RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14385
(228 letters)
>gnl|CDD|239286 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral
inhibitor of apoptosis (IAP)-associated factor (VIAF)
subfamily; VIAF is a Phd-like protein that functions in
caspase activation during apoptosis. It was identified
as an IAP binding protein through a screen of a human
B-cell library using a prototype IAP. VIAF lacks a
consensus IAP binding motif and while it does not
function as an IAP antagonist, it still plays a
regulatory role in the complete activation of caspases.
VIAF itself is a substrate for IAP-mediated
ubiquitination, suggesting that it may be a target of
IAPs in the prevention of cell death. The similarity of
VIAF to Phd points to a potential role distinct from
apoptosis regulation. Phd functions as a cytosolic
regulator of G protein by specifically binding to G
protein betagamma (Gbg)-subunits. The C-terminal domain
of Phd adopts a thioredoxin fold, but it does not
contain a CXXC motif. Phd interacts with G protein beta
mostly through the N-terminal helical domain.
Length = 192
Score = 240 bits (615), Expect = 3e-81
Identities = 98/186 (52%), Positives = 120/186 (64%), Gaps = 10/186 (5%)
Query: 45 TQWNDILRAKGIIPQKEKEVTEDDIVNLVEQTVKEKQGKGEKELGDMDLDDLDELEDE-E 103
T+WNDILR KGI+P K E++ L Q E L LD+LDE DE E
Sbjct: 1 TEWNDILRKKGILPPKPPSPKEEEEEALEL----AIQEAHENALEKKLLDELDEELDEEE 56
Query: 104 DERVLQEYRRKRIAEMKAMAEKSRFGRVLEINGDTYVQEVNNAGEGIWVVLHF----IPL 159
D+R L+EYRRKR+AEMKA+AEKS+FG V EI+ YV+EV A + WVV+H IPL
Sbjct: 57 DDRFLEEYRRKRLAEMKALAEKSKFGEVYEISKPDYVREVTEASKDTWVVVHLYKDGIPL 116
Query: 160 CSLINNHLSELAAKFPTTKFIKSISTTCIPNYPDKNLPTLFIYFEGKMQSQMVGPDEFR- 218
C L+N HLSELA KFP TKF+K IST CIPNYPDKNLPT+ +Y G + Q +G EF
Sbjct: 117 CRLLNQHLSELARKFPDTKFVKIISTQCIPNYPDKNLPTILVYRNGDIVKQFIGLLEFGG 176
Query: 219 TNLSCD 224
N + +
Sbjct: 177 MNTTME 182
>gnl|CDD|239255 cd02957, Phd_like, Phosducin (Phd)-like family; composed of Phd and
Phd-like proteins (PhLP), characterized as cytosolic
regulators of G protein functions. Phd and PhLPs
specifically bind G protein betagamma (Gbg)-subunits
with high affinity, resulting in the solubilization of
Gbg from the plasma membrane and impeding G
protein-mediated signal transduction by inhibiting the
formation of a functional G protein trimer (G protein
alphabetagamma). Phd also inhibits the GTPase activity
of G protein alpha. Phd can be phosphorylated by protein
kinase A and G protein-coupled receptor kinase 2,
leading to its inactivation. Phd was originally isolated
from the retina, where it is highly expressed and has
been implicated to play an important role in light
adaptation. It is also found in the pineal gland, liver,
spleen, striated muscle and the brain. The C-terminal
domain of Phd adopts a thioredoxin fold, but it does not
contain a CXXC motif. Phd interacts with G protein beta
mostly through the N-terminal helical domain. Also
included in this family is a PhLP characterized as a
viral inhibitor of apoptosis (IAP)-associated factor,
named VIAF, that functions in caspase activation during
apoptosis.
Length = 113
Score = 118 bits (299), Expect = 2e-34
Identities = 40/98 (40%), Positives = 59/98 (60%), Gaps = 6/98 (6%)
Query: 126 SRFGRVLEINGDTYVQEVNNAGEGIWVVLHF----IPLCSLINNHLSELAAKFPTTKFIK 181
FG V EI+ +++EV A +G VV+HF P C ++++HL ELAAK+P TKF+K
Sbjct: 1 KGFGEVREISSKEFLEEVTKASKGTRVVVHFYEPGFPRCKILDSHLEELAAKYPETKFVK 60
Query: 182 SIST-TCIPNYPD-KNLPTLFIYFEGKMQSQMVGPDEF 217
+ + NY D K LPTL +Y G++ +VG +E
Sbjct: 61 INAEKAFLVNYLDIKVLPTLLVYKNGELIDNIVGFEEL 98
>gnl|CDD|239285 cd02987, Phd_like_Phd, Phosducin (Phd)-like family, Phd subfamily;
Phd is a cytosolic regulator of G protein functions. It
specifically binds G protein betagamma (Gbg)-subunits
with high affinity, resulting in the solubilization of
Gbg from the plasma membrane. This impedes the formation
of a functional G protein trimer (G protein
alphabetagamma), thereby inhibiting G protein-mediated
signal transduction. Phd also inhibits the GTPase
activity of G protein alpha. Phd can be phosphorylated
by protein kinase A and G protein-coupled receptor
kinase 2, leading to its inactivation. Phd was
originally isolated from the retina, where it is highly
expressed and has been implicated to play an important
role in light adaptation. It is also found in the pineal
gland, liver, spleen, striated muscle and the brain. The
C-terminal domain of Phd adopts a thioredoxin fold, but
it does not contain a CXXC motif. Phd interacts with G
protein beta mostly through the N-terminal helical
domain.
