RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3148
(123 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 = 53.7 bits (130), Expect = 5e-11
Identities = 20/53 (37%), Positives = 29/53 (54%)
Query: 15 YDDGRDGFLDLEELKRMMEKLGAPQTHLGLKAMIKEVDEDNDNKISFREITHL 67
+D DG + +ELK ++ LG + + MI+EVD+D D KI F E L
Sbjct: 9 FDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLEL 61
Score = 26.0 bits (58), Expect = 2.0
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 44 LKAMIKEVDEDNDNKISFRE-ITHLRKLKLGSTDSPVLAM 82
L+ + D+D D IS E L+ L G ++ + M
Sbjct: 2 LREAFRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEM 41
Score = 24.4 bits (54), Expect = 6.7
Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 9/41 (21%)
Query: 1 MNAFLRQLLDNTTR---------YDDGRDGFLDLEELKRMM 32
+ A L+ L + + D DG +D EE +M
Sbjct: 22 LKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDFEEFLELM 62
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 40.8 bits (96), Expect = 5e-06
Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 14 RYDDGRDGFLDLEELKRMMEKLGAPQTHLGLKAMIKE----VDEDNDNKISFREITHL 67
D DG++D+EEL+++++ LG T ++ +I+ +D+D D +ISF E
Sbjct: 2 LLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLEA 59
>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 = 41.9 bits (99), Expect = 9e-06
Identities = 16/50 (32%), Positives = 31/50 (62%)
Query: 14 RYDDGRDGFLDLEELKRMMEKLGAPQTHLGLKAMIKEVDEDNDNKISFRE 63
+D DG++ + EL+R+++ LG + ++ ++KE DED D +I + E
Sbjct: 100 LFDKDHDGYISIGELRRVLKSLGERLSDEEVEKLLKEYDEDGDGEIDYEE 149
Score = 26.1 bits (58), Expect = 3.8
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 16 DDGRDGFLDLEELKRMM-EKLGAPQTHLGLKAMIKEVDEDNDNKISFREITH 66
D + +D E +M KL L+ K D+D+D IS E+
Sbjct: 65 IDAGNETVDFPEFLTVMSVKLKRGDKEEELREAFKLFDKDHDGYISIGELRR 116
>gnl|CDD|222407 pfam13833, EF_hand_6, EF-hand domain pair.
Length = 53
Score = 39.8 bits (94), Expect = 9e-06
Identities = 17/44 (38%), Positives = 23/44 (52%)
Query: 20 DGFLDLEELKRMMEKLGAPQTHLGLKAMIKEVDEDNDNKISFRE 63
G + EELKR + LG + + + +E D D D KISF E
Sbjct: 2 KGLITREELKRALALLGISLSEEEVDILFREFDTDGDGKISFEE 45
>gnl|CDD|185504 PTZ00184, PTZ00184, calmodulin; Provisional.
Length = 149
Score = 41.3 bits (97), Expect = 2e-05
Identities = 24/63 (38%), Positives = 31/63 (49%)
Query: 15 YDDGRDGFLDLEELKRMMEKLGAPQTHLGLKAMIKEVDEDNDNKISFREITHLRKLKLGS 74
+D DG + +EL +M LG T L+ MI EVD D + I F E L K+
Sbjct: 20 FDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTLMARKMKD 79
Query: 75 TDS 77
TDS
Sbjct: 80 TDS 82
Score = 35.1 bits (81), Expect = 0.002
Identities = 17/53 (32%), Positives = 28/53 (52%)
Query: 15 YDDGRDGFLDLEELKRMMEKLGAPQTHLGLKAMIKEVDEDNDNKISFREITHL 67
+D +GF+ EL+ +M LG T + MI+E D D D +I++ E +
Sbjct: 93 FDRDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADVDGDGQINYEEFVKM 145
>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 = 35.9 bits (84), Expect = 6e-04
Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 5/52 (9%)
Query: 17 DGRDGFLDLEELKRMMEK-----LGAPQTHLGLKAMIKEVDEDNDNKISFRE 63
+G L +ELK ++E L + + ++K++D + D K+ F+E
Sbjct: 21 EGDKDTLSKKELKELLETELPNFLKNQKDPEAVDKIMKDLDVNKDGKVDFQE 72
>gnl|CDD|185503 PTZ00183, PTZ00183, centrin; Provisional.
