RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10331
(183 letters)
>gnl|CDD|216928 pfam02204, VPS9, Vacuolar sorting protein 9 (VPS9) domain.
Length = 104
Score = 90.0 bits (224), Expect = 6e-24
Identities = 31/89 (34%), Positives = 54/89 (60%), Gaps = 3/89 (3%)
Query: 96 KLLEMDSVRAPQDKLACVVACCRDIFLLLQSSVGPA--SADEFLPALIFLVLKMNPARLK 153
+L +++ ++P++KL C++ C+ I L S AD+ LP LI++++K NP L
Sbjct: 7 ELKKLNEAKSPREKLKCLLRTCKLITEALSKSNPGEPLGADDLLPILIYVLIKANPPNLY 66
Query: 154 SNIHFVTRFCNANRLMSGEAGYFFTNLVS 182
SN+ F++ F + L+SGE GY+ T L +
Sbjct: 67 SNLQFISLFRD-PDLLSGEEGYYLTTLEA 94
>gnl|CDD|128469 smart00167, VPS9, Domain present in VPS9. Domain present in yeast
vacuolar sorting protein 9 and other proteins.
Length = 117
Score = 66.7 bits (163), Expect = 8e-15
Identities = 29/82 (35%), Positives = 51/82 (62%), Gaps = 2/82 (2%)
Query: 100 MDSVRAPQDKLACVVACCRDIFLLLQSSVGP-ASADEFLPALIFLVLKMNPARLKSNIHF 158
+ ++P DK+ C++ C+ I+ LL++ G A AD+FLP LI++++K +P L N +
Sbjct: 12 LQLYKSPSDKIKCLLRACKLIYTLLETQSGEVAGADDFLPVLIYVIIKCDPRDLLLNAEY 71
Query: 159 VTRFCNANRLMSGEAGYFFTNL 180
+ F L++GE GY+ T+L
Sbjct: 72 MEEFLE-PSLLTGEGGYYLTSL 92
>gnl|CDD|172871 PRK14395, PRK14395, membrane protein; Provisional.
Length = 195
Score = 31.1 bits (70), Expect = 0.20
Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 4/70 (5%)
Query: 106 PQDKLACVVACCRDIFLLLQSSVGPASADEFLPALIFLVLKMNPARLKSNIH--FVTRFC 163
P+ + +V +FL SVG A + L+FL + ++ + I V
Sbjct: 117 PKITVMAIVLFVLVVFLTRYVSVGSVLAALTVGILVFLFNEPMAYKVFAVIAVSGVVIRH 176
Query: 164 NAN--RLMSG 171
N R++ G
Sbjct: 177 RTNIQRVLKG 186
>gnl|CDD|235104 PRK03103, PRK03103, DNA polymerase IV; Reviewed.
Length = 409
Score = 28.0 bits (63), Expect = 2.9
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 17/62 (27%)
Query: 14 NHKLYADVSAQDRELLLDY---VEKYSM------ISLYPLLFCPPFTSDEDQDLEIQERI 64
+ Y DVS Q +L D+ VE +S+ ++ LF P LEI ++I
Sbjct: 77 RMQRYIDVSLQITRILEDFTDLVEPFSIDEQFLDVTGSQKLFGSP--------LEIAQKI 128
Query: 65 RQ 66
+Q
Sbjct: 129 QQ 130
>gnl|CDD|176459 cd03586, PolY_Pol_IV_kappa, DNA Polymerase IV/Kappa. Pol IV, also
known as Pol kappa, DinB, and Dpo4, is a translesion
synthesis (TLS) polymerase. Translesion synthesis is a
process that allows the bypass of a variety of DNA
lesions. TLS polymerases lack proofreading activity and
have low fidelity and low processivity. They use
damaged DNA as templates and insert nucleotides opposite
the lesions. Known primarily as Pol IV in prokaryotes
and Pol kappa in eukaryotes, this polymerase has a
propensity for generating frameshift mutations. The
eukaryotic Pol kappa differs from Pol IV and Dpo4 by an
N-terminal extension of ~75 residues known as the
"N-clasp" region. The structure of Pol kappa shows DNA
that is almost totally encircled by Pol kappa, with the
N-clasp region augmenting the interactions between DNA
and the polymerase. Pol kappa is more resistant than Pol
eta and Pol iota to bulky guanine adducts and is
efficient at catalyzing the incorporation of dCTP.
Bacterial pol IV has a higher error rate than other
Y-family polymerases.
Length = 334
Score = 27.5 bits (62), Expect = 3.9
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 13/62 (20%)
Query: 14 NHKLYADVSAQDRELLLDY---VEKYSM------ISLYPLLFCPPFTSDEDQDLEIQERI 64
Y +VS Q E+L +Y VE S+ ++ Y L F S + EI+ RI
Sbjct: 70 RFDKYREVSRQIMEILREYTPLVEPLSIDEAYLDVTDYVRL----FGSATEIAKEIRARI 125
Query: 65 RQ 66
R+
Sbjct: 126 RE 127
>gnl|CDD|173663 cd05572, STKc_cGK_PKG, Catalytic domain of the Protein
Serine/Threonine Kinase, cGMP-dependent protein kinase.
