RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16078
(111 letters)
>gnl|CDD|113356 pfam04582, Reo_sigmaC, Reovirus sigma C capsid protein.
Length = 326
Score = 30.3 bits (68), Expect = 0.15
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 50 IRRNLGDERPEVAEYEAVLQD----LDEAKAELDQLTATVANLKERLS 93
+ ++ +++ A LQD LD+AKA L+ L TV L+ +
Sbjct: 47 LSESVSTISSRLSDLSADLQDMTTSLDDAKATLNGLITTVQALQTSVD 94
>gnl|CDD|176405 cd01810, ISG15_repeat2, ISG15 ubiquitin-like protein, second repeat
of 2. ISG15 is a ubiquitin-like protein containing two
ubiquitin homology domains and becomes conjugated to a
variety of proteins when cells are treated with type I
interferon or lipopolysaccharide. Although ISG15 has
properties similar to those of other ubiquitin-like
molecules, it is a unique member of the ubiquitin-like
superfamily, whose expression and conjugation to target
proteins are tightly regulated by specific signaling
pathways, indicating it may have specialized functions
in the immune system.
Length = 74
Score = 27.9 bits (62), Expect = 0.34
Identities = 13/23 (56%), Positives = 19/23 (82%)
Query: 80 QLTATVANLKERLSKYEVVESDQ 102
QLT TVA LK+++S+ E V++DQ
Sbjct: 16 QLTQTVATLKQQVSQRERVQADQ 38
>gnl|CDD|184611 PRK14297, PRK14297, chaperone protein DnaJ; Provisional.
Length = 380
Score = 29.4 bits (66), Expect = 0.34
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 4 IPETPNEKNKEAFRRYLEQSG 24
IP+ N K KEA ++E SG
Sbjct: 340 IPKKLNSKQKEALTMFMEASG 360
>gnl|CDD|233130 TIGR00797, matE, putative efflux protein, MATE family. The Multi
Antimicrobial Extrusion (MATE) Family (TC 2.A.66) The
MATE family consists of probable efflux proteins
including a functionally characterized multi drug efflux
system from Vibrio parahaemolyticus, a putative
ethionine resistance protein of Saccharomyces
cerevisiae, and the functionally uncharacterized DNA
damage-inducible protein F (DinF) of E. coli. These
proteins have 12 probable TMS [Transport and binding
proteins, Other].
Length = 342
Score = 29.1 bits (66), Expect = 0.41
Identities = 11/55 (20%), Positives = 18/55 (32%), Gaps = 6/55 (10%)
Query: 10 EKNKEAFRRYLEQSGVVDAITSALVMLYSIEEKPEDPLDFIRRNLGDERPEVAEY 64
N + R +QS ++ + V+L +L EVAE
Sbjct: 62 AGNYQRLGRQAQQSLLLALLLGLPVLLVGY------FFIDPLLSLMGADGEVAEL 110
>gnl|CDD|233547 TIGR01730, RND_mfp, RND family efflux transporter, MFP subunit.
This model represents the MFP (membrane fusion protein)
component of the RND family of transporters. RND refers
to Resistance, Nodulation, and cell Division. It is, in
part, a subfamily of pfam00529 (Pfam release 7.5) but
hits substantial numbers of proteins missed by that
model. The related HlyD secretion protein, for which
pfam00529 is named, is outside the scope of this model.
Attributed functions imply outward transport. These
functions include nodulation, acriflavin resistance,
heavy metal efflux, and multidrug resistance proteins.
Most members of this family are found in Gram-negative
bacteria. The proposed function of MFP proteins is to
bring the inner and outer membranes together and enable
transport to the outside of the outer membrane. Note,
however, that a few members of this family are found in
Gram-positive bacteria, where there is no outer membrane
[Transport and binding proteins, Unknown substrate].
Length = 322
Score = 28.8 bits (65), Expect = 0.45
Identities = 8/36 (22%), Positives = 20/36 (55%)
Query: 62 AEYEAVLQDLDEAKAELDQLTATVANLKERLSKYEV 97
A+ + ++ A+A+L+ A++A+ + L E+
Sbjct: 102 ADLDDAKAAVEAAQADLEAAKASLASAQLNLRYTEI 137
>gnl|CDD|235732 PRK06189, PRK06189, allantoinase; Provisional.
