RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13887
(107 letters)
>gnl|CDD|227498 COG5170, CDC55, Serine/threonine protein phosphatase 2A, regulatory
subunit [Signal transduction mechanisms].
Length = 460
Score = 67.7 bits (165), Expect = 1e-14
Identities = 36/120 (30%), Positives = 56/120 (46%), Gaps = 20/120 (16%)
Query: 7 VHEYLRSKLCSLYENDCIFDKFEVCWSGTDSAIMTGSYNNFFRMF--------DR---IN 55
+H L +L +YEND IFDKFE+ +SG D +++GSY+N F ++ D +N
Sbjct: 320 MHCDLMDELNDVYENDAIFDKFEISFSGDDKHVLSGSYSNNFGIYPTDSSGFKDVGHVVN 379
Query: 56 KRDATLEAAREIAKPKTLLRPRKVCTGGKRKKDEIS---------VDCLDFNKKILHTAW 106
D + E + + + + K+ R + D LD KKILH +W
Sbjct: 380 LADGSAEDFKVKCETNNVEKKDKLKNNDWRSVSSSADGFVVACEDPDNLDLLKKILHRSW 439
>gnl|CDD|235618 PRK05818, PRK05818, DNA polymerase III subunit delta'; Validated.
Length = 261
Score = 32.5 bits (74), Expect = 0.026
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 9/80 (11%)
Query: 2 FPSPQVHEYLRSKLCSLYENDCIFDKFEVCWSGTDSAIMTGSYNNFFRMFDRIN--KRDA 59
F P ++EYL S +C+ C E C I+ G YN+F+ +FD+ N K++
Sbjct: 19 FLKPFLYEYLTSIVCTKANGFC--KTCESCLK-----ILNGKYNDFYLIFDQKNPIKKED 71
Query: 60 TLEAAREIAKPKTLLRPRKV 79
L ++ +P +K+
Sbjct: 72 ALSIINKLNRPSVESNGKKI 91
>gnl|CDD|237258 PRK12903, secA, preprotein translocase subunit SecA; Reviewed.
Length = 925
Score = 27.3 bits (61), Expect = 1.7
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 41 TGSYNNFFRMFDRI 54
T +Y NFFR+F ++
Sbjct: 351 TITYQNFFRLFKKL 364
>gnl|CDD|223242 COG0164, RnhB, Ribonuclease HII [DNA replication, recombination,
and repair].
Length = 199
Score = 26.8 bits (60), Expect = 2.1
Identities = 11/50 (22%), Positives = 16/50 (32%), Gaps = 12/50 (24%)
Query: 52 DRINKRDATLEAAREIAKPKTLLRPRKVCTGGKRKKDEISVDCLDFNKKI 101
D +N +AT A R G + D + VD D +
Sbjct: 71 DELNILEATKLAMRRAVA------------GLSSQPDLVLVDGNDLPLGL 108
>gnl|CDD|163440 TIGR03728, glyco_access_1, glycosyltransferase, SP_1767 family.
Members of this protein family are putative
glycosyltransferases. Some members are found close to
genes for the accessory secretory (SecA2) system, and
are suggested by Partial Phylogenetic Profiling to
correlate with SecA2 systems. Glycosylation, therefore,
may occur in the cytosol prior to secretion.
Length = 265
Score = 26.9 bits (60), Expect = 2.4
Identities = 21/67 (31%), Positives = 28/67 (41%), Gaps = 17/67 (25%)
Query: 25 FDKFEVCWSGTDSAIMTGSY------NNFF---RMFDRI--------NKRDATLEAAREI 67
F+K + W D I+ G N+ F + RI +K D LEA RE
Sbjct: 124 FEKLKQIWKNKDILIVEGETSRSGVGNDLFDNAKSIKRIICPSKNAFSKYDEILEAIREN 183
Query: 68 AKPKTLL 74
AK K +L
Sbjct: 184 AKNKLIL 190
>gnl|CDD|218705 pfam05702, Herpes_UL49_5, Herpesvirus UL49.5 envelope/tegument
protein. UL49.5 protein consists of 98 amino acids
with a calculated molecular mass of 10,155 Da. It
contains putative signal peptide and transmembrane
domains but lacks a consensus sequence for N
glycosylation. UL49.5 protein is an O-glycosylated
structural component of the viral envelope.
Length = 98
Score = 25.5 bits (56), Expect = 3.6
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 28 FEVCWSGTDSAIMTGSYNNFFRMF 51
F + A++ G+YN FR+F
Sbjct: 66 FYISLLAVIVALLAGAYNACFRLF 89
>gnl|CDD|216326 pfam01142, TruD, tRNA pseudouridine synthase D (TruD). TruD is
responsible for synthesis of pseudouridine from
uracil-13 in transfer RNAs. The structure of TruD
reveals an overall V-shaped molecule which contains an
RNA-binding cleft.
