RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8958
(294 letters)
>gnl|CDD|206738 cd08771, DLP_1, Dynamin_like protein family includes dynamins and
Mx proteins. The dynamin family of large
mechanochemical GTPases includes the classical dynamins
and dynamin-like proteins (DLPs) that are found
throughout the Eukarya. 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
interferon-induced Mx proteins that inhibit a wide range
of viruses by blocking an early stage of the replication
cycle. Dynamin oligomerizes into helical structures
around the neck of budding vesicles in a GTP
hydrolysis-dependent manner.
Length = 278
Score = 161 bits (409), Expect = 5e-48
Identities = 74/287 (25%), Positives = 113/287 (39%), Gaps = 78/287 (27%)
Query: 1 MTRSPVKVTLSEGPYH-VAQFKDSSREFDLTKE---SDLVELRKEVERRMMNSVRKGKTV 56
TR P+++ L P K+ EF K +D ELR+E+E+ + K +
Sbjct: 36 CTRRPLELQLRRSPSESDEDEKEEWGEFLHLKSKEFTDFEELREEIEKETDRVAGENKGI 95
Query: 57 SNEVISMSVKGPGLQRMVLVDLPGIISTSTQDMASDTRDLIRQMTQTHMSNPNAIILCIQ 116
S E I + ++ P + + LVDLPG+I D D + IR M ++++SNP +IIL +
Sbjct: 96 SPEPIRLEIESPDVPNLTLVDLPGLIKVPVGDQPEDIEEQIRSMVKSYISNPRSIILAVV 155
Query: 117 DGSVDAERSNVTDLVSQMDPQGKRTIFVLTKVSQQLIRIEKDGSVDAERSNVTDLGSVMD 176
+VD S L ++DP+G+RT
Sbjct: 156 PANVDLANSEALKLAREVDPEGERT----------------------------------- 180
Query: 177 LQGKHTIFVLTKVSQQVSMSPPLSPSGQKHRLIKSFIVCLQVDLAEENHSDPQRIKKILA 236
I VLTK+ DL + +D + I +L
Sbjct: 181 ------IGVLTKL-----------------------------DLMDPG-TDAEDILLLLQ 204
Query: 237 GKLFPMKALGYFAVVTGRGGKKDE--SIQDIKEYEENFFKKSKLFST 281
GK+ P+K LGY VV D SI++ E EE FF+ +
Sbjct: 205 GKVIPLK-LGYVGVVNRSQKDIDSGKSIEEALEAEEEFFETHPWYKL 250
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 114 bits (288), Expect = 2e-31
Identities = 48/149 (32%), Positives = 70/149 (46%), Gaps = 12/149 (8%)
Query: 1 MTRSPVKVTLSEGPY-HVAQFKDSSREFDLTKESDLVELRKEVERRMMNSVRKGKTVSNE 59
TR P+ + L E P K ++ L K D ELR+E+E GK +S+E
Sbjct: 31 TTRRPLVLRLGEEPGAIPGAVKVEYKDG-LKKFEDFSELREEIEDETDKISGTGKGISSE 89
Query: 60 VISMSVKGPGLQRMVLVDLPGIISTSTQDMASDTRDLIRQMTQTHMSNPNAIILCIQDGS 119
I + + P + + LVD PG+ S + D +T+ ++ P IIL + D +
Sbjct: 90 PIILEILSPLVPGLTLVDTPGLDSVAVGDQD---------LTEEYI-KPADIILAVVDAN 139
Query: 120 VDAERSNVTDLVSQMDPQGKRTIFVLTKV 148
D S L ++DP GKRTI VLTK
Sbjct: 140 HDLSTSEALFLAREVDPNGKRTIGVLTKD 168
>gnl|CDD|197491 smart00053, DYNc, Dynamin, GTPase. Large GTPases that mediate
vesicle trafficking. Dynamin participates in the
endocytic uptake of receptors, associated ligands, and
plasma membrane following an exocytic event.
