RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15708
(87 letters)
>gnl|CDD|238008 cd00051, EFh, EF-hand, calcium binding motif; A diverse
superfamily of calcium sensors and calcium signal
modulators; most examples in this alignment model have
2 active canonical EF hands. Ca2+ binding induces a
conformational change in the EF-hand motif, leading to
the activation or inactivation of target proteins.
EF-hands tend to occur in pairs or higher copy numbers.
Length = 63
Score = 40.6 bits (96), Expect = 2e-06
Identities = 20/50 (40%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 11 NSHGYIPTSSLREILAALDEQLTPDQLDEMIEEIDTDASGTVDFDGEFDE 60
+ G I L+ L +L E L+ +++DEMI E+D D G +DF+ EF E
Sbjct: 12 DGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFE-EFLE 60
>gnl|CDD|222407 pfam13833, EF_hand_6, EF-hand domain pair.
Length = 53
Score = 38.6 bits (91), Expect = 1e-05
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 14 GYIPTSSLREILAALDEQLTPDQLDEMIEEIDTDASGTVDFDGEF 58
G I L+ LA L L+ +++D + E DTD G + F+ EF
Sbjct: 3 GLITREELKRALALLGISLSEEEVDILFREFDTDGDGKISFE-EF 46
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 38.8 bits (91), Expect = 5e-05
Identities = 14/46 (30%), Positives = 30/46 (65%)
Query: 10 INSHGYIPTSSLREILAALDEQLTPDQLDEMIEEIDTDASGTVDFD 55
+ GYI LR +L +L E+L+ ++++++++E D D G +D++
Sbjct: 103 KDHDGYISIGELRRVLKSLGERLSDEEVEKLLKEYDEDGDGEIDYE 148
Score = 30.0 bits (68), Expect = 0.077
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 10 INSHGYIPTSSLREILAALDEQLTPDQLDEMIEEIDTDASGTVDFD 55
+S G I + L +IL +L + +++++ EEID TVDF
Sbjct: 31 RDSDGLIDRNELGKILRSLGFNPSEAEINKLFEEIDAGN-ETVDFP 75
>gnl|CDD|185504 PTZ00184, PTZ00184, calmodulin; Provisional.
Length = 149
Score = 36.7 bits (85), Expect = 3e-04
Identities = 16/45 (35%), Positives = 30/45 (66%)
Query: 11 NSHGYIPTSSLREILAALDEQLTPDQLDEMIEEIDTDASGTVDFD 55
+ +G+I + LR ++ L E+LT +++DEMI E D D G ++++
Sbjct: 96 DGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADVDGDGQINYE 140
Score = 34.4 bits (79), Expect = 0.003
Identities = 16/44 (36%), Positives = 26/44 (59%)
Query: 11 NSHGYIPTSSLREILAALDEQLTPDQLDEMIEEIDTDASGTVDF 54
+ G I T L ++ +L + T +L +MI E+D D +GT+DF
Sbjct: 23 DGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDF 66
>gnl|CDD|185503 PTZ00183, PTZ00183, centrin; Provisional.
Length = 158
Score = 31.6 bits (72), Expect = 0.021
Identities = 13/45 (28%), Positives = 24/45 (53%)
Query: 11 NSHGYIPTSSLREILAALDEQLTPDQLDEMIEEIDTDASGTVDFD 55
+ G I +L+ + L E +T ++L EMI+E D + G + +
Sbjct: 102 DKTGKISLKNLKRVAKELGETITDEELQEMIDEADRNGDGEISEE 146
Score = 26.6 bits (59), Expect = 1.6
Identities = 13/49 (26%), Positives = 26/49 (53%)
Query: 11 NSHGYIPTSSLREILAALDEQLTPDQLDEMIEEIDTDASGTVDFDGEFD 59
+ G I L+ + +L + +++ +MI ++D D SG +DF+ D
Sbjct: 29 DGSGTIDPKELKVAMRSLGFEPKKEEIKQMIADVDKDGSGKIDFEEFLD 77
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 30.0 bits (68), Expect = 0.029
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 5/52 (9%)
Query: 11 NSHGYIPTSSLREILAALDEQLTPDQLDEMIEEI----DTDASGTVDFDGEF 58
+ GYI LR++L AL +LT ++++E+IE D D G + F+ EF
Sbjct: 6 DGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFE-EF 56
>gnl|CDD|197492 smart00054, EFh, EF-hand, calcium binding motif. EF-hands are
calcium-binding motifs that occur at least in pairs.