Length = 175
Score = 83.1 bits (206), Expect = 6e-20
Identities = 48/142 (33%), Positives = 74/142 (52%), Gaps = 13/142 (9%)
Query: 83 KGEKELGDMDLDDLDELEDEEDERVLQEYRRKRIAEMKAMAEKSR-FGRVLEI-NGDTYV 140
K KE D DD DE+ E LQ+YR +R+ EM A R FG+V E+ +G+ ++
Sbjct: 20 KQLKESEQEDDDD-----DEDKEEFLQQYREQRMQEMHAKLPFGRRFGKVYELDSGEQFL 74
Query: 141 QEVNNAGEGIWVVLHF----IPLCSLINNHLSELAAKFPTTKFIKSIST-TCIPNYPDKN 195
++ G+ VV+H IP C+ +N+ L LAA++P KF K ++ T + D +
Sbjct: 75 DAIDKEGKDTTVVVHIYEPGIPGCAALNSSLLCLAAEYPAVKFCKIRASATGASDEFDTD 134
Query: 196 -LPTLFIYFEGKMQSQMVGPDE 216
LP L +Y G++ V E
Sbjct: 135 ALPALLVYKGGELIGNFVRVTE 156
>gnl|CDD|202114 pfam02114, Phosducin, Phosducin.
Length = 245
Score = 54.3 bits (130), Expect = 6e-09
Identities = 41/178 (23%), Positives = 79/178 (44%), Gaps = 15/178 (8%)
Query: 48 NDILRAKGIIPQKEKEVTEDDIVNLVEQTVKEKQGKG----EKELGDMDLDDLDELEDE- 102
ND + K + ++ Q + E+ M + + + + +
Sbjct: 27 NDWRKFKLESEDSDSVAHS--KKEILRQMSSPQSRDDKDSKERFSRKMSVQEYELIHKDK 84
Query: 103 EDERVLQEYRRKRIAEMKAMAEKS-RFGRVLEI-NGDTYVQEVNNAGEGIWVVLHF---- 156
EDE L++YRR+ + +M R+G V E+ +G+ +++ + + +V+H
Sbjct: 85 EDENCLRKYRRQCMQDMHQKLSFGPRYGFVYELESGEQFLETIEKEQKITTIVVHIYEDG 144
Query: 157 IPLCSLINNHLSELAAKFPTTKF--IKSISTTCIPNYPDKNLPTLFIYFEGKMQSQMV 212
I C +N+ L LAA++P KF IK+ +T + LPTL +Y G++ S +
Sbjct: 145 IKGCDALNSSLICLAAEYPMVKFCKIKASNTGAGDRFSSDVLPTLLVYKGGELLSNFI 202
>gnl|CDD|239287 cd02989, Phd_like_TxnDC9, Phosducin (Phd)-like family, Thioredoxin
(TRX) domain containing protein 9 (TxnDC9) subfamily;
composed of predominantly uncharacterized eukaryotic
proteins, containing a TRX-like domain without the redox
active CXXC motif. The gene name for the human protein
is TxnDC9. The two characterized members are described
as Phd-like proteins, PLP1 of Saccharomyces cerevisiae
and PhLP3 of Dictyostelium discoideum. Gene disruption
experiments show that both PLP1 and PhLP3 are
non-essential proteins. Unlike Phd and most Phd-like
proteins, members of this group do not contain the Phd
N-terminal helical domain which is implicated in binding
to the G protein betagamma subunit.
Length = 113
Score = 42.6 bits (101), Expect = 2e-05
Identities = 28/102 (27%), Positives = 44/102 (43%), Gaps = 19/102 (18%)
Query: 128 FGRVLEINGD----TYVQEVNNAGEGIWVVLHF----IPLCSLINNHLSELAAKFPTTKF 179
G+ E++ + V+ VV HF C +++ HL LA K TKF
Sbjct: 3 HGKYREVSDEKEFFEIVKSSER------VVCHFYHPEFFRCKIMDKHLEILAKKHLETKF 56
Query: 180 IKSISTTCIP----NYPDKNLPTLFIYFEGKMQSQMVGPDEF 217
IK ++ P K LPT+ ++ GK ++VG +E
Sbjct: 57 IK-VNAEKAPFLVEKLNIKVLPTVILFKNGKTVDRIVGFEEL 97
>gnl|CDD|239245 cd02947, TRX_family, TRX family; composed of two groups: Group I,
which includes proteins that exclusively encode a TRX
domain; and Group II, which are composed of fusion
proteins of TRX and additional domains. Group I TRX is a
small ancient protein that alter the redox state of
target proteins via the reversible oxidation of an
active site dithiol, present in a CXXC motif, partially
exposed at the protein's surface. TRX reduces protein
disulfide bonds, resulting in a disulfide bond at its
active site. Oxidized TRX is converted to the active
form by TRX reductase, using reducing equivalents
derived from either NADPH or ferredoxins. By altering
their redox state, TRX regulates the functions of at
least 30 target proteins, some of which are enzymes and
transcription factors. It also plays an important role
in the defense against oxidative stress by directly
reducing hydrogen peroxide and certain radicals, and by
serving as a reductant for peroxiredoxins. At least two
major types of functional TRXs have been reported in
most organisms; in eukaryotes, they are located in the
cytoplasm and the mitochondria. Higher plants contain
more types (at least 20 TRX genes have been detected in
the genome of Arabidopsis thaliana), two of which (types
f amd m) are located in the same compartment, the
chloroplast. Also included in the alignment are TRX-like
domains which show sequence homology to TRX but do not
contain the redox active CXXC motif. Group II proteins,
in addition to either a redox active TRX or a TRX-like
domain, also contain additional domains, which may or
may not possess homology to known proteins.
