RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14169
(97 letters)
>gnl|CDD|216919 pfam02181, FH2, Formin Homology 2 Domain.
Length = 372
Score = 31.9 bits (73), Expect = 0.029
Identities = 11/60 (18%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 1 MSEFLSDTAQRIIVLSIVHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISEFALEYR 60
M EFL + +++ L + + + F + G T P++ +I+ +F ++
Sbjct: 316 MKEFLEEAEEKLDKLESLLKEAMELFKELTEYFG---EDPKETSPEEFFKILRDFLRMFK 372
>gnl|CDD|189039 cd09869, PIN_GEN1, PIN domain of Gap Endonuclease 1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Gap Endonuclease 1 (GEN1) is a
Holliday junction resolvase reported to symmetrically
cleave Holliday junctions and allow religation without
additional processing. GEN1 is a member 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 (PilT N
terminus) domain with a helical arch/clamp region (I
domain) of variable length (approximately 30 - 50
residues in GEN1 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 binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+).
Length = 233
Score = 31.6 bits (72), Expect = 0.031
Identities = 25/92 (27%), Positives = 32/92 (34%), Gaps = 13/92 (14%)
Query: 13 IVLSIVHRRVLHR--FHRFC--LWLGVPLHRV-----PLTKPQDLARIISEFALEYRTTR 63
+V V + R F R + LGV V P K L II L+ +
Sbjct: 41 VVKYFVVPKPHLRNLFFRTRYLIALGVLPVFVVDGAAPPLK---LPVIIKRNQLQSGIAK 97
Query: 64 ERVIQTREKKASHRERNKTRGKMITECEELSE 95
T K S R R ++ EC EL E
Sbjct: 98 PGDNPT-PKNGSKRNRRSRFSHVLKECVELLE 128
>gnl|CDD|214697 smart00498, FH2, Formin Homology 2 Domain. FH proteins control
rearrangements of the actin cytoskeleton, especially in
the context of cytokinesis and cell polarisation.
Members of this family have been found to interact with
Rho-GTPases, profilin and other actin-assoziated
proteins. These interactions are mediated by the
proline-rich FH1 domain, usually located in front of FH2
(but not listed in SMART). Despite this cytosolic
function, vertebrate formins have been assigned
functions within the nucleus. A set of Formin-Binding
Proteins (FBPs) has been shown to bind FH1 with their WW
domain.
Length = 392
Score = 31.2 bits (71), Expect = 0.049
Identities = 22/96 (22%), Positives = 36/96 (37%), Gaps = 6/96 (6%)
Query: 1 MSEFLSDTAQRIIVLSIVHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISEFALEYR 60
M FL ++ L + RF + + G P++ + +EF E+
Sbjct: 275 MKPFLKAAKEKYDKLQKDLSDLKTRFEKLVEYYGEDPKDTS---PEEFFKDFNEFLKEFS 331
Query: 61 TTRERVIQTREKKASHRERNKTRGKMITECEELSER 96
E + +K+ ER K K TE E+ S R
Sbjct: 332 KAAE---ENIKKEEEEEERRKKLVKETTEYEQSSSR 364
>gnl|CDD|223024 PHA03252, PHA03252, DNA packaging tegument protein UL25;
Provisional.
Length = 589
Score = 30.8 bits (70), Expect = 0.063
Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 5/78 (6%)
Query: 23 LHRFHRF-CLWLGVPLHR--VPLTKPQDLARIISEFALEYRTTRERVIQTREKKASHRER 79
L F++ + + H + +DL R+ + AL R RE +++ R + E
Sbjct: 4 LRTFYQLPIVPIYEG-HVRNILRCPEEDLRRLRDDSALRLRRYREDLLRDRLLRRRLGEE 62
Query: 80 NKTRG-KMITECEELSER 96
++ TECE+L R
Sbjct: 63 LDDLQKRLQTECEDLRSR 80
>gnl|CDD|146789 pfam04337, DUF480, Protein of unknown function, DUF480. This
family consists of several proteins of uncharacterized
function.
Length = 148
Score = 26.0 bits (58), Expect = 2.8
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 8 TAQRIIVLSIVHRRVLHRFHRFCLWLGVP 36
A+ ++ S RV HRFC L +
Sbjct: 59 KAKGLVRESGFGSRVPKYEHRFCNTLQLS 87
>gnl|CDD|117685 pfam09129, Chol_subst-bind, Cholesterol oxidase, substrate-binding.
The substrate-binding domain found in Cholesterol
oxidase is composed of an eight-stranded mixed
beta-pleated sheet and six alpha-helices. This domain is
positioned over the isoalloxazine ring system of the FAD
cofactor bound by FAD_binding_4 (PF:PF01565) and forms
the roof of the active site cavity, allowing for
catalysis of oxidation and isomerisation of cholesterol
to cholest-4-en-3-one.
