RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16982
(116 letters)
>gnl|CDD|227943 COG5656, SXM1, Importin, protein involved in nuclear import
[Posttranslational modification, protein turnover,
chaperones].
Length = 970
Score = 66.0 bits (161), Expect = 7e-14
Identities = 32/116 (27%), Positives = 50/116 (43%), Gaps = 3/116 (2%)
Query: 1 MMSEVDMPVRQAGVVYLKNLITNQWVEKEVDPGTPLAFSLHEQDKAMIRDAIVDAVVMAP 60
E D+ V+ + +Y KN I W K D + K + + I+D + +P
Sbjct: 45 SKDEGDLNVKLSAAIYFKNKIIRSWSSKRDDGIKA---DEKSEAKKYLIENILDVFLYSP 101
Query: 61 EVIRVQLAVCVSNIVKHDFPGKWTQIVDKVSIYLQNPDATPWFGALLCLYQLVKNY 116
EV R L + NI D P + K + L++ +A + LLCL +L K Y
Sbjct: 102 EVTRTALNAILVNIFSEDKPSDLWGLFPKAANLLRSSEANHVYTGLLCLEELFKAY 157
>gnl|CDD|227944 COG5657, CSE1, CAS/CSE protein involved in chromosome segregation
[Cell division and chromosome partitioning].
Length = 947
Score = 61.4 bits (149), Expect = 3e-12
Identities = 27/112 (24%), Positives = 50/112 (44%), Gaps = 7/112 (6%)
Query: 5 VDMPVRQAGVVYLKNLITNQWVEKEVDPGTPLAFSLHEQDKAMIRDAIVDAVVMAPEVIR 64
M +R A ++ KN I W E+ + S+ + +IRD + ++ + ++
Sbjct: 50 NSMSLRWAALIQFKNYIDKHWREENGN-------SILPDENVLIRDELFSLIISSSNQLQ 102
Query: 65 VQLAVCVSNIVKHDFPGKWTQIVDKVSIYLQNPDATPWFGALLCLYQLVKNY 116
+Q A+ VS I + DFP +W +V + L D +L L+ + K
Sbjct: 103 IQNALAVSRIARLDFPDEWPTLVPDLLSLLSEKDMVTNENSLRVLHHIFKRL 154
>gnl|CDD|217743 pfam03810, IBN_N, Importin-beta N-terminal domain.
Length = 71
Score = 45.7 bits (109), Expect = 7e-08
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 10/54 (18%)
Query: 4 EVDMPVRQAGVVYLKNLITNQWVEKEVDPGTPLAFSLHEQDKAMIRDAIVDAVV 57
D+ VRQ +YLKNLIT W SL ++K IR+ +++ +
Sbjct: 27 SSDLQVRQLAALYLKNLITRHWN----------QLSLPPEEKEQIRNNLLNLLG 70
>gnl|CDD|197981 smart00913, IBN_N, Importin-beta N-terminal domain. Members of
the importin-beta (karyopherin-beta) family can bind
and transport cargo by themselves, or can form
heterodimers with importin-alpha. As part of a
heterodimer, importin-beta mediates interactions with
the pore complex, while importin-alpha acts as an
adaptor protein to bind the nuclear localisation signal
(NLS) on the cargo through the classical NLS import of
proteins. Importin-beta is a helicoidal molecule
constructed from 19 HEAT repeats. Many nuclear pore
proteins contain FG sequence repeats that can bind to
HEAT repeats within importins.. which is important for
importin-beta mediated transport.
Length = 67
Score = 41.5 bits (98), Expect = 3e-06
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 12/57 (21%)
Query: 1 MMSEVDMPVRQAGVVYLKNLITNQWVEKEVDPGTPLAFSLHEQDKAMIRDAIVDAVV 57
+ + D VRQ + LKN IT +W SL E++K I++++++ ++
Sbjct: 22 LANSEDQYVRQLAAITLKNKITRRWS------------SLPEEEKEEIKNSLLELLL 66
>gnl|CDD|219817 pfam08389, Xpo1, Exportin 1-like protein. The sequences featured
in this family are similar to a region close to the
N-terminus of yeast exportin 1 (Xpo1, Crm1). This region
is found just C-terminal to an importin-beta N-terminal
domain (pfam03810) in many members of this family.
Exportin 1 is a nuclear export receptor that interacts
with leucine-rich nuclear export signal (NES) sequences,
and Ran-GTP, and is involved in translocation of
proteins out of the nucleus.
Length = 147
Score = 30.3 bits (69), Expect = 0.13
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 60 PEVIRVQLAVCVSNIVKHDFPGKW-TQIVDKVSIYLQNPDATPWFGALLCL 109
P+ IR +LA+ ++ + K ++P W T D VS+ +P +L +
Sbjct: 1 PKFIRNKLALALAELAKQEWPSNWPTFFPDLVSLLSSSPSGCELLLRILKV 51
>gnl|CDD|213736 TIGR02773, addB_Gpos, helicase-exonuclease AddAB, AddB subunit. DNA
repair is accomplished by several different systems in
prokaryotes. Recombinational repair of double-stranded
DNA breaks involves the RecBCD pathway in some lineages,
and AddAB (also called RexAB) in other. The AddA protein
is conserved between the firmicutes and the
alphaproteobacteria, while the partner protein is not.
