RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 047331
(102 letters)
>gnl|CDD|177867 PLN02221, PLN02221, asparaginyl-tRNA synthetase.
Length = 572
Score = 95.4 bits (237), Expect = 2e-24
Identities = 41/66 (62%), Positives = 55/66 (83%)
Query: 33 LVERNGCGGAGEMFQVTTLLSEAEKLEKELMKNPPPSEADREAAKLFVKEKGEGVAKLKS 92
++ + C GAGEMFQVTTL++ E+LE++L+ NPPP+EAD EAA+L VKE+GE VA+LK+
Sbjct: 197 IITTSDCEGAGEMFQVTTLINYTERLEQDLIDNPPPTEADVEAARLIVKERGEVVAQLKA 256
Query: 93 KKASKE 98
KASKE
Sbjct: 257 AKASKE 262
Score = 52.3 bits (125), Expect = 3e-09
Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 8/81 (9%)
Query: 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNGCGGAGEMFQVTTLLSEAEKLEK 60
+ GWVK GR+Q K AF EVNDGSC NLQV+V+ + ++ ++TL++ +
Sbjct: 55 IGGWVKTGREQGKGTFAFLEVNDGSCPANLQVMVDSS-------LYDLSTLVATGTCVTV 107
Query: 61 E-LMKNPPPSEADREAAKLFV 80
+ ++K PP + ++ +L V
Sbjct: 108 DGVLKVPPEGKGTKQKIELSV 128
>gnl|CDD|239813 cd04318, EcAsnRS_like_N, EcAsnRS_like_N: N-terminal, anticodon
recognition domain of the type found in Escherichia
coli asparaginyl-tRNA synthetase (AsnRS) and, in
Arabidopsis thaliana and Saccharomyces cerevisiae
mitochondrial (mt) AsnRS. This domain is a beta-barrel
domain (OB fold) involved in binding the tRNA anticodon
stem-loop. The enzymes in this group are homodimeric
class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs
catalyze the specific attachment of amino acids (AAs)
to their cognate tRNAs during protein biosynthesis.
This 2-step reaction involves i) the activation of the
AA by ATP in the presence of magnesium ions, followed
by ii) the transfer of the activated AA to the
terminal ribose of tRNA. In the case of the class2b
aaRSs, the activated AA is attached to the 3'OH of the
terminal ribose. Eukaryotes contain 2 sets of aaRSs,
both of which are encoded by the nuclear genome. One
set concerns with cytoplasmic protein synthesis,
whereas the other exclusively with mitochondrial
protein synthesis. S. cerevisiae mtAsnRS can charge
E.coli tRNA with asparagines. Mutations in the gene for
S. cerevisiae mtAsnRS has been found to induce a
"petite" phenotype typical for a mutation in a nuclear
gene that results in a non-functioning mitochondrial
protein synthesis system.
Length = 82
Score = 46.4 bits (111), Expect = 3e-08
Identities = 17/32 (53%), Positives = 22/32 (68%), Gaps = 2/32 (6%)
Query: 3 GWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLV 34
GWV+ R K ++F E+NDGSC NLQV+V
Sbjct: 6 GWVRSVRDSKK--ISFIELNDGSCLKNLQVVV 35
>gnl|CDD|215291 PLN02532, PLN02532, asparagine-tRNA synthetase.
Length = 633
Score = 42.9 bits (101), Expect = 5e-06
Identities = 26/65 (40%), Positives = 36/65 (55%), Gaps = 9/65 (13%)
Query: 41 GAGEMFQVTTLLS-EAEKLEKELMKNPPPSEADR---EAAKLFVKEKGEGVAKLKSKKAS 96
G GEMF+VTTLL +K EK P E + EA K +KEK V +LK +++
Sbjct: 269 GFGEMFRVTTLLGKSDDKEEK-----KPVHETEGISLEAVKAAIKEKTNLVEELKRSESN 323
Query: 97 KEVLL 101
+E L+
Sbjct: 324 REALV 328
Score = 29.5 bits (66), Expect = 0.30
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 17 AFFEVNDGSCFDNLQVLVE 35
A+ ++DGSC +LQV+V+
Sbjct: 136 AYLLISDGSCVASLQVVVD 154
>gnl|CDD|235176 PRK03932, asnC, asparaginyl-tRNA synthetase; Validated.
