RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13475
(468 letters)
>gnl|CDD|206740 cd09913, EHD, Eps15 homology domain (EHD), C-terminal domain.
Dynamin-like C-terminal Eps15 homology domain (EHD)
proteins regulate endocytic events; they have been
linked to a number of Rab proteins through their
association with mutual effectors, suggesting a
coordinate role in endocytic regulation. Eukaryotic EHDs
comprise four members (EHD1-4) in mammals and single
members in Caenorhabditis elegans (Rme-1), Drosophila
melanogaster (Past1) as well as several eukaryotic
parasites. EHD1 regulates trafficking of multiple
receptors from the endocytic recycling compartment (ERC)
to the plasma membrane; EHD2 regulates trafficking from
the plasma membrane by controlling Rac1 activity; EHD3
regulates endosome-to-Golgi transport, and preserves
Golgi morphology; EHD4 is involved in the control of
trafficking at the early endosome and regulates exit of
cargo toward the recycling compartment as well as late
endocytic pathway. Rme-1, an ortholog of human EHD1,
controls the recycling of internalized receptors from
the endocytic recycling compartment to the plasma
membrane. In D. melanogaster, deletion of the Past1 gene
leads to infertility as well as premature death of adult
flies. Arabidopsis thaliana also has homologs of EHD
proteins (AtEHD1 and AtEHD2), possibly involved in
regulating endocytosis and signaling.
Length = 241
Score = 330 bits (848), Expect = e-112
Identities = 104/243 (42%), Positives = 144/243 (59%), Gaps = 5/243 (2%)
Query: 97 LVLFMGPWSGGKSSIINYLLDNEYSQNSLRTGAEPSPAYFNILSWGESPTILDGTQLAAD 156
+VLF+G +S GKS+ INYLL +Y LRTG EP+ F ++ GE + G L D
Sbjct: 1 MVLFLGQYSTGKSTFINYLLGQDYPG--LRTGPEPTTDRFTVVMHGEDDGTIPGNALVVD 58
Query: 157 --WTFSGLQKFGQGLLDRLRGLQLPHPLLEKINIVEIPGILEIRKQ-VERQFPFNDACQW 213
F GL KFG G L++ G LPHPLLE + IV+ PGIL KQ R + FN C+W
Sbjct: 59 PDKPFRGLSKFGNGFLNKFEGSTLPHPLLESVTIVDTPGILSGEKQRQSRGYDFNAVCRW 118
Query: 214 FIDRADIIFLVYDPSKLDVGPETEAILDQLKGREYQTRIILNKADQVKPEELMRVQGTLI 273
F +RAD+IFL++DP KLD+ E +++QLKG E + RI+LNKAD V ++LMRV G L+
Sbjct: 119 FAERADLIFLLFDPHKLDISDEFRRVIEQLKGHESKIRIVLNKADMVDTQQLMRVYGALM 178
Query: 274 WNISPLMSSSEPPVMYSTSLWSNPYEVGAPIRLLQAQEHAFLRDLRNAIDKRVENKIASA 333
W++S ++++ E P +Y S W PYE +L +E LRDL + K+
Sbjct: 179 WSLSKVINTPEVPRVYIGSFWDQPYEPDTNRKLFLEEEIDLLRDLNSLPRNAALRKLNDL 238
Query: 334 RRF 336
+
Sbjct: 239 IKR 241
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 54.9 bits (133), Expect = 6e-09
Identities = 42/178 (23%), Positives = 69/178 (38%), Gaps = 28/178 (15%)
Query: 98 VLFMGPWSGGKSSIINYLLDNEYSQNSLRTGAEPSPAYFNILSWGESPTILDGT------ 151
+ +G S GKSS++N LL ++ L G P+ +L GE P + G
Sbjct: 1 IAVVGDQSAGKSSVLNALL----GRDILPRGPGPTTRRPLVLRLGEEPGAIPGAVKVEYK 56
Query: 152 -QLAADWTFSGLQKFGQGLLDRLRGLQLPH-----------PLLEKINIVEIPGILEIRK 199
L FS L++ + D++ G PL+ + +V+ PG+
Sbjct: 57 DGLKKFEDFSELREEIEDETDKISGTGKGISSEPIILEILSPLVPGLTLVDTPGL--DSV 114
Query: 200 QVERQFPFNDACQWFIDRADIIFLVYDPSKLDVGPETEAILDQLKGREYQTRIILNKA 257
V Q D + +I ADII V D + E + ++ +T +L K
Sbjct: 115 AVGDQ----DLTEEYIKPADIILAVVDANHDLSTSEALFLAREVDPNGKRTIGVLTKD 168
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 48.6 bits (116), Expect = 7e-07
Identities = 31/181 (17%), Positives = 56/181 (30%), Gaps = 45/181 (24%)
Query: 99 LFMGPWSGGKSSIINYLLDNEYSQNSLRTGAEPSPAYFNILSWGESPTILDGTQLAADWT 158
+ +G GKSS++N LL E + S G T D