Links between disease states and genes encoding
EF-hands, particularly the S100 subclass, are emerging.
Each motif consists of a 12 residue loop flanked on
either side by a 12 residue alpha-helix. EF-hands
undergo a conformational change unpon binding calcium
ions.
Length = 29
Score = 27.7 bits (63), Expect = 0.12
Identities = 9/23 (39%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 36 QLDEMIEEIDTDASGTVDFDGEF 58
+L E D D G +DF+ EF
Sbjct: 1 ELKEAFRLFDKDGDGKIDFE-EF 22
>gnl|CDD|131452 TIGR02399, salt_tol_Pase, glucosylglycerol 3-phosphatase. Proteins
in this family are glucosylglycerol-phosphate
phosphatase, with the gene symbol stpA (Salt Tolerance
Protein A). A motif characteristic of acid phosphatases
is found, but otherwise this family shows little
sequence similarity to other phosphatases. This enzyme
acts on the glucosylglycerol phosphate, product of
glucosylglycerol phosphate synthase and immediate
precursor of the osmoprotectant glucosylglycerol.
Length = 389
Score = 29.4 bits (66), Expect = 0.16
Identities = 10/44 (22%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 18 TSSLREILAALDEQLTPDQLDEMIEE--IDTDASGTVDFDGEFD 59
SL +I+ + L +++ + +DT S T++ + FD
Sbjct: 119 RPSLEQIVKKIFPNLVQEEIQTHASKSVLDTRFSPTINLNSLFD 162
>gnl|CDD|200946 pfam00036, efhand, EF hand. The EF-hands can be divided into two
classes: signaling proteins and buffering/transport
proteins. The first group is the largest and includes
the most well-known members of the family such as
calmodulin, troponin C and S100B. These proteins
typically undergo a calcium-dependent conformational
change which opens a target binding site. The latter
group is represented by calbindin D9k and do not
undergo calcium dependent conformational changes.
Length = 29
Score = 27.0 bits (61), Expect = 0.19
Identities = 9/23 (39%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 36 QLDEMIEEIDTDASGTVDFDGEF 58
+L E +E D D G + F+ EF
Sbjct: 1 ELKEAFKEFDKDGDGKISFE-EF 22
>gnl|CDD|178335 PLN02734, PLN02734, glycyl-tRNA synthetase.
Length = 684
Score = 28.9 bits (65), Expect = 0.25
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 21 LREILAALDEQLTPDQLDEMIEEIDTDASGT 51
L+++LA LD+ L+ ++L I+E A T
Sbjct: 194 LKDVLAVLDD-LSAEELGAKIKEYGIKAPDT 223
>gnl|CDD|238131 cd00213, S-100, S-100: S-100 domain, which represents the largest
family within the superfamily of proteins carrying the
Ca-binding EF-hand motif. Note that this S-100
hierarchy contains only S-100 EF-hand domains, other
EF-hands have been modeled separately. S100 proteins
are expressed exclusively in vertebrates, and are
implicated in intracellular and extracellular
regulatory activities. Intracellularly, S100 proteins
act as Ca-signaling or Ca-buffering proteins. The most
unusual characteristic of certain S100 proteins is
their occurrence in extracellular space, where they act
in a cytokine-like manner through RAGE, the receptor
for advanced glycation products. Structural data
suggest that many S100 members exist within cells as
homo- or heterodimers and even oligomers;
oligomerization contributes to their functional
diversification. Upon binding calcium, most S100
proteins change conformation to a more open structure
exposing a hydrophobic cleft. This hydrophobic surface
represents the interaction site of S100 proteins with
their target proteins. There is experimental evidence
showing that many S100 proteins have multiple binding
partners with diverse mode of interaction with
different targets. In addition to S100 proteins (such
as S100A1,-3,-4,-6,-7,-10,-11,and -13), this group
includes the ''fused'' gene family, a group of calcium
binding S100-related proteins. The ''fused'' gene
family includes multifunctional epidermal
differentiation proteins - profilaggrin, trichohyalin,
repetin, hornerin, and cornulin; functionally these
proteins are associated with keratin intermediate
filaments and partially crosslinked to the cell
envelope. These ''fused'' gene proteins contain
N-terminal sequence with two Ca-binding EF-hands motif,
which may be associated with calcium signaling in
epidermal cells and autoprocessing in a
calcium-dependent manner. In contrast to S100 proteins,
"fused" gene family proteins contain an extraordinary
high number of almost perfect peptide repeats with
regular array of polar and charged residues similar to
many known cell envelope proteins.