Length = 158
Score = 35.0 bits (81), Expect = 0.003
Identities = 23/63 (36%), Positives = 30/63 (47%)
Query: 15 YDDGRDGFLDLEELKRMMEKLGAPQTHLGLKAMIKEVDEDNDNKISFREITHLRKLKLGS 74
+D G +D +ELK M LG +K MI +VD+D KI F E + KLG
Sbjct: 26 FDTDGSGTIDPKELKVAMRSLGFEPKKEEIKQMIADVDKDGSGKIDFEEFLDIMTKKLGE 85
Query: 75 TDS 77
D
Sbjct: 86 RDP 88
Score = 33.9 bits (78), Expect = 0.007
Identities = 19/49 (38%), Positives = 29/49 (59%)
Query: 15 YDDGRDGFLDLEELKRMMEKLGAPQTHLGLKAMIKEVDEDNDNKISFRE 63
+DD + G + L+ LKR+ ++LG T L+ MI E D + D +IS E
Sbjct: 99 FDDDKTGKISLKNLKRVAKELGETITDEELQEMIDEADRNGDGEISEEE 147
>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 = 29.0 bits (66), Expect = 0.077
Identities = 13/24 (54%), Positives = 14/24 (58%)
Query: 44 LKAMIKEVDEDNDNKISFREITHL 67
LK KE D+D D KISF E L
Sbjct: 2 LKEAFKEFDKDGDGKISFEEFKEL 25
Score = 26.6 bits (60), Expect = 0.49
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 15 YDDGRDGFLDLEELKRMMEKL 35
+D DG + EE K +++KL
Sbjct: 9 FDKDGDGKISFEEFKELLKKL 29
>gnl|CDD|240157 cd05031, S-100A10_like, S-100A10_like: S-100A10 domain found in
proteins similar to S100A10. S100A10 is a member of the
S100 family of EF-hand superfamily of calcium-binding
proteins. Note that the S-100 hierarchy, to which this
S-100A1_like group belongs, 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. A unique feature of S100A10 is
that it contains mutation in both of the calcium
binding sites, making it calcium insensitive. S100A10
has been detected in brain, heart, gastrointestinal
tract, kidney, liver, lung, spleen, testes, epidermis,
aorta, and thymus. Structural data supports the homo-
and hetero-dimeric as well as hetero-tetrameric nature
of the protein. S100A10 has multiple binding partners
in its calcium free state and is therefore involved in
many diverse biological functions.
Length = 94
Score = 30.1 bits (68), Expect = 0.10
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 5/56 (8%)
Query: 17 DGRDGFLDLEELKRMMEK-----LGAPQTHLGLKAMIKEVDEDNDNKISFREITHL 67
DG L +ELK++MEK L + + + ++K++D++ D K++F E L
Sbjct: 21 DGDKNTLSRKELKKLMEKELSEFLKNQKDPMAVDKIMKDLDQNRDGKVNFEEFVSL 76
>gnl|CDD|205583 pfam13405, EF_hand_4, EF-hand domain.
Length = 30
Score = 28.7 bits (65), Expect = 0.11
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 14 RYDDGRDGFLDLEELKRMMEKLG 36
+D DG++ EEL++ + LG
Sbjct: 8 LFDKDGDGYISAEELRKALRSLG 30
>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 = 28.5 bits (65), Expect = 0.11
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 44 LKAMIKEVDEDNDNKISFRE 63
LK + D+D D KI F E
Sbjct: 2 LKEAFRLFDKDGDGKIDFEE 21
Score = 26.6 bits (60), Expect = 0.52
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 15 YDDGRDGFLDLEELKRMMEKL 35
+D DG +D EE K +++ L
Sbjct: 9 FDKDGDGKIDFEEFKDLLKAL 29
>gnl|CDD|178501 PLN02913, PLN02913, dihydrofolate synthetase.
