RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5453
(138 letters)
>gnl|CDD|192486 pfam10224, DUF2205, Predicted coiled-coil protein (DUF2205). This
entry represent a highly conserved 100 residue region
which is likely to be a coiled-coil structure. The exact
function is unknown.
Length = 80
Score = 103 bits (259), Expect = 3e-30
Identities = 53/82 (64%), Positives = 63/82 (76%), Gaps = 2/82 (2%)
Query: 57 SSPGRNSLDPDVSPDEQEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQ 116
SP R+S D+ E+E + RLI Q LELQ++L+DLSQRV++VKEENL+LRSENQ L Q
Sbjct: 1 MSPRRDS--EDLEALEKEARQRLIEQALELQDSLEDLSQRVEAVKEENLKLRSENQFLQQ 58
Query: 117 YIENLMSASSVFQSTSPKSGKK 138
YIENLMS SSV QSTSPK K
Sbjct: 59 YIENLMSNSSVTQSTSPKIKNK 80
>gnl|CDD|218915 pfam06156, DUF972, Protein of unknown function (DUF972). This
family consists of several hypothetical bacterial
sequences. The function of this family is unknown.
Length = 106
Score = 32.7 bits (75), Expect = 0.015
Identities = 17/56 (30%), Positives = 28/56 (50%)
Query: 82 QVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIENLMSASSVFQSTSPKSGK 137
Q+ +L L +L Q++ + EEN LR EN+ L + +E L + K G+
Sbjct: 16 QLNQLLAELGELKQQLAELLEENAELRIENEHLRERLEELEQEQKEKEKGKKKLGE 71
>gnl|CDD|237560 PRK13922, PRK13922, rod shape-determining protein MreC;
Provisional.
Length = 276
Score = 32.3 bits (74), Expect = 0.050
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 73 QEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIENLMSASSVFQSTS 132
+EE L ++LEL++ L Q ++ ++ EN RLR + ++A + +S
Sbjct: 75 REENEELKKELLELESRL----QELEQLEAENARLRELLNLKESLDYQFITARVISRSPD 130
Query: 133 P 133
P
Sbjct: 131 P 131
Score = 25.7 bits (57), Expect = 8.6
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 77 ARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQY 117
+S V E +L DL + + +K+E L L S Q L Q
Sbjct: 58 REFVSGVFESLASLFDLREENEELKKELLELESRLQELEQL 98
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 31.3 bits (72), Expect = 0.12
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 73 QEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVL 114
+E + L Q+ +L+ L DL + ++ E RL+SE + L
Sbjct: 7 EERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKL 48
Score = 28.6 bits (65), Expect = 1.1
Identities = 13/52 (25%), Positives = 23/52 (44%)
Query: 74 EEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIENLMSAS 125
E L + EL+ + L ++ ++ EN +L E + L +E L S
Sbjct: 1 ERLEALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKSPP 52
>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 = 30.4 bits (69), Expect = 0.21
Identities = 14/50 (28%), Positives = 25/50 (50%)
Query: 81 SQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIENLMSASSVFQS 130
++ ELQ L +L + + ++E+ L+ ENQ L Q + L + Q
Sbjct: 66 ERLPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQK 115
Score = 29.6 bits (67), Expect = 0.36
Identities = 12/44 (27%), Positives = 22/44 (50%)
Query: 71 DEQEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVL 114
E +L + +EL +L + + +K+EN L +EN+ L
Sbjct: 115 KELARIKQLSANAIELDEENRELREELAELKQENEALEAENERL 158
Score = 29.6 bits (67), Expect = 0.42
Identities = 16/54 (29%), Positives = 28/54 (51%)
Query: 73 QEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIENLMSASS 126
Q+E A L ++ ELQ L +L Q +K+E L +E + L + + + S+
Sbjct: 72 QQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSA 125
Score = 26.5 bits (59), Expect = 4.3
Identities = 8/34 (23%), Positives = 15/34 (44%)
Query: 73 QEEKARLISQVLELQNTLDDLSQRVDSVKEENLR 106
EE L ++ EL+ + L + ++E R
Sbjct: 131 DEENRELREELAELKQENEALEAENERLQENEQR 164
>gnl|CDD|234342 TIGR03752, conj_TIGR03752, integrating conjugative element protein,
PFL_4705 family. Members of this protein family are
found occasionally on plasmids such as the Pseudomonas
putida toluene catabolic TOL plasmid pWWO_p085. Usually,
however, they are found on the bacterial main chromosome
in regions flanked by markers of conjugative transfer
and/or transposition [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 472
Score = 30.8 bits (70), Expect = 0.22
Identities = 21/89 (23%), Positives = 40/89 (44%), Gaps = 11/89 (12%)
Query: 47 SISSSFTNSSSSPGRNSLDPDVSPDEQEEK-----------ARLISQVLELQNTLDDLSQ 95
I S + S P ++ ++SP+E + L+++V EL+ L L
Sbjct: 21 GIKSFSGSGSPEPTSDTALAELSPEELKALGIEGDTPADTLRTLVAEVKELRKRLAKLIS 80
Query: 96 RVDSVKEENLRLRSENQVLGQYIENLMSA 124
+++K EN RL+ Q + Q I+ + +
Sbjct: 81 ENEALKAENERLQKREQSIDQQIQQAVQS 109
>gnl|CDD|162098 TIGR00900, 2A0121, H+ Antiporter protein. [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 365
Score = 30.4 bits (69), Expect = 0.29
Identities = 9/34 (26%), Positives = 19/34 (55%)
Query: 51 SFTNSSSSPGRNSLDPDVSPDEQEEKARLISQVL 84
+ + +P ++ PD+ P+EQ +A +SQ +
Sbjct: 103 AIAQAFFTPAYQAMLPDLVPEEQLTQANSLSQAV 136
>gnl|CDD|197664 smart00338, BRLZ, basic region leucin zipper.