Length = 450
Score = 42.0 bits (100), Expect = 8e-06
Identities = 15/37 (40%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERN 37
+ GWV+ K+D +AF ++ DGSCF LQV+ +
Sbjct: 21 VRGWVR--TKRDSGKIAFLQLRDGSCFKQLQVVKDNG 55
Score = 29.7 bits (68), Expect = 0.21
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 39 CGGAGEMFQVTTL 51
C GAGE+F+VTTL
Sbjct: 165 CEGAGELFRVTTL 177
>gnl|CDD|178213 PLN02603, PLN02603, asparaginyl-tRNA synthetase.
Length = 565
Score = 38.4 bits (89), Expect = 2e-04
Identities = 31/109 (28%), Positives = 49/109 (44%), Gaps = 24/109 (22%)
Query: 3 GWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNGCG-----------GAGEMFQVTTL 51
GWV+ R Q + F EVNDGSC N+Q ++ + G GA + Q T +
Sbjct: 114 GWVRTLRAQSS--VTFIEVNDGSCLSNMQCVMTPDAEGYDQVESGLITTGASVLVQGTVV 171
Query: 52 LSEAEKLEKELMKNPPPSEADREAAKLFVKEKGEGVAKLKSKKASKEVL 100
S+ K + EL + +K+ V K + ++ K+ S+E L
Sbjct: 172 SSQGGKQKVEL-----------KVSKIVVVGKSDPSYPIQKKRVSREFL 209
Score = 29.9 bits (67), Expect = 0.18
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 39 CGGAGEMFQVTTLLSEAEKLEKELMKNPPPSEADR 73
C GAGE F VTTL+ + + L+ + P ++
Sbjct: 258 CEGAGEQFCVTTLIPNSAENGGSLVDDIPKTKDGL 292
>gnl|CDD|232982 TIGR00457, asnS, asparaginyl-tRNA synthetase. In a multiple
sequence alignment of representative asparaginyl-tRNA
synthetases (asnS), archaeal/eukaryotic type
aspartyl-tRNA synthetases (aspS_arch), and bacterial
type aspartyl-tRNA synthetases (aspS_bact), there is a
striking similarity between asnS and aspS_arch in gap
pattern and in sequence, and a striking divergence of
aspS_bact. Consequently, a separate model was built for
each of the three groups. This model, asnS, represents
asparaginyl-tRNA synthetases from the three domains of
life. Some species lack this enzyme and charge
tRNA(asn) by misacylation with Asp, followed by
transamidation of Asp to Asn [Protein synthesis, tRNA
aminoacylation].
Length = 453
Score = 37.0 bits (86), Expect = 5e-04
Identities = 11/34 (32%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLV 34
++GWV+ K+ + F E+NDGS +Q ++
Sbjct: 21 VSGWVR--TKRSSKKIIFLELNDGSSLGPIQAVI 52
Score = 26.2 bits (58), Expect = 3.3
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 37 NGCGGAGEMFQVTTL 51
N C GAGE+F+V+T
Sbjct: 166 NDCEGAGELFRVSTG 180
>gnl|CDD|240414 PTZ00425, PTZ00425, asparagine-tRNA ligase; Provisional.
Length = 586
Score = 36.9 bits (85), Expect = 7e-04
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVER 36
+ GW K RKQ F +NDGSC NLQ++V++
Sbjct: 86 VCGWSKAVRKQGGGRFCFVNLNDGSCHLNLQIIVDQ 121
Score = 30.8 bits (69), Expect = 0.087
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 33 LVERNGCGGAGEMFQVTTLLSE 54
L+ + C G GEMF VTTLL E
Sbjct: 241 LITTSDCEGGGEMFTVTTLLGE 262
>gnl|CDD|223096 COG0017, AsnS, Aspartyl/asparaginyl-tRNA synthetases
[Translation, ribosomal structure and biogenesis].
