RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5308
(137 letters)
>gnl|CDD|236842 PRK11091, PRK11091, aerobic respiration control sensor protein
ArcB; Provisional.
Length = 779
Score = 33.0 bits (76), Expect = 0.036
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 7/38 (18%)
Query: 39 RQKQEEEREL-------EIMRRKQDEVHLLEQSIRQRS 69
R+K EE R+ EI R++ ++ L +QS RS
Sbjct: 122 REKAEEARQEAFEQLKNEIKEREETQIELEQQSSLLRS 159
>gnl|CDD|224685 COG1771, COG1771, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 471
Score = 29.9 bits (67), Expect = 0.39
Identities = 12/60 (20%), Positives = 21/60 (35%)
Query: 17 DIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAG 76
D D+ L L+ + + +E EL R ++ H I ++ K G
Sbjct: 267 DPKADIELLALDLFCYYFLTSKKLRLKEILELYPGLRDCEDCHYSLFDIPFKNRLDFKIG 326
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 29.8 bits (67), Expect = 0.42
Identities = 11/40 (27%), Positives = 25/40 (62%), Gaps = 3/40 (7%)
Query: 39 RQKQEEERELEIMRRK---QDEVHLLEQSIRQRSEQQKKA 75
R+K+E+++ E+ +++ Q+ + LE+ EQ+K+A
Sbjct: 81 RKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQA 120
>gnl|CDD|234058 TIGR02916, PEP_his_kin, putative PEP-CTERM system histidine kinase.
Members of this protein family have a novel N-terminal
domain, a single predicted membrane-spanning helix, and
a predicted cystosolic histidine kinase domain. We
designate this protein PrsK, and its companion
DNA-binding response regulator protein (TIGR02915) PrsR.
These predicted signal-transducing proteins appear to
enable enhancer-dependent transcriptional activation.
The prsK gene is often associated with exopolysaccharide
biosynthesis genes [Protein fate, Protein and peptide
secretion and trafficking, Signal transduction,
Two-component systems].
Length = 679
Score = 29.7 bits (67), Expect = 0.51
Identities = 22/120 (18%), Positives = 47/120 (39%), Gaps = 14/120 (11%)
Query: 16 ADIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKA 75
D++ + + ++++ +R K EE +L + D V LL ++I + Q +
Sbjct: 511 DDMLETVENAVNRMKKLLAQ--LRSKGLEEEKLCV-----DLVDLLRRAIASKRAQGPRP 563
Query: 76 GVELDATCHICL-KTKFADGVGHMCNYCNIRCCARCGGKVTLR----SNKVSVEVTTRGH 130
V +D + + + +GH+ N G+V +R +E+ G
Sbjct: 564 EVSIDTDLSVRADRERLERVLGHLVQ--NALEATPGEGRVAIRVERECGAARIEIEDSGC 621
>gnl|CDD|217446 pfam03238, ESAG1, ESAG protein. Expression-site-associated gene
(ESAG) proteins are thought to be involved in VSG
activation. This family includes ESAG 117A as well as
ESAG IM.
Length = 231
Score = 29.0 bits (65), Expect = 0.69
Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 49 EIMRRKQDEVHLLEQSIRQRSEQQKKAGV-ELDATC--HICLKTKFADGV 95
EI R D+V + +S + + E QK GV E + C H C ADGV
Sbjct: 60 EITRTVWDDVKAVLESGKAKCEDQKFRGVGEFETECGDHTCP---LADGV 106
>gnl|CDD|131094 TIGR02039, CysD, sulfate adenylyltransferase, small subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. Homologous to this E.coli
activation pathway are nodPQH gene products found among
members of the Rhizobiaceae family. These gene products
have been shown to exhibit ATP sulfurase and APS kinase
activity, yet are involved in Nod factor sulfation, and
sulfation of other macromolecules [Central intermediary
metabolism, Sulfur metabolism].
