RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13824
(226 letters)
>gnl|CDD|216423 pfam01301, Glyco_hydro_35, Glycosyl hydrolases family 35.
Length = 318
Score = 121 bits (307), Expect = 2e-33
Identities = 40/81 (49%), Positives = 55/81 (67%)
Query: 123 TFRMDGRPFRFVSGEFHYFRSPQERWREILRKIRSAGLNAVSTYVGWSSHEAQPGTYSFD 182
+F +DG+ FR +SG HYFR P E W + L+K ++ GLN + TYV W+ HE +PG Y F
Sbjct: 1 SFLIDGQRFRLISGSIHYFRIPPEMWPDRLQKAKALGLNTIETYVFWNLHEPEPGQYDFS 60
Query: 183 GHRDVEYFMRLAAEEGLYVLL 203
G D+ F++LA E GLYV+L
Sbjct: 61 GILDLVKFIKLAQEAGLYVIL 81
>gnl|CDD|224786 COG1874, LacA, Beta-galactosidase [Carbohydrate transport and
metabolism].
Length = 673
Score = 77.1 bits (190), Expect = 2e-16
Identities = 32/88 (36%), Positives = 48/88 (54%), Gaps = 3/88 (3%)
Query: 117 VNYSANTFRMDGRPFRFVSGEFHYFRSPQERWREILRKIRSAGLNAVST-YVGWSSHEAQ 175
V+Y +F DGR G+++ R P+E W + LRK+++ GLN V Y W+ HE +
Sbjct: 1 VSYDGYSFIRDGRRILLYGGDYYPERWPRETWMDDLRKMKALGLNTVRIGYFAWNLHEPE 60
Query: 176 PGTYSFDGHRDVEYFMRLAAEEGLYVLL 203
G + F D F+ A + GLYV+L
Sbjct: 61 EGKFDF-TWLDEI-FLERAYKAGLYVIL 86
>gnl|CDD|166698 PLN03059, PLN03059, beta-galactosidase; Provisional.
Length = 840
Score = 75.4 bits (185), Expect = 9e-16
Identities = 34/98 (34%), Positives = 54/98 (55%)
Query: 109 RPSSQTFTVNYSANTFRMDGRPFRFVSGEFHYFRSPQERWREILRKIRSAGLNAVSTYVG 168
S + +V+Y F ++G+ +SG HY RS E W ++++K + GL+ + TYV
Sbjct: 22 WVSHGSASVSYDHRAFIINGQRRILISGSIHYPRSTPEMWPDLIQKAKDGGLDVIQTYVF 81
Query: 169 WSSHEAQPGTYSFDGHRDVEYFMRLAAEEGLYVLLYSG 206
W+ HE PG Y F+ D+ F+++ GLYV L G
Sbjct: 82 WNGHEPSPGNYYFEDRYDLVKFIKVVQAAGLYVHLRIG 119
>gnl|CDD|217042 pfam02449, Glyco_hydro_42, Beta-galactosidase. This group of
beta-galactosidase enzymes belong to the glycosyl
hydrolase 42 family. The enzyme catalyzes the hydrolysis
of terminal, non-reducing terminal beta-D-galactosidase
residues.
Length = 376
Score = 49.6 bits (119), Expect = 3e-07
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 4/61 (6%)
Query: 144 PQERWREILRKIRSAGLNAVS-TYVGWSSHEAQPGTYSFDGHRDVEYFMRLAAEEGLYVL 202
P+E W E +R ++ AG+N V W+ E + G Y F ++ + L A+ G+ V+
Sbjct: 8 PEETWEEDIRLMKEAGVNVVRLGIFAWAKLEPEEGKYDFGWLDEI---IDLLAKAGIKVI 64
Query: 203 L 203
L
Sbjct: 65 L 65
>gnl|CDD|131325 TIGR02272, gentisate_1_2, gentisate 1,2-dioxygenase. This family
consists of gentisate 1,2-dioxygenases. This
ring-opening enzyme acts in salicylate degradation that
goes via gentisate rather than via catechol. It converts
gentisate to maleylpyruvate. Some putative gentisate
1,2-dioxygenases are excluded by a relatively high
trusted cutoff score because they are too closely
related to known examples of 1-hydroxy-2-naphthoate
dioxygenase. Therefore some homologs may be bona fide
gentisate 1,2-dioxygenases even if they score below the
given cutoffs.