Length = 93
Score = 31.8 bits (73), Expect = 0.056
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 12/87 (13%)
Query: 137 DTYVQEVNNAGEGIWVVLHFI----PLCSLINNHLSELAAKFPTTKFIKSISTTCIPNYP 192
+ + + + +A VV+ F C I L ELA ++P KF+K + P
Sbjct: 1 EEFEELIKSAK---PVVVDFWAPWCGPCKAIAPVLEELAEEYPKVKFVK-VDVDENPELA 56
Query: 193 DKN----LPTLFIYFEGKMQSQMVGPD 215
++ +PT + GK ++VG D
Sbjct: 57 EEYGVRSIPTFLFFKNGKEVDRVVGAD 83
>gnl|CDD|233778 TIGR02207, lipid_A_htrB, lipid A biosynthesis lauroyl (or
palmitoleoyl) acyltransferase. This model represents a
narrow clade of acyltransferases, nearly all of which
transfer a lauroyl group to KDO2-lipid IV-A, a lipid A
precursor; these proteins are termed lipid A
biosynthesis lauroyl acyltransferase, HtrB. An exception
is a closely related paralog of E. coli HtrB, LpxP,
which acts in cold shock conditions by transferring a
palmitoleoyl rather than lauroyl group to the lipid A
precursor. Members of this family are homologous to the
family of acyltransferases responsible for the next step
in lipid A biosynthesis [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 303
Score = 33.1 bits (76), Expect = 0.079
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 98 ELEDEEDERVLQE---YRRKRIAEMKAMA---EKSRFGRVLEINGDTYVQEVNNAGEGIW 151
+ D E ER+L+E + E MA +R + ++I G ++Q G G+
Sbjct: 65 HMSDAERERLLRENFESTGMALFET-GMAWFWSDARIKKWMQIEGLEHLQRAQKQGRGVL 123
Query: 152 VV-LHFIPL 159
+V +HF+ L
Sbjct: 124 LVGVHFLTL 132
>gnl|CDD|235543 PRK05646, PRK05646, lipid A biosynthesis lauroyl acyltransferase;
Provisional.
Length = 310
Score = 32.1 bits (73), Expect = 0.17
Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 8/69 (11%)
Query: 98 ELEDEEDERVLQE-YRRKRIA--EMKAMA---EKSRFGRVLEINGDTYVQEVNNAGEG-I 150
E E ER+L+E + IA EM AM+ K+R R+ I G ++Q+ G+G I
Sbjct: 68 EKSAAERERLLKENFASTGIAFFEM-AMSWWWPKARLARLAHIEGLEHLQQAQQEGQGVI 126
Query: 151 WVVLHFIPL 159
+ LHF L
Sbjct: 127 LMALHFTTL 135
>gnl|CDD|181057 PRK07608, PRK07608, ubiquinone biosynthesis hydroxylase family
protein; Provisional.
Length = 388
Score = 31.8 bits (73), Expect = 0.28
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 86 KELGDMDLDDLDELEDEEDERVLQEYRRKRIAEMKAM 122
L D+ L + D D R+L+ Y R R ++ A+
Sbjct: 308 AALADV-LAGREPFRDLGDLRLLRRYERARREDILAL 343
>gnl|CDD|238613 cd01286, deoxycytidylate_deaminase, Deoxycytidylate deaminase
domain. Deoxycytidylate deaminase catalyzes the
deamination of dCMP to dUMP, providing the nucleotide
substrate for thymidylate synthase. The enzyme binds
Zn++, which is required for catalytic activity. The
activity of the enzyme is allosterically regulated by
the ratio of dCTP to dTTP not only in eukaryotic cells
but also in T-even phage-infected Escherichia coli, with
dCTP acting as an activator and dTTP as an inhibitor.
Length = 131
Score = 30.3 bits (69), Expect = 0.36
Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 92 DLDDLDELEDEEDERVLQEYRRKRIAEMKAMAEKSRFGRVLEINGDTYV 140
++ D+ Q+ R AE A+ + +R G LE YV
Sbjct: 46 HCAEVGCERDDLPSGEDQKCCRTVHAEQNAILQAARHGVSLE-GATLYV 93
>gnl|CDD|224061 COG1138, CcmF, Cytochrome c biogenesis factor [Posttranslational
modification, protein turnover, chaperones].
Length = 648
Score = 31.6 bits (72), Expect = 0.36
Identities = 15/55 (27%), Positives = 20/55 (36%), Gaps = 5/55 (9%)
Query: 110 EYRRKRIAEMKAMAEKSRFGRVLEINGDTYVQEVNNAGEGIWVV-LHFIPLCSLI 163
E R M R G + GD Y + G+G W V L++ P I
Sbjct: 570 EKRFYTARRMLMSEAAIRPGLL----GDLYAVLGESLGQGAWAVRLYYKPFVRWI 620
>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated.
