RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6451
(332 letters)
>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 = 171 bits (436), Expect = 9e-54
Identities = 64/113 (56%), Positives = 83/113 (73%)
Query: 129 QGHGEYEEIPDEKKFFDLCKKSPNMVVHFYKDGSVNCKILDEHMKTLCKKHLETRFIKLN 188
+GHG+Y E+ DEK+FF++ K S +V HFY CKI+D+H++ L KKHLET+FIK+N
Sbjct: 1 KGHGKYREVSDEKEFFEIVKSSERVVCHFYHPEFFRCKIMDKHLEILAKKHLETKFIKVN 60
Query: 189 VERAPFLTERLRIKVIPTLTLVKDSVTKDYIVGFTELGNCADFSTEMLEWRIA 241
E+APFL E+L IKV+PT+ L K+ T D IVGF ELG DFSTE LE R+A
Sbjct: 61 AEKAPFLVEKLNIKVLPTVILFKNGKTVDRIVGFEELGGKDDFSTETLEKRLA 113
Score = 101 bits (254), Expect = 8e-27
Identities = 37/67 (55%), Positives = 50/67 (74%)
Query: 60 GHGEYEEIPDEKKFFDLCKKSPNMVVHFYKDGSVNCKILDEHMKTLCKKHLETRFIKLNV 119
GHG+Y E+ DEK+FF++ K S +V HFY CKI+D+H++ L KKHLET+FIK+N
Sbjct: 2 GHGKYREVSDEKEFFEIVKSSERVVCHFYHPEFFRCKIMDKHLEILAKKHLETKFIKVNA 61
Query: 120 ERAPFLT 126
E+APFL
Sbjct: 62 EKAPFLV 68
>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 = 119 bits (301), Expect = 1e-33
Identities = 54/116 (46%), Positives = 72/116 (62%), Gaps = 6/116 (5%)
Query: 129 QGHGEYEEIPDEKKFFDLCKKSP---NMVVHFYKDGSVNCKILDEHMKTLCKKHLETRFI 185
+G GE EI K+F + K+ +VVHFY+ G CKILD H++ L K+ ET+F+
Sbjct: 1 KGFGEVREI-SSKEFLEEVTKASKGTRVVVHFYEPGFPRCKILDSHLEELAAKYPETKFV 59
Query: 186 KLNVERAPFLTERLRIKVIPTLTLVKDSVTKDYIVGFTELGNCADFSTEMLEWRIA 241
K+N E+A FL L IKV+PTL + K+ D IVGF ELG DF+TE LE +A
Sbjct: 60 KINAEKA-FLVNYLDIKVLPTLLVYKNGELIDNIVGFEELGG-DDFTTEDLEKFLA 113
Score = 69.9 bits (172), Expect = 4e-15
Identities = 29/66 (43%), Positives = 41/66 (62%), Gaps = 4/66 (6%)
Query: 60 GHGEYEEIPDEKKFFDLCKKSP---NMVVHFYKDGSVNCKILDEHMKTLCKKHLETRFIK 116
G GE EI K+F + K+ +VVHFY+ G CKILD H++ L K+ ET+F+K
Sbjct: 2 GFGEVREI-SSKEFLEEVTKASKGTRVVVHFYEPGFPRCKILDSHLEELAAKYPETKFVK 60
Query: 117 LNVERA 122
+N E+A
Sbjct: 61 INAEKA 66
>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 = 53.7 bits (130), Expect = 2e-09
Identities = 20/75 (26%), Positives = 39/75 (52%)
Query: 148 KKSPNMVVHFYKDGSVNCKILDEHMKTLCKKHLETRFIKLNVERAPFLTERLRIKVIPTL 207
K + +VV F+ CK + ++ L +++ + +F+K++V+ P L E ++ IPT
Sbjct: 8 KSAKPVVVDFWAPWCGPCKAIAPVLEELAEEYPKVKFVKVDVDENPELAEEYGVRSIPTF 67
Query: 208 TLVKDSVTKDYIVGF 222
K+ D +VG
Sbjct: 68 LFFKNGKEVDRVVGA 82
Score = 33.7 bits (78), Expect = 0.020
Identities = 13/53 (24%), Positives = 29/53 (54%)
Query: 78 KKSPNMVVHFYKDGSVNCKILDEHMKTLCKKHLETRFIKLNVERAPFLTGQQG 130