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPG----------------TTR--------DPD 36
Query: 159 FSGLQKFGQGLLDRLRGLQLPHPLLEKINIVEIPGILEIRKQVERQFPFNDACQWFIDRA 218
+ K+ +V+ PG+ E + + + A
Sbjct: 37 VYVKEL---------------DKGKVKLVLVDTPGLDEFGGLGREE-----LARLLLRGA 76
Query: 219 DIIFLVYDPSKLDVGPE-TEAILDQLKGREYQTRIILNKADQVKPEELMRVQGTLIWNIS 277
D+I LV D + + + IL +L+ ++ NK D ++ E+ +
Sbjct: 77 DLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNKIDLLEEREVEELLRLEELAKI 136
Query: 278 P 278
Sbjct: 137 L 137
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 37.9 bits (89), Expect = 0.004
Identities = 39/176 (22%), Positives = 65/176 (36%), Gaps = 63/176 (35%)
Query: 97 LVLFMGPWSGGKSSIINYLLDNEYSQNSLRTGAEPSPAYFNILSWGESPTILDGTQLAAD 156
L+ +G +S GKS+++N LL + L TG P+ A +L +G
Sbjct: 2 LLAVVGEFSAGKSTLLNALL----GEEVLPTGVTPTTAVITVLRYG-------------- 43
Query: 157 WTFSGLQKFGQGLLDRLRGLQLPHPLLEKINIVEIPGILEIRKQVERQFPFNDACQW-FI 215
LL+ + +V+ PG+ + + F+
Sbjct: 44 -------------------------LLKGVVLVDTPGLNSTIEH-------HTEITESFL 71
Query: 216 DRADIIFLV--YDPSKLDVGPETEAILDQLKG-REYQTR---IILNKADQVKPEEL 265
RAD + V D P TE+ + LK ++ + +LNK D + EEL
Sbjct: 72 PRADAVIFVLSADQ------PLTESEREFLKEILKWSGKKIFFVLNKIDLLSEEEL 121
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 37.8 bits (89), Expect = 0.004
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 5/52 (9%)
Query: 215 IDRADIIFLVYDPSKLDVGPETEAILDQLKGREYQTRIIL--NKADQVKPEE 264
+ D++ V D S+ +G E IL+ LK + +T +IL NK D VK +E
Sbjct: 80 LKDVDLVLFVVDASE-WIGEGDEFILELLK--KSKTPVILVLNKIDLVKDKE 128
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 36.5 bits (85), Expect = 0.010
Identities = 25/81 (30%), Positives = 37/81 (45%), Gaps = 7/81 (8%)
Query: 185 KINIVEIPGILEI-RKQVERQFPFNDACQWFIDRADIIFLVYDPSKLDVGPETEAILDQL 243
+ +++ PG+ E ER + + DRAD++ LV D V E EA L L
Sbjct: 47 PVVLIDTPGLDEEGGLGRER----VEEARQVADRADLVLLVVDSDLTPV--EEEAKLGLL 100
Query: 244 KGREYQTRIILNKADQVKPEE 264
+ R ++LNK D V E
Sbjct: 101 RERGKPVLLVLNKIDLVPESE 121
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 37.3 bits (88), Expect = 0.012
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 218 ADIIFLVYDPSKLDVGPETEAILDQLKGREYQTRIILNKADQVKPEE 264
D++ V D + +GP E IL++LK + ++LNK D VK +E
Sbjct: 85 VDLVLFVVDADE-KIGPGDEFILEKLKKVKTPVILVLNKIDLVKDKE 130
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 37.4 bits (88), Expect = 0.014
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 215 IDRADIIFLVYDPSKLDVGPETEAILDQLKGREYQTRIILNKADQVKPEELMRVQGTLIW 274
I+ AD++ LV D S+ E + IL++LK + ++LNKAD +L G +
Sbjct: 292 IEEADLVLLVLDASEPL-TEEDDEILEELKDKPVI--VVLNKADLTGEIDLEEENGKPVI 348
Query: 275 NIS 277
IS
Sbjct: 349 RIS 351
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 36.8 bits (86), Expect = 0.019
Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 218 ADIIFLVYDPSKLDVGPETEAILDQLKGREYQTRIILNKADQVKPEELM 266
D+I V D + GP E IL+QLK + +++NK D+VKP+ ++
Sbjct: 86 VDLILFVVDADE-GWGPGDEFILEQLKKTKTPVILVVNKIDKVKPKTVL 133
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 36.7 bits (86), Expect = 0.020
Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 215 IDRADIIFLVYDPSKLDVGPETEAILDQLKGREYQTRIILNKADQVKPEE 264
+D+ D+ LV D + G ++++LK R+ +++NK D +
Sbjct: 83 LDKTDLALLVVDA-GVGPGEYELELIEELKERKIPYIVVINKIDLGEESA 131
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 35.5 bits (83), Expect = 0.021
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 215 IDRADIIFLVYDPSKLDVGPETEAILDQLKGREYQTRIILNKADQVKPEE 264
