RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17384
(295 letters)
>gnl|CDD|214540 smart00164, TBC, Domain in Tre-2, BUB2p, and Cdc16p. Probable
Rab-GAPs. Widespread domain present in Gyp6 and Gyp7,
thereby giving rise to the notion that it performs a
GTP-activator activity on Rab-like GTPases.
Length = 216
Score = 132 bits (335), Expect = 1e-37
Identities = 55/162 (33%), Positives = 87/162 (53%), Gaps = 2/162 (1%)
Query: 5 NTITQIRLDISRTFPHLCLFQ-NEGPYYNTLHYMLASYVSYNTRISYVQGMSYICALFIL 63
+ + QI D+ RTFP FQ EGP +L +L +Y YN + Y QGM+++ A +L
Sbjct: 45 SIVHQIEKDLRRTFPEHSFFQDKEGPGQESLRRVLKAYALYNPEVGYCQGMNFLAAPLLL 104
Query: 64 NISTAYEAFVCFCNFLNKSVFYVFYSLNIRMMQAYYATYNDLFKYNLPKLHRHFHSCGLT 123
+ +AF C + + FY ++ +Q + L K P L++H G+T
Sbjct: 105 VMEDEEDAFWCLVKLMER-YGPNFYLPDMSGLQLDLLQLDRLVKEYDPDLYKHLKDLGIT 163
Query: 124 PDLYLLDWIYTLFSKAMGLDLVCKIWDLVMRDGEVFIFRAAL 165
P LY L W TLF++ + L++V +IWD++ +G F+FR AL
Sbjct: 164 PSLYALRWFLTLFARELPLEIVLRIWDVLFAEGSDFLFRVAL 205
>gnl|CDD|215997 pfam00566, RabGAP-TBC, Rab-GTPase-TBC domain. Identification of a
TBC domain in GYP6_YEAST and GYP7_YEAST, which are
GTPase activator proteins of yeast Ypt6 and Ypt7,
implies that these domains are GTPase activator proteins
of Rab-like small GTPases.
Length = 206
Score = 130 bits (329), Expect = 4e-37
Identities = 55/163 (33%), Positives = 84/163 (51%), Gaps = 2/163 (1%)
Query: 3 YDNTITQIRLDISRTFPHLCLFQNEGPYYNTLHYMLASYVSYNTRISYVQGMSYICALFI 62
QI D+ RTFPH F+N G L +L +Y YN + Y QGM++I A +
Sbjct: 35 DSPDEEQIEKDVPRTFPHHFFFKN-GEGQQQLRRILKAYSIYNPDVGYCQGMNFIAAPLL 93
Query: 63 LNISTAYEAFVCFCNFLNKSVFYVFYSLNIRMMQAYYATYNDLFKYNLPKLHRHFHSCGL 122
L + EAF CF + L F+ + +Q + +L K + P+L++H GL
Sbjct: 94 LVVLDEEEAFWCFVSLLEYL-LRDFFLPSFPGLQRDLYVFEELLKKHDPELYKHLQKLGL 152
Query: 123 TPDLYLLDWIYTLFSKAMGLDLVCKIWDLVMRDGEVFIFRAAL 165
P L+ W TLF++ + L+ V ++WDL + G+ F+FR AL
Sbjct: 153 DPSLFASKWFLTLFARELPLETVLRLWDLFLEGGKFFLFRVAL 195
>gnl|CDD|227535 COG5210, COG5210, GTPase-activating protein [General function
prediction only].
Length = 496
Score = 104 bits (260), Expect = 4e-25
Identities = 48/162 (29%), Positives = 78/162 (48%), Gaps = 1/162 (0%)
Query: 5 NTITQIRLDISRTFPHLCLFQNEGPY-YNTLHYMLASYVSYNTRISYVQGMSYICALFIL 63
I+QI D+SRTFP LFQ E L +L +Y YN + YVQGM+++ A +L
Sbjct: 255 EIISQIEKDLSRTFPDNSLFQTEISIRAENLRRVLKAYSLYNPEVGYVQGMNFLAAPLLL 314
Query: 64 NISTAYEAFVCFCNFLNKSVFYVFYSLNIRMMQAYYATYNDLFKYNLPKLHRHFHSCGLT 123
+ + +AF C L ++ N+ + +DL + P+L+ H G+
Sbjct: 315 VLESEEQAFWCLVKLLKNYGLPGYFLKNLSGLHRDLKVLDDLVEELDPELYEHLLREGVV 374
Query: 124 PDLYLLDWIYTLFSKAMGLDLVCKIWDLVMRDGEVFIFRAAL 165
++ W TLF + L+ +IWD + +G +F+ AL
Sbjct: 375 LLMFAFRWFLTLFVREFPLEYALRIWDCLFLEGSSMLFQLAL 416
>gnl|CDD|215698 pfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA
polymerase). A reverse transcriptase gene is usually
indicative of a mobile element such as a retrotransposon
or retrovirus. Reverse transcriptases occur in a variety
of mobile elements, including retrotransposons,
retroviruses, group II introns, bacterial msDNAs,
hepadnaviruses, and caulimoviruses.