Length = 336
Score = 25.7 bits (57), Expect = 4.9
Identities = 10/18 (55%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 53 RINKRDA-TLEAAREIAK 69
RI KR TL+ ARE+A+
Sbjct: 46 RIEKRGWNTLDVARELAR 63
>gnl|CDD|223911 COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms].
Length = 1009
Score = 25.6 bits (57), Expect = 5.7
Identities = 7/25 (28%), Positives = 10/25 (40%)
Query: 46 NFFRMFDRINKRDATLEAAREIAKP 70
N R + R+A +A EI
Sbjct: 406 NIERHMRGLPPREAAEKAMGEIGGA 430
>gnl|CDD|169983 PRK09579, PRK09579, multidrug efflux protein; Reviewed.
Length = 1017
Score = 25.6 bits (56), Expect = 6.1
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 57 RDATLEAAREIAKP 70
DA LE AREIA P
Sbjct: 420 FDAALEGAREIAMP 433
>gnl|CDD|238665 cd01369, KISc_KHC_KIF5, Kinesin motor domain, kinesin heavy chain
(KHC) or KIF5-like subgroup. Members of this group have
been associated with organelle transport. This
catalytic (head) domain has ATPase activity and belongs
to the larger group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In most kinesins, the motor domain is found
at the N-terminus (N-type). N-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and
move along the microtubule at a speed of about 6400
Angstroms per second. To achieve that, kinesin head
groups work in pairs. Upon replacing ADP with ATP, a
kinesin motor domain increases its affinity for
microtubule binding and locks in place. Also, the neck
linker binds to the motor domain, which repositions the
other head domain through the coiled-coil domain close
to a second tubulin dimer, about 80 Angstroms along the
microtubule. Meanwhile, ATP hydrolysis takes place, and
when the second head domain binds to the microtubule,
the first domain again replaces ADP with ATP,
triggering a conformational change that pulls the first
domain forward.
Length = 325
Score = 25.7 bits (57), Expect = 6.1
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 26 DKFEVCWSGTDSAIMTGSYNNFFRMFDRINKRDATLE-----AAREIAK 69
K V + G D+ + GS + FDR+ + T E A+ I
Sbjct: 22 SKSIVKFPGEDTVSIAGSDDGKTFSFDRVFPPNTTQEDVYNFVAKPIVD 70
>gnl|CDD|184712 PRK14501, PRK14501, putative bifunctional trehalose-6-phosphate
synthase/HAD hydrolase subfamily IIB; Provisional.
Length = 726
Score = 25.7 bits (57), Expect = 6.5
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 9/53 (16%)
Query: 51 FDRINKRDATLEAAREIAKPKTLLRPRKVCTGGKRKKDEISVDCLDFNKKILH 103
+D+ + E EI + + LR RK+ +S+D LD+ K I
Sbjct: 239 YDKFHNSAQDPEVQEEIRRLRQDLRGRKII---------LSIDRLDYTKGIPR 282
>gnl|CDD|217534 pfam03399, SAC3_GANP, SAC3/GANP/Nin1/mts3/eIF-3 p25 family. This
large family includes diverse proteins involved in large
complexes. The alignment contains one highly conserved
negatively charged residue and one highly conserved
positively charged residue that are probably important
for the function of these proteins. The family includes
the yeast nuclear export factor Sac3, and mammalian
GANP/MCM3-associated proteins, which facilitate the
nuclear localisation of MCM3, a protein that associates
with chromatin in the G1 phase of the cell-cycle. The
26S protease (or 26S proteasome) is responsible for
degrading ubiquitin conjugates. It consists of 19S
regulatory complexes associated with the ends of 20S
proteasomes. The 19S regulatory complex is composed of
about 20 different polypeptides and confers
ATP-dependence and substrate specificity to the 26S
enzyme. The conserved region occurs at the C-terminal of
the Nin1-like regulatory subunit. This family includes
several eukaryotic translation initiation factor 3
subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation
factor 3 (eIF3) is a multisubunit complex that is
required for binding of mRNA to 40 S ribosomal subunits,
stabilisation of ternary complex binding to 40 S
subunits, and dissociation of 40 and 60 S subunits.
Length = 155
Score = 24.9 bits (55), Expect = 7.4
Identities = 12/52 (23%), Positives = 19/52 (36%), Gaps = 5/52 (9%)
Query: 1 MFPSPQVHEYLRSKLCSLYENDCIFDKFEVCWSGTDSAIMTGSYNNFFRMFD 52
P H L + + I E+ A+M G+Y+ FFR+
Sbjct: 67 NNPISDFHTELELLPDEIRNDPYIQFALELE-----QALMEGNYHRFFRLLK 113
>gnl|CDD|235208 PRK04036, PRK04036, DNA polymerase II small subunit; Validated.
