RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17185
(121 letters)
>gnl|CDD|237981 cd00014, CH, Calponin homology domain; actin-binding domain which
may be present as a single copy or in tandem repeats
(which increases binding affinity). The CH domain is
found in cytoskeletal and signal transduction proteins,
including actin-binding proteins like spectrin,
alpha-actinin, dystrophin, utrophin, and fimbrin,
proteins essential for regulation of cell shape
(cortexillins), and signaling proteins (Vav).
Length = 107
Score = 61.6 bits (150), Expect = 1e-13
Identities = 25/71 (35%), Positives = 34/71 (47%), Gaps = 2/71 (2%)
Query: 8 EQDKEAQAWIETVTGQKFPAGVL-YEDAIKDGQILCHLINKLKPGSVAKINS-SGGQFKF 65
Q +E WI V G+ P + + +KDG LC L+N L P + K +FK
Sbjct: 1 SQKEELLRWINKVLGEYGPVTINNFSTDLKDGIALCKLLNSLSPDLIDKKKINPLSRFKR 60
Query: 66 MENINKGLTFI 76
+ENIN L F
Sbjct: 61 LENINLALNFA 71
>gnl|CDD|214479 smart00033, CH, Calponin homology domain. Actin binding domains
present in duplicate at the N-termini of spectrin-like
proteins (including dystrophin, alpha-actinin). These
domains cross-link actin filaments into bundles and
networks. A calponin homology domain is predicted in
yeasst Cdc24p.
Length = 101
Score = 55.0 bits (133), Expect = 4e-11
Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 11 KEAQAWIETVTGQKFPAGV--LYEDAIKDGQILCHLINKLKPGSV--AKINSSGGQFKFM 66
K W+ ++ + V D +KDG LC L+N L PG V K+ +S +FK +
Sbjct: 1 KTLLRWVNSLLAEYDKPPVTNFSSD-LKDGVALCALLNSLSPGLVDKKKVAASLSRFKKI 59
Query: 67 ENINKGLTFI 76
ENIN L+F
Sbjct: 60 ENINLALSFA 69
>gnl|CDD|215849 pfam00307, CH, Calponin homology (CH) domain. The CH domain is
found in both cytoskeletal proteins and signal
transduction proteins. The CH domain is involved in
actin binding in some members of the family. However in
calponins there is evidence that the CH domain is not
involved in its actin binding activity. Most member
proteins have from two to four copies of the CH domain,
however some proteins such as calponin have only a
single copy.
Length = 104
Score = 51.9 bits (125), Expect = 6e-10
Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 7/71 (9%)
Query: 10 DKEAQAWIETVTGQKFPAGV--LYEDAIKDGQILCHLINKLKPGSV--AKINSSGGQFKF 65
+K WI V G+ V +ED ++DG LC L+NKL+PG + K+N + +F
Sbjct: 1 EKALLRWINEVLGEYGGLPVTNFFED-LRDGLALCALLNKLRPGLIDLKKVNKN--RFDK 57
Query: 66 MENINKGLTFI 76
+EN+N L F
Sbjct: 58 LENLNLALEFA 68
>gnl|CDD|227526 COG5199, SCP1, Calponin [Cytoskeleton].
Length = 178
Score = 51.5 bits (123), Expect = 3e-09
Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 3 AKRNPEQDKEAQAWIETVTGQKFPAGVLYEDAIKDGQILCHLINKLKPGSVAKINSSGGQ 62
+Q KE WIETV G+KF +KDG LC ++N+ P + K S
Sbjct: 8 CPGMDKQQKEVTLWIETVLGEKFEPPGDLLSLLKDGVRLCRILNEASPLDI-KYKESKMP 66
Query: 63 FKFMENINKGLTF 75
F MENI+ +
Sbjct: 67 FVQMENISSFING 79
>gnl|CDD|227586 COG5261, IQG1, Protein involved in regulation of cellular
morphogenesis/cytokinesis [Cell division and chromosome
partitioning / Signal transduction mechanisms].