Length = 65
Score = 28.3 bits (64), Expect = 0.30
Identities = 11/34 (32%), Positives = 23/34 (67%)
Query: 90 LDDLSQRVDSVKEENLRLRSENQVLGQYIENLMS 123
+++L ++V+ ++ EN RL+ E + L + +E L S
Sbjct: 28 IEELERKVEQLEAENERLKKEIERLRRELEKLKS 61
Score = 28.3 bits (64), Expect = 0.35
Identities = 9/41 (21%), Positives = 22/41 (53%)
Query: 73 QEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQV 113
+ E L +V +L+ + L + ++ ++ E +L+SE +
Sbjct: 25 KAEIEELERKVEQLEAENERLKKEIERLRRELEKLKSELEE 65
>gnl|CDD|203244 pfam05400, FliT, Flagellar protein FliT. This family contains
several bacterial flagellar FliT proteins. The flagellar
proteins FlgN and FliT have been proposed to act as
substrate specific export chaperones, facilitating
incorporation of the enterobacterial hook-associated
axial proteins (HAPs) FlgK/FlgL and FliD into the
growing flagellum. In Salmonella typhimurium flgN and
fliT mutants, the export of target HAPs is reduced,
concomitant with loss of unincorporated flagellin into
the surrounding medium.
Length = 82
Score = 28.8 bits (65), Expect = 0.31
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 61 RNSLDPDVSPDEQEEKARLISQVLEL-QNTLDDLSQRVDSVKEENLRLRSENQVLGQY 117
+ +SP E EEK L+ ++L L R+D + + + R + + Y
Sbjct: 25 ERLREAPLSPPESEEKRELLRRILANDAEIRALLQPRLDELSQLLGQARRQKKANNAY 82
>gnl|CDD|190534 pfam03131, bZIP_Maf, bZIP Maf transcription factor. Maf
transcription factors contain a conserved basic region
leucine zipper (bZIP) domain, which mediates their
dimerisation and DNA binding property. Thus, this family
is probably related to pfam00170.
Length = 93
Score = 28.5 bits (64), Expect = 0.51
Identities = 15/44 (34%), Positives = 21/44 (47%)
Query: 80 ISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIENLMS 123
+ Q EL+ L Q+V+ +K+E RL E L E L S
Sbjct: 50 VQQRHELEKEKSQLQQQVEQLKQEVSRLARERDALKAKYEALQS 93
>gnl|CDD|225803 COG3264, COG3264, Small-conductance mechanosensitive channel [Cell
envelope biogenesis, outer membrane].
Length = 835
Score = 29.7 bits (67), Expect = 0.53
Identities = 14/64 (21%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 72 EQEEKARLISQVL----ELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIENLMSASSV 127
E E +A LI Q L +L L+ ++R++++ ++ +L + L Q + +V
Sbjct: 52 EAELQAELIQQELAINDQLSQALNQQTERLNALASDDRQLANLLLQLLQSSRTIREQIAV 111
Query: 128 FQST 131
+ +
Sbjct: 112 LRGS 115
>gnl|CDD|218184 pfam04632, FUSC, Fusaric acid resistance protein family. This
family includes a conserved region found in two proteins
associated with fusaric acid resistance,from
Burkholderia cepacia and Klebsiella oxytoca. These
proteins are likely to be membrane transporter proteins.
