RanBP2. There is no RanBP2 ortholog in
yeast. Transport complex disassembly is accomplished by
a small ubiquitin-related modifier-1 (SUMO-1)-modified
version of RanGAP that is bound to RanBP2. RanBP1 acts
as a second line of defense against exported
RanGTP#importin complexes which have escaped from
dissociation by RanBP2. RanBP2 also interacts with the
importin subunit beta-1. RabBD shares structural
similarity to the PH domain, but lacks detectable
sequence similarity. The first RanBD2 is present in this
hierarchy.
Length = 112
Score = 50.1 bits (120), Expect = 6e-09
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 69 LFLYDSVKTWIELGRGQLRLNDINNSLSRIVIRVVGSLRVILNTKIWAEMVVQKPSD 125
LF + + W E GRG+LR+N +R+V+R G+ R++LN ++ +M + K
Sbjct: 11 LFEFIT-GGWKERGRGELRVNLSTTGKARLVMRAKGNYRLLLNANLFPDMKLTKMMG 66
>gnl|CDD|241324 cd13170, RanBD_NUP50, Nucleoporin 50 Ran-binding domain. NUP50
acts as a cofactor for the importin-alpha:importin-beta
heterodimer, which allows for transportation of many
nuclear-targeted proteins through nuclear pore
complexes. It is thought to function primarily at the
terminal stages of nuclear protein import to coordinate
import complex disassembly and importin recycling. NUP50
is composed of a N-terminal NUP50 domain which binds the
C-terminus of importin-beta, a central domain which
binds importin-beta, and a C-terminal RanBD which binds
importin-beta through Ran-GTP. NUP50:importin-alpha then
binds cargo and can stimulate nuclear import. The
N-terminal domain of NUP50 is also able to displace
nuclear localization signals from importin-alpha. NUP50
interacts with cyclin-dependent kinase inhibitor 1B
which binds to cyclin E-CDK2 or cyclin D-CDK4 complexes
and prevents its activation, thereby controling the cell
cycle progression at G1. Ran is a Ras-like nuclear small
GTPase, which regulates receptor-mediated transport
between the nucleus and the cytoplasm. RanGTP hydrolysis
is stimulated by RanGAP together with the Ran-binding
domain containing acessory proteins RanBP1 and RanBP2.
These accessory proteins stabilize the active GTP-bound
form of Ran. RabBD shares structural similarity to the
PH domain, but lacks detectable sequence similarity.
Length = 109
Score = 47.3 bits (113), Expect = 9e-08
Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 6/85 (7%)
Query: 67 CKLFLYDSVKTWIELGRGQLRLNDI-NNSLSRIVIRVVGSL-RVILNTKIWAEMVVQKPS 124
CKLF+ W + G G L L + + S +R+++R SL +++LN ++ M V
Sbjct: 9 CKLFVKKDDGEWKDKGVGTLYLKKVKDTSKARLLVRADTSLGKILLNILLYPGMPVTVTG 68
Query: 125 DNSVRLTAIEN----GQAKVYLVKV 145
N+V L + N G +L++V
Sbjct: 69 KNNVMLVCVPNPPAEGGPVTFLLRV 93
>gnl|CDD|109686 pfam00638, Ran_BP1, RanBP1 domain.