K + +VV F+ CK + ++ L +++ + +F+K++V+ P L + G
Sbjct: 8 KSAKPVVVDFWAPWCGPCKAIAPVLEELAEEYPKVKFVKVDVDENPELAEEYG 60
>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 = 50.7 bits (122), Expect = 1e-07
Identities = 33/102 (32%), Positives = 55/102 (53%), Gaps = 10/102 (9%)
Query: 17 EKQIDEEIYRLENLDLDSIEKLREDHLKKLKAKAKRNQELKALGHGEYEEI--PDEKKFF 74
++DEE+ E D +E+ R L ++KA A++++ GE EI PD +
Sbjct: 45 LDELDEELDEEE--DDRFLEEYRRKRLAEMKALAEKSK------FGEVYEISKPDYVREV 96
Query: 75 DLCKKSPNMVVHFYKDGSVNCKILDEHMKTLCKKHLETRFIK 116
K +VVH YKDG C++L++H+ L +K +T+F+K
Sbjct: 97 TEASKDTWVVVHLYKDGIPLCRLLNQHLSELARKFPDTKFVK 138
Score = 45.7 bits (109), Expect = 8e-06
Identities = 34/120 (28%), Positives = 54/120 (45%), Gaps = 14/120 (11%)
Query: 131 HGEYEEI--PDEKKFFDLCKKSPNMVVHFYKDGSVNCKILDEHMKTLCKKHLETRFIKLN 188
GE EI PD + K +VVH YKDG C++L++H+ L +K +T+F+K+
Sbjct: 81 FGEVYEISKPDYVREVTEASKDTWVVVHLYKDGIPLCRLLNQHLSELARKFPDTKFVKII 140
Query: 189 VERAPFLTERLRIKVIPTLTLVKDSVTKDYIVGFTELG----NCADFSTEMLEWRIAQAG 244
+ K +PT+ + ++ +G E G D LEW + Q G
Sbjct: 141 STQC---IPNYPDKNLPTILVYRNGDIVKQFIGLLEFGGMNTTMED-----LEWLLVQVG 192
>gnl|CDD|239282 cd02984, TRX_PICOT, TRX domain, PICOT (for PKC-interacting cousin
of TRX) subfamily; PICOT is a protein that interacts
with protein kinase C (PKC) theta, a calcium independent
PKC isoform selectively expressed in skeletal muscle and
T lymphocytes. PICOT contains an N-terminal TRX-like
domain, which does not contain the catalytic CXXC motif,
followed by one to three glutaredoxin domains. The
TRX-like domain is required for interaction with PKC
theta. PICOT inhibits the activation of c-Jun N-terminal
kinase and the transcription factors, AP-1 and NF-kB,
induced by PKC theta or T-cell activating stimuli.
Length = 97
Score = 41.1 bits (97), Expect = 6e-05
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 154 VVHFYKDGSVNCKILDEHMKTLCKK-HLETRFIKLNVERAPFLTERLRIKVIPTLTLVKD 212
V+HF+ + CK +++ + L K+ F+ + E P ++E+ I +PT ++
Sbjct: 18 VLHFWAPWAEPCKQMNQVFEELAKEAFPSVLFLSIEAEELPEISEKFEITAVPTFVFFRN 77
Query: 213 SVTKDYIVGF 222
D + G
Sbjct: 78 GTIVDRVSGA 87
Score = 29.5 bits (67), Expect = 0.77
Identities = 10/41 (24%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 84 VVHFYKDGSVNCKILDEHMKTLCKK-HLETRFIKLNVERAP 123
V+HF+ + CK +++ + L K+ F+ + E P
Sbjct: 18 VLHFWAPWAEPCKQMNQVFEELAKEAFPSVLFLSIEAEELP 58
>gnl|CDD|173347 PTZ00051, PTZ00051, thioredoxin; Provisional.