Length = 470
Score = 31.0 bits (71), Expect = 0.44
Identities = 25/117 (21%), Positives = 47/117 (40%), Gaps = 11/117 (9%)
Query: 45 TQWN-DILRAKGIIPQKEKEVTE--------DDIVNLVEQTVKEKQGKGEKELGDMDLDD 95
T W DI+ + +++ E DI + Q + E+ +EL + +++
Sbjct: 331 TGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEE 390
Query: 96 LDELE--DEEDERVLQEYRRKRIAEMKAMAEKSRFGRVLEINGDTYVQEVNNAGEGI 150
L E+E DEE L+E ++ + E+ +L + G A +GI
Sbjct: 391 LLEIEGFDEETVEELRERAKEALETEALAQEEKLADDLLSLEGLDRELAFKLAEKGI 447
>gnl|CDD|226907 COG4530, COG4530, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 129
Score = 29.1 bits (65), Expect = 0.94
Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 61 EKEV-TEDDIVNLVEQTVKEKQGKGEKELGDMDLDDLDELEDEEDERVLQE 110
KEV E++ V +V + KG +L D+ D+ +L+D++D+ L++
Sbjct: 58 VKEVDAENEEVEVVSLEDADDDPKGGDDLPDLGDDEDVDLDDDDDDTFLED 108
>gnl|CDD|153124 cd02433, Nodulin-21_like_2, Nodulin-21 and CCC1-related protein
family. Nodulin-21_like_2: This is a family of proteins
closely related to nodulin-21, a plant nodule-specific
protein that may be involved in symbiotic nitrogen
fixation. This family is also related to CCC1, a yeast
vacuole transmembrane protein that functions as an iron
and manganese transporter. .
Length = 234
Score = 28.9 bits (65), Expect = 1.7
Identities = 15/48 (31%), Positives = 21/48 (43%)
Query: 17 SARNQILSLNLSVPFGAVVNLKPNYEEDTQWNDILRAKGIIPQKEKEV 64
S +Q L S+P K EE + I RAKG+ ++ K V
Sbjct: 73 SVTSQRELLEASIPDERRELRKHPLEEAAELALIYRAKGLDEEEAKRV 120
>gnl|CDD|202254 pfam02491, SHS2_FTSA, SHS2 domain inserted in FTSA. FtsA is
essential for bacterial cell division, and co-localises
to the septal ring with FtsZ. The SHS2 domain is
inserted in to the RNAseH fold of FtsA, and is involved
in protein-protein interaction.
Length = 80
Score = 27.5 bits (62), Expect = 1.7
Identities = 7/21 (33%), Positives = 16/21 (76%)
Query: 54 KGIIPQKEKEVTEDDIVNLVE 74
GI+ +++EVT++D+ ++E
Sbjct: 11 NGIVAIEDREVTQEDVERVLE 31
>gnl|CDD|192987 pfam12325, TMF_TATA_bd, TATA element modulatory factor 1 TATA
binding. This is the C-terminal conserved coiled coil
region of a family of TATA element modulatory factor 1
proteins conserved in eukaryotes. The proteins bind to
the TATA element of some RNA polymerase II promoters and
repress their activity. by competing with the binding of
TATA binding protein. TMF1_TATA_bd is the most conserved
part of the TMFs. TMFs are evolutionarily conserved
golgins that bind Rab6, a ubiquitous ras-like
GTP-binding Golgi protein, and contribute to Golgi
organisation in animal and plant cells. The Rab6-binding
domain appears to be the same region as this C-terminal
family.
Length = 121
Score = 28.3 bits (64), Expect = 1.8
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 9/71 (12%)
Query: 59 QKEKEVTEDDIVNLVEQ--TVKEKQG---KGEKELGDMD--LDDLDELEDEEDERVLQEY 111
+ E++ +IV L E+ ++E + + EKEL D++ + EL E+ ERV E
Sbjct: 44 EAERDEARQEIVKLTEENEELRELKKEIEELEKELEDLEQRYETTLELLGEKSERV--EE 101
Query: 112 RRKRIAEMKAM 122
R + ++K M
Sbjct: 102 LRADVVDLKEM 112
>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family. This family of proteins includes
MND1 from S. cerevisiae. The mnd1 protein forms a
complex with hop2 to promote homologous chromosome
pairing and meiotic double-strand break repair.
Length = 188
Score = 28.7 bits (65), Expect = 1.9
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 5/68 (7%)
Query: 59 QKEKEVTEDDIVNLVEQTVKEKQGKGEKELGDMDLDDLDELEDEEDE--RVLQEYRR--- 113
+KE E + I L Q K K+G+ E E L++L +LE E + L++Y +
Sbjct: 75 KKELEELKQRIAELQAQIEKLKKGREETEERTELLEELKQLEKELKKLKAELEKYEKNDP 134
Query: 114 KRIAEMKA 121
+RI ++K
Sbjct: 135 ERIEKLKE 142
>gnl|CDD|185101 PRK15179, PRK15179, Vi polysaccharide biosynthesis protein TviE;
Provisional.