Length = 510
Score = 30.2 bits (68), Expect = 0.22
Identities = 11/25 (44%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 17 DGRDGFLDLEELKRMMEKLGAPQTH 41
D DGF DL ++R+M++LG P +
Sbjct: 51 DSDDGF-DLGRMRRLMDRLGNPHSK 74
>gnl|CDD|222067 pfam13354, Beta-lactamase2, Beta-lactamase enzyme family. This
family is closely related to Beta-lactamase, pfam00144,
the serine beta-lactamase-like superfamily, which
contains the distantly related pfam00905 and PF00768
D-alanyl-D-alanine carboxypeptidase.
Length = 197
Score = 29.9 bits (68), Expect = 0.23
Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 22 FLDLEELKRMMEKLGAPQTHLGLKAMIKEV-DEDNDNKISFREITHL 67
L L+ + +++LG T L K E +D +N + R++ L
Sbjct: 86 RLGLDAVNARLKELGLRDTRLNRKLPDLEAAPKDPENTTTARDMARL 132
>gnl|CDD|226493 COG4004, COG4004, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 96
Score = 28.7 bits (64), Expect = 0.37
Identities = 14/45 (31%), Positives = 18/45 (40%)
Query: 6 RQLLDNTTRYDDGRDGFLDLEELKRMMEKLGAPQTHLGLKAMIKE 50
++LL NTT Y D + +EKL K M KE
Sbjct: 52 KKLLVNTTDYTDDETKLQTAKTYNDFLEKLTGYTAKERKKMMKKE 96
>gnl|CDD|238193 cd00316, Oxidoreductase_nitrogenase, The nitrogenase enzyme system
catalyzes the ATP-dependent reduction of dinitrogen to
ammonia. This group contains both alpha and beta
subunits of component 1 of the three known genetically
distinct types of nitrogenase systems: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium-dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase) and, both
subunits of Protochlorophyllide (Pchlide) reductase and
chlorophyllide (chlide) reductase. The nitrogenase
systems consist of component 1 (MoFe protein, VFe
protein or, FeFe protein respectively) and, component 2
(Fe protein). The most widespread and best characterized
nitrogenase is the Mo-nitrogenase. MoFe is an
alpha2beta2 tetramer, the alternative nitrogenases are
alpha2beta2delta2 hexamers whose alpha and beta subunits
are similar to the alpha and beta subunits of MoFe. For
MoFe, each alphabeta pair contains one P-cluster (at the
alphabeta interface) and, one molecule of iron
molybdenum cofactor (FeMoco) contained within the alpha
subunit. The Fe protein contains a single [4Fe-4S]
cluster from which, electrons are transferred to the
P-cluster of the MoFe and in turn, to FeMoCo at the site
of substrate reduction. The V-nitrogenase requires an
iron-vanadium cofactor (FeVco), the iron
only-nitrogenase an iron only cofactor (FeFeco). These
cofactors are analogous to the FeMoco. The V-nitrogenase
has P clusters identical to those of MoFe. Pchlide
reductase and chlide reductase participate in the
Mg-branch of the tetrapyrrole biosynthetic pathway.
Pchlide reductase catalyzes the reduction of the D-ring
of Pchlide during the synthesis of chlorophylls (Chl)
and bacteriochlorophylls (BChl). Chlide-a reductase
catalyzes the reduction of the B-ring of Chlide-a during
the synthesis of BChl-a. The Pchlide reductase NB
complex is a an N2B2 heterotetramer resembling
nitrogenase FeMo, N and B proteins are homologous to the
FeMo alpha and beta subunits respectively. The NB
complex may serve as a catalytic site for Pchlide
reduction and, the ZY complex as a site of chlide
reduction, similar to MoFe for nitrogen reduction.
Length = 399
Score = 28.8 bits (65), Expect = 0.73
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 21 GFLDLEELKRMMEKLGAP 38
G DL ELKR++E++G
Sbjct: 164 GGGDLRELKRLLEEMGIR 181
>gnl|CDD|205383 pfam13202, EF_hand_3, EF hand.