Length = 294
Score = 28.2 bits (63), Expect = 1.3
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 6/44 (13%)
Query: 6 GMVTSMAQTNADIIPDLSHLTLEERQ------IIESVMMRQKQE 43
G + S A T +II + + ERQ + M +K+E
Sbjct: 248 GAIESDAATVEEIIAETAAARTSERQGRAIDRDQAASMEDKKRE 291
>gnl|CDD|217206 pfam02731, SKIP_SNW, SKIP/SNW domain. This domain is found in
chromatin proteins.
Length = 158
Score = 27.6 bits (62), Expect = 1.4
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 25 LTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQ 71
L + ER+ E V RQ+ E +R+L +++ E L E + R R E+
Sbjct: 114 LYIAERKAREEV--RQRAELQRQLAEKEKQEKEEKLRELAQRAREER 158
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 27.8 bits (62), Expect = 1.8
Identities = 9/44 (20%), Positives = 28/44 (63%)
Query: 28 EERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQ 71
E ++ ++ +++ ++++++ E RRKQ + E+ +Q++E+
Sbjct: 179 EAKKRLQEWELKKLKQQQQKREEERRKQRKKQQEEEERKQKAEE 222
Score = 25.8 bits (57), Expect = 8.1
Identities = 12/48 (25%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 28 EERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKA 75
++ Q + +Q++E+ERE +R++ + E+ RQ+++Q K
Sbjct: 102 KKLQKLLEEKQKQEREKEREEAELRQRLAKEK-YEEWCRQKAQQAAKQ 148
>gnl|CDD|219368 pfam07299, FBP, Fibronectin-binding protein (FBP). This family
consists of several bacterial fibronectin-binding
proteins which are thought to be involved in virulence
in Listeria species.
Length = 208
Score = 27.6 bits (62), Expect = 1.9
Identities = 9/39 (23%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 12 AQTNADIIPDLSHLTLEERQIIESVM-MRQKQEEERELE 49
A I+ L+ E++++++ ++ +R + E E+ LE
Sbjct: 35 ALAIEKILDLFPELSPEQKELLDKLLTVRTRAEAEKFLE 73
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 27.7 bits (62), Expect = 2.1
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 28 EERQIIESVMMRQKQEEE---RELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVEL 79
EE ++ + K+E E ELE RR+ + ++ IR R + ++ EL
Sbjct: 436 EENSELKRELEELKREIEKLESELERFRREVRDKVRKDREIRARDRRIERLEKEL 490
>gnl|CDD|184281 PRK13729, PRK13729, conjugal transfer pilus assembly protein TraB;
Provisional.
Length = 475
Score = 27.5 bits (61), Expect = 2.3
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 27 LEERQIIESVMMRQKQEEERELEIM-RRKQDE---VHLLEQSIRQRSEQQKKAGVELDAT 82
E Q+ + M +Q +E REL+++ +++ D+ + L Q +EQ K G
Sbjct: 71 TTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKALGANPVTA 130
>gnl|CDD|181082 PRK07682, PRK07682, hypothetical protein; Validated.
