RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10640
(242 letters)
>gnl|CDD|238847 cd01714, ETF_beta, The electron transfer flavoprotein (ETF) serves
as a specific electron acceptor for various
mitochondrial dehydrogenases. ETF transfers electrons to
the main respiratory chain via ETF-ubiquinone
oxidoreductase. ETF is an heterodimer that consists of
an alpha and a beta subunit which binds one molecule of
FAD per dimer . A similar system also exists in some
bacteria. The homologous pair of proteins (FixA/FixB)
are essential for nitrogen fixation. The beta subunit
protein is distantly related to and forms a heterodimer
with the alpha subunit.
Length = 202
Score = 162 bits (412), Expect = 5e-50
Identities = 61/176 (34%), Positives = 87/176 (49%), Gaps = 48/176 (27%)
Query: 38 RETIRTALAMGADRGIHVEVSGPEYETLQPFHISKILAKVAQEEKVDMVIVGKQKAKKKP 97
E +R ALAMGADR I V S + +K LA ++ VD+++ GKQ
Sbjct: 66 EEALREALAMGADRAILV--SDRAFAGADTLATAKALAAAIKKIGVDLILTGKQ------ 117
Query: 98 IKKVSPKDMGVDTGAHIEIVTVEDPPVRQAGSIVPDVDTLAIDDDSNQTAQMTAAFLNWP 157
+ID D+ Q + A L WP
Sbjct: 118 ----------------------------------------SIDGDTGQVGPLLAELLGWP 137
Query: 158 QATFASKVDKTDGELTVKREIDGGLETIKVKLPAVISADLRLNEPRYATLPNIMKS 213
Q T+ SK++ G++TV+RE++GG+ET++VKLPAVI+ DL +NEPRY +LP IMK+
Sbjct: 138 QITYVSKIEIEGGKVTVERELEGGVETVEVKLPAVITVDLGINEPRYPSLPGIMKA 193
>gnl|CDD|224997 COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy
production and conversion].
Length = 260
Score = 144 bits (365), Expect = 2e-42
Identities = 60/176 (34%), Positives = 84/176 (47%), Gaps = 49/176 (27%)
Query: 38 RETIRTALAMGADRGIHVEVSGPEYETLQPFHISKILAKVAQEEKVDMVIVGKQKAKKKP 97
E +R ALAMGADR I + + P +K LA ++ D+V+ GKQ
Sbjct: 69 EEALREALAMGADRAILIT--DRAFAGADPLATAKALAAAVKKIGPDLVLTGKQ------ 120
Query: 98 IKKVSPKDMGVDTGAHIEIVTVEDPPVRQAGSIVPDVDTLAIDDDSNQTAQMTAAFLNWP 157
AID D+ Q + A L WP
Sbjct: 121 ----------------------------------------AIDGDTGQVGPLLAELLGWP 140
Query: 158 QATFASKVDKTDG-ELTVKREIDGGLETIKVKLPAVISADLRLNEPRYATLPNIMK 212
Q T+ SK++ DG ++TV+RE++GGLET++ LPAV++ DLR+NEPRY +LP IM
Sbjct: 141 QVTYVSKIEIVDGGKVTVERELEGGLETVEAPLPAVVTVDLRINEPRYPSLPGIMA 196
Score = 38.8 bits (91), Expect = 0.001
Identities = 21/48 (43%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 89 GKQKAKKKPIKKVSPKDMG---VDTGAHIEIVTVEDPPVRQAGSIVPD 133
G AKKKP+KK S D+G G+ +++V V PP R+AG V D
Sbjct: 193 GIMAAKKKPVKKWSLADLGLNVGLAGSPLKVVKVTPPPERKAGVKVKD 240
>gnl|CDD|238943 cd01985, ETF, The electron transfer flavoprotein (ETF) serves as a
specific electron acceptor for various mitochondrial
dehydrogenases. ETF transfers electrons to the main
respiratory chain via ETF-ubiquinone oxidoreductase. ETF
is an heterodimer that consists of an alpha and a beta
subunit which binds one molecule of FAD per dimer . A
similar system also exists in some bacteria. The
homologous pair of proteins (FixA/FixB) are essential
for nitrogen fixation. The alpha subunit of ETF is
structurally related to the bacterial nitrogen fixation
protein fixB which could play a role in a redox process
and feed electrons to ferredoxin. The beta subunit
protein is distantly related to and forms a heterodimer
with the alpha subunit.