Length = 504
Score = 25.3 bits (56), Expect = 8.8
Identities = 20/91 (21%), Positives = 38/91 (41%), Gaps = 8/91 (8%)
Query: 3 PSPQVHEYLRSKLCSLYENDCIFDKFEVCWSGTDSAIMTGSYNNFFRMF-DRINKRDATL 61
S + E + K+ ++ ++ + + EV T + TG +F F DR K
Sbjct: 75 ESESIRESVNPKINTIAKDIEVDIEVEVLSDVTGKSTCTGEVEDFVAYFRDRYEK----- 129
Query: 62 EAAREIAKPKTLLRPRKVCTGGKRKKDEISV 92
+I + + RP + KR +E+S+
Sbjct: 130 --LSKIIRGRVNHRPIESLKKLKRGGEEVSI 158
>gnl|CDD|233848 TIGR02400, trehalose_OtsA, alpha,alpha-trehalose-phosphate synthase
[UDP-forming]. This enzyme catalyzes the key,
penultimate step in biosynthesis of trehalose, a
compatible solute made as an osmoprotectant in some
species in all three domains of life. The gene symbol
OtsA stands for osmotically regulated trehalose
synthesis A. Trehalose helps protect against both
osmotic and thermal stresses, and is made from two
glucose subunits. This model excludes
glucosylglycerol-phosphate synthase, an enzyme of an
analogous osmoprotectant system in many cyanobacterial
strains. This model does not identify archaeal examples,
as they are more divergent than
glucosylglycerol-phosphate synthase. Sequences that
score in the gray zone between the trusted and noise
cutoffs include a number of yeast multidomain proteins
in which the N-terminal domain may be functionally
equivalent to this family. The gray zone also includes
the OtsA of Cornyebacterium glutamicum (and related
species), shown to be responsible for synthesis of only
trace amounts of trehalose while the majority is
synthesized by the TreYZ pathway; the significance of
OtsA in this species is unclear (see Wolf, et al.,
PMID:12890033) [Cellular processes, Adaptations to
atypical conditions].
Length = 456
Score = 25.3 bits (56), Expect = 8.8
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 9/53 (16%)
Query: 51 FDRINKRDATLEAAREIAKPKTLLRPRKVCTGGKRKKDEISVDCLDFNKKILH 103
DR ++ + IA+ + L+ RK+ I VD LD++K +
Sbjct: 233 VDRFAEQAKKPSVQKRIAELRESLKGRKLI---------IGVDRLDYSKGLPE 276
>gnl|CDD|234884 PRK00984, truD, tRNA pseudouridine synthase D; Reviewed.
Length = 341
Score = 25.2 bits (56), Expect = 9.5
Identities = 10/18 (55%), Positives = 11/18 (61%), Gaps = 1/18 (5%)
Query: 53 RINKRDA-TLEAAREIAK 69
RI KR TL AR +AK
Sbjct: 47 RIRKRGWNTLFVARALAK 64
>gnl|CDD|219445 pfam07517, SecA_DEAD, SecA DEAD-like domain. SecA protein binds to
the plasma membrane where it interacts with proOmpA to
support translocation of proOmpA through the membrane.
SecA protein achieves this translocation, in association
with SecY protein, in an ATP dependent manner. This
domain represents the N-terminal ATP-dependent helicase
domain, which is related to the pfam00270.
Length = 381
Score = 25.2 bits (56), Expect = 9.6
Identities = 5/12 (41%), Positives = 10/12 (83%)
Query: 43 SYNNFFRMFDRI 54
+Y NFFR++ ++
Sbjct: 355 TYQNFFRLYPKL 366
>gnl|CDD|224858 COG1947, IspE, 4-diphosphocytidyl-2C-methyl-D-erythritol
2-phosphate synthase [Lipid metabolism].
Length = 289
Score = 24.9 bits (55), Expect = 10.0
Identities = 9/35 (25%), Positives = 14/35 (40%)
Query: 32 WSGTDSAIMTGSYNNFFRMFDRINKRDATLEAARE 66
G A M+GS + F +FD + E +
Sbjct: 237 EYGALPARMSGSGSTVFALFDTEKEAQRVAEQLPK 271
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
0.323 0.137 0.439
Gapped
Lambda K H
0.267 0.0815 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,353,367
Number of extensions: 432922
Number of successful extensions: 425
Number of sequences better than 10.0: 1
Number of HSP's gapped: 424
Number of HSP's successfully gapped: 26
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.0 bits)