RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18081
(82 letters)
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 67.0 bits (164), Expect = 6e-15
Identities = 21/59 (35%), Positives = 36/59 (61%)
Query: 2 STEKMPIKINLIAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAVSI 60
+T++ I I LIAPP YV+ T +K G++ + A++ IK I++ GG F+V+ +
Sbjct: 213 ATDECKITIKLIAPPQYVIVTTCSDKDKGMEIIGAALEAIKEVIKKKGGDFKVKGEPEV 271
>gnl|CDD|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit
(eIF-2alpha) [Translation, ribosomal structure and
biogenesis].
Length = 269
Score = 50.4 bits (121), Expect = 5e-09
Identities = 11/56 (19%), Positives = 24/56 (42%)
Query: 1 MSTEKMPIKINLIAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQM 56
E++ +K+ + P Y + P+ + L++A + I++LGG
Sbjct: 206 NGEEEVELKVYYVGAPRYRIDVQAPDYKKAEEVLEKAAEAAIKTIKKLGGEGTFIR 261
>gnl|CDD|219460 pfam07541, EIF_2_alpha, Eukaryotic translation initiation factor 2
alpha subunit. These proteins share a region of
similarity that falls towards the C terminus from
pfam00575.
Length = 112
Score = 43.7 bits (104), Expect = 4e-07
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 2 STEKMPIKINLIAPPLYVMTTVTPEK 27
STE +PIKI + P Y +T P+
Sbjct: 87 STEDVPIKIKYVGAPRYRITVTAPDY 112
>gnl|CDD|111299 pfam02391, MoaE, MoaE protein. This family contains the MoaE
protein that is involved in biosynthesis of
molybdopterin. Molybdopterin, the universal component of
the pterin molybdenum cofactors, contains a dithiolene
group serving to bind Mo. Addition of the dithiolene
sulfurs to a molybdopterin precursor requires the
activity of the converting factor. Converting factor
contains the MoaE and MoaD proteins.
Length = 117
Score = 28.8 bits (65), Expect = 0.15
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 13 IAPPLYVMTTVTPEKADGLKALQEAIDTIKAKI 45
I ++ P + + +A + AID +K ++
Sbjct: 85 IGEAAVLIAVSAPHRKEAFEACEYAIDELKKRV 117
>gnl|CDD|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit
alpha; Validated.
Length = 262
Score = 27.9 bits (63), Expect = 0.40
Identities = 11/48 (22%), Positives = 21/48 (43%)
Query: 8 IKINLIAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQ 55
++I + P Y + P+ KAL++ + I++LGG
Sbjct: 211 VEIYYVGAPRYRIDVTAPDYKTAEKALKKIAERAIKVIKKLGGEGSFV 258
>gnl|CDD|109985 pfam00950, ABC-3, ABC 3 transport family.
Length = 258
Score = 27.6 bits (62), Expect = 0.60
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 48 LGGVFQVQMAVSILLMSMIQNSQTDLFN 75
+G VF +A+ +LL+S+I+ S DL +
Sbjct: 86 IGIVFSSFLALGLLLISLIKGSAVDLDH 113
>gnl|CDD|216309 pfam01122, Cobalamin_bind, Eukaryotic cobalamin-binding protein.
Length = 305
Score = 27.4 bits (61), Expect = 0.64
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 23 VTPEKADGLK-ALQEAIDTIKAKIEQLGGVFQVQMAVSILLMSMIQNSQTDLFNSD 77
V+PE L A ++A++ + +I+Q G F MA+S +L ++ + D+ D
Sbjct: 231 VSPEPPTKLGWACKKAMNALLTEIKQ--GKFHNPMAISQILPALKGKTYLDVPKVD 284
>gnl|CDD|216505 pfam01441, Lipoprotein_6, Lipoprotein. Members of this family
are lipoproteins that are probably involved in evasion
of the host immune system by pathogens.
Length = 160
Score = 26.9 bits (60), Expect = 1.0
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 12 LIAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIE 46
L+A + T +T K + LK + I +K KIE
Sbjct: 52 LLAGAYSISTLIT-TKLEALKKSEGGISDLKEKIE 85
>gnl|CDD|178014 PLN02390, PLN02390, molybdopterin synthase catalytic subunit.