Length = 378
Score = 27.4 bits (61), Expect = 2.4
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 48 LEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHI 85
LE +R D+V + S R+R + E+ TCH+
Sbjct: 268 LEALRAGNDDVIRMRDSYRKRRNFFVTSFNEIGLTCHV 305
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 27.3 bits (61), Expect = 3.1
Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 31 QIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKA 75
+ E + +QEE + RRKQ + L Q +R ++A
Sbjct: 698 NVEEQSVQETEQEERVQQVQPRRKQRQ---LNQKVRIEQSVAEEA 739
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 26.8 bits (59), Expect = 3.7
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 27 LEERQIIESVMMRQKQEEERELEIMRRKQDE--VHLLEQSIRQRSEQQKKAGVE 78
L+ +Q E ++Q E+ER ++KQ E + +Q+ EQ +KA E
Sbjct: 92 LKPKQAAEQERLKQ-LEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQARKAAAE 144
Score = 26.8 bits (59), Expect = 4.3
Identities = 13/49 (26%), Positives = 30/49 (61%), Gaps = 5/49 (10%)
Query: 27 LEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKA 75
LE+ ++ +Q +E E++ ++ +++Q+ EQ+ + +EQ+KKA
Sbjct: 106 LEKERLKAQEQQKQAEEAEKQAQLEQKQQE-----EQARKAAAEQKKKA 149
>gnl|CDD|233845 TIGR02395, rpoN_sigma, RNA polymerase sigma-54 factor. A sigma
factor is a DNA-binding protein protein that binds to
the DNA-directed RNA polymerase core to produce the
holoenzyme capable of initiating transcription at
specific sites. Different sigma factors act in
vegetative growth, heat shock, extracytoplasmic
functions (ECF), etc. This model represents the clade of
sigma factors called sigma-54, or RpoN (unrelated to
sigma 70-type factors such as RpoD/SigA). RpoN is
responsible for enhancer-dependent transcription, and
its presence characteristically is associated with
varied panels of activators, most of which are
enhancer-binding proteins (but see Brahmachary, et al.,
PMID:15231786). RpoN may be responsible for
transcription of nitrogen fixation genes, flagellins,
pilins, etc., and synonyms for the gene symbol rpoN,
such as ntrA, reflect these observations [Transcription,
Transcription factors].
Length = 429
Score = 26.9 bits (60), Expect = 4.2
Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 7/59 (11%)
Query: 12 AQTNADIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSE 70
+ N +P L + E E + + E+E + +++K E L +++ QR E
Sbjct: 241 VELNGRSLP---ELRINE----EYFKLLKDAEKEAADQYLKQKLKEARWLIKALEQREE 292
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 27.0 bits (59), Expect = 4.4
Identities = 9/48 (18%), Positives = 30/48 (62%)
Query: 28 EERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKA 75
EE +I + ++ +E++++ E ++ +++ +++++ +E+ KKA
Sbjct: 1657 EENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKA 1704
>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria
with the myosin-like domain [Function unknown].
Length = 499
Score = 26.9 bits (59), Expect = 4.6
Identities = 7/54 (12%), Positives = 25/54 (46%)
Query: 28 EERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDA 81
+ER+ + + +Q + + + R + L+ ++ +EQ+++ + +
Sbjct: 116 QEREAVRQELAAARQNLAKAQQELARLTKQAQDLQTRLKTLAEQRRQLEAQAQS 169
>gnl|CDD|218095 pfam04459, DUF512, Protein of unknown function (DUF512). Family of
uncharacterized prokaryotic proteins.
Length = 205
Score = 26.4 bits (59), Expect = 4.6
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 14 TNADIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQ 55
T DII +L L + ++ VM+ K EE L+ M ++
Sbjct: 149 TGQDIIEELDGKELGDTLLLPGVML--KHGEEVFLDDMTVEE 188
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 26.5 bits (59), Expect = 4.8
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 21 DLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVH-LLEQSIRQRSEQQKKA 75
LS L E +ES +++ E E R+++E+ E+ +RQ E+Q +A
Sbjct: 201 LLSKLEEELLARLESKEAALEKQLRLEFE---REKEELRKKYEEKLRQELERQAEA 253
>gnl|CDD|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 336
Score = 26.6 bits (58), Expect = 5.1
Identities = 15/78 (19%), Positives = 35/78 (44%), Gaps = 4/78 (5%)
Query: 3 LTEGMVTSMAQTNADIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLE 62
L EG++ + I + L +++ ++ + E +L+++ D LLE
Sbjct: 140 LLEGLLDPQRELLEIIEEEAERL----LRLVNDLLDLSRLEAGTKLKLLLELVDLAELLE 195
Query: 63 QSIRQRSEQQKKAGVELD 80
+ +R + ++ G+EL
Sbjct: 196 EVVRLLAPLAQEKGIELA 213
>gnl|CDD|191367 pfam05761, 5_nucleotid, 5' nucleotidase family. This family of
eukaryotic proteins includes 5' nucleotidase enzymes,
such as purine 5'-nucleotidase EC:3.1.3.5.