Length = 25
Score = 26.1 bits (59), Expect = 0.86
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 44 LKAMIKEVDEDNDNKISFREITHL 67
LK + ++ D + D KIS E+ L
Sbjct: 1 LKDLFRQFDTNGDGKISKEELKRL 24
Score = 24.9 bits (56), Expect = 2.1
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 14 RYDDGRDGFLDLEELKRMM 32
++D DG + EELKR++
Sbjct: 7 QFDTNGDGKISKEELKRLL 25
>gnl|CDD|146358 pfam03682, UPF0158, Uncharacterized protein family (UPF0158).
Length = 163
Score = 28.0 bits (62), Expect = 0.87
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 7/66 (10%)
Query: 7 QLLDNTTRYDDGRDGFLDLEELKRMMEKLGAPQTHLGLKAMIKEVDEDND-----NKISF 61
+L+D + DD RD +LD E + L PQ L A+ +E++E+ D K+SF
Sbjct: 10 RLMDAFAKSDDERDFYLDRYEGFVLYIDLDKPQPE--LDALYQELEENPDRYCLIPKLSF 67
Query: 62 REITHL 67
E +
Sbjct: 68 YESKKI 73
>gnl|CDD|199847 cd03865, M14_CPE, Peptidase M14 carboxypeptidase subfamily
N/E-like; Carboxypeptidase E subgroup. Peptidase M14
Carboxypeptidase (CP) E (CPE, also known as
carboxypeptidase H, and enkephalin convertase; EC
3.4.17.10) belongs to the N/E subfamily of the M14
family of metallocarboxypeptidases (MCPs).The M14 family
are zinc-binding CPs which hydrolyze single, C-terminal
amino acids from polypeptide chains, and have a
recognition site for the free C-terminal carboxyl group,
which is a key determinant of specificity. CPE is an
important enzyme responsible for the proteolytic
processing of prohormone intermediates (such as
pro-insulin, pro-opiomelanocortin, or
pro-gonadotropin-releasing hormone) by specifically
removing C-terminal basic residues. In addition, it has
been proposed that the regulated secretory pathway (RSP)
of the nervous and endocrine systems utilizes
membrane-bound CPE as a sorting receptor. A naturally
occurring point mutation in CPE reduces the stability of
the enzyme and causes its degradation, leading to an
accumulation of numerous neuroendocrine peptides that
result in obesity and hyperglycemia. Reduced CPE enzyme
and receptor activity could underlie abnormal placental
phenotypes from the observation that CPE is
down-regulated in enlarged placentas of interspecific
hybrid (interspecies hybrid placental dysplasia, IHPD)
and cloned mice.
Length = 323
Score = 28.1 bits (62), Expect = 1.1
Identities = 15/33 (45%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 22 FLDLEELKRMMEKLGAPQTHLGLKAMIKEVDED 54
F DL+ + + E+ G P HL LK M K VDE+
Sbjct: 143 FPDLDRIVYVNEREGGPNNHL-LKNMKKAVDEN 174
>gnl|CDD|237739 PRK14510, PRK14510, putative bifunctional
4-alpha-glucanotransferase/glycogen debranching enzyme;
Provisional.
Length = 1221
Score = 28.3 bits (63), Expect = 1.2
Identities = 14/53 (26%), Positives = 17/53 (32%), Gaps = 3/53 (5%)
Query: 9 LDNTTRYDDGRDGFLDLEELKRMMEKLGAPQTHLGLKAMIKEVDEDNDNKISF 61
LD DGF+D R K L MI EV +D +
Sbjct: 341 LDLADELAREPDGFIDEF---RQFLKAMDQDPVLRRLKMIAEVWDDGLGGYQY 390
>gnl|CDD|99782 cd06185, PDR_like, Phthalate dioxygenase reductase (PDR) is an
FMN-dependent reductase that mediates electron transfer
from NADH to FMN to an iron sulfur cluster. PDR has an
an N-terminal ferrredoxin reductase (FNR)-like NAD(H)
binding domain and a C-terminal iron-sulfur [2Fe-2S]
cluster domain. Although structurally homologous to FNR,
PDR binds FMN rather than FAD in it's FNR-like domain.