Length = 435
Score = 34.1 bits (79), Expect = 0.006
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 1 LAGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNGCGGAGEMFQVTTLLSEA 55
+ GWV R K + F + DGS F +Q +V +N E+F+ L E+
Sbjct: 21 VRGWVHNKRDLGK--IIFLVLRDGSGF--IQAVVPKN--KVYEELFKAKKLTLES 69
>gnl|CDD|176478 cd08641, DNA_pol_gammaA, Pol gammaA is a family A polymerase that
is responsible for DNA replication and repair in
mitochondria. DNA polymerase gamma (Pol gamma), 5'-3'
polymerase domain (Pol gammaA). Pol gammaA is a family A
polymerase that is responsible for DNA replication and
repair in mitochondria. Family A polymerase functions
primarily to fill DNA gaps that arise during DNA repair,
recombination and replication. DNA-dependent DNA
polymerases can be classified into six main groups based
upon phylogenetic relationships with E. coli polymerase
I (classA), E. coli polymerase II (class B), E.coli
polymerase III (class C), euryarchaeota polymerase II
(class D), human polymerase beta (class X), E. coli
UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum
variant (class Y). Family A polymerases are found
primarily in organisms related to prokaryotes and
include prokaryotic DNA polymerase I, mitochondrial
polymerase gammaA, and several bacteriophage polymerases
including those from odd-numbered phage (T3, T5, and
T7). The structure of these polymerases resembles in
overall morphology a cupped human right hand, with
fingers (which bind an incoming nucleotide and interact
with the single-stranded template), palm (which harbors
the catalytic amino acid residues and also binds an
incoming dNTP) and thumb (which binds double-stranded
DNA) subdomains. Pol gammaA has also the right hand
configuration. Pol gammaA has both polymerase and
proofreading exonuclease activities separated by a
spacer. Pol gamma holoenzyme is a heterotrimer
containing one Pol gammaA subunit and a dimeric Pol
gammaB subunit. Pol gamma is important for mitochondria
DNA maintenance and mutation of the catalytic subunit of
Pol gamma is implicated in more than 30 human diseases.
Length = 425
Score = 33.1 bits (76), Expect = 0.012
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 41 GAGEMFQVTTLLSEAEKLEKELMKNPPPSEADREAAKLFVKEKGEGVAKLKSKKASK 97
GAG+ F AE+L + P+EA +A +++ KG +A +S K +
Sbjct: 215 GAGQPF--------AERLLMQFNPRLTPAEATEKAKQMYAATKGIRIAIQRSTKGKR 263
>gnl|CDD|233644 TIGR01932, hflC, HflC protein. HflK and HflC are paralogs encoded
by tandem genes in Proteobacteria, spirochetes, and some
other bacterial lineages. The HflKC complex is anchored
in the membrane and exposed to the periplasm. The
complex is not active as a protease, but rather binds to
and appears to modulate the ATP-dependent protease FtsH.
The overall function of HflKC is not fully described
[Protein fate, Degradation of proteins, peptides, and
glycopeptides, Regulatory functions, Protein
interactions].
Length = 317
Score = 31.7 bits (72), Expect = 0.040
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 5/34 (14%)
Query: 46 FQVTTLLSEAEKLEKELMKNPPPSEADREAAKLF 79
++V +LSEA + ++K E D EAAK++
Sbjct: 245 YEVRKILSEAYR-TARIIK----GEGDAEAAKIY 273
>gnl|CDD|153340 cd07656, F-BAR_srGAP, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase
Activating Proteins. F-BAR domains are dimerization
modules that bind and bend membranes and are found in
proteins involved in membrane dynamics and actin
reorganization. Slit-Robo GTPase Activating Proteins
(srGAPs) are Rho GAPs that interact with Robo1, the
transmembrane receptor of Slit proteins. Slit proteins
are secreted proteins that control axon guidance and the
migration of neurons and leukocytes. Vertebrates contain
three isoforms of srGAPs, all of which are expressed
during embryonic and early development in the nervous
system but with different localization and timing.
srGAPs contain an N-terminal F-BAR domain, a Rho GAP
domain, and a C-terminal SH3 domain. F-BAR domains form
banana-shaped dimers with a positively-charged concave
surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 241
Score = 29.6 bits (67), Expect = 0.20
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 52 LSEAEKLEKELMKNPPPSEADREAAKLFVKEKGEG-----VAKLKSKKASKEVLLN 102
L EAEK E++ ++P ++K KE + AKLK KA E LLN
Sbjct: 154 LKEAEKQEEKQEQSPEKKLERSRSSKKIEKEVEKRQAKYSEAKLKCTKARNEYLLN 209
>gnl|CDD|182913 PRK11029, PRK11029, FtsH protease regulator HflC; Provisional.