Length = 448
Score = 26.5 bits (59), Expect = 5.8
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 2/45 (4%)
Query: 42 QEEERELEIMRRKQDEVHLLE--QSIRQRSEQQKKAGVELDATCH 84
E ERE+EI +Q L+ + +R EL
Sbjct: 324 PELEREIEIWNTEQYRFEELQRLDILLERLYDHLDVHAELSTLRP 368
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 26.4 bits (59), Expect = 6.0
Identities = 12/52 (23%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 24 HLTLEERQIIESVMMRQKQEEERELEIMRRKQDEV-HLLEQSIRQRSEQQKK 74
L+ER+ ++ ++ R ++E+E E + R KQ ++ +++ +R E++++
Sbjct: 92 EERLQEREQMDEIIERIQEEDEAEAQEKREKQKKLREEIDEFNEERIERKEE 143
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 26.3 bits (59), Expect = 6.3
Identities = 15/56 (26%), Positives = 34/56 (60%), Gaps = 3/56 (5%)
Query: 28 EERQIIESVMMRQKQEEE---RELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELD 80
E R ++ + R Q+EE R+LE++ ++++E+ E+ + Q+ ++ +K EL+
Sbjct: 79 ERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELE 134
Score = 25.9 bits (58), Expect = 8.9
Identities = 10/38 (26%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 37 MMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKK 74
+ + + E E+EL R +++E+ LE+ + Q+ E +
Sbjct: 66 IHKLRNEFEKEL---RERRNELQKLEKRLLQKEENLDR 100
>gnl|CDD|204405 pfam10146, zf-C4H2, Zinc finger-containing protein. This is a
family of proteins which appears to have a highly
conserved zinc finger domain at the C terminal end,
described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is
predicted to contain a coiled coil. Members are
annotated as being tumour-associated antigen HCA127 in
humans but this could not confirmed.
Length = 215
Score = 26.0 bits (57), Expect = 6.5
Identities = 12/60 (20%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 18 IIPDLSHLTLEERQIIESVMMRQKQEEERE--LEIMRRKQDEVHLLEQSIRQRSEQQKKA 75
I + L EE+ + E ++ EE+ +E +R+ +++ +E I+Q + ++
Sbjct: 20 IKAEEEALESEEKHLKEYDKEMEELLEEKMQHVEELRQIHADINDMETEIKQSKSELERR 79
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 26.4 bits (59), Expect = 6.8
Identities = 18/58 (31%), Positives = 38/58 (65%), Gaps = 4/58 (6%)
Query: 16 ADIIPDLSHLTLEERQ-IIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQ 72
AD I L LEE+Q I+E++ ++++ E+ L+++ K+ ++ LE+ IR++ ++Q
Sbjct: 167 ADTIAAHLPLKLEEKQEILETLDVKERL--EKLLDLL-EKEIDLLQLEKRIRKKVKEQ 221
>gnl|CDD|218602 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 807
Score = 26.1 bits (58), Expect = 6.9
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 99 CNYCNIRCCARCGGKV 114
+C RCC CGG++
Sbjct: 113 LCFCCCRCCGNCGGRM 128
>gnl|CDD|226880 COG4474, COG4474, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 180
Score = 25.8 bits (57), Expect = 7.0
Identities = 10/32 (31%), Positives = 20/32 (62%)
Query: 47 ELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVE 78
EL I + K EV ++++I+++ E + G+E
Sbjct: 13 ELGIFKDKDPEVSYIKKAIKKKLEALLEEGLE 44
>gnl|CDD|233161 TIGR00870, trp, transient-receptor-potential calcium channel
protein. The Transient Receptor Potential Ca2+ Channel
(TRP-CC) Family (TC. 1.A.4)The TRP-CC family has also
been called the store-operated calcium channel (SOC)
family. The prototypical members include the Drosophila
retinal proteinsTRP and TRPL (Montell and Rubin, 1989;
Hardie and Minke, 1993). SOC members of the family
mediate the entry of extracellular Ca2+ into cells in
responseto depletion of intracellular Ca2+ stores
(Clapham, 1996) and agonist stimulated production of
inositol-1,4,5 trisphosphate (IP3). One member of the
TRP-CCfamily, mammalian Htrp3, has been shown to form a
tight complex with the IP3 receptor (TC #1.A.3.2.1).