Length = 1054
Score = 44.1 bits (104), Expect = 3e-06
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 12 EAQAWIETVTGQKFPAGVLYEDAIKDGQILCHLINKLKPGSVAKI-NSSGGQFKFMENIN 70
EA+ WIE V + P + +ED++++G L L + P I + QF+ +NIN
Sbjct: 48 EAKIWIEEVIEEALPE-LCFEDSLRNGVFLAKLTQRFNPDLTTVIFPADKLQFRHTDNIN 106
Query: 71 KGLTFI 76
L I
Sbjct: 107 AFLDLI 112
>gnl|CDD|99812 cd06216, FNR_iron_sulfur_binding_2, Iron-sulfur binding ferredoxin
reductase (FNR) proteins combine the FAD and NAD(P)
binding regions of FNR with an iron-sulfur binding
cluster domain. Ferredoxin-NADP+ (oxido)reductase is an
FAD-containing enzyme that catalyzes the reversible
electron transfer between NADP(H) and electron carrier
proteins such as ferredoxin and flavodoxin. Isoforms of
these flavoproteins (i.e. having a non-covalently bound
FAD as a prosthetic group) are present in chloroplasts,
mitochondria, and bacteria in which they participate in
a wide variety of redox metabolic pathways. The
C-terminal domain contains most of the NADP(H) binding
residues and the N-terminal domain interacts
non-covalently with the isoalloxazine rings of the
flavin molecule which lies largely in a large gap
betweed the two domains. Ferredoxin-NADP+ reductase
first accepts one electron from reduced ferredoxin to
form a flavin semiquinone intermediate. The enzyme then
accepts a second electron to form FADH2 which then
transfers two electrons and a proton to NADP+ to form
NADPH.
Length = 243
Score = 28.7 bits (65), Expect = 0.69
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 34 AIKDGQILCHLINKLKPGSVAKINSSGGQFKFMENINKGLTFIA----ITP 80
A DG + L+N L PG V +++ G F + + L IA ITP
Sbjct: 86 AQPDGLVSNWLVNHLAPGDVVELSQPQGDFVLPDPLPPRLLLIAAGSGITP 136
>gnl|CDD|218241 pfam04750, Far-17a_AIG1, FAR-17a/AIG1-like protein. This family
includes the hamster androgen-induced FAR-17a protein,
and its human homologue, the AIG1 protein. The function
of these proteins is unknown. This family also includes
homologous regions from a number of other metazoan
proteins.
Length = 203
Score = 28.0 bits (63), Expect = 1.00
Identities = 9/42 (21%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 41 LCHLINKLKPGSVAKINSSGGQFKFMENINKGLTFIAITPQV 82
L + ++L ++ ++ GG+FK++ I L + T +
Sbjct: 16 LFYYDHQLP--TLEIESAYGGKFKYLTFIGLVLQALYFTLAL 55
>gnl|CDD|225593 COG3051, CitF, Citrate lyase, alpha subunit [Energy production and
conversion].
Length = 513
Score = 27.4 bits (61), Expect = 1.9
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 13/62 (20%)
Query: 42 CH--LINKLKPGSVAKINSSGGQFKFMENINKGLTFIAITPQVFSNDSITIHSGTG-SHL 98
CH L+ +K G V +I SSG + E I++GL + + IHS G HL
Sbjct: 106 CHAPLVEHIKNGVVTRIYSSGLRGPLGEEISRGLL----------AEPVQIHSHGGRVHL 155
Query: 99 TQ 100
Q
Sbjct: 156 VQ 157
>gnl|CDD|225839 COG3302, DmsC, DMSO reductase anchor subunit [General function
prediction only].