Length = 451
Score = 28.9 bits (65), Expect = 0.56
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 27 DAITSALVMLYSIEEKPEDPLDFIRRNLGDERPEVAEYEAVLQDLDEAKA 76
DA+T L ++ D D++ + RP VAE EAV + L A+
Sbjct: 187 DALTRHLTTQA-RQQGKTDVRDYL-----ESRPVVAELEAVQRALLYAQE 230
>gnl|CDD|234693 PRK00226, greA, transcription elongation factor GreA; Reviewed.
Length = 157
Score = 28.1 bits (64), Expect = 0.72
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 8/57 (14%)
Query: 50 IRRNLGDERPEVAEYEAVLQDLDEAKAELDQLTATVANLKERLSKYEVVESDQPISD 106
R GD E AEY A AK E + + L+++LS EV++ +
Sbjct: 36 EAREHGDLS-ENAEYHA-------AKEEQGFIEGRIRELEDKLSNAEVIDPSKLSGG 84
>gnl|CDD|224640 COG1726, NqrA, Na+-transporting NADH:ubiquinone oxidoreductase,
subunit NqrA [Energy production and conversion].
Length = 447
Score = 27.8 bits (62), Expect = 1.4
Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 5/74 (6%)
Query: 2 SFIPETPNEKNKEAFRRYLEQSGVVDAI-TSALVMLYSIEEKPEDPLDFIRRNLGDERPE 60
+ E + + E R+ L +SG+ A+ T + + + P F+ N D P
Sbjct: 104 KYDLEQLAQLSLEEVRKNLIESGLWTALRTRPFSKVPAPDSTPRAI--FV--NAMDTNPL 159
Query: 61 VAEYEAVLQDLDEA 74
A+ E V+ + EA
Sbjct: 160 AADPEVVIAEFSEA 173
>gnl|CDD|163313 TIGR03537, DapC, succinyldiaminopimelate transaminase. The four
sequences which make up the seed for this model are not
closely related, although they are all members of the
pfam00155 family of aminotransferases and are more
closely related to each other than to anything else.
Additionally, all of them are found in the vicinity of
genes involved in the biosynthesis of lysine via the
diaminopimelate pathway (GenProp0125), although this
amount to a separation of 12 genes in the case of
Sulfurihydrogenibium azorense Az-Fu1. None of these
genomes contain another strong candidate for this role
in the pathway. Note: the detailed information included
in the EC:2.6.1.17 record includes the assertions that
the enzyme uses the pyridoxal pyrophosphate cofactor,
which is consistent with the pfam00155 family, and the
assertion that the amino group donor is L-glutamate,
which is undetermined for the sequences in this clade.
Length = 350
Score = 27.2 bits (60), Expect = 1.7
Identities = 15/37 (40%), Positives = 23/37 (62%), Gaps = 3/37 (8%)
Query: 43 PEDPL-DFIRRNLGDERPEVAEYEAVL--QDLDEAKA 76
P++P FIR+ L D PEV++Y + L + L EA +
Sbjct: 10 PKEPTPPFIRKALIDAVPEVSQYPSALGTKALREAIS 46
>gnl|CDD|218434 pfam05103, DivIVA, DivIVA protein. The Bacillus subtilis divIVA1
mutation causes misplacement of the septum during cell
division, resulting in the formation of small,
circular, anucleate mini-cells. Inactivation of divIVA
produces a mini-cell phenotype, whereas overproduction
of DivIVA results in a filamentation phenotype. These
proteins appear to contain coiled-coils.
