RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13600
(186 letters)
>gnl|CDD|233194 TIGR00930, 2a30, K-Cl cotransporter. [Transport and binding
proteins, Other].
Length = 953
Score = 104 bits (260), Expect = 3e-26
Identities = 37/121 (30%), Positives = 63/121 (52%), Gaps = 12/121 (9%)
Query: 63 VGDHTENDQTDAEKTVNEVMKDIVTNKTSILDEDTKSSLTPD----------EGNVRRMH 112
+ D QT++ + E+++ +KT E +T + NVR+ +
Sbjct: 829 LMDINAKPQTESMEAFEEMIRPFRLHKTEKDREAKDPKMTWTKPWKITDAELQSNVRKSY 888
Query: 113 TAVKLNEVIVNKSHEAQLVILNLPGPPKETNIERESNYMEFLEVLTEGLERVLMVRGSNS 172
V+LNE+++ S +A LV+L+LP P K + YM +LEVL+E L VL+VRG++
Sbjct: 889 RQVRLNELLLEYSRDAALVVLSLPVPRK--GSIPDELYMAWLEVLSEDLPPVLLVRGNHR 946
Query: 173 S 173
+
Sbjct: 947 N 947
>gnl|CDD|204929 pfam12460, MMS19_N, NER and RNAPII transcription protein n
terminal. This domain family is found in eukaryotes,
and is approximately 60 amino acids in length. MMS19 is
required for both nucleotide excision repair (NER) and
RNA polymerase II (RNAP II) transcription.
Length = 64
Score = 28.3 bits (64), Expect = 0.50
Identities = 9/44 (20%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 68 ENDQTDAEKTVNEVMKDIVTNKTSILD--EDTKSSLTPDEGNVR 109
D + A+ + +++ + + K ++LD E LT ++ +R
Sbjct: 7 SRDSSKADASADQIAELVENGKLTLLDLVESLGEYLTSEDPIIR 50
>gnl|CDD|163556 TIGR03844, cysteate_syn, cysteate synthase. Members of this family
are cysteate synthase, an enzyme of alternate pathway to
sulfopyruvate, a precursor of coenzyme M [Biosynthesis
of cofactors, prosthetic groups, and carriers, Other,
Energy metabolism, Methanogenesis].
Length = 398
Score = 28.5 bits (64), Expect = 2.3
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 68 ENDQTDAEKTVNEVMKDIVTNKT 90
E+D DAE ++ EV D++TN+T
Sbjct: 280 ESDMPDAENSIEEVYSDVLTNRT 302
>gnl|CDD|145046 pfam01691, Adeno_E1B_19K, Adenovirus E1B 19K protein / small
t-antigen. This family consists of adenovirus E1B 19K
protein or small t-antigen. The E1B 19K protein inhibits
E1A induced apoptosis and hence prolongs the viability
of the host cell. It can also inhibit apoptosis mediated
by tumour necrosis factor alpha and Fas antigen. E1B 19K
blocks apoptosis by interacting with and inhibiting the
p53-inducible and death- promoting Bax protein. The E1B
region of adenovirus encodes two proteins E1B 19K the
small t-antigen as found in this family and E1B 55K the
large t-antigen which is not found in this family; both
of these proteins inhibit E1A induced apoptosis.
Length = 135
Score = 26.9 bits (60), Expect = 4.0
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 151 MEFLEVLTE-GLERVLMVRGSNSSHHCYRYLFCGSMA 186
M+ L++L + R L+ SN + +R+LF G +A
Sbjct: 1 MDLLKILEDFKSLRRLLEGASNRTSWFWRFLFGGRLA 37
>gnl|CDD|206770 cd11365, RNase_PH_archRRP42, RRP42 subunit of archaeal exosome.
The RRP42 subunit of the archaeal exosome is a member of
the RNase_PH family, named after the bacterial
Ribonuclease PH, a 3'-5' exoribonuclease. Structurally
all members of this family form hexameric rings (trimers
of dimers). In archaea, the ring is formed by three
Rrp41:Rrp42 dimers. The central chamber within the ring
contains three phosphorolytic active sites located in an
Rrp41 pocket at the interface between Rrp42 and Rrp41.
