RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4090
(112 letters)
>gnl|CDD|227432 COG5101, CRM1, Importin beta-related nuclear transport receptor
[Nuclear structure / Intracellular trafficking and
secretion].
Length = 1053
Score = 104 bits (260), Expect = 2e-27
Identities = 38/83 (45%), Positives = 55/83 (66%)
Query: 14 LLDFNQKLDITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQT 73
+L+F++ LDI LLD +V Y G G +Q+ AQ +LT +E PDAWT+ D IL S Q+
Sbjct: 4 ILEFDKDLDIALLDKVVTTFYQGDGRKQEQAQRILTKFQELPDAWTKADYILNNSKLPQS 63
Query: 74 KFYALQILEQVIKTRWKALPREQ 96
K+ AL +L+++I T+WK LP
Sbjct: 64 KYIALSLLDKLITTKWKLLPEGM 86
>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 = 53.8 bits (130), Expect = 4e-11
Identities = 16/55 (29%), Positives = 27/55 (49%)
Query: 44 AQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCD 98
A++ L ++ P W + IL S +Q + A L+ I RW +LP E+ +
Sbjct: 1 AEKQLEQFQKSPGFWLLLLEILANSEDQYVRQLAAITLKNKITRRWSSLPEEEKE 55
>gnl|CDD|217743 pfam03810, IBN_N, Importin-beta N-terminal domain.
Length = 71
Score = 37.2 bits (87), Expect = 1e-04
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 44 AQEVLTALKE-HPDAWTRVDTILEY-SSNQQTKFYALQILEQVIKTRWKALP 93
A++ L ++ P W+++ IL SS+ Q + A L+ +I W L
Sbjct: 1 AEKQLEQFEKQDPGFWSKLLQILSDTSSDLQVRQLAALYLKNLITRHWNQLS 52
>gnl|CDD|224626 COG1712, COG1712, Predicted dinucleotide-utilizing enzyme
[General function prediction only].
Length = 255
Score = 30.8 bits (70), Expect = 0.11
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 55 PDAWTRVDTILEYSSNQQTKFYALQILEQVI 85
+ VD ++E +S + + Y +IL+ I
Sbjct: 55 DELIAEVDLVVEAASPEAVREYVPKILKAGI 85
>gnl|CDD|200463 cd11324, AmyAc_Amylosucrase, Alpha amylase catalytic domain found
in Amylosucrase. Amylosucrase is a glucosyltransferase
that catalyzes the transfer of a D-glucopyranosyl moiety
from sucrose onto an acceptor molecule. When the
acceptor is another saccharide, only alpha-1,4 linkages
are produced. Unlike most amylopolysaccharide synthases,
it does not require any alpha-D-glucosyl nucleoside
diphosphate substrate. In the presence of glycogen it
catalyzes the transfer of a D-glucose moiety onto a
glycogen branch, but in its absence, it hydrolyzes
sucrose and synthesizes polymers, smaller
maltosaccharides, and sucrose isoforms. The
Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 536
Score = 29.8 bits (68), Expect = 0.27
Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 4/70 (5%)
Query: 44 AQEVLTALKEH-PDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDVKEE 102
A L L H PD + + T+ Y ++ L+ L + + A P + +
Sbjct: 2 ADIFLLRLARHFPDLFELLYTL--YG-DRADFDEHLERLLASLAKAYAARPADLKALDLA 58
Query: 103 KEREQNWFQR 112
+E + +WFQ
Sbjct: 59 READPDWFQS 68
>gnl|CDD|233738 TIGR02124, hypE, hydrogenase expression/formation protein HypE.
This family contains HypE (or HupE), a protein required
for expression of catalytically active hydrogenase in
many systems. It appears to be an accessory protein
involved in maturation rather than a regulatory protein
involved in expression. HypE shows considerable homology
to the thiamine-monophosphate kinase ThiL (TIGR01379)
and other enzymes.
Length = 320
Score = 29.1 bits (66), Expect = 0.42
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 37 MGVEQKAAQEVLTALKEHP 55
+ V +AA++VL LK HP
Sbjct: 259 LAVPPEAAEKVLEILKSHP 277
>gnl|CDD|100033 cd02197, HypE, HypE (Hydrogenase expression/formation protein).
HypE is involved in Ni-Fe hydrogenase biosynthesis.
HypE dehydrates its own carbamoyl moiety in an
ATP-dependent process to yield the enzyme thiocyanate.
The N-terminal domain of HypE is related to the
ATP-binding domains of the AIR synthases,
selenophosphate synthetase (SelD), and FGAM synthase and
is thought to bind ATP.