Length = 131
Score = 26.9 bits (60), Expect = 1.9
Identities = 14/53 (26%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 48 DFIRRNLGDERPEVAEY-EAVLQDLDEAKAELDQLTATVANLKERLSKYEVVE 99
+F ++ G + EV E+ + V++D + E ++L + L+E+L +Y+ +E
Sbjct: 10 EFKKKMRGYDPDEVDEFLDQVIKDYEALYKENEELKEEIERLEEKLEEYKELE 62
>gnl|CDD|237721 PRK14466, PRK14466, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 345
Score = 27.0 bits (60), Expect = 2.1
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 6 ETPNEKNKEAFRRYLEQSGVVDAITSA 32
E + EAFR YL GV I ++
Sbjct: 296 EGSDMARMEAFRDYLTSHGVFTTIRAS 322
>gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein,
HlyD family. Type I secretion is an ABC transport
process that exports proteins, without cleavage of any
signal sequence, from the cytosol to extracellular
medium across both inner and outer membranes. The
secretion signal is found in the C-terminus of the
transported protein. This model represents the adaptor
protein between the ATP-binding cassette (ABC) protein
of the inner membrane and the outer membrane protein,
and is called the membrane fusion protein. This model
selects a subfamily closely related to HlyD; it is
defined narrowly and excludes, for example, colicin V
secretion protein CvaA and multidrug efflux proteins
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 423
Score = 26.9 bits (60), Expect = 2.3
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 64 YEAVLQDLDEAKAELDQLTATVANLKERLSKYEV 97
E VL++L EA+A L +L + ++RL + +
Sbjct: 241 REEVLEELTEAQARLAELRERLNKARDRLQRLII 274
>gnl|CDD|234084 TIGR03007, pepcterm_ChnLen, polysaccharide chain length determinant
protein, PEP-CTERM locus subfamily. Members of this
protein family belong to the family of polysaccharide
chain length determinant proteins (pfam02706). All are
found in species that encode the PEP-CTERM/exosortase
system predicted to act in protein sorting in a number
of Gram-negative bacteria, and are found near the epsH
homolog that is the putative exosortase gene [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 498
Score = 26.9 bits (60), Expect = 2.4
Identities = 31/90 (34%), Positives = 47/90 (52%), Gaps = 8/90 (8%)
Query: 10 EKNKEAFR-RYLEQSGVVDAITSALVMLYSIEEKPEDPLDFIRRNLGDERPEVAE--YEA 66
EK +A R RY ++ V A + L EE+ E+ + +N G ER E+A Y+
Sbjct: 260 EKQLDALRLRYTDKHPDVIATKREIAQL---EEQKEE--EGSAKNGGPERGEIANPVYQQ 314
Query: 67 VLQDLDEAKAELDQLTATVANLKERLSKYE 96
+ +L EA+AE+ L A VA L R+ + E
Sbjct: 315 LQIELAEAEAEIASLEARVAELTARIERLE 344
>gnl|CDD|153097 cd00657, Ferritin_like, Ferritin-like superfamily of
diiron-containing four-helix-bundle proteins.
Ferritin-like, diiron-carboxylate proteins participate
in a range of functions including iron regulation,
mono-oxygenation, and reactive radical production. These
proteins are characterized by the fact that they
catalyze dioxygen-dependent oxidation-hydroxylation
reactions within diiron centers; one exception is
manganese catalase, which catalyzes peroxide-dependent
oxidation-reduction within a dimanganese center.
Diiron-carboxylate proteins are further characterized by
the presence of duplicate metal ligands, glutamates and
histidines (ExxH) and two additional glutamates within a
four-helix bundle. Outside of these conserved residues
there is little obvious homology. Members include
bacterioferritin, ferritin, rubrerythrin, aromatic and
alkene monooxygenase hydroxylases (AAMH), ribonucleotide
reductase R2 (RNRR2), acyl-ACP-desaturases
(Acyl_ACP_Desat), manganese (Mn) catalases,
demethoxyubiquinone hydroxylases (DMQH), DNA protecting
proteins (DPS), and ubiquinol oxidases (AOX), and the
aerobic cyclase system, Fe-containing subunit (ACSF).