Length = 240
Score = 69.1 bits (169), Expect = 8e-14
Identities = 43/147 (29%), Positives = 69/147 (46%), Gaps = 4/147 (2%)
Query: 1 MTRSPVKVTLSEGPYHVAQFKDSSREFDLTKESDLVELRKEVERRMMNSVRKGKTVSNEV 60
+TR P+ + L + A+F K +D E+R E+E K +S
Sbjct: 59 VTRRPLILQLIKSKTEYAEF----LHCKGKKFTDFDEVRNEIEAETDRVTGTNKGISGIP 114
Query: 61 ISMSVKGPGLQRMVLVDLPGIISTSTQDMASDTRDLIRQMTQTHMSNPNAIILCIQDGSV 120
I++ V P + + L+DLPGI + D D I++M + +S +IL + +
Sbjct: 115 INLRVYSPHVLNLTLIDLPGITKVAVGDQPPDIEYQIKKMIKQFISREECLILAVTPANT 174
Query: 121 DAERSNVTDLVSQMDPQGKRTIFVLTK 147
D S+ L ++DPQG RTI V+TK
Sbjct: 175 DLANSDALKLAKEVDPQGLRTIGVITK 201
>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 = 40.9 bits (96), Expect = 2e-04
Identities = 20/100 (20%), Positives = 38/100 (38%), Gaps = 9/100 (9%)
Query: 49 SVRKGKTVSNEVISMSVKGPGLQRMVLVDLPGIISTSTQDMASDTRDLIRQMTQTHMSNP 108
S G T +V + ++ +VLVD PG+ R L+R
Sbjct: 26 SDVPGTTRDPDVYVKELDKGKVK-LVLVDTPGLDEFGGLGREELARLLLRG--------A 76
Query: 109 NAIILCIQDGSVDAERSNVTDLVSQMDPQGKRTIFVLTKV 148
+ I+L + ++E ++ ++ +G I V K+
Sbjct: 77 DLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNKI 116
>gnl|CDD|216255 pfam01031, Dynamin_M, Dynamin central region. This region lies
between the GTPase domain, see pfam00350, and the
pleckstrin homology (PH) domain, see pfam00169.
Length = 296
Score = 34.8 bits (81), Expect = 0.036
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 233 KILAGKLFPMKALGYFAVVTGRGGK---KDESIQDIKEYEENFFKKSKLFST 281
IL K++P+K LGY VV R + +SI++ E E FF+ + T
Sbjct: 3 DILENKVYPLK-LGYVGVVN-RSQQDINDKKSIKEALEDERAFFENHPHYRT 52
>gnl|CDD|206743 cd11383, YfjP, YfjP GTPase. The Era (E. coli Ras-like
protein)-like YfjP subfamily includes several
uncharacterized bacterial GTPases that are similar to
Era. They 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. Era is
characterized by a distinct derivative of the KH domain
(the pseudo-KH domain) which is located C-terminal to
the GTPase domain.
Length = 140
Score = 33.1 bits (76), Expect = 0.061
Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 11/86 (12%)
Query: 67 GPGLQRMVLVDLPGIISTSTQDMASDTRDLIRQMTQTHMSNPNAIILCI--QDGSVDAER 124
G +VL+DLPG+ +D +L R++ + ++ + D ++ A+
Sbjct: 41 QTGGDGLVLLDLPGVGERGRRDREY--EELYRRLLPE----ADLVLWLLDADDRALAADH 94
Query: 125 SNVTDLVSQMDPQGKRTIFVLTKVSQ 150
+ + +FVL +V
Sbjct: 95 ---DFYLLPLAGHDAPLLFVLNQVDP 117
>gnl|CDD|132930 cd07019, S49_SppA_1, Signal peptide peptidase A (SppA), a serine
protease, has catalytic Ser-Lys dyad. Signal peptide
peptidase A (SppA; Peptidase S49; Protease IV): SppAs in
this subfamily are found in all three domains of life
and are involved in the cleavage of signal peptides
after their removal from the precursor proteins by
signal peptidases. Site-directed mutagenesis and
sequence analysis have shown these bacterial, archaeal
and thylakoid SppAs to be serine proteases. The
predicted active site serine for members in this family
occurs in a transmembrane domain. Mutagenesis studies
also suggest that the catalytic center comprises a
Ser-Lys dyad (both residues absolutely conserved within
bacteria, chloroplast and mitochondrial signal peptidase
family members) and not the usual Ser-His-Asp catalytic
triad found in the majority of serine proteases. In
addition to the carboxyl-terminal protease domain that
is conserved in all the S49 family members, the E. coli
SppA contains an amino-terminal domain, similar to
Arabidopsis thaliana SppA1 peptidase. Others, including
sohB peptidase, protein C and archaeal signal peptide
peptidase, do not contain the amino-terminal domain.
Interestingly, the single membrane spanning E. coli SppA
carries out catalysis using a Ser-Lys dyad with the
serine located in the conserved carboxy-terminal
protease domain and the lysine in the non-conserved
amino-terminal domain.