Length = 122
Score = 46.3 bits (110), Expect = 3e-07
Identities = 28/101 (27%), Positives = 50/101 (49%), Gaps = 8/101 (7%)
Query: 52 VVTGEEEEVNILQINCKLFLYDS-VKTWIELGRGQLRLN-DINNSLSRIVIRVVGSLRVI 109
V +GEE+E + + KLF +D+ VK W E G G +++ + ++ RI++R L+V
Sbjct: 2 VKSGEEDEEVLFSVRAKLFRFDAEVKQWKERGVGDIKILKNKDDGKVRILMRRDQVLKVC 61
Query: 110 LNTKIWAEMVVQ--KPSDNS----VRLTAIENGQAKVYLVK 144
N I +M ++ SD S A G+ + ++
Sbjct: 62 ANHYITPDMTLKPLAGSDRSWVWTAADFADGEGKPEQLAIR 102
>gnl|CDD|241333 cd13179, RanBD_RanBP1, Ran-binding domain. RanBP1 interacts
specifically with GTP-charged Ran. RanBP1 does not
activate GTPase activity of Ran, but does markedly
increase GTP hydrolysis by the RanGTPase-activating
protein (RanGAP1). In both mammalian cells and in yeast,
RanBP1 acts as a negative regulator of Regulator of
chromosome condensation 1 (RCC1) by inhibiting
RCC1-stimulated guanine nucleotide release from Ran. In
addition to Ran, RanBP1 has been shown to interact with
Exportin-1 and Importin subunit beta-1 which docks the
NPC at the cytoplasmic side of the nuclear pore complex.
RabBP1 contains a single RanBD. The RanBD is present in
RanBD1, RanBD2, RanBD3, Nuc2, and Nuc50. Most of these
proteins have a single RanBD, with the exception of
RanBD2 which has 4 RanBDs. Ran is a Ras-like nuclear
small GTPase, which regulates receptor-mediated
transport between the nucleus and the cytoplasm. RanGTP
hydrolysis is stimulated by RanGAP together with the
Ran-binding domain containing acessory proteins RanBP1
and RanBP2. These accessory proteins stabilize the
active GTP-bound form of Ran. The Ran-binding domain is
found in multiple copies in Nuclear pore complex
proteins. RabBD shares structural similarity to the PH
domain, but lacks detectable sequence similarity.
Length = 126
Score = 43.0 bits (102), Expect = 5e-06
Identities = 25/86 (29%), Positives = 45/86 (52%), Gaps = 7/86 (8%)
Query: 49 AVAVVTGEEEEVNILQINCKLFLYDSV---KTWIELGRGQLRL--NDINNSLSRIVIRVV 103
V V T EE+E + ++ KL+ +D+ W E G G +++ + N + R+++R
Sbjct: 1 EVEVKTNEEDEEELFKMRAKLYRFDTENDPPEWKERGTGDVKILKHKETNKI-RLLMRRD 59
Query: 104 GSLRVILNTKIWAEMVVQKPSDNSVR 129
+L++ N I EM + KP+ S R
Sbjct: 60 KTLKICANHYITPEMKL-KPNCGSDR 84
>gnl|CDD|241335 cd13181, RanBD_NUP2, Nucleoporin 2 Ran-binding domain. Yeast
protein Nup2 transiently associates with Nuclear pore
complexes (NPCs) and when artificially tethered to DNA,
can prevent the spread of transcriptional activation or
repression between flanking genes, a function termed
boundary activity (BA). Nup2 and the Ran
guanylyl-nucleotide exchange factor, Prp20, interact at
specific chromatin regions and enable the NPC to play an
active role in chromatin organization. Nup60p, the nup
responsible for anchoring Nup2 and the Mlp proteins to
the NPC is required for Nup2-dependent BA. Nup2 contains
an N-terminal Nup50 family domain and a C-terminal
RanBD. Ran is a Ras-like nuclear small GTPase, which
regulates receptor-mediated transport between the
nucleus and the cytoplasm. RanGTP hydrolysis is
stimulated by RanGAP together with the Ran-binding
domain containing acessory proteins RanBP1 and RanBP2.
These accessory proteins stabilize the active GTP-bound
form of Ran. RabBD shares structural similarity to the
PH domain, but lacks detectable sequence similarity.