Length = 130
Score = 26.3 bits (58), Expect = 2.4
Identities = 13/64 (20%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 14 EAFRRYLEQSGVV-DAITSALVMLYSIEEKPEDPLDFIRRNLGDERPEVAEYEAVLQDLD 72
+A L + G + L+ Y++ + +DP + +R L E +A Y +++ D
Sbjct: 45 DALAERLRELGGTPPLPPAHLLAAYALPKTSDDPAEALRAALEVEARAIAAYRELIEQAD 104
Query: 73 EAKA 76
+ +
Sbjct: 105 DPEL 108
>gnl|CDD|213408 cd09758, Csn2, CRISPR/Cas system-associated protein Csn2. Csn2 is
a Nmeni subtype-specific Cas protein, which may function
in the adaptation process which mediates the
incorporation of foreign nucleic acids into the
microbial host genome. Csn 2 may interact directly with
double-stranded DNA. 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. Csn2 has been predicted to be a functional
analog of Cas4 based on anti-correlated phyletic
patterns; also known as SPy1049 family.
Length = 218
Score = 26.5 bits (59), Expect = 2.5
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 62 AEYEAVLQDLDEAKAELDQLTATVANLKERLSKYEVVESD 101
A+ E L + E K+ +++LT T+ L YE +E +
Sbjct: 81 ADLEDQLNEKPEVKSMIEKLTNTITE----LIGYECLEHE 116
>gnl|CDD|215929 pfam00458, WHEP-TRS, WHEP-TRS domain.
Length = 56
Score = 25.4 bits (56), Expect = 2.7
Identities = 8/37 (21%), Positives = 17/37 (45%)
Query: 60 EVAEYEAVLQDLDEAKAELDQLTATVANLKERLSKYE 96
++A +++ L KA + + A V L +Y+
Sbjct: 4 KIAAQGDLVRKLKAKKAPKEDVDAAVKKLLALKKQYK 40
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 26.5 bits (59), Expect = 2.9
Identities = 15/71 (21%), Positives = 27/71 (38%)
Query: 21 EQSGVVDAITSALVMLYSIEEKPEDPLDFIRRNLGDERPEVAEYEAVLQDLDEAKAELDQ 80
E + L L + E+ + L I++ + E + ++L E K E +
Sbjct: 91 ELQQENQELKQELSTLEAELERLQKELARIKQLSANAIELDEENRELREELAELKQENEA 150
Query: 81 LTATVANLKER 91
L A L+E
Sbjct: 151 LEAENERLQEN 161
>gnl|CDD|235136 PRK03598, PRK03598, putative efflux pump membrane fusion protein;
Provisional.
Length = 331
Score = 26.5 bits (59), Expect = 3.0
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 69 QDLDEAKAELDQLTATVANLKERLSKYE 96
DL+ A++ DQ AT+ + +++LS+Y
Sbjct: 145 NDLENARSSRDQAQATLKSAQDKLSQYR 172
>gnl|CDD|129323 TIGR00219, mreC, rod shape-determining protein MreC. MreC (murein
formation C) is involved in the rod shape determination
in E. coli, and more generally in cell shape
determination of bacteria whether or not they are
rod-shaped. Cells defective in MreC are round. Species
with MreC include many of the Proteobacteria,
Gram-positives, and spirochetes [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 283
Score = 26.4 bits (58), Expect = 3.3
Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 4/84 (4%)
Query: 26 VDAITSALVMLYSIEEKPEDPLDFIRRNLGDERPEVAEYEAVLQDLDEAKAELDQLTATV 85
+ +A+ + Y I+ +P + D I NL D E + Q+L + +L+ LT +
Sbjct: 37 RSDMFTAVTLNYYIQNRPREVFDGISENLKDVNNLEYENYKLRQELLKKNQQLEILTQNL 96
Query: 86 ----ANLKERLSKYEVVESDQPIS 105
L+E L+ + + +
Sbjct: 97 KQENVRLRELLNSPLSSDEYKISA 120
>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein. Members of this
protein family belong to a conserved gene four-gene
neighborhood found sporadically in a phylogenetically
broad range of bacteria: Nocardia farcinica,
Symbiobacterium thermophilum, and Streptomyces
avermitilis (Actinobacteria), Geobacillus kaustophilus
(Firmicutes), Azoarcus sp. EbN1 and Ralstonia
solanacearum (Betaproteobacteria). Proteins in this
family average over 1400 amino acids in length
[Hypothetical proteins, Conserved].