Length = 88
Score = 27.5 bits (62), Expect = 0.35
Identities = 11/31 (35%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 28 LDEQLTPDQLDEMIEEIDTDASGTVDFDGEF 58
L Q P+ +D++++++D + G VDF EF
Sbjct: 44 LKNQKDPEAVDKIMKDLDVNKDGKVDFQ-EF 73
>gnl|CDD|173198 PRK14736, atpC, F0F1 ATP synthase subunit epsilon; Provisional.
Length = 133
Score = 27.5 bits (61), Expect = 0.62
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 30 EQLTPDQLDEMIEEIDTDASGTVDFD 55
E+LTP+ +D IE ++ + T D D
Sbjct: 87 EELTPEMIDREIEAVEMERDATQDLD 112
>gnl|CDD|223729 COG0656, ARA1, Aldo/keto reductases, related to diketogulonate
reductase [General function prediction only].
Length = 280
Score = 27.6 bits (62), Expect = 0.68
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 12 SHGY--IPTSS----LREILAALDEQLTPDQLDEMIEEIDTDASGT-VDFDGEFDE 60
G IP S+ +RE LAA D +L+ + + I+ +D T V D EF
Sbjct: 225 QRGVIVIPKSTTPERIRENLAAFDFELSEEDMAA-IDALDRGYGRTRVGPDPEFFG 279
>gnl|CDD|234493 TIGR04189, surface_SprA, cell surface protein SprA. SprA is a cell
surface protein widely distributed in the Bacteroidetes
lineage. In Flavobacterium johnsoniae, a species that
shows gliding motility, mutation disrupts gliding.
Length = 2315
Score = 27.7 bits (62), Expect = 0.73
Identities = 11/34 (32%), Positives = 13/34 (38%), Gaps = 5/34 (14%)
Query: 44 IDTDASGTVDFDGEFDERQAAGSIPARGKISTQQ 77
I T A + F GEF A P K S +
Sbjct: 730 IQTTAPSNISFRGEF-----AQLRPGHNKASDFE 758
>gnl|CDD|218184 pfam04632, FUSC, Fusaric acid resistance protein family. This
family includes a conserved region found in two proteins
associated with fusaric acid resistance,from
Burkholderia cepacia and Klebsiella oxytoca. These
proteins are likely to be membrane transporter proteins.
Length = 649
Score = 27.2 bits (61), Expect = 1.0
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 19 SSLREILAALDEQLTPDQLDEMIEEIDT 46
S+L +LAAL L +++E+
Sbjct: 235 SALARLLAALRAAGAAAALAALLDELAA 262
>gnl|CDD|236676 PRK10376, PRK10376, putative oxidoreductase; Provisional.
Length = 290
Score = 26.9 bits (60), Expect = 1.3
Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 4/29 (13%)
Query: 16 IP-TSS---LREILAALDEQLTPDQLDEM 40
IP TSS LRE LAA + L+ + L E+
Sbjct: 255 IPGTSSVAHLRENLAAAELVLSEEVLAEL 283
>gnl|CDD|217775 pfam03874, RNA_pol_Rpb4, RNA polymerase Rpb4. This family includes
the Rpb4 protein. This family also includes C17 (aka
CGRP-RCP) is an essential subunit of RNA polymerase III.
C17 forms a subcomplex with C25 which is likely to be
the counterpart of subcomplex Rpb4/7 in Pol II.