Length = 98
Score = 35.6 bits (82), Expect = 0.005
Identities = 17/86 (19%), Positives = 41/86 (47%)
Query: 136 EIPDEKKFFDLCKKSPNMVVHFYKDGSVNCKILDEHMKTLCKKHLETRFIKLNVERAPFL 195
+ + +F ++ ++V FY + CK + + K++ + F+K++V+ +
Sbjct: 4 IVTSQAEFESTLSQNELVIVDFYAEWCGPCKRIAPFYEECSKEYTKMVFVKVDVDELSEV 63
Query: 196 TERLRIKVIPTLTLVKDSVTKDYIVG 221
E+ I +PT + K+ D ++G
Sbjct: 64 AEKENITSMPTFKVFKNGSVVDTLLG 89
>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 = 36.9 bits (86), Expect = 0.006
Identities = 19/94 (20%), Positives = 41/94 (43%), Gaps = 8/94 (8%)
Query: 31 DLDSIEKLREDHLKKLKAKAKRNQELKALGHGEY----EEIPDEKKFFDLCKKSPN---M 83
+ D ++ +E+ L++ + + + + L G E+ ++F D K +
Sbjct: 28 EDDDDDEDKEEFLQQYR-EQRMQEMHAKLPFGRRFGKVYELDSGEQFLDAIDKEGKDTTV 86
Query: 84 VVHFYKDGSVNCKILDEHMKTLCKKHLETRFIKL 117
VVH Y+ G C L+ + L ++ +F K+
Sbjct: 87 VVHIYEPGIPGCAALNSSLLCLAAEYPAVKFCKI 120
Score = 29.6 bits (67), Expect = 1.4
Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 4/84 (4%)
Query: 132 GEYEEIPDEKKFFDLCKKSPN---MVVHFYKDGSVNCKILDEHMKTLCKKHLETRFIKLN 188
G+ E+ ++F D K +VVH Y+ G C L+ + L ++ +F K+
Sbjct: 62 GKVYELDSGEQFLDAIDKEGKDTTVVVHIYEPGIPGCAALNSSLLCLAAEYPAVKFCKIR 121
Query: 189 VERAPFLTERLRIKVIPTLTLVKD 212
A ++ +P L + K
Sbjct: 122 AS-ATGASDEFDTDALPALLVYKG 144
>gnl|CDD|182889 PRK10996, PRK10996, thioredoxin 2; Provisional.
Length = 139
Score = 36.2 bits (84), Expect = 0.007
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 183 RFIKLNVERAPFLTERLRIKVIPTLTLVKDSVTKDYIVG 221
RF+K+N E L+ R RI+ IPT+ + K+ D + G
Sbjct: 86 RFVKVNTEAERELSARFRIRSIPTIMIFKNGQVVDMLNG 124
>gnl|CDD|238829 cd01659, TRX_superfamily, Thioredoxin (TRX) superfamily; a large,
diverse group of proteins containing a TRX-fold. Many
members contain a classic TRX domain with a redox active
CXXC motif. They function as protein disulfide
oxidoreductases (PDOs), altering the redox state of
target proteins via the reversible oxidation of their
active site dithiol. The PDO members of this superfamily
include TRX, protein disulfide isomerase (PDI),
tlpA-like, glutaredoxin, NrdH redoxin, and the bacterial
Dsb (DsbA, DsbC, DsbG, DsbE, DsbDgamma) protein
families. Members of the superfamily that do not
function as PDOs but contain a TRX-fold domain include
phosducins, peroxiredoxins and glutathione (GSH)
peroxidases, SCO proteins, GSH transferases (GST,
N-terminal domain), arsenic reductases, TRX-like
ferredoxins and calsequestrin, among others.
Length = 69
Score = 34.2 bits (78), Expect = 0.009
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 3/68 (4%)
Query: 154 VVHFYKDGSVNCKILDEHMKTLCKKHLETRFIKLNVERAPFLTE---RLRIKVIPTLTLV 210
+V FY C+ L + L + +F ++V+ P L + R + +PTL +
Sbjct: 1 LVLFYAPWCPFCQALRPVLAELALLNKGVKFEAVDVDEDPALEKELKRYGVGGVPTLVVF 60
Query: 211 KDSVTKDY 218
+ Y
Sbjct: 61 GPGIGVKY 68
Score = 29.6 bits (66), Expect = 0.44
Identities = 11/55 (20%), Positives = 21/55 (38%)
Query: 84 VVHFYKDGSVNCKILDEHMKTLCKKHLETRFIKLNVERAPFLTGQQGHGEYEEIP 138
+V FY C+ L + L + +F ++V+ P L + +P
Sbjct: 1 LVLFYAPWCPFCQALRPVLAELALLNKGVKFEAVDVDEDPALEKELKRYGVGGVP 55
>gnl|CDD|223600 COG0526, TrxA, Thiol-disulfide isomerase and thioredoxins
[Posttranslational modification, protein turnover,
chaperones / Energy production and conversion].