Length = 335
Score = 31.7 bits (72), Expect = 0.27
Identities = 15/60 (25%), Positives = 21/60 (35%), Gaps = 4/60 (6%)
Query: 100 YGNRIRRFHRPSSQTFTVNYSANTFRMDGRPFRFVSGEFHYFRSPQERWREILRKIRSAG 159
Y + RP + Y N + + S F+Y P ER RE L + G
Sbjct: 170 YPEDQQPVTRPEGDSLA-RYGHNMLPVRHKRSDRSSPIFNY---PYERSREALDDLTRTG 225
>gnl|CDD|215751 pfam00150, Cellulase, Cellulase (glycosyl hydrolase family 5).
Length = 269
Score = 31.6 bits (72), Expect = 0.27
Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 3/79 (3%)
Query: 127 DGRPFRFVSGEFHYFRSPQERWREILRKIRSAGLNAVSTYVGWSSHEAQPGTYSFDGH-- 184
+G+P H+ P + ++ ++ G N V V W + Y D +
Sbjct: 4 NGKPVNLFGMSTHWGN-PYYTTKAMIDLVKDWGFNVVRLPVSWGGYVPNNPDYLIDENWL 62
Query: 185 RDVEYFMRLAAEEGLYVLL 203
V+ + A + G+YV++
Sbjct: 63 NRVDEVVDYAIDNGMYVII 81
>gnl|CDD|225006 COG2095, MarC, Multiple antibiotic transporter [Intracellular
trafficking and secretion].
Length = 203
Score = 31.0 bits (71), Expect = 0.34
Identities = 9/39 (23%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 71 VMSSSKGRHGHLFKFIAILLVAS--VWICLRYGNRIRRF 107
V+ S + +L+AS ++ L +RI R
Sbjct: 129 VIVLSSQYGNSKLAVVLAILLASLLTYLILLSSSRIMRL 167
>gnl|CDD|234910 PRK01158, PRK01158, phosphoglycolate phosphatase; Provisional.
Length = 230
Score = 29.9 bits (68), Expect = 0.74
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 186 DVEYFMRLAAEEGLYV-LLYSGFSWTMKSSW 215
VE L E GL + ++ SGF+ +KS
Sbjct: 125 PVEEVRELLEELGLDLEIVDSGFAIHIKSPG 155
>gnl|CDD|225070 COG2159, COG2159, Predicted metal-dependent hydrolase of the
TIM-barrel fold [General function prediction only].
Length = 293
Score = 30.1 bits (68), Expect = 0.85
Identities = 16/70 (22%), Positives = 25/70 (35%), Gaps = 8/70 (11%)
Query: 149 REILRKIRSAGLNAVSTYVGWSSHEAQPGTYSFDGHRDVEYFMRLAAEEGLYVLLYSGFS 208
E+ R++R G VG H G Y D + A E G+ V++++G
Sbjct: 116 EELERRVRELGF------VGVKLHPVAQGFYPDD--PRLYPIYEAAEELGVPVVIHTGAG 167
Query: 209 WTMKSSWDGT 218
G
Sbjct: 168 PGGAGLEKGH 177
>gnl|CDD|217510 pfam03354, Terminase_1, Phage Terminase. The majority of the
members of this family are bacteriophage proteins,
several of which are thought to be terminase large
subunit proteins. There are also a number of bacterial
proteins of unknown function.
Length = 473
Score = 30.1 bits (68), Expect = 0.97
Identities = 28/153 (18%), Positives = 54/153 (35%), Gaps = 20/153 (13%)
Query: 71 VMSSSKGRHGHLFKFIAILLVASVWICLRYGNRIRRFHRPSSQTFTVN-----YSANTFR 125
V +++ + LFK++ + S ++ + N++ + + + N S N +
Sbjct: 59 VAATTFKQAEKLFKYVKNQVKLSPFLSIANENKLLKSQKDGIEMKINNNVFKALSNNGDQ 118
Query: 126 MDGRPFRFVS-GEFHYFRSPQERWREILRKIRSAGLNAVSTYVGWSSHEAQP---GTYSF 181
DG E H F+ RE++ I + G+ A P G Y
Sbjct: 119 YDGGNPSLAIFDEMHEFKD-----RELVSTIVT-GMRKQDNPQTIQITTAGPNRGGPY-- 170
Query: 182 DGHRDVEYFMR-LAAEEGLYVLLYSGFSWTMKS 213
+ EY R L + Y G + + +
Sbjct: 171 --DEEREYIKRILEGDVERDDDSYFGLIYELDN 201
>gnl|CDD|227449 COG5119, COG5119, Uncharacterized protein, contains ParB-like
nuclease domain [General function prediction only].