Length = 649
Score = 29.1 bits (66), Expect = 0.71
Identities = 11/67 (16%), Positives = 26/67 (38%), Gaps = 7/67 (10%)
Query: 64 LDPDVSPDEQEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIENLMS 123
L +E + RL + +L L+ + E+ R R+ N+ L + +++
Sbjct: 177 LAGAGGAAAREARLRLAADILALEALRSHAAF-------ESPRGRARNRALRRLNARMLA 229
Query: 124 ASSVFQS 130
+ +
Sbjct: 230 LLARLSA 236
>gnl|CDD|224705 COG1792, MreC, Cell shape-determining protein [Cell envelope
biogenesis, outer membrane].
Length = 284
Score = 28.9 bits (65), Expect = 0.91
Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 78 RLISQVLELQNT-LDDLSQRVDSVKEENLRLRSE-NQVLGQYIENLMSASSVFQSTSPKS 135
L ++ L+ + L+ L + V+S++EEN RL+ + + ++A + +S P S
Sbjct: 72 ALENEELKKELAELEQLLEEVESLEEENKRLKELLDFKESSSDYDPIAARVISRSPDPWS 131
>gnl|CDD|183876 PRK13169, PRK13169, DNA replication intiation control protein YabA;
Reviewed.
Length = 110
Score = 27.9 bits (63), Expect = 1.0
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 77 ARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVL 114
L + L L L +++ + EEN LR EN L
Sbjct: 11 DDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKL 48
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 28.7 bits (64), Expect = 1.1
Identities = 18/71 (25%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 64 LDPDVSPDEQEEKARLISQVLELQNTLDDLSQ-RVDSVKEENLRLRSENQVLGQYIENLM 122
L P+ S ++ K L++ EL + DLS +V+ ++++ L+L+ + Q L +I +
Sbjct: 285 LCPEASTHVEQMKDMLLAISNELLDNAADLSPDQVEQLRQDRLQLKKQIQQLEIHIRDKE 344
Query: 123 SASSVFQSTSP 133
S F +++
Sbjct: 345 RQKSQFSASTA 355
>gnl|CDD|226513 COG4026, COG4026, Uncharacterized protein containing TOPRIM domain,
potential nuclease [General function prediction only].
Length = 290
Score = 28.3 bits (63), Expect = 1.3
Identities = 13/51 (25%), Positives = 29/51 (56%)
Query: 71 DEQEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIENL 121
+ Q+EK L+ ++ EL+ +++ +R+ ++ EN RL + L + +L
Sbjct: 146 ELQKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKLPGEVYDL 196
>gnl|CDD|220368 pfam09730, BicD, Microtubule-associated protein Bicaudal-D. BicD
proteins consist of three coiled-coiled domains and are
involved in dynein-mediated minus end-directed transport
from the Golgi apparatus to the endoplasmic reticulum
(ER). For full functioning they bind with GSK-3beta
pfam05350 to maintain the anchoring of microtubules to
the centromere. It appears that amino-acid residues
437-617 of BicD and the kinase activity of GSK-3 are
necessary for the formation of a complex between BicD
and GSK-3beta in intact cells.
Length = 711
Score = 28.3 bits (63), Expect = 1.3
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 77 ARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIENL 121
A + ++LELQ L L + +V+ EN RL S +Q L + E L
Sbjct: 30 AYYLQRILELQAELKQLRAELSNVQAENERLSSLSQELKEENEML 74
>gnl|CDD|218681 pfam05667, DUF812, Protein of unknown function (DUF812). This
family consists of several eukaryotic proteins of
unknown function.
Length = 536
Score = 27.8 bits (62), Expect = 1.9
Identities = 13/90 (14%), Positives = 32/90 (35%), Gaps = 2/90 (2%)
Query: 21 PQAIISDEVESSQNSEGPIRADHSLDSISSSFTNSSSSPGRNSLDPDVSPDEQEEKARLI 80
+ D + S + + ++++ ++ +E K R
Sbjct: 212 GSSSADDLADLLSKFRLDSWDKGSRFTRTEKVEQAATAAA-EVPPAEMDTEEDRTKERE- 269
Query: 81 SQVLELQNTLDDLSQRVDSVKEENLRLRSE 110
+++ LQ +D+L ++ V E L S+
Sbjct: 270 AELEALQEQIDELESSIEEVLSEIKALASK 299
>gnl|CDD|206365 pfam14197, Cep57_CLD_2, Centrosome localisation domain of PPC89.