I+ AD++ LV D S+ + E IL+ + ++LNK+D + E
Sbjct: 80 IEEADLVLLVVDASE-GLDEEDLEILELPAKKPVI--VVLNKSDLLSDAE 126
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily CD represents the first GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 157
Score = 34.7 bits (81), Expect = 0.036
Identities = 24/73 (32%), Positives = 33/73 (45%), Gaps = 15/73 (20%)
Query: 196 EIRKQVERQFPFNDACQWFIDRADIIFLVYDPSKLDVGPETEAILDQLKGREYQTRIIL- 254
EIR+Q E I+ AD+I V D + + P E I L R+ + +IL
Sbjct: 65 EIREQAEIA----------IEEADVILFVVD-GREGLTPADEEIAKYL--RKSKKPVILV 111
Query: 255 -NKADQVKPEELM 266
NK D +K EE
Sbjct: 112 VNKIDNIKEEEEA 124
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ 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. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 34.3 bits (80), Expect = 0.091
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 6/40 (15%)
Query: 91 EIFSKPLVLFMGPWSG-GKSSIINYLLDNEYSQNSLRTGA 129
E+ + +G SG GKS+++N LL L TG
Sbjct: 81 ELLKGKTSVLVGQ-SGVGKSTLLNALLPEL----VLATGE 115
>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 = 32.3 bits (74), Expect = 0.16
Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 185 KINIVEIPGILEIRKQVERQFPFNDACQWFIDRADIIFLVYDPSKLDVGPETEAILDQL- 243
+I +V+ PG++E + + FN + I AD+I LV D + + + E IL++L
Sbjct: 47 QIILVDTPGLIEGASEGKGVEGFNRFLEA-IREADLILLVVD-ASEGLTEDDEEILEELE 104
Query: 244 KGREYQTRIILNK 256
K + ++LNK
Sbjct: 105 KLPKKPIILVLNK 117
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 33.7 bits (78), Expect = 0.21
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 215 IDRADIIFLVYDPSKLDVGPETEAILDQLKGREYQTRIILNKADQVKPEELMRVQ 269
I+ AD++ V D S+ E A+++ L ++ ++LNKAD V EL +
Sbjct: 294 IEEADLVLFVLDASQPLD-KEDLALIELLPKKK-PIIVVLNKADLVSKIELESEK 346
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 32.5 bits (75), Expect = 0.23
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 6/34 (17%)
Query: 97 LVLFMGPWSG-GKSSIINYLLDNEYSQNSLRTGA 129
+ G SG GKS+++N LL + LRTG
Sbjct: 37 TSVLAGQ-SGVGKSTLLNALL----PELDLRTGE 65
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 30.9 bits (70), Expect = 0.97
Identities = 25/80 (31%), Positives = 35/80 (43%), Gaps = 11/80 (13%)
Query: 94 SKPLVLFMGPWSGGKSSIINYLLDNEYSQNSLRTGAEPSPAYFNILSWGESPTILDGTQL 153
S+P V+ G GK+S+ L + T EPS AY +L G S T++D
Sbjct: 2 SQPAVIIAGLCDSGKTSLFTLLTTGTVKKT--VTSQEPSAAYKYMLHKGFSFTLID---- 55
Query: 154 AADWTFSGLQKFGQGLLDRL 173
F G K Q LL+ +
Sbjct: 56 -----FPGHVKLRQKLLETI 70
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 31.1 bits (71), Expect = 0.98
Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 10/76 (13%)
Query: 56 ETTLKELKRLY-DNAIKPLEITYKYRDLSNRHFADPEIFSKPLVLFMGPWSG-GKSSIIN 113
E +KEL R Y D L ++ K D E+ + + + +G SG GKS++IN
Sbjct: 127 EAAVKELLREYEDIGYPVLFVSAKNGDGLE---ELAELLAGKITVLLGQ-SGVGKSTLIN 182
Query: 114 YLLDNEYSQNSLRTGA 129
LL + + +TG
Sbjct: 183 ALL----PELNQKTGE 194
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 31.4 bits (72), Expect = 1.1
Identities = 23/73 (31%), Positives = 31/73 (42%), Gaps = 15/73 (20%)
Query: 196 EIRKQVERQFPFNDACQWFIDRADIIFLVYDPSKLDVGPETEAILDQLKGREYQTRIIL- 254
IR+Q I+ AD+I V D + + P E I L R + +IL
Sbjct: 72 LIREQALIA----------IEEADVILFVVD-GREGITPADEEIAKIL--RRSKKPVILV 118
Query: 255 -NKADQVKPEELM 266
NK D +K EEL
Sbjct: 119 VNKIDNLKAEELA 131
>gnl|CDD|218681 pfam05667, DUF812, Protein of unknown function (DUF812). This
family consists of several eukaryotic proteins of
unknown function.