Length = 694
Score = 28.8 bits (64), Expect = 2.3
Identities = 31/96 (32%), Positives = 37/96 (38%), Gaps = 23/96 (23%)
Query: 75 QTVKEKQGKGEKELGDM------DLDDLDELEDEED-----------ERVLQEYRRKRIA 117
Q + G G ++L DL L L E D E++LQE R+R A
Sbjct: 212 QAGLDAIGDGARKLTRRLVDLNADLAALRRLGVEGDGRDVPVSILVLEKMLQEIGRRRNA 271
Query: 118 EMKAMAEKSRFGRVLEINGD-----TYVQEVNNAGE 148
E A E S G VL ING Q VN A
Sbjct: 272 EYDAGPE-SFVGPVLMINGSLGAGGAERQFVNTAVA 306
>gnl|CDD|227466 COG5137, COG5137, Histone chaperone involved in gene silencing
[Transcription / Chromatin structure and dynamics].
Length = 279
Score = 28.4 bits (63), Expect = 2.6
Identities = 11/50 (22%), Positives = 27/50 (54%)
Query: 59 QKEKEVTEDDIVNLVEQTVKEKQGKGEKELGDMDLDDLDELEDEEDERVL 108
++E E ++D + + + + +GE+E + ++ +L E+E EE+
Sbjct: 213 EEEAEGSDDGEDVVDYEGERIDKKQGEEEEMEEEVINLFEIEWEEESPSE 262
>gnl|CDD|220278 pfam09523, DUF2390, Protein of unknown function (DUF2390). Members
of this family are bacterial hypothetical proteins,
about 160 amino acids in length, found in various
proteobacteria, including members of the genera
Pseudomonas and Vibrio. The C-terminal region is poorly
conserved and is not included in the model.
Length = 109
Score = 27.6 bits (62), Expect = 2.8
Identities = 9/32 (28%), Positives = 11/32 (34%)
Query: 86 KELGDMDLDDLDELEDEEDERVLQEYRRKRIA 117
+ L DL L E V+Q R R
Sbjct: 45 RSLSAEDLQALQAAAAPWREEVVQPLRALRRQ 76
>gnl|CDD|235366 PRK05218, PRK05218, heat shock protein 90; Provisional.
Length = 613
Score = 28.5 bits (65), Expect = 3.2
Identities = 22/67 (32%), Positives = 30/67 (44%), Gaps = 10/67 (14%)
Query: 49 DILRAKGIIPQKEKEV--TEDDIVNLVEQTVKEKQGKGEK--ELGDMDLDDLDELEDEED 104
++ + KGI EV D I ++E GK K GD+DL DE E EE
Sbjct: 434 ELFKKKGI------EVLLLTDPIDEFWISYLEEFDGKPFKSVARGDLDLGKEDEEEKEEK 487
Query: 105 ERVLQEY 111
E +E+
Sbjct: 488 EEAEEEF 494
>gnl|CDD|227563 COG5238, RNA1, Ran GTPase-activating protein (RanGAP) involved in
mRNA processing and transport [Signal transduction
mechanisms / RNA processing and modification].
Length = 388
Score = 28.4 bits (63), Expect = 3.4
Identities = 9/45 (20%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 66 EDDIVNLVEQTVKEKQGKGEKELGDMDLDDLDELEDEEDERVLQE 110
D + E + E EK+ GD+ ++ + E E++ + +
Sbjct: 318 LADFGDYYED-IFEVVEVVEKQEGDVVTEESTDEESEDEVEIDES 361
>gnl|CDD|226591 COG4106, Tam, Trans-aconitate methyltransferase [General function
prediction only].
Length = 257
Score = 28.1 bits (63), Expect = 3.4
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 4/37 (10%)
Query: 96 LDELEDEEDERVLQEYRRKRIAEMKAMAEKSRFGRVL 132
LD L++EE +R L Y A+ GRVL
Sbjct: 211 LDRLDEEERQRFLDRYLALLAEAYPPRAD----GRVL 243
>gnl|CDD|204784 pfam11932, DUF3450, Protein of unknown function (DUF3450). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria and eukaryotes.
Proteins in this family are about 260 amino acids in
length.
Length = 250
Score = 28.0 bits (63), Expect = 3.5
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 96 LDELED--EEDERVLQEYRRKRIAEMKAMAEKS------RFGRVLEI 134
+D LE D L+E R R+A ++ + +++ +F RVLE
Sbjct: 112 IDGLEQFVALDLPFLKEERLARLARLRDLMDRADVSLAEKFRRVLEA 158
>gnl|CDD|237192 PRK12758, PRK12758, DNA topoisomerase IV subunit A; Provisional.
Length = 869
Score = 28.4 bits (64), Expect = 3.5
Identities = 18/39 (46%), Positives = 23/39 (58%), Gaps = 5/39 (12%)
Query: 41 YEEDTQWNDILRA--KGIIPQKE---KEVTEDDIVNLVE 74
EE W ++ A KG+ P K+ +EVTEDDIV L E
Sbjct: 378 IEEAETWEAVIEAIDKGLEPFKKQFIREVTEDDIVRLTE 416
>gnl|CDD|234964 PRK01611, argS, arginyl-tRNA synthetase; Reviewed.