Length = 334
Score = 28.2 bits (63), Expect = 0.76
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 5/36 (13%)
Query: 46 FQVTTLLSEAEKLEKELMKNPPPSEADREAAKLFVK 81
++VT L+EAE+ + +M+ E D EAAKLF
Sbjct: 255 YEVTRTLAEAER-QGRIMR----GEGDAEAAKLFAD 285
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved
in the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 26.1 bits (58), Expect = 1.2
Identities = 14/25 (56%), Positives = 17/25 (68%), Gaps = 2/25 (8%)
Query: 56 EKLEKELMKNPPPSEADRE--AAKL 78
E+LEKE KNP PS +RE A +L
Sbjct: 13 EELEKEFEKNPYPSREEREELAKEL 37
>gnl|CDD|106409 PRK13452, atpC, F0F1 ATP synthase subunit epsilon; Provisional.
Length = 145
Score = 27.0 bits (59), Expect = 1.5
Identities = 20/48 (41%), Positives = 27/48 (56%), Gaps = 6/48 (12%)
Query: 53 SEAEKLE---KELMKNPPPSEADREAAKLFVKEKGEGVAKLKSKKASK 97
+EAEK KE++KNP S+ D EAA K E A+LK+ +S
Sbjct: 93 AEAEKARARAKEVLKNPDASKLDIEAAN---KRLKEADARLKALNSSN 137
>gnl|CDD|225321 COG2524, COG2524, Predicted transcriptional regulator, contains
C-terminal CBS domains [Transcription].
Length = 294
Score = 26.9 bits (60), Expect = 1.7
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 4/54 (7%)
Query: 45 MFQVTTLLSEAEKLEKELMKNPP----PSEADREAAKLFVKEKGEGVAKLKSKK 94
+ ++ ++S ++ K LM P + REAAKLF ++ G + K
Sbjct: 160 LIDISKMVSIPKEKVKNLMSKKLITVRPDDTLREAAKLFYEKGIRGAPVVDDDK 213
>gnl|CDD|221296 pfam11894, DUF3414, Protein of unknown function (DUF3414). This
family of proteins are functionally uncharacterized.
This protein is found in eukaryotes. Proteins in this
family are typically between 764 to 2011 amino acids in
length. This protein has a conserved LLG sequence
motif.
Length = 1612
Score = 27.3 bits (61), Expect = 1.7
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 50 TLLSEAEKLE---KELMKNPPPSEADREAAKLFVKEKGEGV 87
L E EK + L+ NPP ++ R+ + G+G
Sbjct: 27 DLEVELEKHKPDFLNLLDNPPKNDKSRQQLESGKITLGDGD 67
>gnl|CDD|237799 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional.
Length = 1627
Score = 27.1 bits (60), Expect = 1.9
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 4/58 (6%)
Query: 21 VNDGSCFDNLQVLVERNGCGGAGEMFQVTTLLSEAEKLEKELMKNPPPSEADREAAKL 78
VN G +N L+ N C E + L+++ + + E + NP P EA A
Sbjct: 437 VNYGDFLENNHTLLPSNWC----EEWYEQELIAKNIEYDPEFINNPTPEEAIHFALVT 490
>gnl|CDD|236166 PRK08149, PRK08149, ATP synthase SpaL; Validated.