Length = 110
Score = 26.4 bits (59), Expect = 1.3
Identities = 7/26 (26%), Positives = 18/26 (69%)
Query: 21 LREILAALDEQLTPDQLDEMIEEIDT 46
LR I+ +L+ + + +QL+E+++ +
Sbjct: 83 LRAIIESLESRFSEEQLEEILDILSK 108
>gnl|CDD|119408 cd06660, Aldo_ket_red, Aldo-keto reductases (AKRs) are a
superfamily of soluble NAD(P)(H) oxidoreductases whose
chief purpose is to reduce aldehydes and ketones to
primary and secondary alcohols. AKRs are present in all
phyla and are of importance to both health and
industrial applications. Members have very distinct
functions and include the prokaryotic
2,5-diketo-D-gluconic acid reductases and beta-keto
ester reductases, the eukaryotic aldose reductases,
aldehyde reductases, hydroxysteroid dehydrogenases,
steroid 5beta-reductases, potassium channel
beta-subunits and aflatoxin aldehyde reductases, among
others.
Length = 285
Score = 26.4 bits (59), Expect = 1.6
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 5/33 (15%)
Query: 16 IPTSS----LREILAALDEQLTPDQLDEMIEEI 44
IP +S L E LAALD +L+ + L ++ +
Sbjct: 254 IPGASSPERLEENLAALDFELSDEDLAA-LDAL 285
>gnl|CDD|150245 pfam09506, Salt_tol_Pase, Glucosylglycerol-phosphate phosphatase
(Salt_tol_Pase). Proteins in this family are
glucosylglycerol-phosphate phosphatases, with the gene
symbol stpA (Salt Tolerance Protein A). A motif
characteristic of acid phosphatases is found, but
otherwise this family shows little sequence similarity
to other phosphatases. This enzyme acts on the
glucosylglycerol phosphate, product of glucosylglycerol
phosphate synthase and immediate precursor of the
osmoprotectant glucosylglycerol.
Length = 381
Score = 26.5 bits (59), Expect = 1.8
Identities = 9/44 (20%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 18 TSSLREILAALDEQLTPDQLDEMIEE--IDTDASGTVDFDGEFD 59
+ L+E L ++ +L+ +++ ++ + +DT S T++ + F
Sbjct: 113 EALLKERLPSILPELSEEEIAKLAQAAILDTRVSPTINLNSLFS 156
>gnl|CDD|133416 cd04789, HTH_Cfa, Helix-Turn-Helix DNA binding domain of the Cfa
transcription regulator. Putative helix-turn-helix
(HTH) MerR-like transcription regulator; the N-terminal
domain of Cfa, a cyclopropane fatty acid synthase and
other related methyltransferases. Based on sequence
similarity, these proteins are predicted to function as
transcription regulators that mediate responses to
stress in eubacteria. They belong to the MerR
superfamily of transcription regulators that promote
transcription of various stress regulons by
reconfiguring the operator sequence located between the
-35 and -10 promoter elements. A typical MerR regulator
is comprised of distinct domains that harbor the
regulatory (effector-binding) site and the active
(DNA-binding) site. Their N-terminal domains are
homologous and contain a DNA-binding winged HTH motif,
while the C-terminal domains are often dissimilar and
bind specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 102
Score = 25.9 bits (57), Expect = 2.0
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 8/50 (16%)
Query: 2 DQDLDQ----EQINSHGYIPTSSLREILAALDEQLTPDQLDEMIEEIDTD 47
D DL + +Q+ + G SL+E LA L +LT L E + +
Sbjct: 41 DSDLQRLLLIQQLQAGGL----SLKECLACLQGKLTRSLLLERLSSLAEQ 86
>gnl|CDD|234170 TIGR03336, IOR_alpha, indolepyruvate ferredoxin oxidoreductase,
alpha subunit. Indolepyruvate ferredoxin oxidoreductase
(IOR) is an alpha 2/beta 2 tetramer related to ketoacid
oxidoreductases for pyruvate (1.2.7.1, POR),
2-ketoglutarate (1.2.7.3, KOR), and 2-oxoisovalerate
(1.2.7.7, VOR). These multi-subunit enzymes typically
are found in anaerobes and are inactiviated by oxygen.
IOR in Pyrococcus acts in fermentation of all three
aromatic amino acids, following removal of the amino
group by transamination. In Methanococcus maripaludis,
by contrast, IOR acts in the opposite direction, in
pathways of amino acid biosynthesis from phenylacetate,
indoleacetate, and p-hydroxyphenylacetate. In M.
maripaludis and many other species, iorA and iorB are
found next to an apparent phenylacetate-CoA ligase.