Length = 507
Score = 28.2 bits (64), Expect = 3.7
Identities = 17/63 (26%), Positives = 21/63 (33%), Gaps = 16/63 (25%)
Query: 95 DLDELEDEEDERVLQEYRRKRIAEMK-------AMAEKSR-------FGRVLEINGDT-- 138
LD+L DE R + K IAE +SR L G+
Sbjct: 332 TLDDLLDEAVGRARELIEEKEIAEAVGIDAVRYFDLSRSRDKDLDFDLDLALSFEGNNPP 391
Query: 139 YVQ 141
YVQ
Sbjct: 392 YVQ 394
>gnl|CDD|225423 COG2868, COG2868, Predicted ribosomal protein [Translation,
ribosomal structure and biogenesis].
Length = 109
Score = 26.9 bits (60), Expect = 3.9
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 165 NHLSELAAKFPTTKFIKSISTTC-IPNYPDKNLPTLFIYFEG 205
N + ELA + P T+ ++ IPN PD N + E
Sbjct: 45 NGIEELADQEPVTELVEGGYLYFEIPNLPDNNKEEAQLLLES 86
>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 156 to 174 amino acids in length. This domain is
found associated with pfam07780, pfam01728.
Length = 154
Score = 27.6 bits (62), Expect = 4.1
Identities = 10/54 (18%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 72 LVEQTVKEKQGKGEKELGDMDLDDLDELEDEEDERVLQEYRRKRIAEMKAMAEK 125
L ++++ + E+ +++ D +E DE E+ L + +R++ E + ++
Sbjct: 94 LGLDKKEKEEEEEEEV--EVEELDEEEQIDELLEKELAKLKREKRRENERKQKE 145
>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor
[Transcription].
Length = 392
Score = 28.1 bits (62), Expect = 4.1
Identities = 15/49 (30%), Positives = 23/49 (46%)
Query: 78 KEKQGKGEKELGDMDLDDLDELEDEEDERVLQEYRRKRIAEMKAMAEKS 126
KEKQG E+ M +DLD E + + + E +++ E AE
Sbjct: 259 KEKQGAEEEGEEGMSEEDLDVGAAEIENKEVSEGDKEQQQEEVENAEAH 307
>gnl|CDD|236833 PRK11059, PRK11059, regulatory protein CsrD; Provisional.
Length = 640
Score = 28.3 bits (64), Expect = 4.1
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 91 MDLDDLDELEDEEDERVLQEYR 112
+ L D D L++E E ++E
Sbjct: 265 IRLPDFDLLQEEWGESQVEELL 286
>gnl|CDD|216001 pfam00577, Usher, Type VII secretion system (T7SS), usher protein.
The chaperone-usher (CU) pathway or Type VII secretion
system (T7SS) in Gram-negative (diderm) bacteria is
responsible for the secretion and assembly of prepilins
for fimbriae biogenesis, the prototypical Type 1 pili.
Following the prepilins export to the periplasm by the
Sec translocon, the biogenesis of fimbriae requires a
two-component assembly and transport system which is
composed of a periplasmic chaperone and an outer
membrane protein, which has been termed a molecular
'usher'. The usher protein is rather large (from 86 to
100 Kd) and seems to be mainly composed of
membrane-spanning beta-sheets, a structure reminiscent
of porins. Although the degree of sequence similarity of
these proteins is not very high they share a number of
characteristics. One of these is the presence of two
pairs of cysteines, the first one located in the
N-terminal part and the second at the C-terminal
extremity that are probably involved in disulphide
bonds. The best conserved region is located in the
central part of these proteins.
Length = 552
Score = 28.0 bits (63), Expect = 4.3
Identities = 9/32 (28%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 1 MSISGTDTKKEERLIKSARNQILSLNLSVPFG 32
+S++ + ++ + R+ LSLN+S+P G
Sbjct: 348 VSLNWSYSRNAG---SNNRDDSLSLNISIPLG 376
>gnl|CDD|214923 smart00937, PCRF, This domain is found in peptide chain release
factors.
Length = 116
Score = 27.0 bits (61), Expect = 4.7
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 87 ELGDMDLDDLDELEDEEDERVLQEYRRKRIAEM 119
EL + + DD EE+ L+ + + E+
Sbjct: 1 ELLEEEEDDEMRELAEEELEELEAELEEELEEL 33
>gnl|CDD|233300 TIGR01174, ftsA, cell division protein FtsA. This bacterial cell
division protein interacts with FtsZ, the bacterial
homolog of tubulin. It is an ATP-binding protein and
shows structural similarities to actin and heat shock
cognate protein 70 [Cellular processes, Cell division].
Length = 371
Score = 28.0 bits (63), Expect = 4.8
Identities = 9/25 (36%), Positives = 17/25 (68%)
Query: 50 ILRAKGIIPQKEKEVTEDDIVNLVE 74
+ G++ K+KEVT++DI ++E
Sbjct: 82 SQNSIGVVAIKDKEVTQEDIERVLE 106
>gnl|CDD|214850 smart00842, FtsA, Cell division protein FtsA. FtsA is essential
for bacterial cell division, and co-localizes to the
septal ring with FtsZ. It has been suggested that the
interaction of FtsA-FtsZ has arisen through coevolution
in different bacterial strains.