Length = 111
Score = 42.4 bits (100), Expect = 5e-06
Identities = 31/94 (32%), Positives = 53/94 (56%), Gaps = 7/94 (7%)
Query: 58 EEVNILQINCKLFLYDSVKT---WIELGRGQLR-LNDINNSLSRIVIRVVGSLRVILNTK 113
EEV + KL L+D + G G+L+ L + + SRI++R GSLRV+LNT
Sbjct: 2 EEV-LYTKRAKLMLFDPSNKESPYTSKGVGELKLLKNKDTGKSRILVRAEGSLRVLLNTL 60
Query: 114 IWAEMVVQKPSD-NSVRLTAI-ENGQAKVYLVKV 145
+ ++ +K + + VR+ I +G+ + Y++KV
Sbjct: 61 VLKDVKYEKMGNGSLVRVPTINSDGKIETYVIKV 94
>gnl|CDD|241330 cd13176, RanBD1_RanBD3_RanBP2_mammal-like, Ran-binding protein 2,
Ran binding domain repeats 1 and 3. RanBP2 (also called
E3 SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and
nuclear pore complex (NPC) protein Nup358) is a giant
nucleoporin that localizes to the cytosolic face of the
NPC. RanBP2 contains a leucine-rich region, 8
zinc-finger motifs, a cyclophilin A homologous domain,
and 4 RanBDs. Ran is a Ras-like nuclear small GTPase,
which regulates receptor-mediated transport between the
nucleus and the cytoplasm. RanGTP hydrolysis is
stimulated by RanGAP together with the Ran-binding
domain containing acessory proteins RanBP1 and RanBP2.
These accessory proteins stabilize the active GTP-bound
form of Ran. All eukaryotic cells contain RanBP1, but in
vertebrates however, the main RanBP seems to be RanBP2.
There is no RanBP2 ortholog in yeast. Transport complex
disassembly is accomplished by a small ubiquitin-related
modifier-1 (SUMO-1)-modified version of RanGAP that is
bound to RanBP2. RanBP1 acts as a second line of defense
against exported RanGTP-importin complexes which have
escaped from dissociation by RanBP2. RanBP2 also
interacts with the importin subunit beta-1. RabBD shares
structural similarity to the PH domain, but lacks
detectable sequence similarity. The members here include
human, chicken, frog, tunicates, sea urchins, ticks, sea
anemones, and sponges. RanBD repeats 1 and 3 are present
in this hierarchy.
Length = 116
Score = 34.2 bits (79), Expect = 0.005
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 4/78 (5%)
Query: 54 TGEEEEVNILQINCKLFLYDS-VKTWIELGRGQLR-LNDINNSLSRIVIRVVGSLRVILN 111
TGEE+E + KL+ +D K W E G G ++ L + + RI++R L++ N
Sbjct: 1 TGEEDEEELFSHRAKLYRFDKDSKQWKERGIGDIKILQNPESGKVRILMRRDQVLKLCAN 60
Query: 112 TKIWAEMVVQ--KPSDNS 127
I +M ++ SD S
Sbjct: 61 HYITPDMKLKPNAGSDRS 78
>gnl|CDD|241331 cd13177, RanBD2_RanBP2_mammal-like, Ran-binding protein 2, Ran
binding domain repeats 2. RanBP2 (also called E3
SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and
nuclear pore complex (NPC) protein Nup358) is a giant
nucleoporin that localizes to the cytosolic face of the
NPC. RanBP2 contains a leucine-rich region, 8
zinc-finger motifs, a cyclophilin A homologous domain,
and 4 RanBDs. Ran is a Ras-like nuclear small GTPase,
which regulates receptor-mediated transport between the
nucleus and the cytoplasm. RanGTP hydrolysis is
stimulated by RanGAP together with the Ran-binding
domain containing acessory proteins RanBP1 and RanBP2.
These accessory proteins stabilize the active GTP-bound
form of Ran. All eukaryotic cells contain RanBP1, but in
vertebrates however, the main RanBP seems to be RanBP2.