Length = 321
Score = 25.7 bits (56), Expect = 4.5
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 42 LTKPQDLARIISEFALEYRT 61
LT+ ++ R+I+EF Y
Sbjct: 145 LTRRANVQRVINEFTEWYHE 164
>gnl|CDD|235628 PRK05855, PRK05855, short chain dehydrogenase; Validated.
Length = 582
Score = 25.7 bits (57), Expect = 4.7
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 38 HRVPLTKPQDLARIISEFA 56
H +P++ PQ LA ++EF
Sbjct: 271 HWLPMSHPQVLAAAVAEFV 289
>gnl|CDD|130130 TIGR01058, parE_Gpos, DNA topoisomerase IV, B subunit,
Gram-positive. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation step
of chromosome segregation. Not every bacterium has both
a topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 25.6 bits (56), Expect = 4.7
Identities = 11/45 (24%), Positives = 26/45 (57%)
Query: 42 LTKPQDLARIISEFALEYRTTRERVIQTREKKASHRERNKTRGKM 86
L + + A+++ + A++ R +E + RE+K S ++ K +G +
Sbjct: 361 LEENNNDAKLLIDKAIKARDAKEAAKKAREEKKSGKKPKKEKGIL 405
>gnl|CDD|99743 cd06450, DOPA_deC_like, DOPA decarboxylase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). The major groups
in this CD correspond to DOPA/tyrosine decarboxylase
(DDC), histidine decarboxylase (HDC), and glutamate
decarboxylase (GDC). DDC is active as a dimer and
catalyzes the decarboxylation of tyrosine. GDC catalyzes
the decarboxylation of glutamate and HDC catalyzes the
decarboxylation of histidine.
Length = 345
Score = 25.6 bits (57), Expect = 5.2
Identities = 9/42 (21%), Positives = 15/42 (35%), Gaps = 5/42 (11%)
Query: 26 FHRFCLWLGVPLHRVPLTK-----PQDLARIISEFALEYRTT 62
+ +L V + VP+ + P+ L I E E
Sbjct: 108 VEKAAAYLDVKVRLVPVDEDGRMDPEALEAAIDEDKAEGLNP 149
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 25.4 bits (56), Expect = 5.7
Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 2/73 (2%)
Query: 2 SEFLSDTAQRIIVLSIVHRRVLHRFHRFCLWLGVPLHRVPLTK--PQDLARIISEFALEY 59
E L D + + ++ V + L + + G L+ VP T+ +L +++ E
Sbjct: 175 EEPLEDPKKTVFIIFFVGKEDLDKVKKILDSFGFELYDVPETEGERSELISKVNKRIEEL 234
Query: 60 RTTRERVIQTREK 72
+ E+ EK
Sbjct: 235 QRVLEQTESHLEK 247
>gnl|CDD|176774 cd08796, Death_IRAK-M, Death domain of Interleukin 1 Receptor
Associated Kinase-M. Death Domain (DD) of
Interleukin-1 Receptor-Associated Kinase M (IRAK-M).
IRAKs are essential components of innate immunity and
inflammation in mammals and other vertebrates. They are
involved in signal transduction pathways involving IL-1
and IL-18 receptors, Toll-like receptors(TLRs), nuclear
factor-kappaB (NF-kB), and mitogen-activated protein
kinases (MAPKs). IRAKs contain an N-terminal DD domain
and a C-terminal kinase domain. IRAK-M, also called
IRAK-3, is an inactive kinase present only in
macrophages in an inducible manner. It is a negative
regulator of TLR signaling and it contributes to the
attenuation of NF-kB activation. DDs are
protein-protein interaction domains found in a variety
of domain architectures. Their common feature is that
they form homodimers by self-association or
heterodimers by associating with other members of the
DD superfamily including CARD (Caspase activation and
recruitment domain), DED (Death Effector Domain), and
PYRIN. They serve as adaptors in signaling pathways and
can recruit other proteins into signaling complexes.
Length = 89
Score = 24.9 bits (54), Expect = 5.8
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 46 QDLARIISEFALEYRTTRERVIQ----TREKKASHRERNKTRGKMITECEELSER 96
+ LA +S LE R + V+Q TRE S ++NKT G ++ +E+
Sbjct: 28 RTLAERLSSSWLEVRHIEKYVVQGKSGTRELLWSWAQKNKTVGDLLQVLDEMGHA 82
>gnl|CDD|220867 pfam10744, Med1, Mediator of RNA polymerase II transcription
subunit 1. Mediator complexes are basic necessities for
linking transcriptional regulators to RNA polymerase II.