Length = 194
Score = 53.1 bits (128), Expect = 2e-08
Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 8/82 (9%)
Query: 165 LDFKKAYDSIDRETLFNILEEYGADAKTVAIIKESLQATKSKIKFMGDISNPFEIKTGVR 224
LD KKA+DSI + L L +G + + S+ + G+
Sbjct: 58 LDLKKAFDSIPHDPLDRPLTAFGLPQRFIRWRTFSVLVNGN--------PGGRYEWRGLP 109
Query: 225 QGDGLSPLLFNCVLEKVIREWR 246
QG LSPLLFN + +++R R
Sbjct: 110 QGSVLSPLLFNLFMNELLRPLR 131
>gnl|CDD|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat)
retrotransposon and non-LTR retrovirus reverse
transcriptase (RT). This subfamily contains both non-LTR
retrotransposons and non-LTR retrovirus RTs. RTs
catalyze the conversion of single-stranded RNA into
double-stranded DNA for integration into host
chromosomes. RT is a multifunctional enzyme with
RNA-directed DNA polymerase, DNA directed DNA polymerase
and ribonuclease hybrid (RNase H) activities.
Length = 220
Score = 49.6 bits (119), Expect = 4e-07
Identities = 26/88 (29%), Positives = 33/88 (37%), Gaps = 38/88 (43%)
Query: 163 AALDFKKAYDSIDRETLFNILEEYGADAKTVAIIKESLQATKSKIKFMGDISNPFEIKTG 222
LDF+KA+DS+D E L L G
Sbjct: 85 VFLDFEKAFDSVDHEFLLKAL--------------------------------------G 106
Query: 223 VRQGDGLSPLLFNCVLEKVIREWRIISK 250
VRQGD LSPLLFN L+ ++R +
Sbjct: 107 VRQGDPLSPLLFNLALDDLLRLLNKEEE 134
>gnl|CDD|238828 cd01651, RT_G2_intron, RT_G2_intron: Reverse transcriptases (RTs)
with group II intron origin. RT transcribes DNA using
RNA as template. Proteins in this subfamily are found in
bacterial and mitochondrial group II introns. Their most
probable ancestor was a retrotransposable element with
both gag-like and pol-like genes. This subfamily of
proteins appears to have captured the RT sequences from
transposable elements, which lack long terminal repeats
(LTRs).
Length = 226
Score = 43.0 bits (102), Expect = 7e-05
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 166 DFKKAYDSIDRETLFNILEEYGADAKTVAIIKESLQATKSKIKFMGDISNPFEIKTGVRQ 225
D K +D+ID + L IL+ D + + +I++ L+A + E + G Q
Sbjct: 76 DIKGFFDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGVLEDGK------LVETEKGTPQ 129
Query: 226 GDGLSPLLFNCVLEKVIREW 245
G +SPLL N L ++ +
Sbjct: 130 GGVISPLLANIYLHELDKFV 149
>gnl|CDD|100102 cd00387, Ribosomal_L7_L12, Ribosomal protein L7/L12. Ribosomal
protein L7/L12 refers to the large ribosomal subunit
proteins L7 and L12, which are identical except that L7
is acetylated at the N terminus. It is a component of
the L7/L12 stalk, which is located at the surface of the
ribosome. The stalk base consists of a portion of the
23S rRNA and ribosomal proteins L11 and L10. An extended
C-terminal helix of L10 provides the binding site for
L7/L12. L7/L12 consists of two domains joined by a
flexible hinge, with the helical N-terminal domain (NTD)
forming pairs of homodimers that bind to the extended
helix of L10. It is the only multimeric ribosomal
component, with either four or six copies per ribosome
that occur as two or three dimers bound to the L10
helix. L7/L12 is the only ribosomal protein that does
not interact directly with rRNA, but instead has
indirect interactions through L10. The globular
C-terminal domains of L7/L12 are highly mobile. They are
exposed to the cytoplasm and contain binding sites for
other molecules. Initiation factors, elongation factors,
and release factors are known to interact with the
L7/L12 stalk during their GTP-dependent cycles. The
binding site for the factors EF-Tu and EF-G comprises
L7/L12, L10, L11, the L11-binding region of 23S rRNA,
and the sarcin-ricin loop of 23S rRNA. Removal of L7/L12
has minimal effect on factor binding and it has been
proposed that L7/L12 induces the catalytically active
conformation of EF-Tu and EF-G, thereby stimulating the
GTPase activity of both factors. In eukaryotes, the
proteins that perform the equivalent function to L7/L12
are called P1 and P2, which do not share sequence
similarity with L7/L12. However, a bacterial L7/L12
homolog is found in some eukaryotes, in mitochondria and
chloroplasts. In archaea, the protein equivalent to
L7/L12 is called aL12 or L12p, but it is closer in
sequence to P1 and P2 than to L7/L12.