Length = 595
Score = 26.2 bits (58), Expect = 2.0
Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 14/78 (17%)
Query: 16 IPTSSLREILAALDEQLTPDQLDEMIEE--------------IDTDASGTVDFDGEFDER 61
+P + E L+ ++E L ++L+ ++EE + G + +GE +
Sbjct: 267 VPEGLVEEFLSGVEEVLVVEELEPVVEEQVKALAGTAGLNIKVHGKEDGFLPREGELNPD 326
Query: 62 QAAGSIPARGKISTQQIE 79
++ G + E
Sbjct: 327 IVVNALAKFGLAPSVTHE 344
>gnl|CDD|238009 cd00052, EH, Eps15 homology domain; found in proteins implicated
in endocytosis, vesicle transport, and signal
transduction. The alignment contains a pair of EF-hand
motifs, typically one of them is canonical and binds to
Ca2+, while the other may not bind to Ca2+. A
hydrophobic binding pocket is formed by residues from
both EF-hand motifs. The EH domain binds to proteins
containing NPF (class I), [WF]W or SWG (class II), or
H[TS]F (class III) sequence motifs.
Length = 67
Score = 24.9 bits (55), Expect = 2.9
Identities = 13/48 (27%), Positives = 19/48 (39%), Gaps = 3/48 (6%)
Query: 11 NSHGYIPTSSLREILAALDEQLTPDQLDEMIEEIDTDASGTVDFDGEF 58
+ G I R L L L ++ + DTD G +D + EF
Sbjct: 11 DGDGLISGDEARPFLGKS--GLPRSVLAQIWDLADTDKDGKLDKE-EF 55
>gnl|CDD|220449 pfam09867, DUF2094, Uncharacterized protein conserved in bacteria
(DUF2094). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 138
Score = 25.7 bits (57), Expect = 3.0
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 24 ILAALDEQLTPDQLDEMIEEI 44
+LAAL +P+ LD+ + +
Sbjct: 115 LLAALRADASPEALDQALAAL 135
>gnl|CDD|221918 pfam13093, FTA4, Kinetochore complex Fta4 of Sim4 subunit, or
CENP-50. Fission yeast has three kinetochore protein
complexes. Two complexes, Sim4 and Ndc80-MIND-Spc7
(NMS), are constitutive components, whereas the third
complex, DASH, is transiently associated with
kinetochores only in mitosis and is required for
precise chromosome segregation. The Sim4 complex
functions as a loading dock for the DASH complex. Sim4
consists of a number of different proteins including
Ftas 1-7 and Dad1.
Length = 211
Score = 25.8 bits (57), Expect = 3.2
Identities = 9/39 (23%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 6 DQEQINSHGYIPTSSLREILAALD--EQLTPDQLDEMIE 42
Q +I S P+ R LAA ++L+ + ++++
Sbjct: 17 AQVRILSQPLEPSEDWRSYLAAPSTEDELSDKVVQDVLQ 55
>gnl|CDD|217801 pfam03934, T2SK, Type II secretion system (T2SS), protein K.
Members of this family are involved in the Type II
protein secretion system. The T2SK family includes
proteins such as ExeK, PulK, OutX and XcpX.
Length = 282
Score = 25.4 bits (56), Expect = 4.2
Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 3/56 (5%)
Query: 23 EILAALDEQLTPDQLDEMIEEIDTDASGTVDFDGEFDERQAAGSIPARGKISTQQI 78
E+LAAL E L+ Q ++ D +VD +F A + Q+
Sbjct: 194 EVLAALFEGLSLSQAQRLLAARPADGFESVD---DFLALPALSGVDPSLAALKTQL 246
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form
(CCALD), the milder adult form, adrenomyeloneuropathy
(AMN), and variants without neurologic involvement
(i.e. asymptomatic).
Length = 166
Score = 25.2 bits (56), Expect = 4.2
Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 13 HGYIPTSSLREILA-ALDEQLTPDQ 36
Y+P +LRE L D+ L+ +
Sbjct: 72 RPYLPLGTLREQLIYPWDDVLSGGE 96
>gnl|CDD|236267 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau;
Validated.