Length = 428
Score = 26.5 bits (59), Expect = 3.0
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 25 SCFDNLQVLVERNGCGGAGEMFQVTTLLSEAE 56
S FD+L L+ER G AG + T+L E+E
Sbjct: 276 SVFDSLPRLLERPGATLAGSITAFYTVLLESE 307
>gnl|CDD|220095 pfam09037, Sulphotransf, Stf0 sulphotransferase. Members of this
family are essential for the biosynthesis of
sulpholipid-1 in prokaryotes. They adopt a structure
that belongs to the sulphotransferase superfamily,
consisting of a single domain with a core four-stranded
parallel beta-sheet flanked by alpha-helices.
Length = 245
Score = 26.2 bits (58), Expect = 3.1
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 1 LAGWVKIGRKQDKDWLAFFEVND 23
+A V+ R Q+ W +FE
Sbjct: 165 IASCVRRLRDQEAAWRNWFEREG 187
>gnl|CDD|214960 smart00991, WHEP-TRS, A conserved domain of 46 amino acids,
called WHEP-TRS has been shown.to exist in a number of
higher eukaryote aminoacyl-transfer RNA synthetases.
This domain is present one to six times in the several
enzymes. There are three copies in mammalian
multifunctional aminoacyl-tRNA synthetase in a region
that separates the N-terminal glutamyl-tRNA synthetase
domain from the C-terminal prolyl-tRNA synthetase
domain, and six copies in the intercatalytic region of
the Drosophila enzyme. The domain is found at the
N-terminal extremity of the mammalian tryptophanyl-
tRNA synthetase and histidyl-tRNA synthetase, and the
mammalian, insect, nematode and plant glycyl- tRNA
synthetases. This domain could contain a central
alpha-helical region and may play a role in the
association of tRNA-synthetases into multienzyme
complexes.
Length = 56
Score = 25.0 bits (55), Expect = 3.1
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 80 VKEKGEGVAKLKSKKASKEV 99
V +GE V KLK++KASK+
Sbjct: 4 VAAQGELVRKLKAEKASKDE 23
>gnl|CDD|150002 pfam09162, Tap-RNA_bind, Tap, RNA-binding. Members of this
family adopt a structure consisting of an alpha+beta
sandwich with an antiparallel beta-sheet, arranged in a
2(beta-alpha-beta) motif. They are mainly found in mRNA
export factors, and mediate the sequence nonspecific
nuclear export of cellular mRNAs as well as the
sequence-specific export of retroviral mRNAs bearing
the constitutive transport element.
Length = 88
Score = 25.4 bits (56), Expect = 3.3
Identities = 8/20 (40%), Positives = 10/20 (50%), Gaps = 4/20 (20%)
Query: 1 LAGWVKI----GRKQDKDWL 16
W K+ G+K DK WL
Sbjct: 4 SKNWFKVTIPHGKKYDKKWL 23
>gnl|CDD|238605 cd01200, WHEPGMRS_RNA, EPRS-like_RNA binding domain. This short
RNA-binding domain is found in several higher eukaryote
aminoacyl-tRNA synthetases (aaRSs). It is found in
three copies in the mammalian bifunctional EPRS in a
region that separates the N-terminal GluRS from the
C-terminal ProRS. In the Drosophila EPRS, this domain
is repeated six times. It is found at the N-terminus of
TrpRS, HisRS and GlyR and at the C-terminus of MetRS.
This domain consists of a helix- turn- helix structure,
which is similar to other RNA-binding proteins. It is
involved in both protein-RNA interactions by binding
tRNA and protein-protein interactions, which are
important for the formation of aaRSs into multienzyme
complexes.
Length = 42
Score = 24.4 bits (54), Expect = 3.7
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 80 VKEKGEGVAKLKSKKASKEV 99
+ E+G+ V KLK++KA KE
Sbjct: 4 IAEQGDLVRKLKAEKAPKEE 23
>gnl|CDD|233619 TIGR01888, cas_cmr3, CRISPR type III-B/RAMP module-associated
protein Cmr3. CRISPR is a term for Clustered Regularly
Interspaced Short Palidromic Repeats. A number of
protein families appear only in association with these
repeats and are designated Cas (CRISPR associated)
proteins. This highly divergent family is found in at
least ten different archaeal and bacterial species as
part of the CRISPR RAMP modulue but is not a member of
the RAMP superfamily itself. A typical example is TM1793
from Thermotoga maritima [Mobile and extrachromosomal
element functions, Other].