Length = 281
Score = 27.3 bits (61), Expect = 2.2
Identities = 9/23 (39%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 72 GLTFIAITPQVFSNDSI-TIHSG 93
G+ F+ + QV+S ++ T HSG
Sbjct: 121 GVVFVWMMAQVYSITTVPTWHSG 143
>gnl|CDD|185761 cd09034, BRO1_Alix_like, Protein-interacting Bro1-like domain of
mammalian Alix and related domains. This superfamily
includes the Bro1-like domains of mammalian Alix
(apoptosis-linked gene-2 interacting protein X),
His-Domain type N23 protein tyrosine phosphatase
(HD-PTP, also known as PTPN23), RhoA-binding proteins
Rhophilin-1 and Rhophilin-2, Brox, Bro1 and Rim20 (also
known as PalA) from Saccharomyces cerevisiae, and
related domains. Alix, HD-PTP, Brox, Bro1 and Rim20
interact with the ESCRT (Endosomal Sorting Complexes
Required for Transport) system. Alix, also known as
apoptosis-linked gene-2 interacting protein 1 (AIP1),
participates in membrane remodeling processes during the
budding of enveloped viruses, vesicle budding inside
late endosomal multivesicular bodies (MVBs), and the
abscission reactions of mammalian cell division. It also
functions in apoptosis. HD-PTP functions in cell
migration and endosomal trafficking, Bro1 in endosomal
trafficking, and Rim20 in the response to the external
pH via the Rim101 pathway. Bro1-like domains are
boomerang-shaped, and part of the domain is a
tetratricopeptide repeat (TPR)-like structure. Bro1-like
domains bind components of the ESCRT-III complex: CHMP4
(in the case of Alix, HD-PTP, and Brox) and Snf7 (in the
case of yeast Bro1, and Rim20). The single domain
protein human Brox, and the isolated Bro1-like domains
of Alix, HD-PTP and Rhophilin can bind human
immunodeficiency virus type 1 (HIV-1) nucleocapsid.
Alix, HD-PTP, Bro1, and Rim20 also have a V-shaped (V)
domain, which in the case of Alix, has been shown to be
a dimerization domain and to contain a binding site for
the retroviral late assembly (L) domain YPXnL motif,
which is partially conserved in this superfamily. Alix,
HD-PTP and Bro1 also have a proline-rich region (PRR);
the Alix PRR binds multiple partners. Rhophilin-1, and
-2, in addition to this Bro1-like domain, have an
N-terminal Rho-binding domain and a C-terminal PDZ
(PS.D.-95, Disc-large, ZO-1) domain. HD-PTP is encoded
by the PTPN23 gene, a tumor suppressor gene candidate
frequently absent in human kidney, breast, lung, and
cervical tumors. This protein has a C-terminal,
catalytically inactive tyrosine phosphatase domain.
Length = 345
Score = 26.5 bits (59), Expect = 3.5
Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 7/55 (12%)
Query: 28 GVLYEDAIKDGQILCHL------INKLKPGSVAKINSSGGQFK-FMENINKGLTF 75
G+ ++A K G+ + L + + + + + G K E I K L
Sbjct: 258 GLKLDEANKIGEAIARLQAALELLKESERLCKSFLLDVWGNLKKLKEKIEKELEK 312
>gnl|CDD|239519 cd03427, MTH1, MutT homolog-1 (MTH1) is a member of the Nudix
hydrolase superfamily. MTH1, the mammalian counterpart
of MutT, hydrolyzes oxidized purine nucleoside
triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to
monophosphates, thereby preventing the incorporation of
such oxygen radicals during replication. This is an
important step in the repair mechanism in genomic and
mitochondrial DNA. Like other members of the Nudix
family, it requires a divalent cation, such as Mg2+ or
Mn2+, for activity, and contain the Nudix motif, a
highly conserved 23-residue block (GX5EX7REUXEEXGU,
where U = I, L or V), that functions as a metal binding
and catalytic site. MTH1 is predominantly localized in
the cytoplasm and mitochondria. Structurally, this
enzyme adopts a similar fold to MutT despite low
sequence similarity outside the conserved nudix motif.
The most distinctive structural difference between MutT
and MTH1 is the presence of a beta-hairpin, which is
absent in MutT. This results in a much deeper and
narrower substrate binding pocket. Mechanistically,
MTH1 contains dual specificity for nucleotides that
contain 2-OH-adenine bases and those that contain
8-oxo-guanine bases.
Length = 137
Score = 26.0 bits (58), Expect = 3.7
Identities = 8/35 (22%), Positives = 14/35 (40%), Gaps = 2/35 (5%)
Query: 35 IKDGQILCHLINKLKPGSVAKINSSGGQFKFMENI 69
++L L+N+ K N GG+ + E
Sbjct: 9 KDPDKVL--LLNRKKGPGWGGWNGPGGKVEPGETP 41
>gnl|CDD|182582 PRK10602, PRK10602, murein peptide amidase A; Provisional.