This interaction is apparently required for IP3
tostimulate Ca2+ release via Htrp3. The vanilloid
receptor subtype 1 (VR1), which is the receptor for
capsaicin (the ?hot? ingredient in chili peppers) and
servesas a heat-activated ion channel in the pain
pathway (Caterina et al., 1997), is also a member of
this family. The stretch-inhibitable non-selective
cation channel(SIC) is identical to the vanilloid
receptor throughout all of its first 700 residues, but
it exhibits a different sequence in its last 100
residues. VR1 and SICtransport monovalent cations as
well as Ca2+. VR1 is about 10x more permeable to Ca2+
than to monovalent ions. Ca2+ overload probably causes
cell deathafter chronic exposure to capsaicin.
(McCleskey and Gold, 1999) [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 743
Score = 26.2 bits (58), Expect = 7.4
Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 9/50 (18%)
Query: 48 LEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTKFADGVGH 97
L R+ + V LL ++ A V A +K++ D H
Sbjct: 134 LAAHRQNYEIVKLL---------LERGASVPARACGDFFVKSQGVDSFYH 174
>gnl|CDD|72673 pfam09257, BCMA-Tall_bind, BCMA, TALL-1 binding. Members of this
family, which are predominantly found in the tumour
necrosis factor receptor superfamily member 17, BCMA,
are required for binding to tumour necrosis factor
ligand TALL-1.
Length = 39
Score = 24.0 bits (51), Expect = 7.5
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 86 CLKTKFADGVGHMCNYCNIRC 106
C + ++ D + H C C +RC
Sbjct: 1 CSQNEYFDSLLHACIPCQLRC 21
>gnl|CDD|197519 smart00109, C1, Protein kinase C conserved region 1 (C1) domains
(Cysteine-rich domains). Some bind phorbol esters and
diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Length = 50
Score = 24.4 bits (53), Expect = 7.5
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 81 ATCHICLKT-KFADGVGHMCNYCNIRCCARCGGKVTL 116
C +C K+ + G C+ C ++C +C KV
Sbjct: 12 TFCCVCRKSIWGSFKQGLRCSECKVKCHKKCADKVPK 48
>gnl|CDD|216108 pfam00769, ERM, Ezrin/radixin/moesin family. This family of
proteins contain a band 4.1 domain (pfam00373), at their
amino terminus. This family represents the rest of these
proteins.
Length = 244
Score = 25.9 bits (57), Expect = 7.6
Identities = 12/52 (23%), Positives = 23/52 (44%)
Query: 28 EERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVEL 79
EE + +E ++E ER + EV LE+ ++ + ++ EL
Sbjct: 61 EENRRLEEEAAASEEERERLEAEVDEATAEVAKLEEEREKKEAETRQLQQEL 112
>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter
subunit G; Reviewed.
Length = 197
Score = 25.8 bits (56), Expect = 8.0
Identities = 18/55 (32%), Positives = 26/55 (47%)
Query: 17 DIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQ 71
D I L + + QI ++ R++ EE E E K DE E+ R+R EQ
Sbjct: 113 DDIKKKKSLIIRQEQIEKARQEREELEERMEWERREEKIDEREDQEEQEREREEQ 167
>gnl|CDD|177609 PHA03372, PHA03372, DNA packaging terminase subunit 1; Provisional.
Length = 668
Score = 25.9 bits (57), Expect = 9.0
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 41 KQEEERELEI---MRRKQDEVHLLEQSIRQRSEQQK 73
EE R+L I ++ DE+ S QR QQK
Sbjct: 74 NSEERRKLTISDALKSALDELKFRPCSEEQRQYQQK 109
>gnl|CDD|237996 cd00029, C1, Protein kinase C conserved region 1 (C1) .