Length = 211
Score = 31.2 bits (70), Expect = 0.48
Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 10/79 (12%)
Query: 168 VTDLGSVMDLQGKHTIFVLTKVSQQVSMSPPLSPSGQK------HRLIKSFIVCLQVDLA 221
+T + + +D G HT V T VS++ L P Q K FI +A
Sbjct: 112 ITTVENSLDSIGVHTDGVSTSPLADVSITRALPPEAQLGLQLSIENGYKRFITL----VA 167
Query: 222 EENHSDPQRIKKILAGKLF 240
+ HS P++I KI G ++
Sbjct: 168 DARHSTPEQIDKIAQGHVW 186
>gnl|CDD|225316 COG2518, Pcm, Protein-L-isoaspartate carboxylmethyltransferase
[Posttranslational modification, protein turnover,
chaperones].
Length = 209
Score = 30.7 bits (70), Expect = 0.75
Identities = 15/41 (36%), Positives = 26/41 (63%)
Query: 130 LVSQMDPQGKRTIFVLTKVSQQLIRIEKDGSVDAERSNVTD 170
L+ Q+ P G+ I V + +Q+L+RI KDG + ER ++ +
Sbjct: 155 LLDQLKPGGRLVIPVGSGPAQRLLRITKDGDGNFERRDLFN 195
>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 = 29.9 bits (68), Expect = 1.1
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 58 NEVISMSVKGPGLQRMVLVDLPGIISTSTQD 88
N+ ++ P L+ + +VD PGI+S Q
Sbjct: 75 NKFEGSTLPHPLLESVTIVDTPGILSGEKQR 105
>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 = 28.4 bits (64), Expect = 1.7
Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 5/77 (6%)
Query: 71 QRMVLVDLPGIISTSTQDMASDTRDLIRQMTQTHMSNPNAIILCIQDGSVDAERSNVTDL 130
++++LVD PG+I +++ + + + + I+L + D S + L
Sbjct: 46 RQIILVDTPGLIEGASEG---KGVEGFNR-FLEAIREADLILLVV-DASEGLTEDDEEIL 100
Query: 131 VSQMDPQGKRTIFVLTK 147
K I VL K
Sbjct: 101 EELEKLPKKPIILVLNK 117
>gnl|CDD|235602 PRK05776, PRK05776, DNA topoisomerase I; Provisional.
Length = 670
Score = 28.8 bits (65), Expect = 4.1
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 5/39 (12%)
Query: 28 DLTKESDLVELRKEVERRMMNSVRKGKTVSNEVISMSVK 66
D+ VEL ++ E + +R GK EVI + +
Sbjct: 533 DIVS----VELTRDFEE-KLEMIRTGKATREEVIEEAKE 566
>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 = 27.9 bits (63), Expect = 5.1
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 19/84 (22%)
Query: 69 GLQR-MVLVDLPGIISTSTQDMASDTRDLIRQMTQTHMSNPNAIILCIQDGSVDAER--- 124
GL + +VLVD PG+ ST ++T++ + +A+I + A++
Sbjct: 43 GLLKGVVLVDTPGLNSTIEHH---------TEITESFLPRADAVIFV-----LSADQPLT 88
Query: 125 -SNVTDLVSQMDPQGKRTIFVLTK 147
S L + GK+ FVL K
Sbjct: 89 ESEREFLKEILKWSGKKIFFVLNK 112
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 27.4 bits (62), Expect = 6.8
Identities = 25/102 (24%), Positives = 37/102 (36%), Gaps = 24/102 (23%)
Query: 53 GKTVSNEVISMSVKGPGLQRMVLVDLPGIISTSTQDMASD---TRDLIRQMTQTHMSNPN 109
G TV E K G + + +VDLPG S + D RD +
Sbjct: 29 GVTV--EKKEGEFKLGG-KEIEIVDLPGTYSLTPYSE--DEKVARDFLL-------GEEP 76
Query: 110 AIILCIQDGSVDA---ERSNVTDLVSQMDPQGKRTIFVLTKV 148
+I+ + VDA ER+ L Q+ G + L +
Sbjct: 77 DLIVNV----VDATNLERNLY--LTLQLLELGLPVVVALNMI 112
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
0.315 0.131 0.354
Gapped
Lambda K H
0.267 0.0608 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,283,946
Number of extensions: 1338600
Number of successful extensions: 1133
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1129
Number of HSP's successfully gapped: 27
Length of query: 294
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 198
Effective length of database: 6,679,618
Effective search space: 1322564364
Effective search space used: 1322564364
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: 59 (26.8 bits)