Length = 1353
Score = 26.3 bits (58), Expect = 3.7
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 54 LGDERPEVAEYEAVLQDLDEAKAELDQLTATVANLKERLSKY 95
L D+ E+ + L+ LDE + EL++L A L+ L +Y
Sbjct: 217 LDDD--ELTDVADALEQLDEYRDELERLEALERALRNFLQRY 256
>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 = 3.8
Identities = 10/40 (25%), Positives = 18/40 (45%)
Query: 60 EVAEYEAVLQDLDEAKAELDQLTATVANLKERLSKYEVVE 99
VA +++ L KA D++ A VA L ++ +
Sbjct: 3 AVAAQGELVRKLKAEKASKDEIDAAVAKLLALKAQLKEAT 42
>gnl|CDD|235289 PRK04350, PRK04350, thymidine phosphorylase; Provisional.
Length = 490
Score = 26.3 bits (59), Expect = 3.9
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 9/59 (15%)
Query: 13 KEAFRRYLEQSGVVDAITSALVMLYSIEEKPEDPLDFIRRNLGDERPEVAEYEAVLQDL 71
+ AFRR G ++ A PE L IR+ + E+ + E EA+++D+
Sbjct: 57 ESAFRRLGVSEGDEVEVSHA--------PPPES-LSAIRKKIDGEKLDKEEIEAIIRDI 106
>gnl|CDD|238148 cd00244, AlgLyase, Alginate Lyase A1-III; enzymatically
depolymerizes alginate, a complex copolymer of
beta-D-mannuronate and alpha-L-guluronate, by cleaving
the beta-(1,4) glycosidic bond.
Length = 339
Score = 26.4 bits (58), Expect = 4.0
Identities = 10/41 (24%), Positives = 18/41 (43%)
Query: 5 PETPNEKNKEAFRRYLEQSGVVDAITSALVMLYSIEEKPED 45
T NE ++AFR + + ++ VM Y + +P
Sbjct: 52 RATLNEPAEKAFRDFTKDITTLERGYVKTVMQYMRDGRPVY 92
>gnl|CDD|130529 TIGR01462, greA, transcription elongation factor GreA. The GreA
and GreB transcription elongation factors enable to
continuation of RNA transcription past template-encoded
arresting sites. Among the Proteobacteria, distinct
clades of GreA and GreB are found. GreA differs
functionally in that it releases smaller
oligonucleotides. Because members of the family outside
the Proteobacteria resemble GreA more closely than GreB,
the GreB clade (TIGR01461) forms a plausible outgroup
and the remainder of the GreA/B family, included in this
model, is designated GreA. In the Chlamydias and some
spirochetes, the region described by This model is found
as the C-terminal region of a much larger protein
[Transcription, Transcription factors].
Length = 151
Score = 26.0 bits (58), Expect = 4.0
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 50 IRRNLGDERPEVAEYEAVLQDLDEAKAELDQLTATVANLKERLSKYEVVESDQ 102
R GD E AEY A AK E +A L++ L+ +V++ +
Sbjct: 31 EAREHGDLS-ENAEYHA-------AKEEQGFNEGRIAELEDLLANAQVIDDSK 75
>gnl|CDD|147395 pfam05186, Dpy-30, Dpy-30 motif. This motif is found in a wide
variety of domain contexts. It is found in the Dpy-30
proteins hence the motifs name. It is about 40 residues
long and is probably fomed of two alpha-helices. It may
be a dimerisation motif analogous to pfam02197 (Bateman
A pers obs).
Length = 42
Score = 24.5 bits (54), Expect = 4.1
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 17 RRYLEQSGVVDAITSALVMLYSIEEKPEDPLDFI 50
R+YL + V + L L +E+PEDP++F+
Sbjct: 3 RQYLNDT-VAPILLQGLTEL--AKERPEDPIEFL 33
>gnl|CDD|180379 PRK06065, PRK06065, acetyl-CoA acetyltransferase; Provisional.
Length = 392
Score = 26.3 bits (58), Expect = 4.1
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 49 FIRRNLGDERPEVAEYEAVLQDLDEAKAELDQLTATV 85
F RR L E P+ +EA + LDEA EL + V
Sbjct: 21 FRRRLL--ETPQELAWEAASKALDEAGLELKDIDCVV 55
>gnl|CDD|222426 pfam13870, DUF4201, Domain of unknown function (DUF4201). This is
a family of coiled-coil proteins from eukaryotes. The
function is not known.