Length = 337
Score = 25.9 bits (57), Expect = 4.1
Identities = 13/46 (28%), Positives = 20/46 (43%)
Query: 56 EKLEKELMKNPPPSEADREAAKLFVKEKGEGVAKLKSKKASKEVLL 101
KL K L + ++F KE+ G+A + +K KE L
Sbjct: 127 SKLSKYLAGRISELHTLLQEEEIFKKEERIGIALDRERKVVKEGAL 172
>gnl|CDD|218926 pfam06178, KdgM, Oligogalacturonate-specific porin protein (KdgM).
This family consists of several bacterial proteins which
are homologous to the oligogalacturonate-specific porin
protein KdgM from Erwinia chrysanthemi. The
phytopathogenic Gram-negative bacteria Erwinia
chrysanthemi secretes pectinases, which are able to
degrade the pectic polymers of plant cell walls, and
uses the degradation products as a carbon source for
growth. KdgM is a major outer membrane protein, whose
synthesis is strongly induced in the presence of pectic
derivatives. KdgM behaves like a voltage-dependent porin
that is slightly selective for anions and that exhibits
fast block in the presence of trigalacturonate. In
contrast to most porins, KdgM seems to be monomeric.
Length = 218
Score = 25.5 bits (56), Expect = 5.3
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 6/28 (21%)
Query: 5 VKIGRKQDKDWLAFFEVNDGSCFDNLQV 32
VK+ K DK W + EV N+ V
Sbjct: 178 VKLAYKIDKHWTPYVEV------GNVDV 199
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 24.1 bits (53), Expect = 6.2
Identities = 15/25 (60%), Positives = 17/25 (68%), Gaps = 2/25 (8%)
Query: 56 EKLEKELMKNPPPSEADRE--AAKL 78
E+LEKE KNP PS +RE A KL
Sbjct: 14 EELEKEFQKNPYPSREEREELAKKL 38
>gnl|CDD|181599 PRK08972, fliI, flagellum-specific ATP synthase; Validated.
Length = 444
Score = 25.4 bits (56), Expect = 6.2
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 4/38 (10%)
Query: 25 SCFDNLQVLVERNGCGGAGEMFQVT---TLLSEAEKLE 59
S F L LVER G GG G+ +T T+L+E + L+
Sbjct: 287 SVFAKLPALVERAGNGGPGQG-SITAFYTVLTEGDDLQ 323
>gnl|CDD|181182 PRK07960, fliI, flagellum-specific ATP synthase; Validated.
Length = 455
Score = 25.5 bits (56), Expect = 6.5
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 25 SCFDNLQVLVER--NGCGGAGEMFQVTTLLSEAE 56
S F L LVER NG G G + T+L+E +
Sbjct: 300 SVFAKLPALVERAGNGISGGGSITAFYTVLTEGD 333
>gnl|CDD|224180 COG1260, INO1, Myo-inositol-1-phosphate synthase [Lipid
metabolism].
Length = 362
Score = 25.4 bits (56), Expect = 6.8
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 62 LMKNPPPSEADREAAKLFVKE 82
MKNPP D A+ ++E
Sbjct: 338 FMKNPPTQYPDDIEARRALEE 358
>gnl|CDD|215929 pfam00458, WHEP-TRS, WHEP-TRS domain.
Length = 56
Score = 24.2 bits (53), Expect = 6.9
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 80 VKEKGEGVAKLKSKKASKEV 99
+ +G+ V KLK+KKA KE
Sbjct: 5 IAAQGDLVRKLKAKKAPKED 24
>gnl|CDD|216115 pfam00780, CNH, CNH domain. Domain found in NIK1-like kinase,
mouse citron and yeast ROM1, ROM2. Unpublished
observations.
Length = 266
Score = 24.9 bits (55), Expect = 8.1
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 3/34 (8%)
Query: 9 RKQDKDWLAFFEVNDGS---CFDNLQVLVERNGC 39
RK++ LA ++D C+D V V G
Sbjct: 176 RKENLKPLAVVRLSDDEFLLCYDEFAVYVNLQGR 209
>gnl|CDD|236531 PRK09467, envZ, osmolarity sensor protein; Provisional.