Length = 181
Score = 104 bits (261), Expect = 7e-28
Identities = 50/177 (28%), Positives = 69/177 (38%), Gaps = 54/177 (30%)
Query: 39 ETIRTALAMGADRGIHVEVSGPEYETLQPFHISKILAKVAQEEKVDMVIVGKQKAKKKPI 98
+R ALAMGAD+ + VE P P +K LA + ++EK D+++ G
Sbjct: 50 VALREALAMGADKVLLVE--DPALAGYDPEATAKALAALIKKEKPDLILAGAT------- 100
Query: 99 KKVSPKDMGVDTGAHIEIVTVEDPPVRQAGSIVPDVDTLAIDDDSNQTAQMTAAFLNWPQ 158
SI Q A AA L PQ
Sbjct: 101 ------------------------------SI------------GKQLAPRVAALLGVPQ 118
Query: 159 ATFASKVDKTDGELTVKREI--DGGLETIKVK-LPAVISADLRLNEPRYATLPNIMK 212
+ +K++ G+LTV R I GLET++ LPAVI+ EPRY + P K
Sbjct: 119 ISDVTKLEIDGGDLTVTRPIYAGNGLETVESPDLPAVITVRPGAFEPRYPSGPGKKK 175
>gnl|CDD|214890 smart00893, ETF, Electron transfer flavoprotein domain. Electron
transfer flavoproteins (ETFs) serve as specific electron
acceptors for primary dehydrogenases, transferring the
electrons to terminal respiratory systems. They can be
functionally classified into constitutive,
"housekeeping" ETFs, mainly involved in the oxidation of
fatty acids (Group I), and ETFs produced by some
prokaryotes under specific growth conditions, receiving
electrons only from the oxidation of specific substrates
(Group II). ETFs are heterodimeric proteins composed of
an alpha and beta subunit, and contain an FAD cofactor
and AMP. ETF consists of three domains: domains I and II
are formed by the N- and C-terminal portions of the
alpha subunit, respectively, while domain III is formed
by the beta subunit. Domains I and III share an almost
identical alpha-beta-alpha sandwich fold, while domain
II forms an alpha-beta-alpha sandwich similar to that of
bacterial flavodoxins. FAD is bound in a cleft between
domains II and III, while domain III binds the AMP
molecule. Interactions between domains I and III
stabilise the protein, forming a shallow bowl where
domain II resides. This entry represents the N-terminal
domain of both the alpha and beta subunits from Group I
and Group II ETFs.
Length = 185
Score = 92.7 bits (231), Expect = 2e-23
Identities = 50/182 (27%), Positives = 70/182 (38%), Gaps = 60/182 (32%)
Query: 39 ETIRTALAMGADRGIHVEVSGPE-YETLQPFHISKILAKVAQEEKVDMVIVGKQKAKKKP 97
E +R ALAMGAD+ V+ Y+TL +++ LA + +EEK D+V+ G
Sbjct: 41 EALREALAMGADKVYLVDDDALAGYDTLAT--LAEALAALIKEEKPDLVLAGAT------ 92
Query: 98 IKKVSPKDMGVDTGAHIEIVTVEDPPVRQAGSIVPDVDTLAIDDDSNQTAQMTAAFLNWP 157
D Q A AA L P
Sbjct: 93 -------------------------------------------SDGKQLAPRLAALLGVP 109
Query: 158 QATFASKVDKTDGELTVKREIDGGL---ETIKVKLPAVISADLRLNEP----RYATLPNI 210
Q T +K++ DG+ V+R GG E ++ LPAVI+ EP Y +L I
Sbjct: 110 QITDVTKLE-VDGDTFVRRIYGGGAIATEVVEADLPAVITVRPGAFEPAPRDGYPSLVEI 168
Query: 211 MK 212
MK
Sbjct: 169 MK 170
>gnl|CDD|216243 pfam01012, ETF, Electron transfer flavoprotein domain. This family
includes the homologous domain shared between the alpha
and beta subunits of the electron transfer flavoprotein.