Length = 127
Score = 33.7 bits (76), Expect = 0.040
Identities = 23/109 (21%), Positives = 39/109 (35%), Gaps = 4/109 (3%)
Query: 122 APFLTGQQGHGEYEEIPDEKKFFDLCKKSPNMVVHFYKDGSVNCKILDEHMKTLCKKHLE 181
FL G+ E D K ++V F+ C+ ++ L +++
Sbjct: 4 LSFLLGELATAASFEELDGAPLSLSELKGKPVLVDFWAPWCPPCRAEAPLLEELAEEYGG 63
Query: 182 T-RFIKLNV---ERAPFLTERLRIKVIPTLTLVKDSVTKDYIVGFTELG 226
+ +NV + ++ IPTL L KD D +VG L
Sbjct: 64 DVEVVAVNVDDENPDLAAEFGVAVRSIPTLLLFKDGKEVDRLVGGKVLP 112
>gnl|CDD|200072 TIGR01068, thioredoxin, thioredoxin. Several proteins, such as
protein disulfide isomerase, have two or more copies of
a domain closely related to thioredoxin. This model is
designed to recognize authentic thioredoxin, a small
protein that should be hit exactly once by This model.
Any protein that hits once with a score greater than the
second (per domain) trusted cutoff may be taken as
thioredoxin [Energy metabolism, Electron transport].
Length = 101
Score = 32.6 bits (75), Expect = 0.062
Identities = 27/89 (30%), Positives = 40/89 (44%), Gaps = 8/89 (8%)
Query: 139 DEKKFFDLCKKSPNMV-VHFYKDGSVNCK----ILDEHMKTLCKKHLETRFIKLNVERAP 193
+ F + S V V F+ CK IL+E K + + +F+KLNV+ P
Sbjct: 2 TDANFDETIASSDKPVLVDFWAPWCGPCKMIAPILEELAK---EYEGKVKFVKLNVDENP 58
Query: 194 FLTERLRIKVIPTLTLVKDSVTKDYIVGF 222
+ + I+ IPTL L K+ D VG
Sbjct: 59 DIAAKYGIRSIPTLLLFKNGKEVDRSVGA 87
>gnl|CDD|239254 cd02956, ybbN, ybbN protein family; ybbN is a hypothetical protein
containing a redox-inactive TRX-like domain. Its gene
has been sequenced from several gammaproteobacteria and
actinobacteria.
Length = 96
Score = 31.5 bits (72), Expect = 0.13
Identities = 14/61 (22%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 154 VVHFYKDGSVNCKILDEHMKTLCKKHLETRFI--KLNVERAPFLTERLRIKVIPTLTLVK 211
VV F+ S K L ++ L +++ + +F+ K+N + P + ++ ++ +PT+ L
Sbjct: 16 VVDFWAPRSPPSKELLPLLERLAEEY-QGQFVLAKVNCDAQPQIAQQFGVQALPTVYLFA 74
Query: 212 D 212
Sbjct: 75 A 75
>gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional.
Length = 585
Score = 31.9 bits (72), Expect = 0.45
Identities = 15/61 (24%), Positives = 32/61 (52%)
Query: 82 NMVVHFYKDGSVNCKILDEHMKTLCKKHLETRFIKLNVERAPFLTGQQGHGEYEEIPDEK 141
N+ HFYK S + IL+++ +C H + F+ ++ ++ + G++ + D+K
Sbjct: 14 NVGSHFYKQHSFSKIILNKNKNIICPVHCKQCFVTMSEKKEHVMEGEKKVRSVQASKDKK 73
Query: 142 K 142
K
Sbjct: 74 K 74
>gnl|CDD|215704 pfam00085, Thioredoxin, Thioredoxin. Thioredoxins are small
enzymes that participate in redox reactions, via the
reversible oxidation of an active centre disulfide bond.
Some members with only the active site are not separated
from the noise.
Length = 104
Score = 29.9 bits (68), Expect = 0.60
Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 3/84 (3%)
Query: 141 KKFFD--LCKKSPNMVVHFYKDGSVNCKILDEHMKTLCKKHLET-RFIKLNVERAPFLTE 197
+ FD + K ++V FY CK L + L +++ + +F K++ + P L
Sbjct: 7 DENFDEEVAKSDKPVLVDFYAPWCGPCKALAPEYEKLAQEYKDDVKFAKVDADENPDLAS 66
Query: 198 RLRIKVIPTLTLVKDSVTKDYIVG 221
++ PT+ K+ VG
Sbjct: 67 EYGVRGFPTIKFFKNGKKVSDYVG 90
>gnl|CDD|225660 COG3118, COG3118, Thioredoxin domain-containing protein
[Posttranslational modification, protein turnover,
chaperones].