This domain, Med1, is conserved from plants to fungi to
humans and forms part of the Med9 submodule of the
Srb/Med complex. it is one of three subunits essential
for viability of the whole organism via its role in
environmentally-directed cell-fate decisions. Med1 is
part of the tail region of the Mediator complex.
Length = 384
Score = 25.5 bits (56), Expect = 6.0
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 32 WLGVPLHRVPLTKPQDLARIIS 53
LG + VP + P+ L +I+
Sbjct: 343 DLGRLITSVPFSHPRQLPKILP 364
>gnl|CDD|184746 PRK14562, PRK14562, haloacid dehalogenase superfamily protein;
Provisional.
Length = 204
Score = 24.9 bits (55), Expect = 7.6
Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 10/57 (17%)
Query: 46 QDLARIISEFALEYRTTRERVIQ-TREK--------KASHRERNKTRGKMITECEEL 93
+ + I E E RE ++ +RE +A HR + K++ E EEL
Sbjct: 4 EIIDSIREELE-EKDEAREEALKLSREIVRLSGDAIRAIHRGDFEEAEKLLKEAEEL 59
>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 = 25.0 bits (55), Expect = 8.0
Identities = 11/51 (21%), Positives = 17/51 (33%)
Query: 46 QDLARIISEFALEYRTTRERVIQTREKKASHRERNKTRGKMITECEELSER 96
+ L + E E E RE+ S R + + + EE E
Sbjct: 799 KALREALDELRAELTLLNEEAANLRERLESLERRIAATERRLEDLEEQIEE 849
>gnl|CDD|215212 PLN02372, PLN02372, violaxanthin de-epoxidase.
Length = 455
Score = 25.2 bits (55), Expect = 8.1
Identities = 9/68 (13%), Positives = 17/68 (25%)
Query: 14 VLSIVHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISEFALEYRTTRERVIQTREKK 73
S H V HR L ++ + S + + E
Sbjct: 18 STSRTHSSVSRSNHRAVLAPRRRSMSAISSRTSSRSSRASASLRKSDSEEEFDFVGLSSL 77
Query: 74 ASHRERNK 81
+E ++
Sbjct: 78 NELKEWSR 85
>gnl|CDD|181651 PRK09105, PRK09105, putative aminotransferase; Provisional.
Length = 370
Score = 25.0 bits (55), Expect = 8.7
Identities = 5/13 (38%), Positives = 7/13 (53%)
Query: 32 WLGVPLHRVPLTK 44
G P+ +VPL
Sbjct: 138 AQGAPVAKVPLRA 150
>gnl|CDD|179603 PRK03600, nrdI, ribonucleotide reductase stimulatory protein;
Reviewed.
Length = 134
Score = 24.4 bits (54), Expect = 8.7
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 27 HRFCLWLGVPLHRVPLTKPQDL 48
HRF LG+P R+P+ + + L
Sbjct: 15 HRFVQKLGLPATRIPINERERL 36
>gnl|CDD|162157 TIGR01013, 2a58, Phosphate:Na+ Symporter (PNaS) Family. [Transport
and binding proteins, Cations and iron carrying
compounds].
Length = 456
Score = 24.8 bits (54), Expect = 9.4
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 1 MSEFLSDTAQRIIVLSIVHRRVLHRFHRFCLWLGVPLHRVPLTKPQDLARIISEFALEYR 60
++ LS+ +R L I + L L+ +P R P+ AR + +YR
Sbjct: 325 LAALLSEDEKRRSALQIAYCHNLFNISGIVLFYPLPCTRKPIA----AARGFGDDGSKYR 380
Query: 61 T 61
Sbjct: 381 W 381
>gnl|CDD|235440 PRK05387, PRK05387, histidinol-phosphate aminotransferase;
Provisional.
Length = 353
Score = 24.8 bits (55), Expect = 9.4
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 48 LARIISEFALE----YRTTRERVIQTREK 72
LA+ + A+E + TR +VI TRE+
Sbjct: 247 LAQAGAIAAIEDEAYFEETRAKVIATRER 275
>gnl|CDD|215465 PLN02863, PLN02863, UDP-glucoronosyl/UDP-glucosyl transferase
family protein.
Length = 477
Score = 24.8 bits (54), Expect = 9.6
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 45 PQDLARIISEFALEYRTTRERVIQTR 70
+LAR+ E E + RER + R
Sbjct: 420 SDELARVFMESVSENQVERERAKELR 445
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
0.326 0.137 0.403
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,971,502
Number of extensions: 421198
Number of successful extensions: 638
Number of sequences better than 10.0: 1
Number of HSP's gapped: 637
Number of HSP's successfully gapped: 45
Length of query: 97
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 33
Effective length of database: 8,098,946
Effective search space: 267265218
Effective search space used: 267265218
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: 53 (24.2 bits)