Length = 237
Score = 26.1 bits (58), Expect = 4.2
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 39 QILCHLINKLKPGSV 53
Q LC LI++L+P V
Sbjct: 139 QALCQLIHRLQPAWV 153
>gnl|CDD|130646 TIGR01584, citF, citrate lyase, alpha subunit. This is a model of
the alpha subunit of the holoenzyme citrate lyase (EC
4.1.3.6) composed of alpha (EC 2.8.3.10), beta (EC
4.1.3.34), and acyl carrier protein subunits in a
stoichiometric relationship of 6:6:6. Citrate lyase is
an enzyme which converts citrate to oxaloacetate. In
bacteria, this reaction is involved in citrate
fermentation. The alpha subunit catalyzes the reaction
Acetyl-CoA + citrate = acetate + (3S)-citryl-CoA. The
seed contains an experimentally characterized member
from Lactococcus lactis subsp. lactis. The model covers
both Gram positive and Gram negative bacteria. It is
quite robust with queries scoring either quite well or
quite poorly against the model. There are currently no
hits in between the noise cutoff and trusted cutoff
[Energy metabolism, Fermentation].
Length = 492
Score = 26.3 bits (58), Expect = 4.2
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 42 CH--LINKLKPGSVAKINSSGGQFKFMENINKGL 73
H L+ +K G V I SSG + + I+KG+
Sbjct: 84 VHDPLVEHIKKGVVTGITSSGLRGTLGDEISKGI 117
>gnl|CDD|113013 pfam04223, CitF, Citrate lyase, alpha subunit (CitF). In
citrate-utilising prokaryotes, citrate lyase EC:4.1.3.6
cleaves intracellular citrate into acetate and
oxaloacetate, and is organised as a functional complex
consisting of alpha, beta, and gamma subunits. The gamma
subunit serves as an acyl carrier protein (ACP), and has
a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic
group. The citrate lyase is active only if this
prosthetic group is acetylated; this acetylation is
catalyzed by an acetate:SH-citrate lyase ligase. The
alpha subunit substitutes citryl for the acetyl group to
form citryl-S-ACP. The beta subunit completes the
reaction by cleaving the citryl to yield oxaloacetate
and (regenerated) acetyl-S-ACP. This family represents
the alpha subunit EC:2.8.3.10.
Length = 466
Score = 26.3 bits (58), Expect = 5.0
Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 13/62 (20%)
Query: 42 CH--LINKLKPGSVAKINSSGGQFKFMENINKGLTFIAITPQVFSNDSITIHSGTG-SHL 98
H L+ +K G V I SSG + K + I++GL + + I S G +
Sbjct: 61 VHEPLVEHIKNGVVTNITSSGLRGKLGDAISRGLL----------ENPVIIRSHGGRARA 110
Query: 99 TQ 100
Q
Sbjct: 111 IQ 112
>gnl|CDD|233926 TIGR02556, cas_TM1802, CRISPR-associated protein, TM1802 family.
This minor cas protein is found in CRISPR/cas regions
of at least five prokaryotic genomes: Methanosarcina
mazei, Sulfurihydrogenibium azorense, Thermotoga
maritima, Carboxydothermus hydrogenoformans, and
Dictyoglomus thermophilum, the first of which is
archaeal while the rest are bacterial [Mobile and
extrachromosomal element functions, Other].
Length = 555
Score = 26.0 bits (57), Expect = 5.9
Identities = 8/34 (23%), Positives = 12/34 (35%)
Query: 53 VAKINSSGGQFKFMENINKGLTFIAITPQVFSND 86
V S +F + N + FI I + F
Sbjct: 25 VEYDESGNYKFIVIMNFSLDSVFINIYSREFKKQ 58
>gnl|CDD|99780 cd06183, cyt_b5_reduct_like, Cytochrome b5 reductase catalyzes the
reduction of 2 molecules of cytochrome b5 using NADH as
an electron donor. Like ferredoxin reductases, these
proteins have an N-terminal FAD binding subdomain and a
C-terminal NADH binding subdomain, separated by a cleft,
which accepts FAD. The NADH-binding moiety interacts
with part of the FAD and resembles a Rossmann fold.
However, NAD is bound differently than in canonical
Rossmann fold proteins. Nitrate reductases,
flavoproteins similar to pyridine nucleotide cytochrome
reductases, catalyze the reduction of nitrate to
nitrite. The enzyme can be divided into three functional
fragments that bind the cofactors molybdopterin,
heme-iron, and FAD/NADH.