Length = 304
Score = 30.4 bits (69), Expect = 1.1
Identities = 9/32 (28%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 183 RFI--KLNVERAPFLTERLRIKVIPTLTLVKD 212
+F K+N + P + + ++ IPT+ KD
Sbjct: 75 KFKLAKVNCDAEPMVAAQFGVQSIPTVYAFKD 106
>gnl|CDD|240266 PTZ00102, PTZ00102, disulphide isomerase; Provisional.
Length = 477
Score = 30.1 bits (68), Expect = 1.9
Identities = 16/94 (17%), Positives = 32/94 (34%), Gaps = 6/94 (6%)
Query: 124 FLTGQQGHGEYEEIPD--EKKFFDLCKKSPNMVVHFYKDGSVNCKIL----DEHMKTLCK 177
+ H E + + F ++ ++V FY +CK L + K L +
Sbjct: 21 VFGSAEEHFISEHVTVLTDSTFDKFITENEIVLVKFYAPWCGHCKRLAPEYKKAAKMLKE 80
Query: 178 KHLETRFIKLNVERAPFLTERLRIKVIPTLTLVK 211
K E ++ L + ++ PT+
Sbjct: 81 KKSEIVLASVDATEEMELAQEFGVRGYPTIKFFN 114
>gnl|CDD|236544 PRK09506, mrcB, bifunctional glycosyl transferase/transpeptidase;
Reviewed.
Length = 830
Score = 29.4 bits (66), Expect = 3.0
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 301 IKKKQKKRLIEKKKIIRGRNSSDEDSDDPDDW 332
I +K K K+K+ R R D+D DD DD+
Sbjct: 9 IGRKGKPSRPVKQKVSRRRYRDDDDYDDYDDY 40
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 29.3 bits (67), Expect = 3.5
Identities = 15/36 (41%), Positives = 25/36 (69%), Gaps = 2/36 (5%)
Query: 25 YRLENLDLDS-IEKLREDHLKKLKAKAKRNQELKAL 59
L+N+DL++ E+LRE+ LK+ ++ KR + LK L
Sbjct: 177 ELLKNIDLEAEAEELREE-LKETGSEQKRKKALKRL 211
>gnl|CDD|218623 pfam05524, PEP-utilisers_N, PEP-utilising enzyme, N-terminal.
Length = 123
Score = 28.0 bits (63), Expect = 3.9
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 4 VLQDTVLNVAKNVEKQIDEEIYRLENLDLDSIEKLREDHLKKLKAKAKRN 53
VL + V + + ++ EI RLE ++EK RE+ L+ L +A +
Sbjct: 17 VLDEPEPEVPERSVEDVEAEIARLEA----ALEKAREE-LEALAERAAES 61
>gnl|CDD|219841 pfam08438, MMR_HSR1_C, GTPase of unknown function C-terminal. This
domain is found at the C-terminus of pfam01926 in
archaeal and eukaryotic GTP-binding proteins. The
C-terminal domain of the GTP-binding proteins is
necessary for the complete activity of the protein of
interacting with the 50S ribosome and binding of both
adenine and guanine nucleotides, with a preference for
guanine nucleotides.
Length = 109
Score = 27.5 bits (62), Expect = 4.1
Identities = 17/49 (34%), Positives = 29/49 (59%), Gaps = 6/49 (12%)
Query: 239 RIAQAGVIDYE-GDL-FNPPD---IKKKQKKRMIE-KKKIIRGRNSTGV 281
+ A+AG+IDY GD F + +KQKK + + ++ +++ STGV
Sbjct: 39 KAAKAGLIDYLPGDSDFEITGEDKLSEKQKKALEKIREFVLKRYGSTGV 87
>gnl|CDD|181812 PRK09381, trxA, thioredoxin; Provisional.
Length = 109
Score = 27.7 bits (61), Expect = 4.2
Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 1/88 (1%)
Query: 145 DLCKKSPNMVVHFYKDGSVNCKILDEHMKTLCKKHL-ETRFIKLNVERAPFLTERLRIKV 203
D+ K ++V F+ + CK++ + + ++ + KLN+++ P + I+
Sbjct: 16 DVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRG 75
Query: 204 IPTLTLVKDSVTKDYIVGFTELGNCADF 231
IPTL L K+ VG G +F
Sbjct: 76 IPTLLLFKNGEVAATKVGALSKGQLKEF 103
>gnl|CDD|184003 PRK13364, PRK13364, protocatechuate 4,5-dioxygenase subunit beta;
Provisional.