Length = 111
Score = 26.6 bits (59), Expect = 1.1
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 25 PEKADGLKALQEAIDTIKAKI 45
+AD L A + ID +KA +
Sbjct: 78 VHRADALDACKFLIDELKASV 98
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 26.4 bits (59), Expect = 1.9
Identities = 8/37 (21%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 29 DGLKA-LQEAIDTIKAK---IEQLGGVFQVQMAVSIL 61
+ L ++ AID I AK ++ + +F +++
Sbjct: 116 EALFIRIEYAIDKIGAKRVVLDSIEALFSGFSNEAVV 152
>gnl|CDD|237730 PRK14493, PRK14493, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobB/MoaE;
Provisional.
Length = 274
Score = 25.7 bits (57), Expect = 2.5
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 26 EKADGLKALQEAIDTIKAKIEQLGGVFQVQM 56
EK DG+ E + I+ +++Q GVF+V +
Sbjct: 186 EKYDGVA--DERMAAIREELKQRDGVFEVLL 214
>gnl|CDD|149709 pfam08734, GYD, GYD domain. This protein is found in a range of
bacteria. It is usually less than 100 amino acids in
length. The function of the protein is unknown. It may
belong to the dimeric alpha/beta barrel superfamily.
Length = 91
Score = 25.2 bits (56), Expect = 2.9
Identities = 9/33 (27%), Positives = 16/33 (48%)
Query: 18 YVMTTVTPEKADGLKALQEAIDTIKAKIEQLGG 50
V+ T + GLK + + ++ +E LGG
Sbjct: 2 IVLANYTDQGIKGLKDSPKRAEAVRELLESLGG 34
>gnl|CDD|233390 TIGR01385, TFSII, transcription elongation factor S-II. This model
represents eukaryotic transcription elongation factor
S-II. This protein allows stalled RNA transcription
complexes to perform a cleavage of the nascent RNA and
restart at the newly generated 3-prime end.
Length = 299
Score = 25.6 bits (56), Expect = 2.9
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 9/54 (16%)
Query: 23 VTPEKADGLKALQEAIDTIKAKIEQLG--GVFQVQMAVSILLMSMIQNSQTDLF 74
+TPEK + A + A +K + E++ +F+ Q A IQ + TDLF
Sbjct: 213 ITPEKLATMTAEEMASAELKQEREEITKENLFEAQGAK-------IQKAVTDLF 259
>gnl|CDD|224431 COG1514, LigT, 2'-5' RNA ligase [Translation, ribosomal structure
and biogenesis].
Length = 180
Score = 25.4 bits (56), Expect = 3.7
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 23 VTPEKADGLKALQEAIDTIKAKIE 46
V E+ + L+AL E ++ A++
Sbjct: 90 VGVEETEELRALAEELERALARLG 113
>gnl|CDD|226908 COG4531, ZnuA, ABC-type Zn2+ transport system, periplasmic
component/surface adhesin [Inorganic ion transport and
metabolism].
Length = 318
Score = 25.5 bits (56), Expect = 3.7
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 4/28 (14%)
Query: 22 TVTPEKADGLKALQEAIDTIKAKIEQLG 49
TV+PE G K L E I+ ++++
Sbjct: 235 TVSPEVQPGAKRLAE----IRTQLKEQK 258
>gnl|CDD|132903 cd06927, RNAP_L, L subunit of Archaeal RNA polymerase. The
archaeal L subunit of RNA polymerase (RNAP) is involved
in the assembly of RNAP subunits. RNAP is a large
multi-subunit complex responsible for the synthesis of
RNA. It is the principal enzyme of the transcription
process, and is a final target in many regulatory
pathways that control gene expression in all living
cells. A single distinct RNAP complex is found in
archaea, which may be responsible for the synthesis of
all RNAs. The archaeal RNAP harbors homologues of all
eukaryotic RNAP II subunits with two exceptions (RPB8
and RPB9). The 12 archaeal subunits are designated by
letters and can be divided into three functional groups
that are engaged in: (I) catalysis (A'/A", B'/B" or B);
(II) assembly (L, N, D and P); and (III) auxiliary
functions (F, E, H and K). The assembly of the two
largest archaeal RNAP subunits that provide most of the
enzyme's catalytic functions depends on the presence of
the archaeal D/L heterodimer.