Length = 119
Score = 28.1 bits (62), Expect = 1.8
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 123 TFRMDGRPFRFVSGEFHYFRSPQERWREILR--KIRSAGLNAVSTYVGWS 170
TF +DG+P+ + G H + RE + ++R A + Y+G S
Sbjct: 66 TFEVDGQPYYYAFGGCHRLEACDRAGRETILAKRVRCAPNTVLRMYLGAS 115
>gnl|CDD|235554 PRK05673, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1135
Score = 29.3 bits (67), Expect = 1.8
Identities = 9/20 (45%), Positives = 11/20 (55%), Gaps = 1/20 (5%)
Query: 127 DGRPFRFVSGEFHYFRSPQE 146
D FRF S E Y +S +E
Sbjct: 228 DPDRFRFYSPE-QYLKSAEE 246
>gnl|CDD|214770 smart00666, PB1, PB1 domain. Phox and Bem1p domain, present in
many eukaryotic cytoplasmic signalling proteins. The
domain adopts a beta-grasp fold, similar to that found
in ubiquitin and Ras-binding domains. A motif, variously
termed OPR, PC and AID, represents the most conserved
region of the majority of PB1 domains, and is necessary
for PB1 domain function. This function is the formation
of PB1 domain heterodimers, although not all PB1 domain
pairs associate.
Length = 81
Score = 27.2 bits (61), Expect = 2.2
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 93 SVWICLRYGNRIRRFHRPSSQTFTVNYS--ANTFRMDGRPFRF 133
+V + LRYG RR P +F S A F +D + F
Sbjct: 1 TVDVKLRYGGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTL 43
>gnl|CDD|180714 PRK06827, PRK06827, phosphoribosylpyrophosphate synthetase;
Provisional.
Length = 382
Score = 28.8 bits (65), Expect = 2.4
Identities = 8/36 (22%), Positives = 15/36 (41%)
Query: 103 RIRRFHRPSSQTFTVNYSANTFRMDGRPFRFVSGEF 138
R R+ + YS ++ + + RF +GE
Sbjct: 32 RERKENENIESLAFKGYSRESYLIPAKFIRFSNGEA 67
>gnl|CDD|239240 cd02930, DCR_FMN, 2,4-dienoyl-CoA reductase (DCR) FMN-binding
domain. DCR in E. coli is an iron-sulfur flavoenzyme
which contains FMN, FAD, and a 4Fe-4S cluster. It is
also a monomer, unlike that of its eukaryotic
counterparts which form homotetramers and lack the
flavin and iron-sulfur cofactors. Metabolism of
unsaturated fatty acids requires auxiliary enzymes in
addition to those used in b-oxidation. After a given
number of cycles through the b-oxidation pathway, those
unsaturated fatty acyl-CoAs with double bonds at
even-numbered carbon positions contain 2-trans, 4-cis
double bonds that can not be modified by enoyl-CoA
hydratase. DCR utilizes NADPH to remove the C4-C5 double
bond. DCR can catalyze the reduction of both natural
fatty acids with cis double bonds, as well as substrates
containing trans double bonds. The reaction is initiated
by hybrid transfer from NADPH to FAD, which in turn
transfers electrons, one at a time, to FMN via the
4Fe-4S cluster. The fully reduced FMN provides a hydrid
ion to the C5 atom of substrate, and Tyr and His are
proposed to form a catalytic dyad that protonates the C4
atom of the substrate and completes the reaction.
Length = 353
Score = 28.4 bits (64), Expect = 3.2
Identities = 10/31 (32%), Positives = 20/31 (64%), Gaps = 5/31 (16%)
Query: 148 WREIL---RKIRSAGLNAVSTYVGWSSHEAQ 175
W E++ + + +AG + ++T +GW HEA+
Sbjct: 223 WEEVVALAKALEAAGADILNTGIGW--HEAR 251
>gnl|CDD|215022 smart01094, CpcD, CpcD/allophycocyanin linker domain.