The N-terminal region of the fission yeast spindle pole
body protein PPC89 has low similarity to the human Cep57
protein. The CLD or centrosome localisation domain of
Cep57 and PPC89 is found at the N-terminus. This region
localises to the centrosome internally to gamma-tubulin,
suggesting that it is either on both centrioles or on a
centromatrix component. This N-terminal region can also
multimerise with the N-terminus of other Cep57
molecules. The C-terminal part, Family Cep57_MT_bd,
pfam06657, is the microtubule-binding region of Cep57
and PPC89.
Length = 69
Score = 26.1 bits (58), Expect = 2.0
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 78 RLISQVLELQNTLDDLSQRVDSVKEENLRLRSEN 111
RL ++ L L+N LD +++V + E RL E
Sbjct: 2 RLEAENLTLRNRLDSATRKVAVHEIELKRLNRER 35
>gnl|CDD|226873 COG4467, COG4467, Regulator of replication initiation timing
[Replication, recombination, and repair].
Length = 114
Score = 27.1 bits (60), Expect = 2.1
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 78 RLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVL 114
L Q+ L L L Q + S+ EEN LR EN+ L
Sbjct: 12 NLEEQLGVLLAELGGLKQHLGSLVEENTALRLENEKL 48
>gnl|CDD|218311 pfam04888, SseC, Secretion system effector C (SseC) like family.
SseC is a secreted protein that forms a complex together
with SecB and SecD on the surface of Salmonella. All
these proteins are secreted by the type III secretion
system. Many mucosal pathogens use type III secretion
systems for the injection of effector proteins into
target cells. SecB, SseC and SecD are inserted into the
target cell membrane. where they form a small pore or
translocon. In addition to SseC, this family includes
the bacterial secreted proteins PopB, PepB, YopB and
EspD which are thought to be directly involved in pore
formation, and type III secretion system translocon.
Length = 303
Score = 27.4 bits (61), Expect = 2.4
Identities = 11/62 (17%), Positives = 26/62 (41%), Gaps = 3/62 (4%)
Query: 71 DEQEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIENLMSASSVFQS 130
Q+E +L + + L+ ++ L + +KEE + + Q ++++ A
Sbjct: 238 VLQKEAGKLEADLALLRAEMEQLQAVIKQLKEE---FKKLQEQFQQAMKSISQAIQQSGD 294
Query: 131 TS 132
T
Sbjct: 295 TL 296
>gnl|CDD|218816 pfam05936, DUF876, Bacterial protein of unknown function (DUF876).
This family consists of a series of hypothetical
bacterial sequences of unknown function.
Length = 427
Score = 27.6 bits (62), Expect = 2.6
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 66 PDVSPDEQEE-KARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYI 118
+VS DE AR ++ E+++ + V NLRL E++ L Y+
Sbjct: 93 NNVSEDEAAARLARYRAEEEEVRDLNSGGGEAEIQVARLNLRLLLESEDLSGYV 146
>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain. Axonemal
dynein light chain proteins play a dynamic role in
flagellar and cilia motility. Eukaryotic cilia and
flagella are complex organelles consisting of a core
structure, the axoneme, which is composed of nine
microtubule doublets forming a cylinder that surrounds a
pair of central singlet microtubules. This
ultra-structural arrangement seems to be one of the most
stable micro-tubular assemblies known and is responsible
for the flagellar and ciliary movement of a large number
of organisms ranging from protozoan to mammals. This
light chain interacts directly with the N-terminal half
of the heavy chains.
Length = 189
Score = 27.2 bits (61), Expect = 2.7
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 8/56 (14%)
Query: 74 EEKARLISQVLELQNTLDDLSQRV----DSV----KEENLRLRSENQVLGQYIENL 121
EEK L +V EL+ L+ + +R +E L+ +NQ L +E +
Sbjct: 134 EEKEELEKRVAELEAKLEAIEKREEEERQIEEKRHADEIAFLKKQNQQLKSQLEQI 189
>gnl|CDD|216301 pfam01105, EMP24_GP25L, emp24/gp25L/p24 family/GOLD. Members of
this family are implicated in bringing cargo forward
from the ER and binding to coat proteins by their
cytoplasmic domains. This domain corresponds closely to
the beta-strand rich GOLD domain described in. The GOLD
domain is always found combined with lipid- or
membrane-association domains.
Length = 178
Score = 26.8 bits (60), Expect = 2.9
Identities = 13/58 (22%), Positives = 27/58 (46%)
Query: 52 FTNSSSSPGRNSLDPDVSPDEQEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRS 109
F+NS S+ ++ D+ E+ + ++ L+ L L +++ +K E LR
Sbjct: 78 FSNSFSTFSSKTVSFDIKVGEEAKDIAKKEKLDPLEEELKKLEDQLNDIKREQKYLRE 135
>gnl|CDD|221101 pfam11382, DUF3186, Protein of unknown function (DUF3186). This
bacterial family of proteins has no known function.