Electron transfer between pyrimidines and iron-sulfur
clusters (Rieske center [2Fe-2S]) or heme groups is
mediated by flavins in respiration, photosynthesis, and
oxygenase systems. Type I dioxygenase systems, including
the hydroxylate phthalate system, have 2 components, a
monomeric reductase consisting of a flavin and a 2Fe-2S
center and a multimeric oxygenase. In contrast to other
Rieske dioxygenases the ferredoxin like domain is C-,
not N-terminal.
Length = 211
Score = 27.4 bits (62), Expect = 1.5
Identities = 19/58 (32%), Positives = 23/58 (39%), Gaps = 15/58 (25%)
Query: 3 AF---LRQLL-DNTTRYDDGRDGFLDLEELKRMMEKLGAPQ--THL---GLKAMIKEV 51
AF L L D + D G LDL L L AP TH+ G + M+ V
Sbjct: 140 AFLDELAALPGDRVHLHFDDEGGRLDLAAL------LAAPPAGTHVYVCGPEGMMDAV 191
>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175).
Length = 820
Score = 27.2 bits (61), Expect = 2.7
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 25 LEELKRMMEKLGAPQ 39
LE+L++MME L Q
Sbjct: 563 LEQLQQMMENLQVTQ 577
>gnl|CDD|220451 pfam09873, DUF2100, Uncharacterized protein conserved in archaea
(DUF2100). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 215
Score = 26.7 bits (59), Expect = 2.8
Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 3/71 (4%)
Query: 3 AFLRQLLDNTTRYDDGRDGFLDLEELKRMMEKLGAPQTHLGLKAMIKEVDEDNDN---KI 59
+ + D + G +D E K+ + L +L A E++ + K+
Sbjct: 22 VKPIVTKTDKKIFTDAKPGKIDSGEFKKAVHSLIEADEYLYKSAPTHELNGEQAKEFCKL 81
Query: 60 SFREITHLRKL 70
F H+ K+
Sbjct: 82 LFAAQKHINKI 92
>gnl|CDD|218791 pfam05879, RHD3, Root hair defective 3 GTP-binding protein (RHD3).
This family consists of several eukaryotic root hair
defective 3 like GTP-binding proteins. It has been
speculated that the RHD3 protein is a member of a novel
class of GTP-binding proteins that is widespread in
eukaryotes and required for regulated cell enlargement.
The family also contains the homologous yeast synthetic
enhancement of YOP1 (SEY1) protein which is involved in
membrane trafficking.
Length = 743
Score = 27.0 bits (60), Expect = 3.0
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 1 MNAFLRQLLDNTTRYDDGRDGF-LDLEELKRMMEKL 35
+ F R++ D +R+ D + GF L EE +M++ L
Sbjct: 458 LKLFKREVEDAVSRFTDRKSGFDLSEEENDKMLKNL 493
>gnl|CDD|149931 pfam09032, Siah-Interact_N, Siah interacting protein, N terminal.
The N terminal domain of Siah interacting protein
(SIP) adopts a helical hairpin structure with a
hydrophobic core stabilised by a classic
knobs-and-holes arrangement of side chains contributed
by the two amphipathic helices. Little is known about
this domain's function, except that it is crucial for
interactions with Siah. It has also been hypothesised
that SIP can dimerise through this N terminal domain.
Length = 79
Score = 25.5 bits (56), Expect = 3.7
Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 9/57 (15%)
Query: 23 LDLEELKRMMEKLGAPQTHLGLKAMIKEVDEDNDNKISFREITHLRKLKLGSTDSPV 79
LDLEELK ++EK + LK I++++ EI ++ K
Sbjct: 10 LDLEELKSLLEKATRKRVQDLLKQEIRKIE---------TEIAQKQQAKAAQKQQQE 57
>gnl|CDD|134340 PRK00650, PRK00650, 4-diphosphocytidyl-2-C-methyl-D-erythritol
kinase; Provisional.