Length = 51
Score = 25.6 bits (57), Expect = 3.7
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 4/27 (14%)
Query: 94 VWICLRYGNRIRRFHRPSSQTFTVNYS 120
LR G R+RR S+QT+ V Y
Sbjct: 7 EVTGLRQGGRVRR----SNQTYFVPYD 29
>gnl|CDD|176675 cd07252, BphC1-RGP6_N_like, N-terminal domain of
2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC
1.13.11.39) 1 from Rhodococcus globerulus P6
(BphC1-RGP6) and similar proteins. This subfamily
contains the N-terminal, non-catalytic, domain of
BphC1-RGP6 and similar proteins. BphC catalyzes the
extradiol ring cleavage reaction of
2,3-dihydroxybiphenyl, the third step in the
polychlorinated biphenyls (PCBs) degradation pathway
(bph pathway). This subfamily of BphCs belongs to the
type I extradiol dioxygenase family, which require a
metal in the active site in its catalytic mechanism.
Polychlorinated biphenyl degrading bacteria demonstrate
a multiplicity of 2,3-dihydroxybiphenyl
1,2-dioxygenases. For example, three types of BphC
enzymes have been found in Rhodococcus globerulus
(BphC1-RGP6 - BphC3-RGP6), all three enzymes are type I
extradiol dioxygenases. BphC1-RGP6 has an internal
duplication, it is a two-domain dioxygenase which forms
octamers, and has Fe(II) at the catalytic site. Its
N-terminal repeat is represented in this subfamily.
BphC2-RGP6 and BphC3-RGP6 are one-domain dioxygenases,
they belong to a different family, the
ED_TypeI_classII_C (C-terminal domain of type I, class
II extradiol dioxygenases) family.
Length = 120
Score = 27.1 bits (61), Expect = 3.9
Identities = 9/46 (19%), Positives = 16/46 (34%), Gaps = 10/46 (21%)
Query: 123 TFRMDGRPFRFV-----SGEFHY----FRSPQERWREILRKIRSAG 159
RMD R +R + + Y + ++R+AG
Sbjct: 38 YLRMDDRAWRIAVHPGEADDLAYAGWEVADEAA-LDALAARLRAAG 82
>gnl|CDD|213628 TIGR01487, Pglycolate_arch, phosphoglycolate phosphatase,
TA0175-type. This group of Archaeal sequences, now
known to be phosphoglycolate phosphatases, is most
closely related to the sucrose-phosphate phosphatases
from plants and cyanobacteria (TIGR01485). Together,
these two models comprise a subfamily model (TIGR01482).
TIGR01482, in turn, is a member of the IIB subfamily
(TIGR01484) of the Haloacid Dehalogenase (HAD)
superfamily of aspartate-nucleophile hydrolases.
Length = 215
Score = 27.8 bits (62), Expect = 4.4
Identities = 10/53 (18%), Positives = 20/53 (37%), Gaps = 1/53 (1%)
Query: 169 WSSHEAQPGTYSFDGHRDVEYFMRLAAEEGLYVLLYSGFSWTMKSSWDGTCIG 221
S+ + +DV+ + E GL ++ SGF+ + +G
Sbjct: 100 LSNEYPRASLVIMREGKDVDEVREIIKERGLNLV-ASGFAIHIMKKGVDKGVG 151
>gnl|CDD|99734 cd00609, AAT_like, Aspartate aminotransferase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). Pyridoxal
phosphate combines with an alpha-amino acid to form a
compound called a Schiff base or aldimine intermediate,
which depending on the reaction, is the substrate in
four kinds of reactions (1) transamination (movement of
amino groups), (2) racemization (redistribution of
enantiomers), (3) decarboxylation (removing COOH
groups), and (4) various side-chain reactions depending
on the enzyme involved. Pyridoxal phosphate (PLP)
dependent enzymes were previously classified into alpha,
beta and gamma classes, based on the chemical
characteristics (carbon atom involved) of the reaction
they catalyzed. The availability of several structures
allowed a comprehensive analysis of the evolutionary
classification of PLP dependent enzymes, and it was
found that the functional classification did not always
agree with the evolutionary history of these enzymes.
The major groups in this CD corresponds to Aspartate
aminotransferase a, b and c, Tyrosine, Alanine,
Aromatic-amino-acid, Glutamine phenylpyruvate,
1-Aminocyclopropane-1-carboxylate synthase,
Histidinol-phosphate, gene products of malY and cobC,
Valine-pyruvate aminotransferase and Rhizopine
catabolism regulatory protein.