Length = 536
Score = 31.6 bits (72), Expect = 1.1
Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 6 ERKKIAQRLQTQKQEDIEIPDNLRDKRHVHGILKLDEE-FKEEEELLAKTIETTLKELKR 64
+ K++ + L T +QE+ E+ + + K+ +L E + + L+ + E L EL +
Sbjct: 299 KIKQVNEELTTVRQENEELEEEYKIKKRTVELLPDAENNVAKLQALVVASSE-RLLELAQ 357
Query: 65 LYDNAIKPLEITYK 78
++ PL Y+
Sbjct: 358 QWEAHRTPLIDEYR 371
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 29.7 bits (67), Expect = 2.0
Identities = 20/100 (20%), Positives = 37/100 (37%), Gaps = 13/100 (13%)
Query: 177 QLPHPLLEKINIVEIPGILE-IRKQVERQFPFNDACQWFIDRADIIFLVYDPSKLDVG-- 233
I I+++PG+L+ + + R+D+I V D S+ VG
Sbjct: 38 VFEFGDGVDIQIIDLPGLLDGASEGRGLGEQILAH----LYRSDLILHVIDASEDCVGDP 93
Query: 234 -PETEAILDQLKGREYQ-----TRIILNKADQVKPEELMR 267
+ + + +++ G I+ NK D L R
Sbjct: 94 LEDQKTLNEEVSGSFLFLKNKPEMIVANKIDMASENNLKR 133
>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 = 29.4 bits (67), Expect = 2.3
Identities = 20/91 (21%), Positives = 36/91 (39%), Gaps = 13/91 (14%)
Query: 42 EEFKEEEELLAKTIETTLKELKRLYDNAIKPLEITYKYRDLSNRHFADPEIFSKPLVLFM 101
+ FK + E + K +K+L A K L+ K + + + + +
Sbjct: 69 KYFKSQGEPVLFVNAKNGKGVKKLLKKAKKLLKENEKLK---AKGLLPRPLR----AMVV 121
Query: 102 G-PWSGGKSSIINYLLDNEYSQNSLRTGAEP 131
G P G KS++IN L + + G +P
Sbjct: 122 GIPNVG-KSTLINRLR----GKKVAKVGNKP 147
>gnl|CDD|129413 TIGR00313, cobQ, cobyric acid synthase CobQ. [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 475
Score = 30.1 bits (68), Expect = 2.5
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 8/65 (12%)
Query: 36 GILKLDEEFKEEEELLAKTIETTLKELKRLYD-----NAIKPLEITYKYRDLSN---RHF 87
G + E +K + + K I+ +L+ L R YD A P EI RDL+N
Sbjct: 93 GDMNYQEYYKNKVDFFLKAIKESLEILAREYDYVVIEGAGSPAEINLLKRDLANMRIAEL 152
Query: 88 ADPEI 92
A+ +
Sbjct: 153 ANADA 157
>gnl|CDD|225930 COG3395, COG3395, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 413
Score = 30.1 bits (68), Expect = 2.8
Identities = 29/153 (18%), Positives = 46/153 (30%), Gaps = 45/153 (29%)
Query: 209 DACQWFIDR-ADIIFLVYDPSKLD------VGPETEAILDQLKGR------EYQT--RII 253
A W + A + + V S D +GPET+A+LD L R +
Sbjct: 65 AALSWLKEAGAQVHYKVC--STFDSTLRGNIGPETDALLDALGFSIAVVVPALPLNGRTV 122
Query: 254 LNKADQVKPEELMRVQGTLIWNISPLMSSSEPPVMYSTSLWSNPYEVGAPIRLLQAQEH- 312
+ V G L+ E + P + R + Q
Sbjct: 123 FGGY--------LFVNGVLV---------DESGMARDP---VTPMKDSYLPRHVAKQTKG 162
Query: 313 -------AFLRDLRNAIDKRVENKIASARRFAV 338
A +R +A+ + + A R AV
Sbjct: 163 KIGLVDLADVRQGADAVRAALADLQAEGCRVAV 195
>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 29.9 bits (68), Expect = 2.9
Identities = 15/68 (22%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 2 KIREERKKIAQRLQTQKQEDIEIPDNLRDKRHVHGILKLDEEFKEEEELLA----KTIET 57
+ + E + Q L +KQ++ E +++ + + +L E+ + E E L + +E
Sbjct: 210 RAKAEAAEAEQELLREKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREKLLAEQERMLEH 269
Query: 58 TLKELKRL 65
L+E + L
Sbjct: 270 KLQEQEEL 277
>gnl|CDD|233198 TIGR00938, thrB_alt, homoserine kinase, Neisseria type. Homoserine
kinase is required in the biosynthesis of threonine from
aspartate.The member of this family from Pseudomonas
aeruginosa was shown by direct assay and complementation
to act specifically as a homoserine kinase [Amino acid
biosynthesis, Aspartate family].