Length = 293
Score = 29.0 bits (66), Expect = 0.46
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 37 MGVEQKAAQEVLTALKEHP 55
V + A+EVL AL+ HP
Sbjct: 264 AIVPPEDAEEVLEALRSHP 282
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 28.1 bits (63), Expect = 0.99
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 4 VIPPNEQFKKLLDFNQKLDITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPD 56
+ E+ +KLLD ++ +I LL V+ Y G A L E P+
Sbjct: 157 TVATLEELEKLLDLAKEHNILLL---VDEAYAGFVFGSLDAVATRALLAEGPN 206
>gnl|CDD|191637 pfam06908, DUF1273, Protein of unknown function (DUF1273). This
family consists of several hypothetical bacterial
proteins of around 180 residues in length. The function
of this family is unknown.
Length = 177
Score = 27.6 bits (62), Expect = 1.1
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 23 ITLLDNIVECMYTG--MGVEQKAAQEVLTALKEHPD 56
I LL+ +E TG +G EQ AA+ VL KE+P+
Sbjct: 36 IELLEEGLEWFITGGQLGFEQWAAEVVLELKKEYPE 71
>gnl|CDD|223386 COG0309, HypE, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 339
Score = 27.2 bits (61), Expect = 1.6
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 37 MGVEQKAAQEVLTALKEHP 55
+ V + A+EVL AL+ H
Sbjct: 280 IAVPPEHAEEVLEALRSHG 298
>gnl|CDD|238498 cd01016, TroA, Metal binding protein TroA. These proteins have been
shown to function as initial receptors in ABC transport
of Zn2+ and possibly Fe3+ in many eubacterial species.
The TroA proteins belong to the TroA superfamily of
periplasmic metal binding proteins that share a distinct
fold and ligand binding mechanism. A typical TroA
protein is comprised of two globular subdomains
connected by a single helix and can bind the metal ion
in the cleft between these domains. In addition, these
proteins sometimes have a low complexity region
containing a metal-binding histidine-rich motif
(repetitive HDH sequence).
Length = 276
Score = 26.9 bits (60), Expect = 2.4
Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 5/55 (9%)
Query: 42 KAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQ 96
A + V L E E+ +N + L L+ K + +P +Q
Sbjct: 112 YAVKAVAEVLSEKLPEHKD-----EFQANSEAYVEELDSLDAYAKKKIAEIPEQQ 161
>gnl|CDD|217564 pfam03447, NAD_binding_3, Homoserine dehydrogenase, NAD binding
domain. This domain adopts a Rossmann NAD binding
fold. The C-terminal domain of homoserine dehydrogenase
contributes a single helix to this structural domain,
which is not included in the Pfam model.
Length = 116
Score = 26.1 bits (58), Expect = 2.7
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 57 AWTRVDTILEYSSNQQTKFYALQILEQ 83
A R D ++E +S++ Y L+ L+
Sbjct: 55 ADPRPDVVVECASSEAVAEYVLKALKA 81
>gnl|CDD|223056 PHA03362, PHA03362, single-stranded binding protein UL29;
Provisional.
Length = 1189
Score = 26.9 bits (60), Expect = 2.8
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 42 KAAQEVLTALKEHPDAWT 59
AA+ VL L P AWT
Sbjct: 934 SAAEYVLEKLAGRPAAWT 951
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 26.3 bits (58), Expect = 3.5
Identities = 14/30 (46%), Positives = 16/30 (53%)
Query: 78 LQILEQVIKTRWKALPREQCDVKEEKEREQ 107
L I E+ IK K L RE KEE +R Q
Sbjct: 34 LDIQEEYIKEEQKNLKRELIRAKEEVKRIQ 63
>gnl|CDD|183987 PRK13343, PRK13343, F0F1 ATP synthase subunit alpha; Provisional.
Length = 502
Score = 26.4 bits (59), Expect = 3.8
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 10/39 (25%)
Query: 18 NQKLDITLLDNIVECMYTGMGVEQKAA--QEVLTALKEH 54
NQK D+ V C+Y +G QKA+ V+ L+EH
Sbjct: 185 NQK------DSDVICVYVAIG--QKASAVARVIETLREH 215
>gnl|CDD|216043 pfam00651, BTB, BTB/POZ domain. The BTB (for BR-C, ttk and bab)
or POZ (for Pox virus and Zinc finger) domain is
present near the N-terminus of a fraction of zinc
finger (pfam00096) proteins and in proteins that
contain the pfam01344 motif such as Kelch and a family
of pox virus proteins. The BTB/POZ domain mediates
homomeric dimerisation and in some instances
heteromeric dimerisation. The structure of the
dimerised PLZF BTB/POZ domain has been solved and
consists of a tightly intertwined homodimer. The
central scaffolding of the protein is made up of a
cluster of alpha-helices flanked by short beta-sheets
at both the top and bottom of the molecule. POZ domains
from several zinc finger proteins have been shown to
mediate transcriptional repression and to interact with
components of histone deacetylase co-repressor
complexes including N-CoR and SMRT. The POZ or BTB
domain is also known as BR-C/Ttk or ZiN.