The ring is capped by three copies of Rrp4 and/or Csl4
which contain putative RNA interaction domains. The
archaeal exosome degrades single-stranded RNA (ssRNA) in
the 3'-5' direction, but also can catalyze the reverse
reaction of adding nucleoside diphosphates to the 3'-end
of RNA which has been shown to lead to the formation of
poly-A-rich tails on RNA. It is required for 3'
processing of the 5.8S rRNA.
Length = 256
Score = 27.6 bits (62), Expect = 4.2
Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 29/79 (36%)
Query: 102 TPDEGNVRRMHTAVKLNEVIVNKSHEAQLVIL----NLPGPPKETNIE---------RES 148
TP+EG + IVN A+L+ L PGPP E IE RES
Sbjct: 67 TPNEGVL------------IVN----AELLPLASPTFEPGPPDENAIELARVVDRGIRES 110
Query: 149 NYMEFLEVLTEGLERVLMV 167
++ +++ E ++V +V
Sbjct: 111 KAIDLEKLVIEPGKKVWVV 129
>gnl|CDD|151407 pfam10960, DUF2762, Protein of unknown function (DUF2762). Members
in this family of proteins are annotated as holin-like
protein BhlA however this cannot be confirmed.
Length = 64
Score = 25.8 bits (57), Expect = 4.4
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 142 TNIERESNYMEFLEVLTEGLERV 164
N ERES Y +E +T+ LE
Sbjct: 29 ENKERESKYQNIIEEITDKLEIF 51
>gnl|CDD|131233 TIGR02178, yeiP, elongation factor P-like protein YeiP. This model
represents the family of Escherichia coli protein YeiP,
a close homolog of elongation factor P (TIGR00038) and
probably itself a translation factor. Member of this
family are found only in some Gammaproteobacteria,
including E. coli and Vibrio cholerae [Protein
synthesis, Translation factors].
Length = 186
Score = 27.2 bits (60), Expect = 4.5
Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 4/64 (6%)
Query: 6 FRQRFDAVPTHSRRPPSTETVHCLDNIDSPLHLVDGTLIDGVDYVFQNQ----PLKITKL 61
++ R VPT S+ + LD ++ + DG +YVF ++ P K
Sbjct: 37 YKFRMYDVPTGSKVEERFKADDMLDTVELLRREASFSYKDGEEYVFMDEEDYTPYTFDKD 96
Query: 62 DVGD 65
+ D
Sbjct: 97 AIED 100
>gnl|CDD|233406 TIGR01420, pilT_fam, pilus retraction protein PilT. This model
represents the PilT subfamily of proteins related to
GspE, a protein involved in type II secretion (also
called the General Secretion Pathway). PilT is an
apparent cytosolic ATPase associated with type IV pilus
systems. It is not required for pilin biogenesis, but is
required for twitching motility and social gliding
behaviors, shown in some species, powered by pilus
retraction. Members of this family may be found in some
species that type IV pili but have related structures
for DNA uptake and natural transformation [Cell
envelope, Surface structures, Cellular processes,
Chemotaxis and motility].
Length = 343
Score = 26.9 bits (60), Expect = 6.5
Identities = 11/39 (28%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 31 NIDSPLHLVDGTLIDGVDYVFQNQPLKITKLDVGDHTEN 69
N + H++ T+ D ++YV +N+ I + +VG+ T +
Sbjct: 147 NKNKAYHII--TIEDPIEYVHKNKRSLINQREVGEDTLS 183
>gnl|CDD|215186 PLN02327, PLN02327, CTP synthase.