Length = 127
Score = 30.2 bits (69), Expect = 0.46
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 14/54 (25%)
Query: 178 TLFN-ILEEYGADAKTVAIIKE-------SLQATKSKIKFMGDISNPFEIKTGV 223
T F+ +LE +GA K +A+IKE L+ K ++ S P +K GV
Sbjct: 59 TEFDVVLESFGAAKK-IAVIKEVREITGLGLKEAKDLVE-----SAPKVLKEGV 106
>gnl|CDD|238452 cd00887, MoeA, MoeA family. Members of this family are involved in
biosynthesis of the molybdenum cofactor (MoCF), an
essential cofactor of a diverse group of redox enzymes.
MoCF biosynthesis is an evolutionarily conserved pathway
present in eubacteria, archaea and eukaryotes. MoCF
contains a tricyclic pyranopterin, termed molybdopterin
(MPT). MoeA, together with MoaB, is responsible for the
metal incorporation into MPT, the third step in MoCF
biosynthesis. The plant homolog Cnx1 is a MoeA-MogA
fusion protein. The mammalian homolog gephyrin is a
MogA-MoeA fusion protein, that plays a critical role in
postsynaptic anchoring of inhibitory glycine receptors
and major GABAa receptor subtypes.
Length = 394
Score = 29.8 bits (68), Expect = 1.8
Identities = 10/38 (26%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 171 YDSIDRETLFNILEEYGADAKTVAIIKESLQATKSKIK 208
YDS L +L E GA+ + I+ + +A + ++
Sbjct: 193 YDSN-SYMLAALLRELGAEVVDLGIVPDDPEALREALE 229
>gnl|CDD|129294 TIGR00190, thiC, thiamine biosynthesis protein ThiC. The thiC
ortholog is designated thiA in Bacillus subtilis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Thiamine].
Length = 423
Score = 28.9 bits (65), Expect = 3.4
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 156 GEVFIFRAALDFKKAYDSIDRETLFNILEEY---GADAKTV--AIIKESLQATKSKIKFM 210
G V I++AA A + +D + +F +E+ G D T+ ++ E ++ K +
Sbjct: 119 GTVPIYQAAEKVHGAVEDMDEDDMFRAIEKQAKDGVDFMTIHAGVLLEYVERLKRSGRIT 178
Query: 211 GDIS 214
G +S
Sbjct: 179 GIVS 182
>gnl|CDD|238824 cd01646, RT_Bac_retron_I, RT_Bac_retron_I: Reverse transcriptases
(RTs) in bacterial retrotransposons or retrons. The
polymerase reaction of this enzyme leads to the
production of a unique RNA-DNA complex called msDNA
(multicopy single-stranded (ss)DNA) in which a small
ssDNA branches out from a small ssRNA molecule via a
2'-5'phosphodiester linkage. Bacterial retron RTs
produce cDNA corresponding to only a small portion of
the retron genome.
Length = 158
Score = 27.7 bits (62), Expect = 5.7
Identities = 8/37 (21%), Positives = 14/37 (37%)
Query: 165 LDFKKAYDSIDRETLFNILEEYGADAKTVAIIKESLQ 201
LD YDSI +L L + + +++
Sbjct: 1 LDISNFYDSIYTHSLPWALHGKIKAKQLLKLLRLLGN 37
>gnl|CDD|205299 pfam13118, DUF3972, Protein of unknown function (DUF3972). This is
a Proteobacterial family of unknown function. Some of
the proteins in this family are annotated as being
kinesin-like proteins.
Length = 126
Score = 26.9 bits (60), Expect = 6.7
Identities = 9/26 (34%), Positives = 18/26 (69%)
Query: 176 RETLFNILEEYGADAKTVAIIKESLQ 201
+E L+++ E Y D KT+ +++E L+
Sbjct: 98 KEALYSMQELYDEDRKTIDLLREQLK 123
>gnl|CDD|173552 PTZ00359, PTZ00359, hypothetical protein; Provisional.