Length = 535
Score = 25.4 bits (56), Expect = 4.3
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 5 LDQEQINSHGYIPTSSLREILAALDEQLTPDQLDEMIEEI 44
LDQ I I S + ++L LD P +L++ + I
Sbjct: 219 LDQAIIYCKNAITESKVADMLGLLD----PSKLEDFFQAI 254
>gnl|CDD|234425 TIGR03974, rSAM_six_Cys, SCIFF radical SAM maturase. Members of
this protein family are predicted radical SAM enzymes
universally associated with Six Cysteines in Forty-Five
protein, or SCIFF (family TIGR03973), a predicted
ribosomal natural product precursor that is nearly
universal in the class Clostridia. Similarity of this
family to radical SAM maturases (PqqE and subtilosin A
maturase) found in the vicinity of other peptide
precursors suggests this protein is the SCIFF radical
SAM maturase [Cellular processes, Biosynthesis of
natural products].
Length = 451
Score = 25.3 bits (56), Expect = 4.9
Identities = 6/29 (20%), Positives = 13/29 (44%)
Query: 17 PTSSLREILAALDEQLTPDQLDEMIEEID 45
+ EI L + + + ++E +EI
Sbjct: 39 DKETPEEIKEKLKGKYSEEDIEEAYDEIT 67
>gnl|CDD|222428 pfam13872, AAA_34, P-loop containing NTP hydrolase pore-1.
Length = 303
Score = 25.2 bits (56), Expect = 5.0
Identities = 11/27 (40%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 53 DFDG--EFDERQAAGSIPARGKISTQQ 77
DFDG FDE A + K +QQ
Sbjct: 171 DFDGVIVFDECHKAKNAAGGEKKPSQQ 197
>gnl|CDD|173796 cd04857, Peptidases_S8_Tripeptidyl_Aminopeptidase_II, Peptidase
S8 family domain in Tripeptidyl aminopeptidases_II.
Tripeptidyl aminopeptidases II are member of the
peptidase S8 or Subtilase family. Subtilases, or
subtilisin-like serine proteases, have an Asp/His/Ser
catalytic triad similar to that found in trypsin-like
proteases, but do not share their three-dimensional
structure (an example of convergent evolution).
Tripeptidyl aminopeptidase II removes tripeptides from
the free N terminus of oligopeptides as well as having
endoproteolytic activity. Some tripeptidyl
aminopeptidases have been shown to cleave tripeptides
and small peptides, e.g. angiotensin II and glucagon,
while others are believed to be involved in MHC I
processing.
Length = 412
Score = 25.3 bits (56), Expect = 5.1
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 26 AALDEQLTPDQLDEMIEEIDTDASGTVD 53
A Q+T D ++I+ ID SG VD
Sbjct: 37 GAPGLQVTTDGKPKIIDIIDCTGSGDVD 64
>gnl|CDD|217740 pfam03803, Scramblase, Scramblase. Scramblase is palmitoylated
and contains a potential protein kinase C
phosphorylation site. Scramblase exhibits
Ca2+-activated phospholipid scrambling activity in
vitro. There are also possible SH3 and WW binding
motifs. Scramblase is involved in the redistribution of
phospholipids after cell activation or injury.
Length = 223
Score = 25.0 bits (55), Expect = 5.1
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 75 TQQIEFMEMMTG 86
QQIE +E+ TG
Sbjct: 27 HQQIEPLEIFTG 38
>gnl|CDD|213327 cd12119, ttLC_FACS_AlkK_like, Fatty acyl-CoA synthetases similar to
LC-FACS from Thermus thermophiles. This family includes
fatty acyl-CoA synthetases that can activate
medium-chain to long-chain fatty acids. They catalyze
the ATP-dependent acylation of fatty acids in a two-step
reaction. The carboxylate substrate first reacts with
ATP to form an acyl-adenylate intermediate, which then
reacts with CoA to produce an acyl-CoA ester. The fatty
acyl-CoA synthetases are responsible for fatty acid
degradation as well as physiological regulation of
cellular functions via the production of fatty acyl-CoA
esters. The fatty acyl-CoA synthetase from Thermus
thermophiles in this family was shown catalyzing the
long-chain fatty acid, myristoyl acid, while another
member in this family, the AlkK protein identified from
Pseudomonas oleovorans, targets medium chain fatty
acids. This family also includes uncharacterized FACS
proteins.
Length = 517
Score = 25.2 bits (56), Expect = 5.5
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 5/28 (17%)
Query: 38 DEMIEEIDTDASGTVDFDGEFDERQAAG 65
+E++EE S ++ E DE AAG
Sbjct: 144 EELLEE----ESPEYEWP-ELDENTAAG 166
>gnl|CDD|237724 PRK14481, PRK14481, dihydroxyacetone kinase subunit DhaK;
Provisional.
