RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12906
(303 letters)
>gnl|CDD|149875 pfam08941, USP8_interact, USP8 interacting. This domain interacts
with the UBP deubiquitinating enzyme USP8.
Length = 179
Score = 258 bits (660), Expect = 4e-87
Identities = 103/179 (57%), Positives = 134/179 (74%)
Query: 125 ELRSIVHKQQQKMVNMETEMSEQRFQMTELKRQLTVLQELMRAMKVSNPGVRVLAENMER 184
ELRSIV Q ++ ++ + Q+ E KR+L +L+ +RA++ +NP +R + E +ER
Sbjct: 1 ELRSIVQDQATEIAELKHTQVDHEIQINEQKRELELLKYYIRALRSTNPIMRNIGEQLER 60
Query: 185 DDVARWSNSLSRARVTRWGGMISTPDVMLQAMIKRSLAESGCPGHILDQLMHNSHERNWP 244
++V W N L ARVTRWGGMISTPD +LQ MI+RSL ESGCP HIL++L+ N HER WP
Sbjct: 61 NEVLEWCNGLPPARVTRWGGMISTPDNVLQLMIRRSLRESGCPMHILNELVENCHERRWP 120
Query: 245 QGLSSLETRQNNRRQYENYVCKRIPSKQAVVVLLCDNVHLPEDMISAPGLVMIFAHGIE 303
GL++LETRQ NRRQYE YVC+RIP KQAVVVL C+N H+PE++ PGLVMIFAHG+E
Sbjct: 121 AGLATLETRQANRRQYEQYVCRRIPGKQAVVVLGCENTHMPENLRPEPGLVMIFAHGVE 179
>gnl|CDD|217894 pfam04102, SlyX, SlyX. The SlyX protein has no known function. It
is short less than 80 amino acids and is found close to
the slyD gene. The SlyX protein has a conserved PPH(Y/W)
motif at its C-terminus. The protein may be a
coiled-coil structure.
Length = 68
Score = 28.6 bits (65), Expect = 0.74
Identities = 11/32 (34%), Positives = 21/32 (65%)
Query: 143 EMSEQRFQMTELKRQLTVLQELMRAMKVSNPG 174
++EQ+ Q+ L+RQL +L E ++ ++ SN
Sbjct: 26 VVAEQQRQIDRLQRQLRLLVERLKEVESSNIA 57
>gnl|CDD|204784 pfam11932, DUF3450, Protein of unknown function (DUF3450). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are about 260 amino acids in
length.
Length = 250
Score = 29.9 bits (68), Expect = 1.2
Identities = 17/88 (19%), Positives = 37/88 (42%), Gaps = 23/88 (26%)
Query: 123 VKELRSIVHKQQQKMVNMETEMSEQRFQMTELKRQLTVLQELMRAMKVSNPGVRVLAEN- 181
+L+ +V QQQ++ +++ ++ Q+ + ++ L L M + L +
Sbjct: 73 NDQLQRLVANQQQEIASLQQQIE----QIEKTRQGLVPLMYRM---------IDGLEQFV 119
Query: 182 --------MERDD-VARWSNSLSRARVT 200
ER +AR + + RA V+
Sbjct: 120 ALDLPFLKEERLARLARLRDLMDRADVS 147
>gnl|CDD|213374 cd12085, DD_cGKI-alpha, Dimerization/Docking domain of Cyclic
GMP-dependent Protein Kinase I alpha. Cyclic
GMP-dependent Protein Kinase I (PKG1 or cGKI) is a
Serine/Threonine Kinase (STK), catalyzing the transfer
of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. cGKI
exists as two splice variants, cGKI-alpha and cGKI-beta.