Serine/Threonine Kinases (STKs), cGMP-dependent protein
kinase (cGK or PKG) subfamily, catalytic (c) domain.
STKs catalyze the transfer of the gamma-phosphoryl group
from ATP to serine/threonine residues on protein
substrates. The cGK subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein STKs, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. Mammals have two cGK isoforms
from different genes, cGKI and cGKII. cGKI exists as two
splice variants, cGKI-alpha and cGKI-beta. cGK consists
of an N-terminal regulatory domain containing a
dimerization and an autoinhibitory pseudosubstrate
region, two cGMP-binding domains, and a C-terminal
catalytic domain. Binding of cGMP to both binding sites
releases the inhibition of the catalytic center by the
pseudosubstrate region, allowing autophosphorylation and
activation of the kinase. cGKI is a soluble protein
expressed in all smooth muscles, platelets, cerebellum,
and kidney. It is also expressed at lower concentrations
in other tissues. cGKII is a membrane-bound protein that
is most abundantly expressed in the intestine. It is
also present in the brain nuclei, adrenal cortex,
kidney, lung, and prostate. cGKI is involved in the
regulation of smooth muscle tone, smooth cell
proliferation, and platelet activation. cGKII plays a
role in the regulation of secretion, such as renin
secretion by the kidney and aldosterone secretion by the
adrenal. It also regulates bone growth and the circadian
rhythm.
Length = 262
Score = 27.2 bits (61), Expect = 4.4
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 3/28 (10%)
Query: 39 ISLYPLLFC--PPFTSDEDQDLEIQERI 64
I LY LL PPF D++ +EI I
Sbjct: 180 ILLYELL-TGRPPFGEDDEDPMEIYNDI 206
>gnl|CDD|221100 pfam11380, DUF3184, Protein of unknown function (DUF3184). This
eukaryotic family of proteins has no known function.
Length = 629
Score = 27.6 bits (61), Expect = 4.5
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 8/84 (9%)
Query: 76 DCGIEETNATVRDLVYNSMTKLLEMDSVRAPQDKLACVVACCRDIFLLLQSSVGPASADE 135
CG VR V ++ T+ + S A +D LA V A + +VGP+ D
Sbjct: 525 TCGGGGAGLRVRGFVVDARTRGAPLRSAAALRDALA-VPAQTLSLEDFRAVAVGPSEGD- 582
Query: 136 FLPALIFLVLKMNPARLKSNIHFV 159
+ LV+ A K+ +H+V
Sbjct: 583 -----VVLVVSREDAEAKA-VHWV 600
>gnl|CDD|216002 pfam00578, AhpC-TSA, AhpC/TSA family. This family contains
proteins related to alkyl hydroperoxide reductase
(AhpC) and thiol specific antioxidant (TSA).
Length = 124
Score = 26.4 bits (59), Expect = 5.4
Identities = 10/45 (22%), Positives = 19/45 (42%), Gaps = 3/45 (6%)
Query: 29 LLDYVEKYSMISLYPLLFCPPFTSDEDQDLEIQERIRQLKWVNAK 73
L DY K+ ++ YP F P T + + + + K + +
Sbjct: 20 LSDYKGKWVVLFFYPKDFTPVCT---TELPALADLYEEFKKLGVE 61
>gnl|CDD|223466 COG0389, DinP, Nucleotidyltransferase/DNA polymerase involved in
DNA repair [DNA replication, recombination, and repair].
Length = 354
Score = 26.9 bits (60), Expect = 6.3
Identities = 17/73 (23%), Positives = 23/73 (31%), Gaps = 12/73 (16%)
Query: 14 NHKLYADVSAQDRELLLDY---VEKYSM----ISLYPLLFCPPFTSDEDQDLEIQERIRQ 66
N Y SA+ R +L Y VE S+ + L L LEI+ I
Sbjct: 73 NFAAYRLASAEIRAILERYTPLVEPLSIDEAFLDLTDALRLLGLADAPRIALEIRFGILL 132
Query: 67 LKWVNAKHLDCGI 79
L +
Sbjct: 133 E-----LGLTASV 140
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
0.325 0.137 0.407
Gapped
Lambda K H
0.267 0.0660 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,129,251
Number of extensions: 828904
Number of successful extensions: 972
Number of sequences better than 10.0: 1
Number of HSP's gapped: 967
Number of HSP's successfully gapped: 18
Length of query: 183
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 92
Effective length of database: 6,901,388
Effective search space: 634927696
Effective search space used: 634927696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.5 bits)