Length = 160
Score = 76.1 bits (188), Expect = 3e-17
Identities = 39/161 (24%), Positives = 53/161 (32%), Gaps = 53/161 (32%)
Query: 44 ALAMGADRGIHVEVSGPEYETLQPFHISKILAKVAQEEKVDMVIVGKQKAKKKPIKKVSP 103
AMGAD+ VE P P + LA + ++E D+V+ G
Sbjct: 51 LAAMGADKVYLVE--DPALAGYDPEAYAAALAALIKKEGPDLVLAGAT------------ 96
Query: 104 KDMGVDTGAHIEIVTVEDPPVRQAGSIVPDVDTLAIDDDSNQTAQMTAAFLNWPQATFAS 163
+I D A AA L P T +
Sbjct: 97 ----------------------------------SIGKD---LAPRLAALLGAPLITDVT 119
Query: 164 KVDKTDGELTVKREIDGGLETIKVKLP--AVISADLRLNEP 202
++ G+LTV R I GG VKLP AV++ EP
Sbjct: 120 ALEVEGGKLTVTRPIYGGNAIATVKLPDPAVLTVRPGAFEP 160
>gnl|CDD|179569 PRK03359, PRK03359, putative electron transfer flavoprotein FixA;
Reviewed.
Length = 256
Score = 40.9 bits (96), Expect = 2e-04
Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 154 LNWPQATFASK-VDKTDGELTVKREIDGGLETIKVKLPAVISADLRLNEPRYATLPNIM 211
LN P SK + TD LTV+RE++ +ET+ + LPAVI+ +N P+ ++ I+
Sbjct: 138 LNIPAINGVSKIISLTDDTLTVERELEDEVETLSIPLPAVIAVSTDINSPQIPSMKAIL 196
>gnl|CDD|183455 PRK12342, PRK12342, hypothetical protein; Provisional.
Length = 254
Score = 38.9 bits (91), Expect = 0.001
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 144 NQTAQMTAAFLNWPQATFASKVDKTDGELTVKREIDGGLETIKVKLPAVISADLRLNEPR 203
++ L P SK+ + +L V+R ++ +E +++ LPAV+ +N PR
Sbjct: 129 LLLGEL----LQLPVINAVSKIQRQGNKLIVERTLEDDVEVLELSLPAVLCVTSDINVPR 184
Query: 204 YATLPNIM 211
++ I+
Sbjct: 185 IPSMKAIL 192
>gnl|CDD|222610 pfam14228, MOR2-PAG1_mid, Cell morphogenesis central region. This
family is the conserved central region of proteins that
are involved in cell morphogenesis.
Length = 1120
Score = 30.7 bits (69), Expect = 0.81
Identities = 24/94 (25%), Positives = 45/94 (47%), Gaps = 4/94 (4%)
Query: 70 ISKILAKVAQEEKVD-MVIVGKQKAKKKPIKKVSPKDMGVDTGAHIEIVTVEDPPVRQAG 128
+S LA++ ++ +D +V Q+ + P + V P D VDT + + + PP+ Q
Sbjct: 735 VSLYLARICPQQTIDHLVCELAQRMLEDPPEPVRPADPKVDTSENGVLEFSQGPPLSQVA 794
Query: 129 SIV---PDVDTLAIDDDSNQTAQMTAAFLNWPQA 159
+IV P + L + + T + + L+W A
Sbjct: 795 TIVDSQPHMSPLLVRGSLDGTIRNVSGNLSWRTA 828
>gnl|CDD|217251 pfam02844, GARS_N, Phosphoribosylglycinamide synthetase, N
domain. Phosphoribosylglycinamide synthetase catalyzes
the second step in the de novo biosynthesis of purine.
The reaction catalyzed by Phosphoribosylglycinamide
synthetase is the ATP- dependent addition of
5-phosphoribosylamine to glycine to form
5'phosphoribosylglycinamide. This domain is related to
the N-terminal domain of biotin carboxylase/carbamoyl
phosphate synthetase (see pfam00289).
Length = 101
Score = 28.6 bits (65), Expect = 1.1
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 74 LAKVAQEEKVDMVIVG 89
LA A+EE +D+V+VG
Sbjct: 55 LADFAKEENIDLVVVG 70
>gnl|CDD|234856 PRK00885, PRK00885, phosphoribosylamine--glycine ligase;
Provisional.