Length = 307
Score = 29.8 bits (67), Expect = 3.0
Identities = 16/86 (18%), Positives = 28/86 (32%), Gaps = 2/86 (2%)
Query: 354 YYNHKTFFGNRKKVADDIIEHPQDYHIYAGLSTLTNISRYDLPDPEVYRDFFRLNPVFEF 413
+ A + H + L L DLP ++ D F N +F+
Sbjct: 145 LEAWHILAEKCFEAAPQLEAHMGA-ELDKELDYLDKFWPRDLPRGVIHADLFPDNVLFDG 203
Query: 414 KKLSDTCTYFRGCPINRL-DVAIAYD 438
+ ++ C R D+AI +
Sbjct: 204 DSVKGVIDFYFACTDARAYDLAITVN 229
>gnl|CDD|227321 COG4988, CydD, ABC-type transport system involved in cytochrome bd
biosynthesis, ATPase and permease components [Energy
production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 559
Score = 29.9 bits (68), Expect = 3.1
Identities = 27/108 (25%), Positives = 47/108 (43%), Gaps = 16/108 (14%)
Query: 56 ETTLKELKRLYDNAIKPLEITYKYRD----LSNRHFADPEIFSKPLVLFMGPWSG-GKSS 110
E+ I ++++Y D LS+ + I + L +G SG GKS+
Sbjct: 307 SGEKAEVANEPPIEISLENLSFRYPDGKPALSDLNL---TIKAGQLTALVGA-SGAGKST 362
Query: 111 IINYLLD-NEYSQNSLR----TGAEPSP-AYFNILSW-GESPTILDGT 151
++N LL +Q +R + SP A+ +SW ++P + GT
Sbjct: 363 LLNLLLGFLAPTQGEIRVNGIDLRDLSPEAWRKQISWVSQNPYLFAGT 410
>gnl|CDD|232848 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
Members of this protein were designated YjeQ and are now
designated RsgA (ribosome small subunit-dependent GTPase
A). The strongest motif in the alignment of these
proteins is GXSGVGKS[ST], a classic P-loop for
nucleotide binding. This protein has been shown to
cleave GTP and remain bound to GDP. A role as a
regulator of translation has been suggested. The Aquifex
aeolicus ortholog is split into consecutive open reading
frames. Consequently, this model was build in fragment
mode (-f option) [Protein synthesis, Translation
factors].
Length = 245
Score = 29.3 bits (66), Expect = 3.4
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 91 EIFSKPLVLFMGPWSGGKSSIINYLLDNEYSQ 122
E + +F G GKSS+IN LD Q
Sbjct: 116 EALQNRISVFAGQSGVGKSSLIN-ALDPSVKQ 146
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 29.7 bits (67), Expect = 3.5
Identities = 25/121 (20%), Positives = 48/121 (39%), Gaps = 22/121 (18%)
Query: 23 EIPDNLRDKRHVHGILKLD-----------EEFKEEEELLAKTIETTLKELKRLYDNAIK 71
E+ +++K + + K D + FK+EE + K I + K +
Sbjct: 54 ELERIVKEKPKLLVLNKADLAPKEVTKKWKKYFKKEEGI--KPIFVSAKSRQGGKKIRKA 111
Query: 72 PLEITY-KYRDLSNRHFADPEIFSKPLVLFMGPWSGGKSSIINYLLDNEYSQNSLRTGAE 130
+++ K + L + +I V +G + GKS++IN LL + +T
Sbjct: 112 LEKLSEEKIKRLKKKGLLKRKI----RVGVVGYPNVGKSTLINRLL----GKKVAKTSNR 163
Query: 131 P 131
P
Sbjct: 164 P 164
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 29.1 bits (66), Expect = 3.5
Identities = 27/125 (21%), Positives = 48/125 (38%), Gaps = 41/125 (32%)
Query: 168 GLLDRLRGLQLPHPLLEKINIVEIPGILEIRKQVERQFPFNDACQWFIDRADIIFLVYDP 227
G+LDR PL E+ N +E+ I + + RA ++F + DP
Sbjct: 56 GILDR--------PL-EERNTIEMQAITALA---------------HL-RAAVLFFI-DP 89
Query: 228 SKLDVGPET--------EAILDQLKGR-EYQTRIILNKADQVKPEELMRVQGTLIWNISP 278
S ET ++ ++K ++LNK D + E+L ++ L
Sbjct: 90 S------ETCGYSIEEQLSLFKEIKPLFNKPVIVVLNKIDLLTEEDLSEIEKELEKEGEE 143
Query: 279 LMSSS 283
++ S
Sbjct: 144 VIKIS 148
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 29.6 bits (68), Expect = 3.6
Identities = 21/71 (29%), Positives = 29/71 (40%), Gaps = 15/71 (21%)
Query: 196 EIRKQVERQFPFNDACQWFIDRADIIFLVYDPSKLDVGPETEAILDQLKGREYQTRIIL- 254
+IR+Q E I+ AD+I V D + + P E I L R+ +IL
Sbjct: 69 QIREQAELA----------IEEADVILFVVD-GRAGLTPADEEIAKIL--RKSNKPVILV 115
Query: 255 -NKADQVKPEE 264
NK D E
Sbjct: 116 VNKVDGPDEEA 126
>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 = 28.6 bits (65), Expect = 4.0
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 9/53 (16%)
Query: 221 IFLVYD----PSKLDVGPETEAILDQLKGREYQTRIILNKADQVKPEELMRVQ 269
+ L+ D P+ +D+ +L+ L+ I+L KAD++K EL +V
Sbjct: 85 VVLLIDARHGPTPIDL-----EMLEFLEELGIPFLIVLTKADKLKKSELAKVL 132
>gnl|CDD|185311 PRK15413, PRK15413, glutathione ABC transporter substrate-binding
protein GsiB; Provisional.