Length = 307
Score = 27.3 bits (61), Expect = 3.0
Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 86 LQNTL-DDLSQRVDSVKEENLRLRSENQVLGQYIEN 120
LQ L L ++ EN RLR+E + L +
Sbjct: 29 LQENLLSGLEDEFSDLRTENDRLRAEREALNEQASA 64
>gnl|CDD|221400 pfam12059, DUF3540, Protein of unknown function (DUF3540). This
family of proteins is functionally uncharacterized. This
protein is found in bacteria. Proteins in this family
are typically between 212 to 238 amino acids in length.
This protein has a conserved SCL sequence motif.
Length = 195
Score = 27.0 bits (60), Expect = 3.1
Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 23/97 (23%)
Query: 39 IRADHSLDSISSSFTNSSSSPGRNSLDPDVSPDE---QEEKARLISQVLELQNTLDDLSQ 95
+ + L S S+ + + + + Q E RL+++ LE D L+Q
Sbjct: 85 LASPQRLSLESPELRLSARQADLTTEELNAHSQKMKGQVETVRLVARTLES--VADRLTQ 142
Query: 96 R----------VDSVK--------EENLRLRSENQVL 114
R D V+ E+ LR+ ++N V+
Sbjct: 143 RAKNSFRTVEGTDQVRAGNLDQTAEQTLRVHAKNTVI 179
>gnl|CDD|216560 pfam01544, CorA, CorA-like Mg2+ transporter protein. The CorA
transport system is the primary Mg2+ influx system of
Salmonella typhimurium and Escherichia coli. CorA is
virtually ubiquitous in the Bacteria and Archaea. There
are also eukaryotic relatives of this protein. The
family includes the MRS2 protein from yeast that is
thought to be an RNA splicing protein. However its
membership of this family suggests that its effect on
splicing is due to altered magnesium levels in the cell.
Length = 291
Score = 27.3 bits (61), Expect = 3.1
Identities = 11/51 (21%), Positives = 24/51 (47%)
Query: 62 NSLDPDVSPDEQEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQ 112
+ P + +E+E L+ ++ L + L +R+ S+++ L L S
Sbjct: 179 SDDGPLIDEEEKEYLRDLLDELERLLEMAEILRERLRSLQDAYLSLLSNRL 229
>gnl|CDD|182548 PRK10559, PRK10559, p-hydroxybenzoic acid efflux subunit AaeA;
Provisional.
Length = 310
Score = 27.0 bits (60), Expect = 3.8
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 44 SLDSISSSFTNSSSSPGRNSLDPDVSPDEQEEKARLISQV 83
++DS+++ TNSSS+ + + D E RL +V
Sbjct: 225 TVDSVAAGVTNSSSTRDSKGM---ATIDSNLEWVRLAQRV 261
>gnl|CDD|234421 TIGR03970, Rv0697, dehydrogenase, Rv0697 family. This model
describes a set of dehydrogenases belonging to the
glucose-methanol-choline oxidoreductase (GMC
oxidoreductase) family. Members of the present family
are restricted to Actinobacterial genome contexts
containing also members of families TIGR03962 and
TIGR03969 (the mycofactocin system), and are proposed to
be uniform in function.
Length = 487
Score = 27.1 bits (60), Expect = 3.9
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 8/44 (18%)
Query: 35 SEGPI--RADHSLDSISSSFTNSSSSPG------RNSLDPDVSP 70
+ GPI R LD IS++F ++ G N PD
Sbjct: 136 TAGPIPVRRTAELDGISAAFVAAALGAGFGWIADLNGSGPDAPT 179
>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 = 27.0 bits (60), Expect = 4.5
Identities = 13/51 (25%), Positives = 27/51 (52%)
Query: 71 DEQEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIENL 121
+E++ + +L + EL+ L+DL ++ V +E R E + + +E L
Sbjct: 347 EERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYREKLEKL 397
>gnl|CDD|215198 PLN02348, PLN02348, phosphoribulokinase.