There is no RanBP2 ortholog in yeast. Transport complex
disassembly is accomplished by a small ubiquitin-related
modifier-1 (SUMO-1)-modified version of RanGAP that is
bound to RanBP2. RanBP1 acts as a second line of defense
against exported RanGTP-importin complexes which have
escaped from dissociation by RanBP2. RanBP2 also
interacts with the importin subunit beta-1. RabBD shares
structural similarity to the PH domain, but lacks
detectable sequence similarity. The members here include
human, chicken, frog, tunicates, sea urchins, ticks, sea
anemones, and sponges. RanBD repeats 2 is present in
this hierarchy.
Length = 117
Score = 33.5 bits (76), Expect = 0.012
Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 4/68 (5%)
Query: 54 TGEEEEVNILQINCKLFLYDS-VKTWIELGRGQLRL--NDINNSLSRIVIRVVGSLRVIL 110
TGEE+E + KLF +D+ V W E G G L++ N++N L R+++R L+V
Sbjct: 1 TGEEDEKVLYSQRVKLFRFDAEVSQWKERGVGNLKILKNEVNGKL-RMLMRREQVLKVCA 59
Query: 111 NTKIWAEM 118
N I M
Sbjct: 60 NHWITTTM 67
>gnl|CDD|227499 COG5171, YRB1, Ran GTPase-activating protein (Ran-binding protein)
[Intracellular trafficking and secretion].
Length = 211
Score = 33.8 bits (77), Expect = 0.017
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 46 KYEAVAVVTGEEEEVNILQINCKLFLYD-SVKTWIELGRGQLR-LNDINNSLSRIVIRVV 103
+ + V + T EE+E + + KLF +D K W E G G + L + +RI +R
Sbjct: 76 ELQRVHLKTNEEDETVLFKARAKLFRFDEEAKEWKERGTGDMIILKHKKTNKARITMRRD 135
Query: 104 GSLRVILNTKIWAEMVVQ 121
+L++ N I E +Q
Sbjct: 136 KTLKLCANHFINPEFKLQ 153
>gnl|CDD|241326 cd13172, RanBD2_RanBP2_insect-like, Ran-binding protein 2, Ran
binding domain repeat 2. RanBP2 (also called E3
SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and
nuclear pore complex (NPC) protein Nup358) is a giant
nucleoporin that localizes to the cytosolic face of the
NPC. RanBP2 contains a leucine-rich region, 8
zinc-finger motifs, a cyclophilin A homologous domain,
and 4 RanBDs. Ran is a Ras-like nuclear small GTPase,
which regulates receptor-mediated transport between the
nucleus and the cytoplasm. RanGTP hydrolysis is
stimulated by RanGAP together with the Ran-binding
domain containing acessory proteins RanBP1 and RanBP2.
These accessory proteins stabilize the active GTP-bound
form of Ran. All eukaryotic cells contain RanBP1, but in
vertebrates however, the main RanBP seems to be RanBP2.
There is no RanBP2 ortholog in yeast. Transport complex
disassembly is accomplished by a small ubiquitin-related
modifier-1 (SUMO-1)-modified version of RanGAP that is
bound to RanBP2. RanBP1 acts as a second line of defense
against exported RanGTP-importin complexes which have
escaped from dissociation by RanBP2. RanBP2 also
interacts with the importin subunit beta-1. RabBD shares
structural similarity to the PH domain, but lacks
detectable sequence similarity. The members here include
insects and nematodes. The second RanBD is present in
this hierarchy.
Length = 113
Score = 30.1 bits (68), Expect = 0.16
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 68 KLFLYDS-VKTWIELGRGQLRL--NDINNSLSRIVIRVVGSLRVILNTKIWAEMVVQKPS 124
KL +D K W E G G ++L N +N+ R+++R L+V N ++ +M + +
Sbjct: 10 KLLRFDKATKEWKERGLGNIKLLRNKEDNNKVRLLMRREQVLKVCCNQRLTKDMEFKYLT 69
Query: 125 DNSVRLT 131
+N LT
Sbjct: 70 NNPKALT 76
>gnl|CDD|220918 pfam10972, DUF2803, Protein of unknown function (DUF2803). This
family of proteins with unknown function appears to be
restricted to Gammaproteobacteria.