Length = 187
Score = 27.4 bits (62), Expect = 4.9
Identities = 7/37 (18%), Positives = 17/37 (45%)
Query: 50 ILRAKGIIPQKEKEVTEDDIVNLVEQTVKEKQGKGEK 86
+ G++ +KE+T++DI ++E +
Sbjct: 81 SVNVSGVVAIPDKEITQEDIDRVLEAAKAVALPPDRE 117
>gnl|CDD|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated.
Length = 325
Score = 27.6 bits (62), Expect = 5.2
Identities = 9/35 (25%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 48 NDILRAKGIIPQKE-KEVTEDDIVNLVEQTVKEKQ 81
N LRA + K E + ++I L+++ V +
Sbjct: 173 NVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVS 207
>gnl|CDD|233914 TIGR02538, type_IV_pilB, type IV-A pilus assembly ATPase PilB.
This model describes a protein of type IV pilus
biogenesis designated PilB in Pseudomonas aeruginosa but
PilF in Neisseria gonorrhoeae; the more common usage,
reflected here, is PilB. This protein is an ATPase
involved in protein export for pilin assembly and is
closely related to GspE (TIGR02533) of type II
secretion, also called the main terminal branch of the
general secretion pathway. Note that type IV pilus
systems are often divided into type IV-A and IV-B, with
the latter group including bundle-forming pilus,
mannose-sensitive hemagglutinin, etc. Members of this
family are found in type IV-A systems [Cell envelope,
Surface structures, Protein fate, Protein and peptide
secretion and trafficking].
Length = 564
Score = 28.1 bits (63), Expect = 5.2
Identities = 12/44 (27%), Positives = 26/44 (59%), Gaps = 4/44 (9%)
Query: 64 VTEDDIVNLVEQ----TVKEKQGKGEKELGDMDLDDLDELEDEE 103
V ED + L+E+ + + G++++GD++ D+D ++DE
Sbjct: 123 VEEDKLSALIEKYYGGSDSLAKELGDEDIGDLEELDVDAIDDEG 166
>gnl|CDD|219512 pfam07683, CobW_C, Cobalamin synthesis protein cobW C-terminal
domain. This is a large and diverse family of putative
metal chaperones that can be separated into up to 15
subgroups. In addition to known roles in cobalamin
biosynthesis and the activation of the Fe-type nitrile
hydratase, this family is also known to be involved in
the response to zinc limitation. The CobW subgroup
involved in cobalamin synthesis represents only a small
sub-fraction of the family.
Length = 94
Score = 26.4 bits (59), Expect = 5.2
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 42 EEDTQWNDILRAKGII 57
E+ ILRAKGI+
Sbjct: 22 EDLLLPEGILRAKGIL 37
>gnl|CDD|180975 PRK07429, PRK07429, phosphoribulokinase; Provisional.
Length = 327
Score = 27.7 bits (62), Expect = 5.2
Identities = 10/43 (23%), Positives = 20/43 (46%)
Query: 131 VLEINGDTYVQEVNNAGEGIWVVLHFIPLCSLINNHLSELAAK 173
VLE++G +++ +N E I++ H + L+ L
Sbjct: 247 VLEVDGHATLEQFDNLEEMIYIEPHLSNTSTKYYGELTGLLLG 289
>gnl|CDD|223136 COG0058, GlgP, Glucan phosphorylase [Carbohydrate transport and
metabolism].
Length = 750
Score = 27.7 bits (62), Expect = 6.4
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 86 KELGDMDLDDLDELEDEEDERVLQEYRRKRIAEMKAMAEKSRFGRVLEING 136
+++GD L+DLD L++ + R+ IAE+K +K + + G
Sbjct: 431 EKIGDEWLNDLDILDELLWFADDKA-FRELIAEIKRENKKRLAEEIADRTG 480
>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional.
Length = 191
Score = 27.3 bits (61), Expect = 6.4
Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 5/82 (6%)
Query: 57 IPQKEKEVTEDDIVNLVEQTVKEKQGKGEKELGDMDLDDLDELEDEEDERVLQ-----EY 111
+E EV E + E+TV+E+ + + +L+ DE +ER L+ E
Sbjct: 10 EEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELEAKLDELEERYLRLQADFEN 69
Query: 112 RRKRIAEMKAMAEKSRFGRVLE 133
++RI + AEK R +
Sbjct: 70 YKRRIQKENEAAEKYRAQSLAS 91
>gnl|CDD|215003 smart01060, Catalase, Catalases are antioxidant enzymes that
catalyse the conversion of hydrogen peroxide to water
and molecular oxygen, serving to protect cells from its
toxic effects. Hydrogen peroxide is produced as a
consequence of oxidative cellular metabolism and can be
converted to the highly reactive hydroxyl radical via
transition metals, this radical being able to damage a
wide variety of molecules within a cell, leading to
oxidative stress and cell death. Catalases act to
neutralise hydrogen peroxide toxicity, and are produced
by all aerobic organisms ranging from bacteria to man.
Most catalases are mono-functional, haem-containing
enzymes, although there are also bifunctional
haem-containing peroxidase/catalases that are closely
related to plant peroxidases, and non-haem,
manganese-containing catalases that are found in
bacteria.
Length = 373
Score = 27.4 bits (62), Expect = 6.9
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 143 VNNAGEGIWVVLHFIPL---CSLINNHLSELAAKFP 175
VN GE +V HF P +L ++LA K P
Sbjct: 193 VNAEGERFYVKFHFKPDQGIKNLTWEEAAKLAGKDP 228
>gnl|CDD|215923 pfam00445, Ribonuclease_T2, Ribonuclease T2 family.