Length = 395
Score = 26.7 bits (59), Expect = 4.5
Identities = 25/82 (30%), Positives = 39/82 (47%), Gaps = 16/82 (19%)
Query: 25 ISDEVESSQNSEGPIRAD-----HSLDSISSSFTNSSSSPGRNSLDPDVSPDEQEEKARL 79
ISD+V+ + I+ D HSL+SI +S + P D D D Q++ A +
Sbjct: 191 ISDDVKFAWK----IQRDMAERGHSLESIKASI--EARKP-----DFDAYIDPQKQYADV 239
Query: 80 ISQVLELQNTLDDLSQRVDSVK 101
+ +VL Q DD +V V+
Sbjct: 240 VIEVLPTQLIPDDNEGKVLRVR 261
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 26.6 bits (59), Expect = 4.8
Identities = 14/66 (21%), Positives = 24/66 (36%), Gaps = 2/66 (3%)
Query: 67 DVSPDEQEEKARLISQVLELQNTLDDLSQRVDSVKEENLR-LRSENQVLGQYIENLMSAS 125
+ + + L+L+ + DL + V EENL L E L +++ L
Sbjct: 53 PLKDTGGKPDVPPSKEFLDLEEEILDLEAEIKEV-EENLESLEKEINELEEWLNVLDEEK 111
Query: 126 SVFQST 131
S
Sbjct: 112 SFLDEN 117
>gnl|CDD|201054 pfam00170, bZIP_1, bZIP transcription factor. The Pfam entry
includes the basic region and the leucine zipper region.
Length = 64
Score = 25.0 bits (55), Expect = 5.3
Identities = 11/37 (29%), Positives = 21/37 (56%)
Query: 90 LDDLSQRVDSVKEENLRLRSENQVLGQYIENLMSASS 126
+++L ++V ++ EN LRSE + L + L S +
Sbjct: 28 IEELEEKVKELEAENKTLRSELERLKKECAKLKSENE 64
>gnl|CDD|216105 pfam00761, Polyoma_coat2, Polyomavirus coat protein.
Length = 322
Score = 26.3 bits (58), Expect = 5.6
Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 2/70 (2%)
Query: 66 PDVSPDEQEEKARLISQVLELQNTLDDLSQRVDS--VKEENLRLRSENQVLGQYIENLMS 123
P ++P + + AR + L ++ + DS K++ L G+YIE +
Sbjct: 222 PPINPIQVRQVARREGTYVNLGHSYPESIDDADSIQEKKQRKELGGPEVQSGEYIEKYTA 281
Query: 124 ASSVFQSTSP 133
Q +P
Sbjct: 282 PGGANQRVAP 291
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 26.7 bits (59), Expect = 5.7
Identities = 14/63 (22%), Positives = 26/63 (41%)
Query: 64 LDPDVSPDEQEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIENLMS 123
L SP + L+ + E DDL QR+ +++ + R E + L + + M
Sbjct: 726 LGGRASPAGALDALELLQNIKEKLQAADDLRQRIAAMERDLARFEEEVEALAEAVAPEML 785
Query: 124 ASS 126
+
Sbjct: 786 GTP 788
>gnl|CDD|237717 PRK14455, PRK14455, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 356
Score = 26.5 bits (59), Expect = 5.8
Identities = 7/22 (31%), Positives = 15/22 (68%)
Query: 79 LISQVLELQNTLDDLSQRVDSV 100
+++QV+ +Q LD+ +RV +
Sbjct: 142 IVAQVMLVQKYLDETEERVSHI 163
>gnl|CDD|217933 pfam04156, IncA, IncA protein. Chlamydia trachomatis is an
obligate intracellular bacterium that develops within a
parasitophorous vacuole termed an inclusion. The
inclusion is non-fusogenic with lysosomes but intercepts
lipids from a host cell exocytic pathway. Initiation of
chlamydial development is concurrent with modification
of the inclusion membrane by a set of C.
trachomatis-encoded proteins collectively designated
Incs. One of these Incs, IncA, is functionally
associated with the homotypic fusion of inclusions. This
family probably includes members of the wider Inc family
rather than just IncA.
Length = 186
Score = 26.3 bits (58), Expect = 5.9
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 70 PDEQEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVL 114
+ Q E + L Q+ ELQ L+DL +R+ ++ E L+ + Q+L
Sbjct: 75 EELQGELSELKQQLSELQEELEDLEERIAELESELEDLKEDLQLL 119
>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing
protein; Provisional.
Length = 697
Score = 26.4 bits (58), Expect = 6.1
Identities = 16/66 (24%), Positives = 24/66 (36%), Gaps = 4/66 (6%)
Query: 19 DDPQAIISDEVESSQNSEGPIRADHSLDSISSSFTNSSSSPGRNSLDPDVSPDEQEEKAR 78
+ S + Q+ E + D + IS N L PDV DE++ R
Sbjct: 572 KQDHSFFSGDRLHPQSREIYQKLDELMKEISEY----GYVAEENELLPDVDEDEEKVSGR 627
Query: 79 LISQVL 84
S+ L
Sbjct: 628 YHSEKL 633
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 26.6 bits (59), Expect = 6.2
Identities = 14/49 (28%), Positives = 31/49 (63%)
Query: 73 QEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIENL 121
+EE A L +++ E++N L++L + ++S++E RL + L + ++ L
Sbjct: 382 REELAELEAELAEIRNELEELKREIESLEERLERLSERLEDLKEELKEL 430
>gnl|CDD|169691 PRK09173, PRK09173, F0F1 ATP synthase subunit B; Validated.