They contain an N-terminal regulatory domain containing
a dimerization/docking region 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 involved in the
regulation of smooth muscle tone, smooth cell
proliferation, and platelet activation. The
dimerization/docking (D/D) domain is a
leucine/isoleucine zipper that mediates both
homodimerization and interaction with isotype-specific
G-kinase-anchoring proteins (GKAPs). The D/D domain of
the two variants (alpha and beta) differ, allowing for
their targeting to different subcellular compartments
and intracellular substrates. cGKI-alpha specifically
binds to myosin light chain phosphatase targeting
subunit (MYPT1) and the regulator of G-protein
signaling-2 (RGS-2). cGKI-alpha activates the
phosphatase activity of MYPT1, resulting in
vasorelaxation. It increases the activity of RGS-2
toward G proteins, with implications in the downstream
signaling for vasoconstrictive agents.
Length = 48
Score = 27.2 bits (61), Expect = 1.5
Identities = 9/40 (22%), Positives = 25/40 (62%)
Query: 123 VKELRSIVHKQQQKMVNMETEMSEQRFQMTELKRQLTVLQ 162
V+EL+ ++ +++++ +E + ++ ++ EL+ QL Q
Sbjct: 4 VEELQKLLQAKEERIRELEQLLQQRDEEIQELRSQLDKFQ 43
>gnl|CDD|189029 cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuclease of Taq DNA
polymerase I and homologs. The 5'-3' exonuclease
(53EXO) PIN (PilT N terminus) domain of multi-domain DNA
polymerase I and single domain protein homologs are
included in this family. Taq contains a polymerase
domain for synthesizing a new DNA strand and a 53EXO PIN
domain for cleaving RNA primers or damaged DNA strands.
Taq's 53EXO PIN domain recognizes and
endonucleolytically cleaves a structure-specific DNA
substrate that has a bifurcated downstream duplex and an
upstream template-primer duplex that overlaps the
downstream duplex by 1 bp. The 53EXO PIN domain cleaves
the unpaired 5'-arm of the overlap flap DNA substrate.
5'-3' exonucleases are members of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN domain with
a helical arch/clamp region (I domain) of variable
length (approximately 16 residues in 53EXO PIN domains)
and a H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA/RNA binding. The active site
includes a set of conserved acidic residues that are
essential for binding divalent metal ions required for
nuclease activity.
Length = 174
Score = 29.3 bits (67), Expect = 1.6
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 6/36 (16%)
Query: 153 ELKRQLTVLQELMRAMKVSNPGVRVL-AENMERDDV 187
EL+ QL +++EL+ A+ G+ VL E E DDV
Sbjct: 80 ELRPQLPLIKELLEAL-----GIPVLEVEGYEADDV 110
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 30.4 bits (69), Expect = 1.6
Identities = 10/79 (12%), Positives = 32/79 (40%), Gaps = 1/79 (1%)
Query: 123 VKELRSIVHKQQQKMVNMETEMSEQRFQMTELKRQLTVLQELMRAMKVSNPGVRVLAENM 182
+ L ++++ ++E ++ ++ +L+ Q+ L E + ++ + L E +
Sbjct: 812 LTLLNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEEL 871
Query: 183 ERDDVARWSNSLSRARVTR 201
E ++ N +
Sbjct: 872 E-SELEALLNERASLEEAL 889
>gnl|CDD|182906 PRK11022, dppD, dipeptide transporter ATP-binding subunit;
Provisional.
Length = 326
Score = 29.7 bits (67), Expect = 1.6
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 124 KELRSIVHKQQQKMVNMETEMSEQRFQ--MTELKRQLTVLQELMRAMKVSNPGVR 176
++L+ I K+++ +V E M FQ MT L TV ++M A+KV G +
Sbjct: 73 QDLQRISEKERRNLVGAEVAMI---FQDPMTSLNPCYTVGFQIMEAIKVHQGGNK 124
>gnl|CDD|233557 TIGR01746, Thioester-redct, thioester reductase domain. This model
includes the terminal domain from the fungal alpha
aminoadipate reductase enzyme (also known as
aminoadipate semialdehyde dehydrogenase) which is
involved in the biosynthesis of lysine , as well as the
reductase-containing component of the myxochelin
biosynthetic gene cluster, MxcG. The mechanism of
reduction involves activation of the substrate by
adenylation and transfer to a covalently-linked
pantetheine cofactor as a thioester. This thioester is
then reduced to give an aldehyde (thus releasing the
product) and a regenerated pantetheine thiol. (In
myxochelin biosynthesis this aldehyde is further reduced
to an alcohol or converted to an amine by an
aminotransferase.) This is a fundamentally different
reaction than beta-ketoreductase domains of polyketide
synthases which act at a carbonyl two carbons removed
from the thioester and forms an alcohol as a product.