Length = 331
Score = 25.2 bits (56), Expect = 5.7
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 33 TPDQLDEMIEEIDTDA 48
TPDQ+ E I+ +DT A
Sbjct: 82 TPDQILEAIKAVDTGA 97
>gnl|CDD|118950 pfam10429, Mtr2, Nuclear pore RNA shuttling protein Mtr2. Mtr2
is a monomeric, dual-action, RNA-shuttle protein found
in yeasts. Transport across the nuclear-cytoplasmic
membrane is via the macro-molecular membrane-spanning
nuclear pore complex, NPC. The pore is lined by a
subset of NPC members called nucleoporins that present
FG (Phe-Gly) receptors, characteristically GLFG and
FXFG motifs, for shuttling RNAs and proteins. RNA cargo
is bound to soluble transport proteins (nuclear export
factors) such as Mex67 in yeasts, and TAP in metazoa,
which pass along the pore by binding to successive FG
receptors. Mtr2 when bound to Mex67 maximises this
FG-binding. Mtr2 also acts independently of Mex67 in
transporting the large ribosomal RNA subunit through
the pore.
Length = 166
Score = 24.8 bits (54), Expect = 6.2
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 11 NSHGYIPTSSLREILAALDEQLTPD 35
N + L++ LA LDEQ P
Sbjct: 1 NGQTQQTETFLKKFLAHLDEQDPPK 25
>gnl|CDD|236499 PRK09404, sucA, 2-oxoglutarate dehydrogenase E1 component;
Reviewed.
Length = 924
Score = 25.1 bits (56), Expect = 6.6
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 2 DQDLDQE-QINSHGYIP-TSSLREILAALDE 30
+ DLD+ S T++LREI+ AL +
Sbjct: 123 EADLDRTFNTGSLALGKETATLREIIEALKK 153
>gnl|CDD|223739 COG0667, Tas, Predicted oxidoreductases (related to aryl-alcohol
dehydrogenases) [Energy production and conversion].
Length = 316
Score = 25.0 bits (55), Expect = 6.8
Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 21 LREILAALDEQLTPDQLDEMIEEI 44
L E LAALD +L+ ++L ++EI
Sbjct: 285 LEENLAALDIKLSEEELAA-LDEI 307
>gnl|CDD|197477 smart00027, EH, Eps15 homology domain. Pair of EF hand motifs
that recognise proteins containing Asn-Pro-Phe (NPF)
sequences.
Length = 96
Score = 24.2 bits (53), Expect = 6.9
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 3/45 (6%)
Query: 14 GYIPTSSLREILAALDEQLTPDQLDEMIEEIDTDASGTVDFDGEF 58
G + + + IL L L ++ D D G +D D EF
Sbjct: 25 GTVTGAQAKPILLKSG--LPQTLLAKIWNLADIDNDGELDKD-EF 66
>gnl|CDD|240152 cd05025, S-100A1, S-100A1: S-100A1 domain found in proteins
similar to S100A1. S100A1 is a calcium-binding protein
belonging to a large S100 vertebrate-specific protein
family within the EF-hand superfamily of
calcium-binding proteins. Note that the S-100
hierarchy, to which this S-100A1 group belongs,
contains only S-100 EF-hand domains, other EF-hands
have been modeled separately. As is the case with many
other members of S100 protein family, S100A1 is
implicated in intracellular and extracellular
regulatory activities, including interaction with
myosin-associated twitchin kinase, actin-capping
protein CapZ, sinapsin I, and tubulin. Structural data
suggests that S100A1 proteins exist within cells as
antiparallel homodimers, while heterodimers with
S100A4 and S100B also has been reported. Upon binding
calcium S100A1 changes conformation to expose a
hydrophobic cleft which is the interaction site of
S100A1 with its more that 20 known target proteins.