Length = 159
Score = 25.9 bits (57), Expect = 6.3
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 89 TLDDLSQRVDSVKEENLRLRSENQ-VLGQY 117
+LD + R+ + E RLR E Q +L +Y
Sbjct: 30 SLDARADRIKNELAEARRLREEAQQLLAEY 59
>gnl|CDD|132396 TIGR03353, VI_chp_4, type VI secretion protein, VC_A0114 family.
Work by Mougous, et al. (2006), describes IAHP-related
loci as a type VI secretion system (PMID:16763151). This
protein family is associated with type VI secretion
loci, although not treated explicitly by Mougous, et al
[Protein fate, Protein and peptide secretion and
trafficking, Cellular processes, Pathogenesis].
Length = 439
Score = 26.4 bits (59), Expect = 6.4
Identities = 13/63 (20%), Positives = 25/63 (39%), Gaps = 2/63 (3%)
Query: 57 SSPGRNSLDPDVSPDEQEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQ 116
PG N++ Q +R ++ E+++ + + NLRL E + L
Sbjct: 100 LRPGGNNVSTPERRAAQ--VSRYVAVEEEVRDLNSGGDEETIQLARLNLRLLLEGEDLSG 157
Query: 117 YIE 119
Y+
Sbjct: 158 YVS 160
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 26.2 bits (59), Expect = 6.9
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 72 EQEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVL 114
EQE + ++ L+ +L +RV+++ EE L E + L
Sbjct: 698 EQEALLKELAA--LLKAKPSELPERVEALLEELKELEKELEQL 738
>gnl|CDD|182755 PRK10816, PRK10816, DNA-binding transcriptional regulator PhoP;
Provisional.
Length = 223
Score = 25.9 bits (57), Expect = 7.4
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 79 LISQVLELQNTLDDLSQRVDSVKEENLRL 107
L SQV+ L DLS+R S+ +E ++L
Sbjct: 122 LASQVISLPPFQVDLSRRELSINDEVIKL 150
>gnl|CDD|203738 pfam07716, bZIP_2, Basic region leucine zipper.
Length = 54
Score = 24.5 bits (54), Expect = 7.6
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 91 DDLSQRVDSVKEENLRLRSENQVL 114
++L +RV ++EEN +LR + + L
Sbjct: 28 EELEERVKELEEENAQLRQKVEQL 51
>gnl|CDD|221918 pfam13093, FTA4, Kinetochore complex Fta4 of Sim4 subunit, or
CENP-50. Fission yeast has three kinetochore protein
complexes. Two complexes, Sim4 and Ndc80-MIND-Spc7
(NMS), are constitutive components, whereas the third
complex, DASH, is transiently associated with
kinetochores only in mitosis and is required for precise
chromosome segregation. The Sim4 complex functions as a
loading dock for the DASH complex. Sim4 consists of a
number of different proteins including Ftas 1-7 and
Dad1.
Length = 211
Score = 25.8 bits (57), Expect = 7.9
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 65 DPDVSPDEQEEKARLISQVLELQNTLDDLSQRVDSVKE 102
D D SP+E E L +++EL L +R+D +++
Sbjct: 131 DADASPEEAERYDELRERLIELDARRQQLQERLDQLRQ 168
>gnl|CDD|163695 cd08064, MPN_eIF3f, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in eIF3f.
Eukaryotic translation initiation factor 3 (eIF3)
subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic
translation initiation factor 3, subunit 5 epsilon,
47kDa; Mov34/MPN/PAD-1 family protein) is an
evolutionarily non-conserved subunit of the functional
core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f,
and eIF3h, and contains the MPN domain. However, it
lacks the canonical JAMM motif, and therefore does not
show catalytic isopeptidase activity. It has been shown
that eIF3f mRNA expression is significantly decreased in
many human tumors including pancreatic cancer and
melanoma. EIF3f is a potent inhibitor of HIV-1
replication; it mediates restriction of HIV-1 expression
through several factors including the
serine/arginine-rich (SR) protein 9G8, and
cyclin-dependent kinase 11 (CDK11). EIF3f
phosphorylation by CDK11 is important in regulating its
function in translation and apoptosis. It enhances its
association with the core eIF3 subunits during
apoptosis, suggesting that eIF3f may inhibit translation
by increasing the binding to the eIF3 complex during
apoptosis. Thus, eIF3f may be an important negative
regulator of cell growth and proliferation.