This domain is invariably found at the C-terminus of the
proteins which contain it (presumably because it results
in the release of the product). The majority of hits to
this model are non-ribosomal peptide synthetases in
which this domain is similarly located proximal to a
thiolation domain (pfam00550). In some cases this domain
is found at the end of a polyketide synthetase enzyme,
but is unlike ketoreductase domains which are found
before the thiolase domains. Exceptions to this observed
relationship with the thiolase domain include three
proteins which consist of stand-alone reductase domains
(GP|466833 from M. leprae, GP|435954 from Anabaena and
OMNI|NTL02SC1199 from Strep. coelicolor) and one protein
(OMNI|NTL01NS2636 from Nostoc) which contains N-terminal
homology with a small group of hypothetical proteins but
no evidence of a thiolation domain next to the putative
reductase domain. Below the noise cutoff to this model
are proteins containing more distantly related
ketoreductase and dehydratase/epimerase domains. It has
been suggested that a NADP-binding motif can be found in
the N-terminal portion of this domain that may form a
Rossman-type fold.
Length = 367
Score = 29.7 bits (67), Expect = 1.9
Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 190 WSNSLSRARVTRWGGMISTPDVMLQAMIKRSLAESGCPGHILDQLMHNSHERNWPQGLSS 249
W L+R R+ G +S P + L LAE+ +D ++HN NW S
Sbjct: 54 WHEDLARERIEVVAGDLSEPRLGLSDAEWERLAEN------VDTIVHNGALVNWVYPYSE 107
Query: 250 LE 251
L
Sbjct: 108 LR 109
>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease.
Length = 259
Score = 29.1 bits (66), Expect = 2.7
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 6/37 (16%)
Query: 153 ELKRQLTVLQELMRAMKVSNPGVRVL-AENMERDDVA 188
EL Q+ +++EL+ A+ G+ VL E E DDV
Sbjct: 81 ELLEQIPLIKELLDAL-----GIPVLEVEGYEADDVI 112
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria [DNA
metabolism, Restriction/modification].
Length = 650
Score = 29.3 bits (66), Expect = 2.9
Identities = 9/49 (18%), Positives = 21/49 (42%)
Query: 119 DHNCVKELRSIVHKQQQKMVNMETEMSEQRFQMTELKRQLTVLQELMRA 167
+ +L + + Q ++ E E+ E Q+ LK + L++ +
Sbjct: 419 SEEQIAQLLEELGEAQNELFRSEAEIEELLRQLETLKEAIEALRKTLDE 467
>gnl|CDD|148473 pfam06874, FBPase_2, Firmicute fructose-1,6-bisphosphatase. This
family consists of several bacterial
fructose-1,6-bisphosphatase proteins (EC:3.1.3.11) which
seem to be specific to phylum Firmicutes.
Fructose-1,6-bisphosphatase (FBPase) is a well known
enzyme involved in gluconeogenesis. This family does not
seem to be structurally related to pfam00316.