Length = 234
Score = 26.0 bits (58), Expect = 5.9
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 45 INKLKPGSVAKINSSGGQFKFMENIN-KGLTFIA----ITP 80
++ LKPG +I G+F++ N K + IA ITP
Sbjct: 78 LHSLKPGDTVEIRGPFGKFEYKPNGKVKHIGMIAGGTGITP 118
>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative
DEAH-box helicase. A conserved gene neighborhood widely
spread in the Actinobacteria contains this
uncharacterized DEAH-box family helicase encoded
convergently towards an operon of genes for protein
homologous to type II secretion and pilus formation
proteins. The context suggests that this helicase may
play a role in conjugal transfer of DNA.
Length = 742
Score = 25.8 bits (57), Expect = 7.4
Identities = 15/48 (31%), Positives = 18/48 (37%), Gaps = 11/48 (22%)
Query: 80 PQVFSNDSITIHSGTG-----SHLTQPEW---GREKPAACDCPDGHPS 119
P VF D H G EW R+ A+C+C G PS
Sbjct: 668 PTVFVYDG---HPGGAGFAERGFAKAREWLAATRDAIASCECESGCPS 712
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 24.5 bits (54), Expect = 8.2
Identities = 9/40 (22%), Positives = 13/40 (32%), Gaps = 8/40 (20%)
Query: 25 FPAGVLYED--------AIKDGQILCHLINKLKPGSVAKI 56
AG+ D + L +I KPG K+
Sbjct: 27 AKAGLKPGDIILSIDGKKVNSLTELIEVILNGKPGDTVKL 66
>gnl|CDD|238662 cd01366, KISc_C_terminal, Kinesin motor domain,
KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Ncd is a
spindle motor protein necessary for chromosome
segregation in meiosis. KIFC2/KIFC3-like kinesins have
been implicated in motility of the Golgi apparatus as
well as dentritic and axonal transport in neurons. This
catalytic (head) domain has ATPase activity and belongs
to the larger group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In this subgroup the motor domain is found at
the C-terminus (C-type). C-type kinesins are (-)
end-directed motors, i.e. they transport cargo towards
the (-) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 329
Score = 25.6 bits (57), Expect = 8.9
Identities = 9/26 (34%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 51 GS--VAKINSSGGQFKFMENINKGLT 74
GS + K ++G + K + INK L+
Sbjct: 235 GSERLKKSGATGDRLKEAQAINKSLS 260
>gnl|CDD|238737 cd01460, vWA_midasin, VWA_Midasin: Midasin is a member of the AAA
ATPase family. The proteins of this family are unified
by their common archetectural organization that is based
upon a conserved ATPase domain. The AAA domain of
midasin contains six tandem AAA protomers. The AAA
domains in midasin is followed by a D/E rich domain that
is following by a VWA domain. The members of this
subgroup have a conserved MIDAS motif. The function of
this domain is not exactly known although it has been
speculated to play a crucial role in midasin function.
Length = 266
Score = 25.4 bits (56), Expect = 9.2
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 3/62 (4%)
Query: 37 DGQILCHLINKLKPGSVAKINSSGGQFKFMENINKGLTFIAITPQVFSNDSITIHSGTGS 96
D QIL + S +I + QF F ++ + T Q+F + SG+
Sbjct: 109 DVQILHPFDEQFSSQSGPRILN---QFTFQQDKTDIANLLKFTAQIFEDARTQSSSGSLW 165
Query: 97 HL 98
L
Sbjct: 166 QL 167
>gnl|CDD|215452 PLN02843, PLN02843, isoleucyl-tRNA synthetase.
Length = 974
Score = 25.5 bits (56), Expect = 9.2
Identities = 13/27 (48%), Positives = 14/27 (51%)
Query: 80 PQVFSNDSITIHSGTGSHLTQPEWGRE 106
P V D IT SGTG T P G+E
Sbjct: 324 PVVIGGDYITTESGTGLVHTAPGHGQE 350
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
0.315 0.134 0.412
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,146,586
Number of extensions: 515605
Number of successful extensions: 291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 288
Number of HSP's successfully gapped: 23
Length of query: 121
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 37
Effective length of database: 7,211,866
Effective search space: 266839042
Effective search space used: 266839042
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: 42 (22.0 bits)
S2: 53 (24.2 bits)