Length = 265
Score = 25.6 bits (57), Expect = 8.6
Identities = 11/68 (16%), Positives = 28/68 (41%), Gaps = 3/68 (4%)
Query: 61 RNSLDPDVSPDEQEEKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQVLGQYIEN 120
+ P S + +L + + +LQ LD + + V+ V + +G+Y+ +
Sbjct: 165 KTLASPSRSAPLTSDLEQLEASLEKLQEMLDRVLRYVEDVLAGK---VKADNAIGRYLMD 221
Query: 121 LMSASSVF 128
+++
Sbjct: 222 ALTSVPKL 229
>gnl|CDD|237624 PRK14143, PRK14143, heat shock protein GrpE; Provisional.
Length = 238
Score = 25.8 bits (57), Expect = 8.9
Identities = 14/86 (16%), Positives = 27/86 (31%)
Query: 25 ISDEVESSQNSEGPIRADHSLDSISSSFTNSSSSPGRNSLDPDVSPDEQEEKARLISQVL 84
D +E A+ + S T + D + + +
Sbjct: 4 EQDPLEVKLAVISESEAEDNSPESSEEVTEQEAELTNPEGDAAEAESSPDSGSAASETAA 63
Query: 85 ELQNTLDDLSQRVDSVKEENLRLRSE 110
+ L L Q ++S+K+E L S+
Sbjct: 64 DNAARLAQLEQELESLKQELEELNSQ 89
>gnl|CDD|218654 pfam05605, Di19, Drought induced 19 protein (Di19). This family
consists of several drought induced 19 (Di19) like
proteins. Di19 has been found to be strongly expressed
in both the roots and leaves of Arabidopsis thaliana
during progressive drought. The precise function of Di19
is unknown.
Length = 209
Score = 25.5 bits (56), Expect = 9.0
Identities = 16/56 (28%), Positives = 28/56 (50%)
Query: 31 SSQNSEGPIRADHSLDSISSSFTNSSSSPGRNSLDPDVSPDEQEEKARLISQVLEL 86
S ++ ++D S + +S+ ++ RNS D +S +E EEKA+ V L
Sbjct: 149 PSADTSSTSKSDSSTEGSASAKSSDQKLSERNSSDSSLSKEELEEKAKRSEFVQGL 204
>gnl|CDD|217902 pfam04111, APG6, Autophagy protein Apg6. In yeast, 15 Apg proteins
coordinate the formation of autophagosomes. Autophagy is
a bulk degradation process induced by starvation in
eukaryotic cells. Apg6/Vps30p has two distinct functions
in the autophagic process, either associated with the
membrane or in a retrieval step of the carboxypeptidase
Y sorting pathway.
Length = 356
Score = 26.0 bits (57), Expect = 9.1
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 75 EKARLISQVLELQNTLDDLSQRVDSVKEENLRLRSENQ 112
E+ RL+ ++ EL+ DDL + ++EE +L +E
Sbjct: 78 EEERLLDELEELEKEDDDLDGELVELQEEKEQLENEEL 115
>gnl|CDD|226133 COG3605, PtsP, Signal transduction protein containing GAF and PtsI
domains [Signal transduction mechanisms].
Length = 756
Score = 25.8 bits (57), Expect = 9.2
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 71 DEQEEKARLISQVLELQNTLDDLSQR--VDSVKEE 103
D E+ RL + L+ ++ + +R V KE
Sbjct: 211 DPDAERERLTGALESLRASIRRMLKRRDVGLEKEH 245
>gnl|CDD|183614 PRK12595, PRK12595, bifunctional 3-deoxy-7-phosphoheptulonate
synthase/chorismate mutase; Reviewed.
Length = 360
Score = 25.7 bits (57), Expect = 9.3
Identities = 9/32 (28%), Positives = 15/32 (46%)
Query: 87 QNTLDDLSQRVDSVKEENLRLRSENQVLGQYI 118
L+ L + +D + + L L S+ L Q I
Sbjct: 3 NEELEQLRKEIDEINLQLLELLSKRGELVQEI 34
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
0.303 0.122 0.315
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,548,557
Number of extensions: 552938
Number of successful extensions: 803
Number of sequences better than 10.0: 1
Number of HSP's gapped: 790
Number of HSP's successfully gapped: 165
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 17 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.8 bits)
S2: 54 (24.6 bits)