Length = 149
Score = 28.8 bits (65), Expect = 0.59
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 73 DSVKTWIELGRGQLRLNDINNSLSRIVIRVVGSLRVILNTKIWAEMVVQKPSDNSVRLTA 132
+ K + L QL+LNDI N L R G +V+L+ W + V + + +RL A
Sbjct: 60 PAAKGFQLLPESQLQLNDIANRLER-----SGGYQVLLH-LAWRQPVGGRDNAPPIRLFA 113
Query: 133 IEN 135
++
Sbjct: 114 GKD 116
>gnl|CDD|236477 PRK09355, PRK09355, hydroxyethylthiazole kinase; Validated.
Length = 263
Score = 29.0 bits (66), Expect = 0.83
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 38 EAARACKRKYEAVAVVTGEE 57
E A+A +KY V VVTGE
Sbjct: 147 EIAKAAAKKYGTVVVVTGEV 166
>gnl|CDD|215056 PLN00104, PLN00104, MYST -like histone acetyltransferase;
Provisional.
Length = 450
Score = 28.6 bits (64), Expect = 1.3
Identities = 20/76 (26%), Positives = 28/76 (36%), Gaps = 18/76 (23%)
Query: 11 EPDSDSGGEDNGTTRHKSLSEAAREYEEAARACKRKYEAVAVVTGEEE-EVNILQINCKL 69
E D ED + + R KRK + V G EE + L+ + +
Sbjct: 117 ETVGDEKVEDKVASL------------KMTRHQKRKIDETHVEEGHEELDAASLREHEE- 163
Query: 70 FLYDSVKT--WIELGR 83
+ VK IELGR
Sbjct: 164 --FTKVKNIATIELGR 177
>gnl|CDD|238575 cd01170, THZ_kinase, 4-methyl-5-beta-hydroxyethylthiazole (Thz)
kinase catalyzes the phosphorylation of the
hydroxylgroup of Thz. A reaction that allows cells to
recycle Thz into the thiamine biosynthesis pathway, as
an alternative to its synthesis from cysteine, tyrosine
and 1-deoxy-D-xylulose-5-phosphate.
Length = 242
Score = 27.5 bits (62), Expect = 2.6
Identities = 13/19 (68%), Positives = 14/19 (73%)
Query: 38 EAARACKRKYEAVAVVTGE 56
E A+A RKY AV VVTGE
Sbjct: 143 ELAKALARKYGAVVVVTGE 161
>gnl|CDD|173033 PRK14569, PRK14569, D-alanyl-alanine synthetase A; Provisional.
Length = 296
Score = 27.3 bits (60), Expect = 3.2
Identities = 26/68 (38%), Positives = 33/68 (48%), Gaps = 14/68 (20%)
Query: 16 SGGEDNGTTRHKSLSEAAREYEEAARACKRKYEAVAV---VTGEEEEVNILQINCKLFLY 72
SGG T + KS+ E YEEA+ KY V + VTG+E V I+ +Y
Sbjct: 139 SGGSSIATFKVKSIQELKHAYEEAS-----KYGEVMIEQWVTGKEITVAIVNDE----VY 189
Query: 73 DSVKTWIE 80
SV WIE
Sbjct: 190 SSV--WIE 195
>gnl|CDD|214890 smart00893, ETF, Electron transfer flavoprotein domain. Electron
transfer flavoproteins (ETFs) serve as specific
electron acceptors for primary dehydrogenases,
transferring the electrons to terminal respiratory
systems. They can be functionally classified into
constitutive, "housekeeping" ETFs, mainly involved in
the oxidation of fatty acids (Group I), and ETFs
produced by some prokaryotes under specific growth
conditions, receiving electrons only from the oxidation
of specific substrates (Group II). ETFs are
heterodimeric proteins composed of an alpha and beta
subunit, and contain an FAD cofactor and AMP. ETF
consists of three domains: domains I and II are formed
by the N- and C-terminal portions of the alpha subunit,
respectively, while domain III is formed by the beta
subunit. Domains I and III share an almost identical
alpha-beta-alpha sandwich fold, while domain II forms
an alpha-beta-alpha sandwich similar to that of
bacterial flavodoxins. FAD is bound in a cleft between
domains II and III, while domain III binds the AMP
molecule. Interactions between domains I and III
stabilise the protein, forming a shallow bowl where
domain II resides. This entry represents the N-terminal
domain of both the alpha and beta subunits from Group I
and Group II ETFs.