Length = 420
Score = 29.3 bits (67), Expect = 2.1
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 74 LAKVAQEEKVDMVIVG 89
L A+EE +D+ +VG
Sbjct: 54 LVAFAKEEGIDLTVVG 69
>gnl|CDD|227558 COG5233, GRH1, Peripheral Golgi membrane protein [Intracellular
trafficking and secretion].
Length = 417
Score = 28.9 bits (64), Expect = 2.5
Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 2/85 (2%)
Query: 59 GPEYETLQPFHISKILAKVAQEEKVDMVIVGKQKAKKKPIKKVSPKDMGVDTGAHIEIVT 118
G PF + + +E + V ++K + K I+ KD+ V + +HI V+
Sbjct: 136 GMGELYKIPFSQRRCKVEFNSDEIRNDVRRLRRKLRGKDIQWSRLKDV-VCSDSHILNVS 194
Query: 119 VEDPPVRQAGSIVPDVDTLAIDDDS 143
++D P A + PD D + D
Sbjct: 195 IQDKPPAYAL-LSPDEDYIDGSSDG 218
>gnl|CDD|235798 PRK06416, PRK06416, dihydrolipoamide dehydrogenase; Reviewed.
Length = 462
Score = 28.6 bits (65), Expect = 3.1
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 160 TFASKVDKTDGELTVKREIDGGLETIKVKLPAVISA 195
A KV++TD +TV E G ET++ V+ A
Sbjct: 234 AKAKKVEQTDDGVTVTLEDGGKEETLEAD--YVLVA 267
>gnl|CDD|227297 COG4962, CpaF, Flp pilus assembly protein, ATPase CpaF
[Intracellular trafficking and secretion].
Length = 355
Score = 28.5 bits (64), Expect = 3.2
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 35 ITQRETIRTALAMGADRGIHVEVSGPEYETL 65
+T R+ ++ AL M DR I EV G E L
Sbjct: 235 VTMRDLVKNALRMRPDRIIVGEVRGVEALDL 265
>gnl|CDD|223229 COG0151, PurD, Phosphoribosylamine-glycine ligase [Nucleotide
transport and metabolism].
Length = 428
Score = 27.9 bits (63), Expect = 5.2
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 74 LAKVAQEEKVDMVIVG 89
L A+E+ VD+V+VG
Sbjct: 55 LVAFAKEKNVDLVVVG 70
>gnl|CDD|200328 TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase.
Members of this protein family comprise a distinct
clade of putative ATPase associated with an integral
membrane complex likely to act in pilus formation,
secretion, or conjugal transfer. The association of most
members with a nearby gene for a DEAH-box helicase
suggests a role in conjugal transfer.
Length = 340
Score = 27.7 bits (62), Expect = 6.6
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 35 ITQRETIRTALAMGADRGIHVEVSGPE 61
+T + +R AL M DR + EV G E
Sbjct: 240 VTLTDLVRQALRMRPDRIVVGEVRGAE 266
>gnl|CDD|233852 TIGR02404, trehalos_R_Bsub, trehalose operon repressor, B.
subtilis-type. This family consists of repressors of
the GntR family typically associated with trehalose
utilization operons. Trehalose is imported as
trehalose-6-phosphate and then hydrolyzed by
alpha,alpha-phosphotrehalase to glucose and
glucose-6-P. This family includes repressors mostly
from Gram-positive lineages and does not include the
TreR from E. coli [Regulatory functions, DNA
interactions].
Length = 233
Score = 27.3 bits (61), Expect = 6.7
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 25 SEAEKSQQHTITQRETIRTALAMGADRG 52
SE E Q+ + RET+R AL + +RG
Sbjct: 26 SEHELMDQYGAS-RETVRKALNLLTERG 52
>gnl|CDD|227265 COG4928, COG4928, Predicted P-loop ATPase [General function
prediction only].