Length = 288
Score = 26.7 bits (59), Expect = 3.7
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 23 LDLEELKRMMEKLGAP-QTHLGL 44
LDL+E K +E L A H+GL
Sbjct: 207 LDLKEKKHWLESLWAELPVHVGL 229
>gnl|CDD|238931 cd01971, Nitrogenase_VnfN_like, Nitrogenase_vnfN_like: VnfN subunit
of the VnfEN complex-like. This group in addition to
VnfN contains a subset of the beta subunit of the
nitrogenase MoFe protein and NifN-like proteins. The
nitrogenase enzyme system catalyzes the ATP-dependent
reduction of dinitrogen to ammonia. NifEN participates
in the synthesis of the iron-molybdenum cofactor
(FeMoco) of MoFe protein of the
molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur
containing precursor of the FeMoco) from NifB is
transferred to NifEN where it is further processed to
FeMoco. VnfEN may similarly be a scaffolding protien
for the iron-vanadium cofactor (FeVco) of the
vanadium-dependent (V)-nitrogenase. NifE and NifN are
essential for the Mo-nitrogenase, VnfE and VnfN are not
essential for the V-nitrogenase. NifE and NifN can
substitute when the vnfEN genes are inactivated.
Length = 427
Score = 26.2 bits (58), Expect = 4.7
Identities = 8/13 (61%), Positives = 12/13 (92%)
Query: 24 DLEELKRMMEKLG 36
DLEE+KR++E +G
Sbjct: 174 DLEEIKRVLEGIG 186
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 26.4 bits (59), Expect = 4.8
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 10/42 (23%)
Query: 6 RQLL-DNTTRYDDGRDGFLDL---------EELKRMMEKLGA 37
+QL + TR+D GR+ FL ++ + +LG
Sbjct: 92 KQLAAEGITRHDLGREEFLKKCWEWKEESGGTIREQLRRLGV 133
>gnl|CDD|119344 cd06552, ASCH_yqfb_like, ASC-1 homology domain, subfamily similar
to Escherichia coli Yqfb. The ASCH domain, a small
beta-barrel domain found in all three kingdoms of life,
resembles the RNA-binding PUA domain and may also
interact with RNA. ASCH has been proposed to function
as an RNA-binding domain during coactivation,
RNA-processing and the regulation of prokaryotic
translation.
Length = 100
Score = 25.7 bits (57), Expect = 4.8
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 6 RQLLDNTTRYDDGRDGFLDLEELKRMMEK 34
+ L T D ++GF LEELK +++
Sbjct: 54 EKTLGELTDEDARQEGFPSLEELKEALKE 82
>gnl|CDD|215749 pfam00148, Oxidored_nitro, Nitrogenase component 1 type
Oxidoreductase.
Length = 397
Score = 26.1 bits (58), Expect = 5.7
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 21 GFLDLEELKRMMEKLG 36
G DL E+KR++EKLG
Sbjct: 157 GPGDLREIKRLLEKLG 172
>gnl|CDD|227424 COG5093, COG5093, Uncharacterized conserved protein [Function
unknown].
Length = 185
Score = 25.6 bits (56), Expect = 6.1
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 20 DGFLDLEELKRMMEKLGAPQTHLGLKAMIKEVDED--NDNKISFREITHLRKLKLGSTD 76
D D+EE + ++E + + LK +K ++E N + ++ EI +R L L S D
Sbjct: 116 DDVEDIEESRMIVEDIREIRQAKTLKG-LKCLNEKALNLDNLTLFEINEIRPLILESMD 173
>gnl|CDD|213963 TIGR04350, C_S_lyase_PatB, putative C-S lyase. Members of this
subfamily are probable C-S lyases from a family of
pyridoxal phosphate-dependent enzymes that tend to be
(mis)annotated as probable aminotransferases. One member
is PatB of Bacillus subtilis, a proven C-S-lyase.
Another is the virulence factor cystalysin from
Treponema denticola, whose hemolysin activity may stem
from H2S production. Members of the seed alignment occur
next to examples of the enzyme 5-histidylcysteine
sulfoxide synthase, from ovothiol A biosynthesis, and
would be expected to perform a C-S cleavage of
5-histidylcysteine sulfoxide to leave
1-methyl-4-mercaptohistidine (ovothiol A).