Cysteine-rich zinc binding domain. Some members of this
domain family bind phorbol esters and diacylglycerol,
some are reported to bind RasGTP. May occur in tandem
arrangement. Diacylglycerol (DAG) is a second messenger,
released by activation of Phospholipase D. Phorbol
Esters (PE) can act as analogues of DAG and mimic its
downstream effects in, for example, tumor promotion.
Protein Kinases C are activated by DAG/PE, this
activation is mediated by their N-terminal conserved
region (C1). DAG/PE binding may be phospholipid
dependent. C1 domains may also mediate DAG/PE signals in
chimaerins (a family of Rac GTPase activating proteins),
RasGRPs (exchange factors for Ras/Rap1), and Munc13
isoforms (scaffolding proteins involved in exocytosis).
Length = 50
Score = 24.0 bits (52), Expect = 9.3
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 80 DATCHICLKT-KFADGVGHMCNYCNIRCCARCGGKVT 115
C +C K+ G C++C ++C +C KV
Sbjct: 11 PTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADKVP 47
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 25.7 bits (57), Expect = 9.4
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 38 MRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQ 71
+ + E EREL+ R +E+ LE+ + QR E
Sbjct: 61 HKLRAELERELKERR---NELQRLERRLLQREET 91
>gnl|CDD|99969 cd03795, GT1_like_4, This family is most closely related to the
GT1 family of glycosyltransferases.
Glycosyltransferases catalyze the transfer of sugar
moieties from activated donor molecules to specific
acceptor molecules, forming glycosidic bonds. The
acceptor molecule can be a lipid, a protein, a
heterocyclic compound, or another carbohydrate residue.
This group of glycosyltransferases is most closely
related to the previously defined glycosyltransferase
family 1 (GT1). The members of this family may transfer
UDP, ADP, GDP, or CMP-linked sugars. The diverse
enzymatic activities among members of this family
reflect a wide range of biological functions. The
protein structure available for this family has the GTB
topology, one of the two protein topologies observed
for nucleotide-sugar-dependent glycosyltransferases.
GTB proteins have distinct N- and C- terminal domains
each containing a typical Rossmann fold. The two
domains have high structural homology despite minimal
sequence homology. The large cleft that separates the
two domains includes the catalytic center and permits a
high degree of flexibility. The members of this family
are found mainly in bacteria and eukaryotes.
Length = 357
Score = 25.6 bits (57), Expect = 9.5
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 62 EQSIRQRSEQQKKAGVELDATCH 84
EQ IR +E G+E+ C
Sbjct: 17 EQVIRDLAEGLAARGIEVAVLCA 39
>gnl|CDD|220402 pfam09787, Golgin_A5, Golgin subfamily A member 5. Members of this
family of proteins are involved in maintaining Golgi
structure. They stimulate the formation of Golgi stacks
and ribbons, and are involved in intra-Golgi retrograde
transport. Two main interactions have been
characterized: one with RAB1A that has been activated by
GTP-binding and another with isoform CASP of CUTL1.
Length = 509
Score = 26.0 bits (57), Expect = 9.5
Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 8/78 (10%)
Query: 2 CLTEGMVTSMAQTNADIIPDLS-----HLTLEERQIIESVMMRQKQEEE--RELEIMRRK 54
CL EG+ +S AQ + + S +T E QII+ Q +E E E E R++
Sbjct: 260 CLFEGLDSSTAQIELEELKHESEHVQEEITKLEGQIIQLRSEAQDREAEASGEAESFRKQ 319
Query: 55 QDEVH-LLEQSIRQRSEQ 71
E+ + I + E
Sbjct: 320 PRELSQQIAPQITTKQEL 337
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
0.319 0.131 0.379
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,385,278
Number of extensions: 544440
Number of successful extensions: 1212
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1153
Number of HSP's successfully gapped: 155
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (24.6 bits)