Length = 350
Score = 27.7 bits (62), Expect = 4.9
Identities = 18/66 (27%), Positives = 24/66 (36%), Gaps = 5/66 (7%)
Query: 146 ERWREILRKIRSAGLNAVSTYVGWSSHEAQPGTY----SFDGHRDVEYFMRLAAEEGLYV 201
E RE R+ R A L A+ + G + D E+ RL E G+ V
Sbjct: 258 EELRERYRRRRDALLEALKELGPLVVVKPS-GGFFLWLDLPEGDDEEFLERLLLEAGVVV 316
Query: 202 LLYSGF 207
S F
Sbjct: 317 RPGSAF 322
>gnl|CDD|224346 COG1429, CobN, Cobalamin biosynthesis protein CobN and related
Mg-chelatases [Coenzyme metabolism].
Length = 1388
Score = 28.1 bits (63), Expect = 5.2
Identities = 12/63 (19%), Positives = 18/63 (28%), Gaps = 12/63 (19%)
Query: 137 EFHYFRSPQERWREILRKIRSAGLNAVSTYVGWSSHEAQPGTYSFDGHRDVEYFMRLAAE 196
+Y ++R + GLN + P S D V L E
Sbjct: 211 RTYYTNGNLAPIDALIRALEERGLNVI------------PVFLSSDALYVVLRAFFLGLE 258
Query: 197 EGL 199
+ L
Sbjct: 259 KVL 261
>gnl|CDD|213993 cd07438, PHP_HisPPase_AMP, Polymerase and Histidinol Phosphatase
domain of Histidinol phosphate phosphatase (HisPPase)
AMP bound. The PHP domain of this HisPPase family has
an unknown function. It has a second domain inserted in
the middle that binds adenosine 5-monophosphate (AMP).
The PHP (also called histidinol phosphatase-2/HIS2)
domain is associated with several types of DNA
polymerases, such as PolIIIA and family X DNA
polymerases, stand alone histidinol phosphate
phosphatases (HisPPases), and a number of
uncharacterized protein families. HisPPase catalyzes the
eighth step of histidine biosynthesis, in which
L-histidinol phosphate undergoes dephosphorylation to
give histidinol. The PHP domain has four conserved
sequence motifs and contains an invariant histidine that
is involved in metal ion coordination. The PHP domain of
HisPPase is structurally homologous to the other members
of the PHP family that have a distorted (beta/alpha)7
barrel fold with a trinuclear metal site on the
C-terminal side of the barrel.
Length = 155
Score = 27.0 bits (61), Expect = 5.5
Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 13/62 (20%)
Query: 140 YFRSPQERWREILRKIRSAGLNAVSTYVGWSSHEAQPGTYSFDGHRDVEYFMRLAAEEGL 199
Y S ++ E++ +++ AGL+ + Y + + D E + LA E GL
Sbjct: 99 YKLSRKKL-EELIEELKEAGLDGIEVY------------HPYHSPEDRERLLELAKEYGL 145
Query: 200 YV 201
V
Sbjct: 146 LV 147
>gnl|CDD|213997 cd12113, PHP_PolIIIA_DnaE3, Polymerase and Histidinol Phosphatase
domain of alpha-subunit of bacterial polymerase III
DnaE3. PolIIIAs that contain an N-terminal PHP domain
have been classified into four basic groups based on
genome composition, phylogenetic, and domain structural
analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also
called histidinol phosphatase-2/HIS2) domain is
associated with several types of DNA polymerases, such
as PolIIIA and family X DNA polymerases, stand alone
histidinol phosphate phosphatases (HisPPases), and a
number of uncharacterized protein families. DNA
polymerase III holoenzyme is one of the five eubacterial
DNA polymerases that is responsible for the replication
of the DNA duplex. The alpha subunit of DNA polymerase
III core enzyme catalyzes the reaction for polymerizing
both DNA strands. The PolIIIA PHP domain has four
conserved sequence motifs and contains an invariant
histidine that is involved in metal ion coordination,
and like other PHP structures, the PolIIIA PHP exhibits
a distorted (beta/alpha) 7 barrel and coordinates up to
3 metals. Initially, it was proposed that PHP region
might be involved in pyrophosphate hydrolysis, but such
an activity has not been found. It has been shown that
the PHP of PolIIIA has a trinuclear metal complex and is
capable of proofreading activity. Bacterial genome
replication and DNA repair mechanisms is related to the
GC content of its genomes. There is a correlation
between GC content variations and the dimeric
combinations of PolIIIA subunits. Eubacteria can be
grouped into different GC variable groups: the
full-spectrum or dnaE1 group, the high-GC or dnaE2-dnaE1
group, and the low GC or polC-dnaE3 group.