Length = 185
Score = 26.8 bits (60), Expect = 3.9
Identities = 14/46 (30%), Positives = 16/46 (34%), Gaps = 3/46 (6%)
Query: 19 EDNGTTRHKSLSEAAREYEEAARACKRKYEAVAVVTGEEEEVNILQ 64
E + A E AAR K K E AVV G L+
Sbjct: 2 EHGVGALINPVDLEALE---AARRLKEKGEVTAVVVGPPAAEEALR 44
>gnl|CDD|183676 PRK12679, cbl, transcriptional regulator Cbl; Reviewed.
Length = 316
Score = 27.1 bits (60), Expect = 4.1
Identities = 14/35 (40%), Positives = 25/35 (71%), Gaps = 1/35 (2%)
Query: 55 GEEEEVNILQINCKLFLYDSVKTWIELGRGQLRLN 89
GE+EE N+++++ + L+D+ W+ L RGQL+ N
Sbjct: 249 GEQEESNLIRLDTR-HLFDANTVWLGLKRGQLQRN 282
>gnl|CDD|219956 pfam08658, Rad54_N, Rad54 N terminal. This is the N terminal of
the DNA repair protein Rad54.
Length = 191
Score = 26.5 bits (59), Expect = 4.2
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 3 QNPSETFDEPDSDSGGEDNGTTRHKSLSE 31
+ +E EP+ NG HKSL+E
Sbjct: 149 EEKAEKDQEPEESETKLSNGPKVHKSLAE 177
>gnl|CDD|140267 PTZ00240, PTZ00240, 60S ribosomal protein P0; Provisional.
Length = 323
Score = 26.5 bits (58), Expect = 5.2
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 28 SLSEAAREYEEAARACKRKYEAV 50
S++ A REYEE C KY V
Sbjct: 3 SITTAKREYEERLVDCLTKYSCV 25
>gnl|CDD|145326 pfam02110, HK, Hydroxyethylthiazole kinase family.
Length = 246
Score = 26.2 bits (58), Expect = 6.4
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 30 SEAAREYEEAARACKRKYEAVAVVTGEEEEV 60
E A + AA+ RKY V VVTGE + V
Sbjct: 134 GEGATDAIRAAQQAARKYGTVVVVTGEVDYV 164
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 24.9 bits (55), Expect = 6.4
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 27 KSLSEAARE-YEEAARACKRKYEA 49
K+LSE ++ YEE A K +YE
Sbjct: 40 KNLSEEEKKPYEEKAEKEKARYEK 63
>gnl|CDD|182694 PRK10746, PRK10746, putative transport protein YifK; Provisional.
Length = 461
Score = 26.3 bits (58), Expect = 6.9
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 91 INNSLSRIVIRVVGSLRVILNTKIWAEM 118
+ L RI+I VG++ VI+ W E+
Sbjct: 237 VGKVLWRILIFYVGAIFVIVTIFPWNEI 264
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
0.313 0.129 0.358
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,213,754
Number of extensions: 642282
Number of successful extensions: 501
Number of sequences better than 10.0: 1
Number of HSP's gapped: 494
Number of HSP's successfully gapped: 35
Length of query: 145
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 57
Effective length of database: 7,034,450
Effective search space: 400963650
Effective search space used: 400963650
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 (21.9 bits)
S2: 54 (24.5 bits)