Length = 512
Score = 29.5 bits (66), Expect = 4.1
Identities = 10/25 (40%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 274 WNISPLMSS-SEPPVMYSTSLWSNP 297
W +SPL +S + PP +++T+ +SN
Sbjct: 418 WALSPLFASQNWPPTLFNTAFYSNK 442
>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 29.2 bits (66), Expect = 4.5
Identities = 24/113 (21%), Positives = 39/113 (34%), Gaps = 15/113 (13%)
Query: 162 LQKFGQGLLDRLRGLQLPHPLLEKINIVEIPGILEIRKQVERQFPFNDACQWFIDRADII 221
L + LL R ++E G+ + ++ + R D +
Sbjct: 71 LLPALERLLRRRDRP--------DRLVIETTGLADPAPVIQTFLTDPELADGV--RLDGV 120
Query: 222 FLVYDPS--KLDVGPETEAILDQLKGREYQTRIILNKADQVKPEELMRVQGTL 272
V D + + E DQL + I+LNK D V EEL ++ L
Sbjct: 121 VTVVDAAHFLEGLDAIAELAEDQL---AFADVIVLNKTDLVDAEELEALEARL 170
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 29.2 bits (66), Expect = 5.1
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 9/56 (16%)
Query: 218 ADIIFLVYDPS------KLDVGPETEAILDQLKGREYQTRIILNKADQVKPEELMR 267
AD++ V D S KL+ E +L ++ E ++LNK D ++ EE++
Sbjct: 272 ADLLLHVVDASDPEILEKLEA---VEDVLAEIGADEIPIILVLNKIDLLEDEEILA 324
>gnl|CDD|236216 PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
Length = 278
Score = 29.1 bits (66), Expect = 5.1
Identities = 11/22 (50%), Positives = 13/22 (59%), Gaps = 3/22 (13%)
Query: 261 KPEELMRVQGTLIWNISPLMSS 282
KPEEL+ GTL+W SS
Sbjct: 241 KPEELL---GTLLWLADEKASS 259
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 28.8 bits (64), Expect = 5.1
Identities = 33/247 (13%), Positives = 80/247 (32%), Gaps = 51/247 (20%)
Query: 98 VLFMGPWSGGKSSIINYLLDNEYSQNSLRTGAEPSPAYFNILSWGESPTILDGTQLAADW 157
++ +G GK++++N L+ +E+ + T PA ++ W
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPA--------KTIEPYRRNIKLQLW 59
Query: 158 TFSGLQKFGQGLLDRLRGLQLPHP--LLEKINIVEIPGILEIRKQVERQFPFNDACQWFI 215
+G +++ LR +L + E+ ++ + +
Sbjct: 60 DTAGQEEY-----RSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEEL------RELA 108
Query: 216 DRADIIFLVYDPSKLDVGPETEAILDQLKGREYQTRIILNKADQVKPEELMRVQGTLIWN 275
I LV +K+D L + + ILN+ ++ ++
Sbjct: 109 PDDVPILLV--GNKID-----------LFDEQSSSEEILNQLNREVVLL-------VLAP 148
Query: 276 ISPLMSSSEPPVMYSTSLWSNPYEVGAPIRLLQAQEHAFLRDLRNAIDKRVENKIASARR 335
+ L + P ++ +++ V F LR +++ + + + R
Sbjct: 149 KAVLPEVANPALLETSAKSLTGPNVNE----------LFKELLRKLLEEIEKLVLKNELR 198
Query: 336 FAVRVRN 342
R+ N
Sbjct: 199 QLDRLNN 205
>gnl|CDD|202974 pfam04327, DUF464, Protein of unknown function (DUF464).