Length = 92
Score = 24.1 bits (52), Expect = 7.4
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 23 EILAALDEQLTPDQLDEMIEEIDTDASGTVDF 54
E+ LD Q D +D++++E+D + G VDF
Sbjct: 40 ELSDFLDAQKDADAVDKIMKELDENGDGEVDF 71
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 24.6 bits (54), Expect = 8.1
Identities = 10/44 (22%), Positives = 15/44 (34%), Gaps = 11/44 (25%)
Query: 13 HGYIPTSSLREILA-ALDEQLTPDQ----------LDEMIEEID 45
Y+P +LRE L D L ++ E +D
Sbjct: 464 RPYLPQGTLREALCYPNAAPDFSDAELVAVLHKVGLGDLAERLD 507
>gnl|CDD|217779 pfam03885, DUF327, Protein of unknown function (DUF327). The
proteins in this family are around 140-170 residues in
length. The proteins contain many conserved residues.
with the most conserved motifs found in the central and
C-terminal region. The function of these proteins is
unknown.
Length = 146
Score = 24.4 bits (54), Expect = 8.3
Identities = 9/27 (33%), Positives = 19/27 (70%)
Query: 19 SSLREILAALDEQLTPDQLDEMIEEID 45
SS E+L + ++ + ++L E+++EID
Sbjct: 26 SSFSEVLEEIRKKKSEERLKELLDEID 52
>gnl|CDD|239716 cd03747, Ntn_PGA_like, Penicillin G acylase (PGA) belongs to a
family of beta-lactam acylases that includes
cephalosporin acylase (CA) and aculeacin A acylase. PGA
and CA are crucial for the production of backbone
chemicals like 6-aminopenicillanic acid and
7-aminocephalosporanic acid (7-ACA), which can be used
to synthesize semi-synthetic penicillins and
cephalosporins, respectively. While both PGA and CA
have a conserved Ntn (N-terminal nucleophile) hydrolase
fold and the structural similarity at their active
sites is very high, their sequence similarity is low.
Length = 312
Score = 24.5 bits (54), Expect = 8.7
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 32 LTPDQLDEMIEEIDTDASGTVDFDGE 57
D +D E++D + +DGE
Sbjct: 70 SYADVVDLYREKLDPEDPTRYRYDGE 95
>gnl|CDD|225248 COG2373, COG2373, Large extracellular alpha-helical protein
[General function prediction only].
Length = 1621
Score = 24.7 bits (54), Expect = 8.7
Identities = 8/27 (29%), Positives = 11/27 (40%)
Query: 29 DEQLTPDQLDEMIEEIDTDASGTVDFD 55
DE+ +E +E TD G D
Sbjct: 559 DEEPNSLTFEEELELTVTDGKGKASLD 585
>gnl|CDD|214935 smart00955, RNB, This domain is the catalytic domain of
ribonuclease II.
Length = 286
Score = 24.1 bits (53), Expect = 9.8
Identities = 8/35 (22%), Positives = 18/35 (51%)
Query: 29 DEQLTPDQLDEMIEEIDTDASGTVDFDGEFDERQA 63
+LT +++D ++E+I D G ++ + A
Sbjct: 120 KARLTYEEVDAILEKIVLDEEGKIEDIVPRERNDA 154
>gnl|CDD|176248 cd08288, MDR_yhdh, Yhdh putative quinone oxidoreductases. Yhdh
putative quinone oxidoreductases (QOR). QOR catalyzes
the conversion of a quinone + NAD(P)H to a hydroquinone
+ NAD(P)+. Quinones are cyclic diones derived from
aromatic compounds. Membrane bound QOR actin the
respiratory chains of bacteria and mitochondria, while
soluble QOR acts to protect from toxic quinones (e.g.
DT-diaphorase) or as a soluble eye-lens protein in some
vertebrates (e.g. zeta-crystalin). QOR reduces quinones
through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 324
Score = 24.4 bits (54), Expect = 9.9
Identities = 9/30 (30%), Positives = 11/30 (36%)
Query: 15 YIPTSSLREILAALDEQLTPDQLDEMIEEI 44
P R A L L P L+ + EI
Sbjct: 270 MAPIERRRAAWARLARDLDPALLEALTREI 299
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
0.310 0.130 0.351
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,743,655
Number of extensions: 410963
Number of successful extensions: 639
Number of sequences better than 10.0: 1
Number of HSP's gapped: 637
Number of HSP's successfully gapped: 91
Length of query: 87
Length of database: 10,937,602
Length adjustment: 55
Effective length of query: 32
Effective length of database: 8,498,132
Effective search space: 271940224
Effective search space used: 271940224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (24.1 bits)