Nevertheless, the partner is designated AddB in both
systems. This model describes the AddB protein as found
Bacillus subtilis and related species. Although the RexB
protein of Streptococcus and Lactococcus is considered to
be orthologous, functionally equivalent, and merely named
differently, all members of this protein family have a
P-loop nucleotide binding motif GxxGxGK[ST] at the
N-terminus, unlike RexB proteins, and a CxxCxxxxxC motif
at the C-terminus, both of which may be relevant to
function [DNA metabolism, DNA replication, recombination,
and repair].
Length = 1160
Score = 28.5 bits (64), Expect = 0.90
Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 6/48 (12%)
Query: 15 VYLKNLITN--QWVEKEVDPGTPLAFSLHEQ----DKAMIRDAIVDAV 56
YL ++TN +W+ + P L F +H+ + + I +
Sbjct: 981 TYLDIVLTNSAKWLGNQATPAGVLYFHIHDPMIQAKGDLTEEEIEQEI 1028
>gnl|CDD|232971 TIGR00425, CBF5, rRNA pseudouridine synthase, putative. This
family, found in archaea and eukaryotes, includes the
only archaeal proteins markedly similar to bacterial
TruB, the tRNA pseudouridine 55 synthase. However, among
two related yeast proteins, the archaeal set matches
yeast YLR175w far better than YNL292w. The first, termed
centromere/microtubule binding protein 5 (CBF5), is an
apparent rRNA pseudouridine synthase, while the second
is the exclusive tRNA pseudouridine 55 synthase for both
cytosolic and mitochondrial compartments. It is unclear
whether archaeal proteins found by this model modify
tRNA, rRNA, or both [Protein synthesis, tRNA and rRNA
base modification].
Length = 322
Score = 27.0 bits (60), Expect = 2.3
Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 7/78 (8%)
Query: 8 PVRQAGVVYLKNLITNQWVEKEVDPGT-------PLAFSLHEQDKAMIRDAIVDAVVMAP 60
+ +V L +L+ KE + P+ + L + +++D+ VDA+
Sbjct: 195 CFGEDDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRHLKRVVVKDSAVDAICHGA 254
Query: 61 EVIRVQLAVCVSNIVKHD 78
+++ +A I K D
Sbjct: 255 DLMVRGIARLEKGIEKGD 272
>gnl|CDD|241426 cd13272, PH_INPP4A_INPP4B, Type I inositol 3,4-bisphosphate
4-phosphatase and Type II inositol 3,4-bisphosphate
4-phosphatase Pleckstrin homology (PH) domain. INPP4A
(also called Inositol polyphosphate 4-phosphatase type
I) and INPP4B (also called Inositol polyphosphate
4-phosphatase type II) both catalyze the hydrolysis of
the 4-position phosphate of phosphatidylinositol
3,4-bisphosphate and inositol 1,3,4-trisphosphate. They
differ in that INPP4A additionally catalyzes the
hydrolysis of the 4-position phosphate of inositol
3,4-bisphosphate, while INPP4B catalyzes the hydrolysis
of the 4-position phosphate of inositol
1,4-bisphosphate. They both have a single PH domain
followed by a C2 domain. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold, which
is electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 116
Score = 26.4 bits (59), Expect = 2.7
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 14/66 (21%)
Query: 12 AGVVYLKNLITNQWVEKEVDPGTPLAFSL-HEQDKAMI--------RDAIVDAVVMAP-E 61
AGV+ L+N V++E AFSL + +K RD ++A+ A E
Sbjct: 40 AGVIVLENCR----VQREEPDPGGFAFSLVFKDEKKYRFSCRSEEERDEWIEAIKQASYE 95
Query: 62 VIRVQL 67
+R QL
Sbjct: 96 YLRSQL 101
>gnl|CDD|226945 COG4579, COG4579, Isocitrate dehydrogenase kinase/phosphatase
[Signal transduction mechanisms].
Length = 578
Score = 26.3 bits (58), Expect = 5.0
Identities = 10/35 (28%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 20 LITNQWVEKEVDPGTPLAFSLHEQDKAMIRDAIVD 54
+I + ++E+ + TPL L + + +RDAI +
Sbjct: 409 VIRHLYIERRM---TPLNIWLEQVEGQQLRDAIEE 440
>gnl|CDD|233538 TIGR01701, Fdhalpha-like, oxidoreductase alpha (molybdopterin)
subunit. This model represents a well-defined clade of
oxidoreductase alpha subunits most closely related to a
group of formate dehydrogenases including the E. coli
FdhH protein (TIGR01591). These alpha subunits contain a
molybdopterin cofactor and generally associate with two
other subunits which contain iron-sulfur clusters and
cytochromes. The particular subunits with which this
enzyme interacts and the substrate which is reduced is
unknown at this time. In Ralstonia, the gene is
associated with the cbb operon , but is not essential
for CO2 fixation.
Length = 743
Score = 25.5 bits (56), Expect = 8.8
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 28 KEVDPGTPLAFSLHEQDKAMIRDAI 52
K + P TP+A+ + IRDAI
Sbjct: 546 KALLPETPVAWEILVDTYDQIRDAI 570
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
0.322 0.136 0.420
Gapped
Lambda K H
0.267 0.0764 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,057,616
Number of extensions: 516157
Number of successful extensions: 393
Number of sequences better than 10.0: 1
Number of HSP's gapped: 389
Number of HSP's successfully gapped: 20
Length of query: 116
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 37
Effective length of database: 7,433,636
Effective search space: 275044532
Effective search space used: 275044532
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 (21.9 bits)
S2: 53 (24.1 bits)