Length = 646
Score = 27.4 bits (61), Expect = 7.1
Identities = 9/45 (20%), Positives = 16/45 (35%)
Query: 62 YETLQPFHISKILAKVAQEEKVDMVIVGKQKAKKKPIKKVSPKDM 106
ET + F S I Q +K+ VI + + + +
Sbjct: 158 SETKEEFQDSGINQTKEQNKKILGVIDDIDELHNEEEELLFKVIK 202
>gnl|CDD|206637 cd11304, Cadherin_repeat, Cadherin tandem repeat domain. Cadherins
are glycoproteins involved in Ca2+-mediated cell-cell
adhesion. The cadherin repeat domains occur as tandem
repeats in the extracellular regions, which are thought
to mediate cell-cell contact when bound to calcium. They
play numerous roles in cell fate, signalling,
proliferation, differentiation, and migration; members
include E-, N-, P-, T-, VE-, CNR-, proto-, and
FAT-family cadherin, desmocollin, and desmoglein, a
large variety of domain architectures with varying
repeat copy numbers. Cadherin-repeat containing proteins
exist as monomers, homodimers, or heterodimers.
Length = 98
Score = 26.1 bits (58), Expect = 7.5
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 9/65 (13%)
Query: 117 VTV-EDPPVRQAGSIVPDVDTLAIDDDSNQTAQMTAAFL-NWPQATFASKVDKTDGELTV 174
V+V E+ P G++V V A D DS + ++T + + F +D + GE+T
Sbjct: 4 VSVPENAPP---GTVVLTV--SATDPDSGENGEVTYSIVSGNEDGLF--SIDPSTGEITT 56
Query: 175 KREID 179
+ +D
Sbjct: 57 AKPLD 61
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and host
eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 26.9 bits (60), Expect = 7.9
Identities = 15/49 (30%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 17 QFTTSSSLSEAEKSQQHTITQRETIRTALAMGADRGIHVEVSGPEYETL 65
+ T E +T + +R+AL M DR I EV G E L
Sbjct: 73 RLVTRPGNVEGSGE----VTMADLLRSALRMRPDRIIVGEVRGGEALDL 117
>gnl|CDD|216006 pfam00582, Usp, Universal stress protein family. The universal
stress protein UspA is a small cytoplasmic bacterial
protein whose expression is enhanced when the cell is
exposed to stress agents. UspA enhances the rate of cell
survival during prolonged exposure to such conditions,
and may provide a general "stress endurance" activity.
The crystal structure of Haemophilus influenzae UspA
reveals an alpha/beta fold similar to that of the
Methanococcus jannaschii MJ0577 protein, which binds
ATP, though UspA lacks ATP-binding activity.
Length = 139
Score = 26.3 bits (58), Expect = 8.7
Identities = 13/67 (19%), Positives = 26/67 (38%), Gaps = 9/67 (13%)
Query: 23 SLSEAEKSQQHTITQRETIRTALAMGADRGIHVEVSGPEYETLQPFHISKILAKVAQEEK 82
E E+ + + E + A G V G ++ + +VA+EE
Sbjct: 51 LEEEEEEELEEEEAEAEALAAAAEAGGVVVEVVVRGG---------DPAEAILEVAEEED 101
Query: 83 VDMVIVG 89
D++++G
Sbjct: 102 ADLIVMG 108
>gnl|CDD|238182 cd00293, USP_Like, Usp: Universal stress protein family. The
universal stress protein Usp is a small cytoplasmic
bacterial protein whose expression is enhanced when the
cell is exposed to stress agents. Usp enhances the rate
of cell survival during prolonged exposure to such
conditions, and may provide a general "stress endurance"
activity. The crystal structure of Haemophilus
influenzae Usp reveals an alpha/beta fold similar to
that of the Methanococcus jannaschii MJ0577 protein,
which binds ATP, athough Usp lacks ATP-binding activity.
Length = 130
Score = 26.2 bits (58), Expect = 8.8
Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 12/55 (21%)
Query: 38 RETIRTALAMGADRGIHVE---VSGPEYETLQPFHISKILAKVAQEEKVDMVIVG 89
R + A+ G+ VE + G E + + A+E D++++G
Sbjct: 55 RALLEALREALAEAGVKVETVVLEGDPAEAI---------LEAAEELGADLIVMG 100
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 0.130 0.362
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,904,601
Number of extensions: 1104715
Number of successful extensions: 867
Number of sequences better than 10.0: 1
Number of HSP's gapped: 856
Number of HSP's successfully gapped: 43
Length of query: 242
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 148
Effective length of database: 6,768,326
Effective search space: 1001712248
Effective search space used: 1001712248
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 (22.0 bits)
S2: 58 (26.1 bits)