Length = 435
Score = 25.3 bits (56), Expect = 8.2
Identities = 7/21 (33%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 3 GWVKIGRKQDKDWLAFFEVND 23
GW+K+ + A+F+V D
Sbjct: 349 GWIKVSSGTEGKR-AWFQVED 368
>gnl|CDD|184048 PRK13428, PRK13428, F0F1 ATP synthase subunit delta; Provisional.
Length = 445
Score = 25.1 bits (55), Expect = 8.4
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 40 GGAGEMFQVTT-LLSEAEKLEKELMKNPPPSEADREAAKLFVKEKGEGVAKLKS 92
GGA + VT LLS+ EL++ P EA A+L V +GE VA++ +
Sbjct: 332 GGASTVNPVTVALLSQT----VELLRGQPAEEAVLFLAELAVARRGEVVAQVSA 381
>gnl|CDD|187787 cd09656, Cmr3_III-B, CRISPR/Cas system-associated RAMP superfamily
protein Cmr3. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
RAMP superfamily protein; This protein is a subunit of
Cmr complex.
Length = 318
Score = 25.1 bits (55), Expect = 8.9
Identities = 14/46 (30%), Positives = 20/46 (43%)
Query: 56 EKLEKELMKNPPPSEADREAAKLFVKEKGEGVAKLKSKKASKEVLL 101
KL K L N ++F KE+ G+A + +K KE L
Sbjct: 113 SKLSKYLAGNISELHTVDGEEEIFKKEERIGIALDRERKVVKEGAL 158
>gnl|CDD|193489 cd04084, CBM6_xylanase-like, Carbohydrate Binding Module 6
(CBM6); many are appended to glycoside hydrolase (GH)
family 11 and GH43 xylanase domains. This family
includes carbohydrate binding module 6 (CBM6) domains
that are appended mainly to glycoside hydrolase (GH)
family domains, including GH3, GH11, and GH43 domains.
These CBM6s are non-catalytic carbohydrate binding
domains that facilitate the strong binding of the GH
catalytic modules with their dedicated, insoluble
substrates. Examples of proteins having CMB6s belonging
to this family are Microbispora bispora GghA, a
1,4-beta-D-glucan glucohydrolase (GH3); Clostridium
thermocellum xylanase U (GH11), and Penicillium
purpurogenum ABF3, a bifunctional
alpha-L-arabinofuranosidase/xylobiohydrolase (GH43).
GH3 comprises enzymes with activities including
beta-glucosidase (hydrolyzes beta-galactosidase) and
beta-xylosidase (hydrolyzes 1,4-beta-D-xylosidase).
GH11 family comprises enzymes with xylanase
(endo-1,4-beta-xylanase) activity which catalyze the
hydrolysis of beta-1,4 bonds of xylan, the major
component of hemicelluloses, to generate
xylooligosaccharides and xylose. GH43 includes
beta-xylosidases and beta-xylanases, using
aryl-glycosides as substrates. CBM6 is an unusual CBM
as it represents a chimera of two distinct binding
sites with different modes of binding: binding site I
within the loop regions and binding site II on the
concave face of the beta-sandwich fold.
Length = 124
Score = 24.6 bits (54), Expect = 9.4
Identities = 13/43 (30%), Positives = 20/43 (46%)
Query: 2 AGWVKIGRKQDKDWLAFFEVNDGSCFDNLQVLVERNGCGGAGE 44
G + +G ++ DW+AF V+ G + V G GG E
Sbjct: 22 GGGLYVGNIKNGDWIAFKNVDFGGGATSFTARVASAGAGGTIE 64
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
0.313 0.132 0.380
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,033,897
Number of extensions: 415863
Number of successful extensions: 416
Number of sequences better than 10.0: 1
Number of HSP's gapped: 414
Number of HSP's successfully gapped: 61
Length of query: 102
Length of database: 10,937,602
Length adjustment: 68
Effective length of query: 34
Effective length of database: 7,921,530
Effective search space: 269332020
Effective search space used: 269332020
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 (21.9 bits)
S2: 53 (24.2 bits)