Length = 102
Score = 27.6 bits (62), Expect = 5.8
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 37 ILKLDEEFKEEEELLAKTIETTLKELKRLYDNAIK 71
+ E E+ +LL +T+ LK + Y IK
Sbjct: 68 LPDDLLEKNEKAQLLLETLLLGLKTIAEQYPEYIK 102
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 29.0 bits (66), Expect = 6.3
Identities = 21/75 (28%), Positives = 42/75 (56%), Gaps = 9/75 (12%)
Query: 3 IREERKKIAQ---RLQTQKQEDIEIPDNLRDKRHVHGILKLDEEFKEEEELLAKTIETTL 59
+RE R ++ + RL QK+E+++ L +KR +L+++ KE E+ + +E
Sbjct: 77 LRERRNELQKLEKRLL-QKEENLDRKLELLEKREE----ELEKKEKELEQKQ-QELEKKE 130
Query: 60 KELKRLYDNAIKPLE 74
+EL+ L + ++ LE
Sbjct: 131 EELEELIEEQLQELE 145
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 28.9 bits (65), Expect = 6.7
Identities = 30/150 (20%), Positives = 61/150 (40%), Gaps = 11/150 (7%)
Query: 1 MKIREERKKIAQRLQTQKQEDIEIPDNLRDKRHVHGILKLDEEFKEEE---ELLAKTIET 57
K+ E ++ + ++ + ++D EI RD+R I +L++E +E++ E L + +
Sbjct: 453 EKLESELERFRREVRDKVRKDREI--RARDRR----IERLEKELEEKKKRVEELERKLAE 506
Query: 58 TLKELKRLYDNAIKPLEITYKYRDLSNRHFADPEIFSKPLVLFMGPWSGGKSSIINYLLD 117
K K P+++ K + + + V+ + SGG + L+D
Sbjct: 507 LRKMRKLELSGKGTPVKVVEKLTLEAIEEAEEEYGIKEGDVILVEDPSGGGARTAEELID 566
Query: 118 NEYSQNSLRTGAEPSPAYFNILSWGESPTI 147
++ G E S A E P +
Sbjct: 567 --KKPRAIIRGEEMSHAAAEEFFKNEIPVL 594
>gnl|CDD|211740 TIGR02385, RelE_StbE, addiction module toxin, RelE/StbE family.
Plasmids may be maintained stably in bacterial
populations through the action of addiction modules, in
which a toxin and antidote are encoded in a cassette on
the plasmid. In any daughter cell that lacks the
plasmid, the toxin persists and is lethal after the
antidote protein is depleted. Toxin/antitoxin pairs are
also found on main chromosomes, and likely represent
selfish DNA. Sequences in the seed for this alignment
all are found adjacent to RelB/DinJ family antitoxin
genes (TIGR02384), as are most genes found by the
resulting model. StbE from Morganella morganii plasmid
R485 shows typical behaviour for an addiction module
toxin. It cannot be cloned without its partner (the
antitoxin), whereas its partner cannot confer plasmid
stability without StbE [Cellular processes, Toxin
production and resistance, Mobile and extrachromosomal
element functions, Other].
Length = 88
Score = 26.9 bits (60), Expect = 7.1
Identities = 11/44 (25%), Positives = 22/44 (50%)
Query: 38 LKLDEEFKEEEELLAKTIETTLKELKRLYDNAIKPLEITYKYRD 81
+ E+FK++ + + K I L +L + + I + +YRD
Sbjct: 2 IVYTEQFKKDLKKIKKYIRKDLPKLLEVIELLINGKPLERRYRD 45
>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 = 28.2 bits (64), Expect = 7.4
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 9/53 (16%)
Query: 221 IFLVYD----PSKLDVGPETEAILDQLKGREYQTRIILNKADQVKPEELMRVQ 269
+ L+ D +LD +++ L+ R I+L KAD++K EL +
Sbjct: 104 VVLLMDIRHPLKELD-----LEMIEWLRERGIPVLIVLTKADKLKKSELNKQL 151
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 28.0 bits (63), Expect = 7.6
Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 15/86 (17%)
Query: 185 KINIVEIPGILEIRKQVERQFPFNDACQWFIDRADIIFLVYDPSKLDVGPETEAILDQLK 244
+IN ++ PG + K+ R D +D + V P+T L+
Sbjct: 63 RINFIDTPGHEDFSKETVRGLAQADGALLVVDANE-----------GVEPQTREHLNIA- 110
Query: 245 GREYQTRII--LNKADQVKPEELMRV 268
II +NK D+V E+ V
Sbjct: 111 -LAGGLPIIVAVNKIDRVGEEDFDEV 135
>gnl|CDD|238699 cd01408, SIRT1, SIRT1: Eukaryotic group (class1) which includes
human sirtuins SIRT1-3 and yeast Hst1-4; and are members
of the SIR2 family of proteins, silent information
regulator 2 (Sir2) enzymes which catalyze NAD+-dependent
protein/histone deacetylation. Sir2 proteins have been
shown to regulate gene silencing, DNA repair, and life
span. The most-studied function, gene silencing,
involves the inactivation of chromosome domains
containing key regulatory genes by packaging them into a
specialized chromatin structure that is inaccessible to
DNA-binding proteins. The nuclear SIRT1 has been shown
to target the p53 tumor suppressor protein for
deacetylation to suppress DNA damage, and the
cytoplasmic SIRT2 homolog has been shown to target
alpha-tubulin for deacetylation for the maintenance of
cell integrity.