Length = 83
Score = 24.5 bits (54), Expect = 3.9
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 19 VMTTVTPEKADGLKALQEAIDTIKAKIEQL 48
V+ T D L+AL+EA + E+
Sbjct: 52 VLKIKTDGGVDPLEALKEAAKRLIDLCEEF 81
>gnl|CDD|143411 cd07092, ALDH_ABALDH-YdcW, Escherichia coli NAD+-dependent
gamma-aminobutyraldehyde dehydrogenase YdcW-like.
NAD+-dependent, tetrameric, gamma-aminobutyraldehyde
dehydrogenase (ABALDH), YdcW of Escherichia coli K12,
catalyzes the oxidation of gamma-aminobutyraldehyde to
gamma-aminobutyric acid. ABALDH can also oxidize n-alkyl
medium-chain aldehydes, but with a lower catalytic
efficiency.
Length = 450
Score = 25.4 bits (56), Expect = 4.1
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 12 LIAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGG 50
L+A P M ++T G K + A DT+K +LGG
Sbjct: 191 LVAHPRVRMVSLTGSVRTGKKVARAAADTLKRVHLELGG 229
>gnl|CDD|187656 cd08953, KR_2_SDR_x, ketoreductase (KR), subgroup 2, complex (x)
SDRs. Ketoreductase, a module of the multidomain
polyketide synthase (PKS), has 2 subdomains, each
corresponding to a SDR family monomer. The C-terminal
subdomain catalyzes the NADPH-dependent reduction of the
beta-carbonyl of a polyketide to a hydroxyl group, a
step in the biosynthesis of polyketides, such as
erythromycin. The N-terminal subdomain, an interdomain
linker, is a truncated Rossmann fold which acts to
stabilizes the catalytic subdomain. Unlike typical SDRs,
the isolated domain does not oligomerize but is composed
of 2 subdomains, each resembling an SDR monomer. The
active site resembles that of typical SDRs, except that
the usual positions of the catalytic Asn and Tyr are
swapped, so that the canonical YXXXK motif changes to
YXXXN. Modular PKSs are multifunctional structures in
which the makeup recapitulates that found in (and may
have evolved from) FAS. Polyketide synthesis also
proceeds via the addition of 2-carbon units as in fatty
acid synthesis. The complex SDR NADP-binding motif,
GGXGXXG, is often present, but is not strictly conserved
in each instance of the module. This subfamily includes
both KR domains of the Bacillus subtilis Pks J,-L, and
PksM, and all three KR domains of PksN, components of
the megacomplex bacillaene synthase, which synthesizes
the antibiotic bacillaene. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) contributing to
the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G
NAD(P)-binding motif. Some atypical SDRs have lost
catalytic activity and/or have an unusual NAD(P)-binding
motif and missing or unusual active site residues.
Reactions catalyzed within the SDR family include
isomerization, decarboxylation, epimerization, C=N bond
reduction, dehydratase activity, dehalogenation,
Enoyl-CoA reduction, and carbonyl-alcohol
oxidoreduction.
Length = 436
Score = 25.0 bits (55), Expect = 4.9
Identities = 10/41 (24%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 12 LIAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVF 52
L A LY+ VT D A++ ++ ++ + + GV
Sbjct: 258 LGARVLYISADVT----D-AAAVRRLLEKVRERYGAIDGVI 293
>gnl|CDD|224033 COG1108, ZnuB, ABC-type Mn2+/Zn2+ transport systems, permease
components [Inorganic ion transport and metabolism].
Length = 274
Score = 24.8 bits (55), Expect = 5.4
Identities = 9/28 (32%), Positives = 20/28 (71%)
Query: 48 LGGVFQVQMAVSILLMSMIQNSQTDLFN 75
+G VF +A+ ++L+S++ +S+ DL +
Sbjct: 95 IGIVFSSGLALGLVLLSLVPSSRVDLMH 122
>gnl|CDD|150467 pfam09803, DUF2346, Uncharacterized conserved protein (DUF2346).
Members of this family of proteins have no known
function.
Length = 80
Score = 24.4 bits (53), Expect = 5.5
Identities = 6/23 (26%), Positives = 11/23 (47%)
Query: 25 PEKADGLKALQEAIDTIKAKIEQ 47
PE K L++ + ++ K E
Sbjct: 45 PENEQHRKELEDFKERLREKHEA 67
>gnl|CDD|223391 COG0314, MoaE, Molybdopterin converting factor, large subunit
[Coenzyme metabolism].