Length = 641
Score = 28.3 bits (64), Expect = 5.3
Identities = 21/99 (21%), Positives = 42/99 (42%), Gaps = 18/99 (18%)
Query: 74 FCTPYQSLHTANTAIMGYEIV---RFIGEVDEELICSICSGVFEEPLQDHNCVKELRSIV 130
F YQ T I GY ++ + V E S E+ +++ + +V
Sbjct: 556 FSKAYQK----TTGIAGYTLIYNSYGLQLVSHEPFTSK-----EKAIEEGTDILSTTRVV 606
Query: 131 HKQQQKMVNMETEMSEQRFQMTELKRQLTVLQELMRAMK 169
+ Q+ + +T++ + ELK Q+ L++L+ A +
Sbjct: 607 EQVLQRKLVKDTDIGK------ELKEQIADLKKLLDAYR 639
>gnl|CDD|173670 cd05579, STKc_MAST_like, Catalytic domain of Microtubule-associated
serine/threonine kinase-like proteins. Serine/Threonine
Kinases (STKs), Microtubule-associated serine/threonine
(MAST) kinase subfamily, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The MAST kinase 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. The MAST kinase subfamily
includes MAST kinases, MAST-like (MASTL) kinases, and
fungal kinases with similarity to Saccharomyces
cerevisiae Rim15 and Schizosaccharomyces pombe cek1.
MAST kinases contain an N-terminal domain of unknown
function, a central catalytic domain, and a C-terminal
PDZ domain that mediates protein-protein interactions.
MASTL kinases carry only a catalytic domain which
contains a long insert relative to other kinases. The
fungal kinases in this subfamily harbor other domains in
addition to a central catalytic domain, which also
contains an insert relative to MAST kinases like MASTL.
Rim15 contains a C-terminal signal receiver (REC) domain
while cek1 contains an N-terminal PAS domain. MAST
kinases are cytoskeletal associated kinases of unknown
function that are also expressed at neuromuscular
junctions and postsynaptic densities. The fungal
proteins Rim15 and cek1 are involved in the regulation
of meiosis and mitosis, respectively.
Length = 265
Score = 28.0 bits (63), Expect = 5.5
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 10/64 (15%)
Query: 73 SFCTPYQSLHTANTAIMGYE----IVRFIGEVDEELICSICSGVFEEPLQDHNCVKELRS 128
S + SL + YE I F GE EE+ +I +G E P +D E
Sbjct: 179 SKTVDWWSL-----GCILYEFLVGIPPFHGETPEEIFQNILNGKIEWP-EDVEVSDEAID 232
Query: 129 IVHK 132
++ K
Sbjct: 233 LISK 236
>gnl|CDD|181818 PRK09393, ftrA, transcriptional activator FtrA; Provisional.
Length = 322
Score = 28.0 bits (63), Expect = 5.6
Identities = 8/9 (88%), Positives = 9/9 (100%)
Query: 105 ICSICSGVF 113
+CSICSGVF
Sbjct: 109 LCSICSGVF 117
>gnl|CDD|235511 PRK05574, holA, DNA polymerase III subunit delta; Reviewed.
Length = 340
Score = 27.8 bits (63), Expect = 6.4
Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 17/63 (26%)
Query: 124 KELRSI--VHKQQQKMVNMETEMSE---------------QRFQMTELKRQLTVLQELMR 166
+E R + + Q+ ++ E QR + +LK+ + +L E
Sbjct: 256 REFRLLLQLKILSQQGYPLQQLAKELRVWPYRVKLALRALQRLSLKQLKQAIQLLAETDY 315
Query: 167 AMK 169
+K
Sbjct: 316 QIK 318
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 28.1 bits (64), Expect = 6.5
Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 6/36 (16%)
Query: 153 ELKRQLTVLQELMRAMKVSNPGVRVL-AENMERDDV 187
+L+ Q+ +++EL+RA+ G+ +L E E DDV
Sbjct: 83 DLREQIPLIRELLRAL-----GIPLLELEGYEADDV 113
>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain. Axonemal
dynein light chain proteins play a dynamic role in
flagellar and cilia motility. Eukaryotic cilia and
flagella are complex organelles consisting of a core
structure, the axoneme, which is composed of nine
microtubule doublets forming a cylinder that surrounds a
pair of central singlet microtubules. This
ultra-structural arrangement seems to be one of the most
stable micro-tubular assemblies known and is responsible
for the flagellar and ciliary movement of a large number
of organisms ranging from protozoan to mammals. This
light chain interacts directly with the N-terminal half
of the heavy chains.