Length = 177
Score = 25.6 bits (57), Expect = 4.7
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 64 YEAVLQDLDEAKAELDQLTATVANLKERLSKYE 96
A+L D D+ ++++ +V L+ + E
Sbjct: 140 VPALLYDYDKTVEKVEEKRKSVEKLRRKHKILE 172
>gnl|CDD|184688 PRK14457, PRK14457, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 345
Score = 25.7 bits (57), Expect = 5.5
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 8 PNEKNKEAFRRYLEQSGV 25
P+ K +AF+R LEQ GV
Sbjct: 303 PSPKRIQAFQRVLEQRGV 320
>gnl|CDD|237616 PRK14127, PRK14127, cell division protein GpsB; Provisional.
Length = 109
Score = 25.4 bits (56), Expect = 5.6
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 64 YEAVLQDLDEAKAELDQLTATVANLKERLSKYEVVES 100
YEA ++++E + E +L A V L +++S S
Sbjct: 39 YEAFQKEIEELQQENARLKAQVDELTKQVSVGASSSS 75
>gnl|CDD|219780 pfam08286, Spc24, Spc24 subunit of Ndc80. Spc24 is a component of
the evolutionarily conserved kinetochore-associated
Ndc80 complex and is involved in chromosome segregation.
Length = 117
Score = 25.4 bits (56), Expect = 5.9
Identities = 12/40 (30%), Positives = 25/40 (62%)
Query: 69 QDLDEAKAELDQLTATVANLKERLSKYEVVESDQPISDDN 108
++L++ ++EL+ L + + LKERL + E E + D++
Sbjct: 13 KELNDLESELNNLQSELEELKERLEELEEQEVEGDEVDED 52
>gnl|CDD|219855 pfam08463, EcoEI_R_C, EcoEI R protein C-terminal. The restriction
enzyme EcoEI recognises 5'-GAGN(7)ATGC-3' and is
composed of the three proteins R, M, and S. The domain
described here is found at the C-terminus of the R
protein (HsdR) which is required for both nuclease and
ATPase activity.
Length = 162
Score = 25.3 bits (56), Expect = 6.1
Identities = 13/67 (19%), Positives = 32/67 (47%)
Query: 41 EKPEDPLDFIRRNLGDERPEVAEYEAVLQDLDEAKAELDQLTATVANLKERLSKYEVVES 100
EK ED L+ R + + ++ + + + + +L +L + + +E S+ + E+
Sbjct: 1 EKAEDYLEKFREYIREHFDDIEALQKLWNNPPLTREDLKELEEKLIDDEELFSEERLQEA 60
Query: 101 DQPISDD 107
+ I+ D
Sbjct: 61 YEDIAAD 67
>gnl|CDD|212587 cd11718, THUMP_SPOUT, THUMP domain associated with SPOUT RNA
Methylases. Members of this archaeal protein family
are characterized by containing an N-terminal THUMP
domain and a C-terminal SPOUT RNA methyltransferase
domain. No functional information is available The
THUMP domain is named after thiouridine synthases,
methylases and PSUSs. The domain consists of about 110
amino acid residues. It is predicted to be an
RNA-binding domain and probably functions by delivering
a variety of RNA modification enzymes to their targets.