Length = 278
Score = 28.5 bits (64), Expect = 4.3
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 8/42 (19%)
Query: 61 HGEYEEIPDEKKFFD--------LCKKSPNMVVHFYKDGSVN 94
++ P K FFD L K P++ V FY D +N
Sbjct: 21 AKGLQQDPYWKPFFDGFPPVREWLEKVKPDVAVVFYNDHGLN 62
Score = 28.5 bits (64), Expect = 4.3
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 8/42 (19%)
Query: 131 HGEYEEIPDEKKFFD--------LCKKSPNMVVHFYKDGSVN 164
++ P K FFD L K P++ V FY D +N
Sbjct: 21 AKGLQQDPYWKPFFDGFPPVREWLEKVKPDVAVVFYNDHGLN 62
>gnl|CDD|223432 COG0355, AtpC, F0F1-type ATP synthase, epsilon subunit
(mitochondrial delta subunit) [Energy production and
conversion].
Length = 135
Score = 27.6 bits (62), Expect = 4.4
Identities = 10/50 (20%), Positives = 21/50 (42%)
Query: 9 VLNVAKNVEKQIDEEIYRLENLDLDSIEKLREDHLKKLKAKAKRNQELKA 58
L V N + + R +++D E+ +E K+L++ +A
Sbjct: 69 FLEVQPNEVTILADSAERADDIDEARAEEAKERAEKELESAKDDKDYRRA 118
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 28.8 bits (65), Expect = 4.6
Identities = 14/71 (19%), Positives = 37/71 (52%), Gaps = 12/71 (16%)
Query: 14 KNVEKQIDE---------EIYRLENLDLDSIEKLRE--DHLKKLKAKAKRNQELKALGHG 62
+++EK++ E E ++ E + I++++E + ++ +A+R +L
Sbjct: 437 EDLEKELAELEEEYADLEEQWKAEKAAIQGIQQIKEEIEQVRLELEQAEREGDLAKAAEL 496
Query: 63 EYEEIPD-EKK 72
+Y ++P+ EK+
Sbjct: 497 QYGKLPELEKR 507
>gnl|CDD|225971 COG3437, COG3437, Response regulator containing a CheY-like
receiver domain and an HD-GYP domain [Transcription /
Signal transduction mechanisms].
Length = 360
Score = 28.5 bits (64), Expect = 5.1
Identities = 8/40 (20%), Positives = 15/40 (37%)
Query: 284 YEAGVIDYEGDLFNPPDIKKKQKKRLIEKKKIIRGRNSSD 323
EAG DY +P ++ + L K+ + +
Sbjct: 108 LEAGADDYLSKPISPKELVARVSSHLQLKRNEDFLLDQNL 147
>gnl|CDD|222346 pfam13728, TraF, F plasmid transfer operon protein. TraF protein
undergoes proteolytic processing associated with export.
The 19 amino acids at the amino terminus of the
polypeptides appear to constitute a typical membrane
leader peptide - not included in this family, while the
remainder of the molecule is predicted to be primarily
hydrophilic in character. F plasmid TraF and TraH are
required for F pilus assembly and F plasmid transfer,
and they are both localised to the outer membrane in the
presence of the complete F transfer region, especially
TraV, the putative anchor.
Length = 215
Score = 27.6 bits (62), Expect = 7.6
Identities = 15/77 (19%), Positives = 26/77 (33%), Gaps = 12/77 (15%)
Query: 157 FYKDGSVNCKILDEHMKTLCKKH-LETRFIKLNVERAPFLT---------ERLRIKVIPT 206
FY+ C+ ++ K+ + ++ P +RL +K P
Sbjct: 127 FYRGDCPYCQAQAPILQAFADKYGFSVIPVSVDGGPLPGFPNNRVDTGQAQRLGVKTTPA 186
Query: 207 LTLVKDSVTKDYI-VGF 222
L LV D T V +
Sbjct: 187 LFLV-DPKTGKVKPVAY 202
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
0.317 0.137 0.399
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,668,981
Number of extensions: 1785605
Number of successful extensions: 2264
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2245
Number of HSP's successfully gapped: 101
Length of query: 332
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 235
Effective length of database: 6,635,264
Effective search space: 1559287040
Effective search space used: 1559287040
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: 41 (21.6 bits)
S2: 59 (26.5 bits)