Length = 557
Score = 26.9 bits (60), Expect = 6.8
Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 124 KSHEAQLVILNLPGPPKETNIERESNYMEFLEVLTEGLERVLMV 167
K+HEA L +LNL +E ++E + E + LTE + R+ MV
Sbjct: 261 KAHEAILKVLNLLSVAREPDLEEWTARAESCDNLTEPV-RIAMV 303
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 27.0 bits (60), Expect = 7.6
Identities = 23/132 (17%), Positives = 49/132 (37%), Gaps = 4/132 (3%)
Query: 31 NIDSPLHLVDGTLIDGVDY-VFQNQPLKITKLDVGDHTENDQTDAEKTVNEVMKDI--VT 87
++ ++D G DY V Q ++ D+ ND + + ++++I
Sbjct: 258 DVKRVFTVLDDVYYSGKDYEVLIQQAIEDLVEDLERERANDIIQVSRQLLNILREIKFAE 317
Query: 88 NKTSILDEDTKSSLTPDEGNVRRMHTAVKLNEVIVNKSHEAQLVILNLPGPPKETNIERE 147
K + + S T + + + N+ + E + + K+ +IE E
Sbjct: 318 EKRLVCKLGSASIATRFSSPNVQENDVEEKNDNSNVQQKEKKKE-ESKAKEEKQEDIEFE 376
Query: 148 SNYMEFLEVLTE 159
+ E +E L E
Sbjct: 377 KRFKELMEELKE 388
>gnl|CDD|111411 pfam02509, Rota_NS35, Rotavirus non-structural protein 35.
Rotavirus non-structural protein 35 (NS35) is a basic
protein which possesses RNA-binding activity and is
essential for genome replication.
Length = 316
Score = 26.4 bits (58), Expect = 8.9
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 42 TLIDGVDYVFQNQPLKITKLDVGDH 66
+G + VFQN + KLD H
Sbjct: 150 PTAEGGEIVFQNSYFTMWKLDYSSH 174
>gnl|CDD|176544 cd08602, GDPD_ScGlpQ1_like, Glycerophosphodiester phosphodiesterase
domain of Streptomycin coelicolor (GlpQ1) and similar
proteins. This subfamily corresponds to the
glycerophosphodiester phosphodiesterase domain (GDPD)
present in a group of putative bacterial and eukaryotic
glycerophosphodiester phosphodiesterases (GP-GDE, EC
3.1.4.46) similar to Escherichia coli periplasmic
phosphodiesterase GlpQ, as well as plant
glycerophosphodiester phosphodiesterases (GP-PDEs), all
of which catalyzes the Ca2+-dependent degradation of
periplasmic glycerophosphodiesters to produce
sn-glycerol-3-phosphate (G3P) and the corresponding
alcohols. The prototypes of this family include putative
secreted phosphodiesterase encoded by gene glpQ1
(SCO1565) from the pho regulon in Streptomyces
coelicolor genome, and in plants, two distinct
Arabidopsis thaliana genes, AT5G08030 and AT1G74210,
coding putative GP-PDEs from the cell walls and
vacuoles, respectively.
Length = 309
Score = 26.5 bits (59), Expect = 8.9
Identities = 14/63 (22%), Positives = 21/63 (33%), Gaps = 7/63 (11%)
Query: 59 TKLDVGDHTENDQTDAEKTVNEVMKDIVT-------NKTSILDEDTKSSLTPDEGNVRRM 111
T + +T A+ T + +K+I T K I+ D L V
Sbjct: 203 TIPPQDTPEGDSRTYADLTTDAGLKEIATYADGIGPWKDLIIPSDANGRLGTPTDLVEDA 262
Query: 112 HTA 114
H A
Sbjct: 263 HAA 265
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 0.132 0.377
Gapped
Lambda K H
0.267 0.0852 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,049,709
Number of extensions: 799710
Number of successful extensions: 494
Number of sequences better than 10.0: 1
Number of HSP's gapped: 493
Number of HSP's successfully gapped: 23
Length of query: 186
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 95
Effective length of database: 6,901,388
Effective search space: 655631860
Effective search space used: 655631860
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: 42 (22.0 bits)
S2: 56 (25.1 bits)