Length = 101
Score = 25.7 bits (57), Expect = 3.9
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 8/48 (16%)
Query: 11 FKKLLDFNQKLDITLLD-------NIVECMYTGMG-VEQKAAQEVLTA 50
FK L N++++ITL D ++E +YTG + ++ ++L
Sbjct: 36 FKALFTGNKEVEITLEDVSPEDFEALLEFIYTGKLEITEENVDDLLAL 83
>gnl|CDD|131015 TIGR01960, ndhF3_CO2, NAD(P)H dehydrogenase, subunit NdhF3 family.
This family represents a subfamily of NAD(P)H
dehydrogenase subunit 5, or ndhF. It is restricted to
two paralogs in each completed cyanobacterial genome, in
which several subtypes of ndhF are found. Included in
this family is NdhF3, shown to play a role in
high-affinity CO2 uptake in Synechococcus sp. PCC7002.
In all cases, neighboring genes include a paralog of
ndhD but do include other NAD(P)H dehydrogenase
subunits. Instead, genes related to C02 uptake tend to
be found nearby.
Length = 606
Score = 25.8 bits (57), Expect = 6.1
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 65 LEYSSNQQTKFYALQIL 81
L+YS + Q++FY L IL
Sbjct: 580 LKYSVSGQSQFYLLTIL 596
>gnl|CDD|99941 cd05509, Bromo_gcn5_like, Bromodomain; Gcn5_like subfamily. Gcn5p
is a histone acetyltransferase (HAT) which mediates
acetylation of histones at lysine residues; such
acetylation is generally correlated with the activation
of transcription. Bromodomains are 110 amino acid long
domains, that are found in many chromatin associated
proteins. Bromodomains can interact specifically with
acetylated lysine.
Length = 101
Score = 24.8 bits (55), Expect = 6.3
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 45 QEVLTALKEHPDAW 58
++VL +LK H AW
Sbjct: 7 KKVLDSLKNHKSAW 20
>gnl|CDD|234734 PRK00349, uvrA, excinuclease ABC subunit A; Reviewed.
Length = 943
Score = 25.4 bits (57), Expect = 8.1
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 7/31 (22%)
Query: 73 TKFYALQILEQV-------IKTRWKALPREQ 96
+ Y Q+L+ + + T WK LP E
Sbjct: 316 SSSYYFQMLKSLAEHYGFDLDTPWKDLPEEV 346
>gnl|CDD|234195 TIGR03396, PC_PLC, phospholipase C, phosphocholine-specific,
Pseudomonas-type. Members of this protein family are
bacterial, phosphatidylcholine-hydrolyzing phospholipase
C enzymes, with a characteristic domain architecture as
found in hemolytyic (PlcH) and nonhemolytic (PlcN)
secreted enzymes of Pseudomonas aeruginosa. PlcH
hydrolyzes phosphatidylcholine to diacylglycerol and
phosphocholine, but unlike PlcN can also hydrolyze
sphingomyelin to ceramide ((N-acylsphingosine)) and
phosphocholine. Members of this family share the
twin-arginine signal sequence for Sec-independent
transport across the plasma membrane. PlcH is secreted
as a heterodimer with a small chaperone, PlcR, encoded
immediately downstream [Cellular processes,
Pathogenesis].
Length = 689
Score = 25.4 bits (56), Expect = 8.3
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 45 QEVLTALKEHPDAWTRVDTILEYSSN 70
VL AL +P+ W++ +L Y N
Sbjct: 313 SRVLDALTANPEVWSKTVLLLNYDEN 338
>gnl|CDD|233176 TIGR00898, 2A0119, cation transport protein. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 505
Score = 25.4 bits (56), Expect = 9.7
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 68 SSNQQTKFYALQILEQVIKTRWKALPREQCDVKEEKER 105
S + + AL+IL+++ K K LP E + EK+
Sbjct: 272 SQGRIEE--ALKILQRIAKINGKKLPAEVLSLSLEKDL 307
>gnl|CDD|226406 COG3889, COG3889, Predicted solute binding protein [General
function prediction only].
Length = 872
Score = 25.2 bits (55), Expect = 9.9
Identities = 12/58 (20%), Positives = 21/58 (36%)
Query: 29 IVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIK 86
IV Y + +A + ++ A+ I E+ YA Q +EQ +
Sbjct: 123 IVNRAYIVNTIFCGSAYPMYGLYRKLTPAYVIYADIWEWLGVTYDGDYANQYVEQAMA 180
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
0.317 0.131 0.387
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: 5,605,405
Number of extensions: 460267
Number of successful extensions: 547
Number of sequences better than 10.0: 1
Number of HSP's gapped: 547
Number of HSP's successfully gapped: 42
Length of query: 112
Length of database: 10,937,602
Length adjustment: 76
Effective length of query: 36
Effective length of database: 7,566,698
Effective search space: 272401128
Effective search space used: 272401128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.1 bits)