Length = 149
Score = 24.6 bits (54), Expect = 6.3
Identities = 4/26 (15%), Positives = 12/26 (46%)
Query: 18 YVMTTVTPEKADGLKALQEAIDTIKA 43
++ + + + +A + ID +K
Sbjct: 95 VLVGVASAHRKEAFEACEYIIDRLKH 120
>gnl|CDD|220375 pfam09742, Dymeclin, Dyggve-Melchior-Clausen syndrome protein.
Dymeclin (Dyggve-Melchior-Clausen syndrome protein)
contains a large number of leucine and isoleucine
residues and a total of 17 repeated dileucine motifs. It
is characteristically about 700 residues long and
present in plants and animals. Mutations in the gene
coding for this protein in humans give rise to the
disorder Dyggve-Melchior-Clausen syndrome (DMC, MIM
223800) which is an autosomal-recessive disorder
characterized by the association of a
spondylo-epi-metaphyseal dysplasia and mental
retardation. DYM transcripts are widely expressed
throughout human development and Dymeclin is not an
integral membrane protein of the ER, but rather a
peripheral membrane protein dynamically associated with
the Golgi apparatus.
Length = 659
Score = 24.7 bits (54), Expect = 6.5
Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 9/61 (14%)
Query: 18 YVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAVSILLMSMIQNSQTDLFNSD 77
YV++ ++D + ++ + + MA+ ILL+ SQ FN
Sbjct: 380 YVLS-----RSDLDNLIVPILELLYDAESDQSNSHHIYMALIILLIL----SQDRNFNRS 430
Query: 78 V 78
+
Sbjct: 431 L 431
>gnl|CDD|236121 PRK07868, PRK07868, acyl-CoA synthetase; Validated.
Length = 994
Score = 24.7 bits (54), Expect = 6.5
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 28 ADGLKALQEAIDTIKA 43
AD + AL EAIDT+K
Sbjct: 122 ADHVVALSEAIDTVKD 137
>gnl|CDD|198434 cd10284, growth_hormone_like, Somatotropin/prolactin hormone
family. The somatotropin/prolactin hormone family
includes growth hormones 1 and 2, prolactin, prolactin
2, and other members that play vital roles in a variety
of processes, including growth control. They are
long-chain class-I helical cytokines, most of which are
secreted by the pituitary gland, and are active as
monomers, binding to cellular receptors with EpoR-like
ligand binding domains.
Length = 178
Score = 24.4 bits (53), Expect = 7.6
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 28 ADGLKALQEAIDTIKAKIEQLGGVFQVQMAV 58
++ LK L++ ++T+ +I+ L F A+
Sbjct: 103 SEMLKLLEDGVETLSERIKDLPLEFNSVGAL 133
>gnl|CDD|163693 cd08062, MPN_RPN7_8, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in 19S
proteasomal subunits Rpn7 and Rpn8. This family
includes lid subunits of the 26 S proteasome regulatory
particles, Rpn7 (PSMD7; proteasome 26S non-ATPase
subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S
non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be
critical for the integrity of the 26 S proteasome
complex by establishing a correct lid structure. It is
necessary for the incorporation/anchoring of Rpn3 and
Rpn12 to the lid and essential for viability and normal
mitosis. Rpn7 and Rpn8 are ATP-independent components of
the 19S regulator subunit, and contain the MPN
structural motif on its N-terminal region. However,
while they show a typical MPN metalloprotease fold, they
lack the canonical JAMM motif, and therefore do not show
catalytic isopeptidase activity. It is suggested that
Rpn7 function is primarily structural.
Length = 280
Score = 24.5 bits (54), Expect = 8.1
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 19 VMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAVSILLMSMIQNSQTDLFN 75
+ T VT K + LK LQ + IK + L V + ++ ++ ++ +Q D+FN
Sbjct: 180 LSTRVT-NKLNSLKGLQSKLKEIK---DYLQLVVEGKLPINHQIIYNLQ----DIFN 228
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
0.318 0.131 0.361
Gapped
Lambda K H
0.267 0.0779 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,938,641
Number of extensions: 303450
Number of successful extensions: 614
Number of sequences better than 10.0: 1
Number of HSP's gapped: 614
Number of HSP's successfully gapped: 38
Length of query: 82
Length of database: 10,937,602
Length adjustment: 51
Effective length of query: 31
Effective length of database: 8,675,548
Effective search space: 268941988
Effective search space used: 268941988
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)