Length = 283
Score = 27.4 bits (62), Expect = 6.2
Identities = 9/23 (39%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 127 DGRPFRFVSGEFHYFRSPQERWR 149
D RF + EF Y +SP+E
Sbjct: 231 DPNRMRFDTDEF-YLKSPEEMRE 252
>gnl|CDD|215431 PLN02801, PLN02801, beta-amylase.
Length = 517
Score = 27.5 bits (61), Expect = 7.7
Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 146 ERWREILRKIRSAGLNAVSTYVGWSSHEAQ-PGTYSFDGHRDVEYFMRLAAEEGL 199
E + L++++ AG++ V V W E++ P Y + +R + L GL
Sbjct: 37 EGLEKQLKRLKEAGVDGVMVDVWWGIVESKGPKQYDWSAYRSL---FELVQSFGL 88
>gnl|CDD|233773 TIGR02193, heptsyl_trn_I, lipopolysaccharide heptosyltransferase I.
This family consists of examples of ADP-heptose:LPS
heptosyltransferase I, an enzyme of LPS inner core
region biosynthesis. LPS, composed of lipid A, a core
region, and O antigen, is found in the outer membrane of
Gram-negative bacteria [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 319
Score = 26.9 bits (60), Expect = 8.0
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 144 PQERWREILRKIRSAGLNAVSTYVGWSS-HEAQ 175
P+ERWRE+ R + + GL + W + E Q
Sbjct: 196 PEERWRELARLLLARGLQ---IVLPWGNDAEKQ 225
>gnl|CDD|227665 COG5373, COG5373, Predicted membrane protein [Function unknown].
Length = 931
Score = 27.5 bits (61), Expect = 8.4
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 69 PVVMSSSKGRHGHLFKFIAILLVASVWI 96
P+++S+ G H LF ++A++ A+ I
Sbjct: 263 PILVSTGAGNHWALFGYLALVNAATFAI 290
>gnl|CDD|233193 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 27.3 bits (61), Expect = 8.7
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 125 RMDGRPFRFVSGEFH-YFRSPQ--ERWREILRKIRSAG 159
+DGRPF + E Y +P + R+ L+ +R A
Sbjct: 625 ALDGRPFLIIIDEAWQYLGNPVFAAKIRDWLKTLRKAN 662
>gnl|CDD|239201 cd02803, OYE_like_FMN_family, Old yellow enzyme (OYE)-like FMN
binding domain. OYE was the first flavin-dependent
enzyme identified, however its true physiological role
remains elusive to this day. Each monomer of OYE
contains FMN as a non-covalently bound cofactor, uses
NADPH as a reducing agent with oxygens, quinones, and
alpha,beta-unsaturated aldehydes and ketones, and can
act as electron acceptors in the catalytic reaction.
Members of OYE family include trimethylamine
dehydrogenase, 2,4-dienoyl-CoA reductase, enoate
reductase, pentaerythriol tetranitrate reductase,
xenobiotic reductase, and morphinone reductase.
Length = 327
Score = 26.8 bits (60), Expect = 9.0
Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 6/60 (10%)
Query: 143 SPQERWR---EILRKIRSAGLNAVSTYVGWSSHEAQPGTYSFDGHRDVEYFMRLAAEEGL 199
S + R R EI+ +R A V S+ + PG + + + + E G+
Sbjct: 186 SLENRARFLLEIVAAVREAVGPDFPVGVRLSADDFVPGGLTLE---EAIEIAKALEEAGV 242
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
0.326 0.139 0.473
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,753,482
Number of extensions: 1069155
Number of successful extensions: 1589
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1584
Number of HSP's successfully gapped: 35
Length of query: 226
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 133
Effective length of database: 6,812,680
Effective search space: 906086440
Effective search space used: 906086440
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 57 (25.6 bits)