Length = 145
Score = 25.3 bits (56), Expect = 6.1
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 3/51 (5%)
Query: 46 PLDFIRRNLGDERPEVAEYEAVLQDLDEAKAELDQLTATVANLKERLSKYE 96
+ + L PEV E V+ E KA+LD++ + + +S+ E
Sbjct: 41 SDEDKKDELALRVPEV---ERVIPVDAEVKADLDEIVRVAEEIAKHISEGE 88
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 25.8 bits (57), Expect = 6.7
Identities = 9/36 (25%), Positives = 18/36 (50%)
Query: 61 VAEYEAVLQDLDEAKAELDQLTATVANLKERLSKYE 96
+ EYE V + +E K++ + L L E + + +
Sbjct: 969 IEEYEEVEERYEELKSQREDLEEAKEKLLEVIEELD 1004
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 25.8 bits (57), Expect = 6.7
Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 3/92 (3%)
Query: 13 KEAFRRYLEQSGVVDAITSALVMLYSIEEKPEDPLDFIRRNLGDERPEVAEYEAVLQDLD 72
E + + S + I + L EEK ++ L+ + +L E+ ++ L++L+
Sbjct: 705 DELSQELSDASRKIGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELE 764
Query: 73 EAKAELDQLTATVANLKERLSKYEVVESDQPI 104
A +++L + L+E L+ E S I
Sbjct: 765 ---ARIEELEEDLHKLEEALNDLEARLSHSRI 793
Score = 25.4 bits (56), Expect = 9.0
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 63 EYEAVLQDLDEAKAELDQLTATVANLKERLSKYE 96
EYE VL+ LDE K + +L + ER+ +YE
Sbjct: 980 EYEEVLKRLDELKEKRAKLEEERKAILERIEEYE 1013
>gnl|CDD|225471 COG2919, COG2919, Septum formation initiator [Cell division and
chromosome partitioning].
Length = 117
Score = 25.0 bits (55), Expect = 6.8
Identities = 7/36 (19%), Positives = 18/36 (50%)
Query: 61 VAEYEAVLQDLDEAKAELDQLTATVANLKERLSKYE 96
A+ + + + +AEL++L+A L+ + +
Sbjct: 49 AADVLQLQRQIAAQQAELEKLSARNTALEAEIKDLK 84
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 25.5 bits (56), Expect = 8.1
Identities = 9/59 (15%), Positives = 26/59 (44%), Gaps = 9/59 (15%)
Query: 62 AEYEAVLQDLDEAKAELDQLTATVANLKERLSKYE---------VVESDQPISDDNSAI 111
E A+ + + E + + +L + +L+ ++ E + + + I+D N+ +
Sbjct: 45 KEIAALEKKIREQQDQRAKLEKQLKSLETEIASLEAQLIETADDLKKLRKQIADLNARL 103
>gnl|CDD|218689 pfam05681, Fumerase, Fumarate hydratase (Fumerase). This family
consists of several bacterial fumarate hydratase
proteins FumA and FumB. Fumarase, or fumarate hydratase
(EC 4.2.1.2), is a component of the citric acid cycle.
In facultative anaerobes such as Escherichia coli,
fumarase also engages in the reductive pathway from
oxaloacetate to succinate during anaerobic growth. Three
fumarases, FumA, FumB, and FumC, have been reported in
E. coli. fumA and fumB genes are homologous and encode
products of identical sizes which form thermolabile
dimers of Mr 120,000. FumA and FumB are class I enzymes
and are members of the iron-dependent hydrolases, which
include aconitase and malate hydratase. The active FumA
contains a 4Fe-4S centre, and it can be inactivated upon
oxidation to give a 3Fe-4S centre.
Length = 271
Score = 25.1 bits (56), Expect = 9.5
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 45 DPLDFIRRNLGDERPEVAEYEAV 67
DPL+ R+N GD P V E V
Sbjct: 104 DPLE--RKNTGDNTPAVIHIEIV 124
>gnl|CDD|216037 pfam00637, Clathrin, Region in Clathrin and VPS. Each region is
about 140 amino acids long. The regions are composed of
multiple alpha helical repeats. They occur in the arm
region of the Clathrin heavy chain.
Length = 143
Score = 24.9 bits (55), Expect = 9.6
Identities = 12/37 (32%), Positives = 23/37 (62%)
Query: 28 AITSALVMLYSIEEKPEDPLDFIRRNLGDERPEVAEY 64
A+ +AL+ LY+ E PE +F+++N + +VA+
Sbjct: 43 ALQTALLELYAKYEDPEKLEEFLKKNNNYDLEKVAKL 79
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
0.309 0.129 0.340
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,753,808
Number of extensions: 516658
Number of successful extensions: 1187
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1166
Number of HSP's successfully gapped: 206
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.3 bits)