Length = 182
Score = 27.0 bits (60), Expect = 6.9
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 49 DILRAKGIIPQKEKEVTEDDIVNLVEQ 75
DIL + GI P K T +I N +++
Sbjct: 116 DILASAGIKPSDGKTYTLSEIENALKK 142
>gnl|CDD|224246 COG1327, COG1327, Predicted transcriptional regulator, consists of
a Zn-ribbon and ATP-cone domains [Transcription].
Length = 156
Score = 26.4 bits (59), Expect = 8.2
Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 13/77 (16%)
Query: 64 VTEDDIVNLVEQTVKEKQGKGE-----KELGDMDLDDLDELEDEEDERVLQEYRR----- 113
V+ + I V ++ + GE KE+G++ +++L +L++ R YR
Sbjct: 79 VSSEQIEEAVSHIERQLRSSGEREVPSKEIGELVMEELKKLDEVAYVRFASVYRSFKDVD 138
Query: 114 ---KRIAEMKAMAEKSR 127
+ I E+ EK R
Sbjct: 139 DFEEEIEELTKEGEKKR 155
>gnl|CDD|223824 COG0753, KatE, Catalase [Inorganic ion transport and metabolism].
Length = 496
Score = 27.3 bits (61), Expect = 8.3
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 143 VNNAGEGIWVVLHFIPL---CSLINNHLSELAAKFP 175
VN G+ +WV HF P +L + ++LA K P
Sbjct: 212 VNAKGKRVWVKFHFKPKQGIKNLTWDEAAKLAGKDP 247
>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen;
Provisional.
Length = 1136
Score = 27.4 bits (60), Expect = 8.8
Identities = 21/91 (23%), Positives = 50/91 (54%)
Query: 36 NLKPNYEEDTQWNDILRAKGIIPQKEKEVTEDDIVNLVEQTVKEKQGKGEKELGDMDLDD 95
N++ N EE+ + N + + + +E E+++ VE+ ++E + +E + ++++
Sbjct: 962 NVEENVEENVEENVEENVEENVEENVEENVEENVEENVEENIEENVEENVEENIEENVEE 1021
Query: 96 LDELEDEEDERVLQEYRRKRIAEMKAMAEKS 126
DE EE E ++EY + + E++ AE++
Sbjct: 1022 YDEENVEEVEENVEEYDEENVEEIEENAEEN 1052
>gnl|CDD|224477 COG1561, COG1561, Uncharacterized stress-induced protein [Function
unknown].
Length = 290
Score = 26.8 bits (60), Expect = 9.1
Identities = 23/108 (21%), Positives = 48/108 (44%), Gaps = 21/108 (19%)
Query: 49 DILRAKGIIPQKEKEVTEDDIVNLV----EQTVK------EKQGKGEKELGDMDLDDLDE 98
D+LR G++ +E+E + + L+ E+ + E++G K LD ++E
Sbjct: 109 DLLRLPGVLAIEEEEEDLEALEALILAALEEALDDLIEMREREGAALKADLLQRLDAIEE 168
Query: 99 LEDEEDER---VLQEYRRKRIAEMKAMAEKSRFGRVLEINGDTYVQEV 143
L ++ + +L+ YR + +A + +++ D QEV
Sbjct: 169 LVEKVESLMPEILEWYRERLVARLNEA--------QDQLDEDRLEQEV 208
>gnl|CDD|234032 TIGR02855, spore_yabG, sporulation peptidase YabG. Members of this
family are the protein YabG, demonstrated for Bacillus
subtilis to be an endopeptidase able to release
N-terminal peptides from a number of sporulation
proteins, including CotT, CotF, and SpoIVA. It appears
to be expressed under control of sigma-K [Cellular
processes, Sporulation and germination].
Length = 283
Score = 26.9 bits (60), Expect = 9.3
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 66 EDDIVNLVEQTVKEKQGKGEKELGDMDLDDLDELEDEEDERVLQEYRRKRIAEMKAMAEK 125
DD+ LV+++ ++K+ K KE + +D + + +EYR + +
Sbjct: 46 LDDLE-LVDESERKKRKKRFKERMETSYRLF--RQDYKLMKEKKEYRATGGYKNNQLY-F 101
Query: 126 SRFGRVLEINGD 137
GRVL I+GD
Sbjct: 102 GMPGRVLHIDGD 113
>gnl|CDD|172358 PRK13831, PRK13831, conjugal transfer protein TrbI; Provisional.
Length = 432
Score = 27.0 bits (60), Expect = 9.5
Identities = 10/25 (40%), Positives = 20/25 (80%)
Query: 99 LEDEEDERVLQEYRRKRIAEMKAMA 123
L+ E++E+ L+E +R+R+A ++A A
Sbjct: 132 LKREQEEQYLRERQRQRMARLQANA 156
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
0.314 0.134 0.378
Gapped
Lambda K H
0.267 0.0853 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,683,079
Number of extensions: 1129896
Number of successful extensions: 1605
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1527
Number of HSP's successfully gapped: 143
Length of query: 228
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 134
Effective length of database: 6,768,326
Effective search space: 906955684
Effective search space used: 906955684
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.5 bits)