Length = 235
Score = 28.4 bits (64), Expect = 8.0
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 8/32 (25%)
Query: 380 IYAGLSTLTNISRYDLPDPEVYRD--FFRLNP 409
+YA N++RY+LP PE D +FR NP
Sbjct: 27 LYA------NLARYNLPYPEAMFDISYFRKNP 52
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 28.7 bits (64), Expect = 8.0
Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 9/59 (15%)
Query: 17 QKQEDIEIPDNLRDKRHVHGILKLDEEFKEEEELLAKTIETTLKELKRLYDNA-IKPLE 74
+K ED+++P +L+D +L E+ + + + + +E + E+ Y NA ++P E
Sbjct: 8 EKIEDLDLPRSLKD--------ELFEKLSKRDGVTEEMVEEIIDEVVSAYLNALVEPYE 58
>gnl|CDD|137467 PRK09677, PRK09677, putative lipopolysaccharide biosynthesis
O-acetyl transferase WbbJ; Provisional.
Length = 192
Score = 27.9 bits (62), Expect = 8.4
Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 9/67 (13%)
Query: 314 FLRDLRNAIDKRVENKIASARRFAVRVRNHAKM---------VDCYLTTYYNHKTFFGNR 364
F+R +R+ + +V + RF +RN + V L + K FFG+
Sbjct: 12 FIRLVRDVLLTKVFYRNCRIIRFPFYIRNDGSINFGEGFTSGVGLRLDAFGRGKLFFGDN 71
Query: 365 KKVADDI 371
+V D +
Sbjct: 72 VQVNDYV 78
>gnl|CDD|148133 pfam06335, DUF1054, Protein of unknown function (DUF1054). This
family consists of several hypothetical bacterial
proteins of unknown function.
Length = 194
Score = 28.0 bits (63), Expect = 9.0
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 8 KKIAQRLQTQKQEDIEIPDNLRDKRHVHGILKLDEEFKEEEELLAKTIETTLKELKRLY 66
++ +R + K+ + + RH I K D +E LA TIE T K+L LY
Sbjct: 146 EQALERFRDVKKAEFLV------GRH---IPKEDPLLMSPDEFLA-TIEDTFKQLLPLY 194
>gnl|CDD|184740 PRK14553, PRK14553, hypothetical protein; Provisional.
Length = 108
Score = 26.8 bits (60), Expect = 9.6
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 37 ILKLDEEFKEEEELLAKTIETTLKELKRLYDNAIK 71
+ DEE E+ +LL +T+E LK L+ Y IK
Sbjct: 68 LPDFDEENNEKLQLLLETLELGLKSLEFQYPKYIK 102
>gnl|CDD|206745 cd11385, RagC_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins C and D. RagC
and RagD are closely related Rag GTPases (ras-related
GTP-binding protein C and D) that constitute a unique
subgroup of the Ras superfamily, and are functional
homologs of Saccharomyces cerevisiae Gtr2. These domains
form heterodimers with RagA or RagB, and similarly, Gtr2
dimerizes with Gtr1 in order to function. They play an
essential role in regulating amino acid-induced target
of rapamycin complex 1 (TORC1) kinase signaling,
exocytic cargo sorting at endosomes, and epigenetic
control of gene expression. In response to amino acids,
the Rag GTPases guide the TORC1 complex to activate the
platform containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 175
Score = 27.6 bits (62), Expect = 9.9
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 98 VLFMGPWSGGKSSI 111
+L MG GKSSI
Sbjct: 2 ILLMGLRRSGKSSI 15
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
0.319 0.137 0.406
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,975,027
Number of extensions: 2536201
Number of successful extensions: 3247
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3230
Number of HSP's successfully gapped: 114
Length of query: 468
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 368
Effective length of database: 6,502,202
Effective search space: 2392810336
Effective search space used: 2392810336
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 (21.7 bits)
S2: 61 (27.3 bits)