Length = 443
Score = 27.8 bits (62), Expect = 6.8
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 2/38 (5%)
Query: 74 CF--CNFLNKSVFYVFYSLNIRMMQAYYATYNDLFKYN 109
CF C LNK VFY F + + + A+ T + +
Sbjct: 173 CFGGCMTLNKKVFYTFAFIYMLVFAAHAYTLGEFKENG 210
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 27.8 bits (63), Expect = 7.0
Identities = 11/35 (31%), Positives = 15/35 (42%)
Query: 174 IDRETLFNILEEYGADAKTVAIIKESLQATKSKIK 208
I E L LEE G + + + E+L K I
Sbjct: 188 ISVEELIEKLEEEGYEVEESLLSPEALVIEKGNIA 222
>gnl|CDD|223380 COG0303, MoeA, Molybdopterin biosynthesis enzyme [Coenzyme
metabolism].
Length = 404
Score = 28.0 bits (63), Expect = 7.2
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 165 LDFKKAYDSIDRETLFNILEEYGADAKTVAIIKESLQATKSKIK 208
L+ + YDS L +LE G + + I+ + +A + I+
Sbjct: 195 LEPGQIYDSN-SYMLAALLERAGGEVVDLGIVPDDPEALREAIE 237
>gnl|CDD|198211 cd10348, SH2_Cterm_shark_like, C-terminal Src homology 2 (SH2)
domain found in SH2 domains, ANK, and kinase domain
(shark) proteins. These non-receptor protein-tyrosine
kinases contain two SH2 domains, five ankyrin
(ANK)-like repeats, and a potential tyrosine
phosphorylation site in its carboxyl-terminal tail
which resembles the phosphorylation site in members of
the src family. Like, mammalian non-receptor
protein-tyrosine kinases, ZAP-70 and syk proteins, they
do not have SH3 domains. However, the presence of ANK
makes these unique among protein-tyrosine kinases. Both
tyrosine kinases and ANK repeats have been shown to
transduce developmental signals, and SH2 domains are
known to participate intimately in tyrosine kinase
signaling. These tyrosine kinases are believed to be
involved in epithelial cell polarity. The members of
this family include the shark (SH2 domains, ANK, and
kinase domain) gene in Drosophila and yellow fever
mosquitos, as well as the hydra protein HTK16.
Drosophila Shark is proposed to transduce
intracellularly the Crumbs, a protein necessary for
proper organization of ectodermal epithelia,
intercellular signal. In general SH2 domains are
involved in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 86
Score = 26.2 bits (58), Expect = 7.5
Identities = 8/46 (17%), Positives = 20/46 (43%), Gaps = 8/46 (17%)
Query: 1 MLYDNTITQIRLDISRTFPHLCLFQNEGPYYNTL-----HYMLASY 41
++Y+N + + + + ++GPY+ +L HY +
Sbjct: 42 LVYENHVYHFEI---QNRDDKWFYIDDGPYFESLEHLIEHYTQFAD 84
>gnl|CDD|163707 cd08151, AOS, Allene oxide synthase. Allene oxide synthase
converts a fatty acid hydroperoxide to an allene oxide,
which is an unstable epoxide. In corals, the enzyme is
part of a eiconaosid synthesis pathway that is initiated
by a lipoxygenase, which generates the fatty acid
hydroperoxides in the first step. The structure of
allene oxide synthase closely resembles that of
catalase, but allene oxide synthase does not have
catalase activity.
Length = 328
Score = 27.4 bits (61), Expect = 8.4
Identities = 10/20 (50%), Positives = 10/20 (50%)
Query: 148 IWDLVMRDGEVFIFRAALDF 167
DLVM GE F F A F
Sbjct: 98 PLDLVMNTGESFGFWTAASF 117
>gnl|CDD|151318 pfam10869, DUF2666, Protein of unknown function (DUF2666). This
Archaeal family of proteins has no known function.
Length = 131
Score = 26.7 bits (59), Expect = 8.4
Identities = 23/92 (25%), Positives = 42/92 (45%), Gaps = 9/92 (9%)
Query: 169 KAYDSIDRETLFNILEEYGADAKTVAIIKESLQATKS--KIKFMGDISNPFEIKTGVRQG 226
+ ID + + I +E+ K I E+L KS + + +I+ E K +++
Sbjct: 46 PEFAPIDMDKIREIADEF-KKVKKEEEISEALVKLKSPATTRKLNEITEEKEGKYALKE- 103
Query: 227 DGLSPLLFNCVLEKVIREWRIISKEGSKFLTK 258
+L N VLE++ + + SK K+L K
Sbjct: 104 -----ILNNIVLERLGLKLDVPSKNLEKYLEK 130
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
0.327 0.140 0.426
Gapped
Lambda K H
0.267 0.0731 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,064,154
Number of extensions: 1452236
Number of successful extensions: 1839
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1829
Number of HSP's successfully gapped: 33
Length of query: 295
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 199
Effective length of database: 6,679,618
Effective search space: 1329243982
Effective search space used: 1329243982
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 59 (26.5 bits)