Length = 384
Score = 26.1 bits (58), Expect = 6.2
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 6 RQLLDNTTRYDDGRDGFLDLEELKR 30
R+L+ N + D GR F DLE+L+
Sbjct: 129 RELVLNPLKLDPGRYRF-DLEDLED 152
>gnl|CDD|238934 cd01974, Nitrogenase_MoFe_beta, Nitrogenase_MoFe_beta: Nitrogenase
MoFe protein, beta subunit. The nitrogenase enzyme
catalyzes the ATP-dependent reduction of dinitrogen to
ammonia. The Molybdenum (Mo-) nitrogenase is the most
widespread and best characterized of these systems.
Mo-nitrogenase consists of the MoFe protein (component
1) and the Fe protein (component 2). MoFe is an
alpha2beta2 tetramer. This group contains the beta
subunit of the MoFe protein. Each alphabeta pair of MoFe
contains one P-cluster (at the alphabeta interface) and,
one molecule of iron molybdenum cofactor (FeMoco)
contained within the alpha subunit. The Fe protein
contains a single [4Fe-4S] cluster. Electrons are
transferred from the [4Fe-4S] cluster of the Fe protein
to the P-cluster of the MoFe and in turn to FeMoCo, the
site of substrate reduction.
Length = 435
Score = 25.7 bits (57), Expect = 7.4
Identities = 9/27 (33%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 18 GRDGFLD-LEELKRMMEKLGAPQTHLG 43
G D + + E+KR++E +G T L
Sbjct: 168 GFDTYAGNMREIKRLLELMGVDYTILP 194
>gnl|CDD|238927 cd01965, Nitrogenase_MoFe_beta_like, Nitrogenase_MoFe_beta_like:
Nitrogenase MoFe protein, beta subunit_like. The
nitrogenase enzyme catalyzes the ATP-dependent reduction
of dinitrogen (N2) to ammonia. This group contains the
beta subunits of component 1 of the three known
genetically distinct types of nitrogenase systems: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium-dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase). These
nitrogenase systems consist of component 1 (MoFe
protein, VFe protein or, FeFe protein respectively) and,
component 2 (Fe protein). The most widespread and best
characterized of these systems is the Mo-nitrogenase.
MoFe is an alpha2beta2 tetramer, the alternative
nitrogenases are alpha2beta2delta2 hexamers having
alpha and beta subunits similar to the alpha and beta
subunits of MoFe. For MoFe, each alphabeta pair contains
one P-cluster (at the alphabeta interface) and, one
molecule of iron molybdenum cofactor (FeMoco) contained
within the alpha subunit. The Fe protein contains, a
single [4Fe-4S] cluster from which electrons are
transferred to the P-cluster of the MoFe and in turn,
to FeMoCo, the site of substrate reduction. The
V-nitrogenase requires an iron-vanadium cofactor
(FeVco), the iron only-nitrogenase an iron only cofactor
(FeFeco). These cofactors are analogous to the FeMoco.
The V-nitrogenase has P clusters identical to those of
MoFe. In addition to N2, nitrogenase also catalyzes the
reduction of a variety of other substrates such as
acetylene The V-nitrogenase differs from the
Mo-nitrogenase in that it produces free hydrazine, as a
minor product during N2-reduction and, ethane as a minor
product during acetylene reduction.
Length = 428
Score = 25.6 bits (57), Expect = 7.4
Identities = 6/13 (46%), Positives = 10/13 (76%)
Query: 24 DLEELKRMMEKLG 36
D+ E+KR++E G
Sbjct: 170 DVREIKRILEAFG 182
>gnl|CDD|183318 PRK11797, PRK11797, D-ribose pyranase; Provisional.
Length = 139
Score = 25.2 bits (56), Expect = 7.9
Identities = 6/29 (20%), Positives = 15/29 (51%)
Query: 38 PQTHLGLKAMIKEVDEDNDNKISFREITH 66
P+ H L ++++++ N I ++H
Sbjct: 78 PELHEALLTQLEQLEQHQGNTIEIEYVSH 106
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 0.141 0.411
Gapped
Lambda K H
0.267 0.0908 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,519,065
Number of extensions: 589230
Number of successful extensions: 743
Number of sequences better than 10.0: 1
Number of HSP's gapped: 738
Number of HSP's successfully gapped: 78
Length of query: 123
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 38
Effective length of database: 7,167,512
Effective search space: 272365456
Effective search space used: 272365456
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 (23.9 bits)