Length = 189
Score = 27.2 bits (61), Expect = 8.7
Identities = 11/57 (19%), Positives = 28/57 (49%)
Query: 132 KQQQKMVNMETEMSEQRFQMTELKRQLTVLQELMRAMKVSNPGVRVLAENMERDDVA 188
+ +Q +E E+ + + EL++++ L+ + A++ R + E D++A
Sbjct: 117 QAEQGKSELEQEIKKLEEEKEELEKRVAELEAKLEAIEKREEEERQIEEKRHADEIA 173
>gnl|CDD|182747 PRK10807, PRK10807, paraquat-inducible protein B; Provisional.
Length = 547
Score = 27.7 bits (62), Expect = 8.8
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 7/81 (8%)
Query: 115 EPL--QDHNCVKELRSIVHKQQQKMVNMETEMSEQRFQMTELKRQLTVLQELMRAMKVSN 172
P+ Q + + E + + + Q + ++ S Q Q Q T L+EL R+M+
Sbjct: 435 NPMIEQATSTLSESQRTMRELQTTLDSLNKITSSQSMQQLPADMQKT-LRELNRSMQGFQ 493
Query: 173 PGVRV---LAENMER-DDVAR 189
PG + +M+R D V R
Sbjct: 494 PGSPAYNKMVADMQRLDQVLR 514
>gnl|CDD|219633 pfam07905, PucR, Purine catabolism regulatory protein-like family.
The bacterial proteins found in this family are similar
to the purine catabolism regulatory protein expressed by
Bacillus subtilis (PucR). PucR is thought to be a
transcriptional activator involved in the induction of
the purine degradation pathway, and may contain a
LysR-like DNA-binding domain. It is similar to LysR-type
regulators in that it represses its own expression. The
other members of this family are also annotated as being
putative regulatory proteins.
Length = 122
Score = 26.7 bits (60), Expect = 9.0
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 79 QSLHTANTAIMGYEIVRFIGEVDEELI 105
+ L A A +G + R+I E+ EELI
Sbjct: 65 RELAEAGAAGLGIKTGRYIPEIPEELI 91
>gnl|CDD|144972 pfam01576, Myosin_tail_1, Myosin tail. The myosin molecule is a
multi-subunit complex made up of two heavy chains and
four light chains it is a fundamental contractile
protein found in all eukaryote cell types. This family
consists of the coiled-coil myosin heavy chain tail
region. The coiled-coil is composed of the tail from two
molecules of myosin. These can then assemble into the
macromolecular thick filament. The coiled-coil region
provides the structural backbone the thick filament.
Length = 859
Score = 27.7 bits (62), Expect = 9.0
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 131 HKQQQK-MVNMETEMSEQRFQMTELKRQLTVLQELM 165
H + QK + ME + E +FQ+ E K+ L LQ+L+
Sbjct: 766 HAETQKNLRKMERRVKELQFQVEEDKKNLERLQDLV 801
>gnl|CDD|226447 COG3937, COG3937, Uncharacterized conserved protein [Function
unknown].
Length = 108
Score = 26.3 bits (58), Expect = 9.5
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 8/40 (20%)
Query: 132 KQQQKMVNME--------TEMSEQRFQMTELKRQLTVLQE 163
K +K+ M +EM E ++ L+RQ+ L+
Sbjct: 65 KIPRKIEEMLSDLEVARQSEMDELTERVDALERQVADLEN 104
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
0.319 0.132 0.399
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,847,363
Number of extensions: 1358552
Number of successful extensions: 1340
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1334
Number of HSP's successfully gapped: 42
Length of query: 303
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 207
Effective length of database: 6,679,618
Effective search space: 1382680926
Effective search space used: 1382680926
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.4 bits)