RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780281|ref|YP_003064694.1| cytochrome-c oxidase assembly
factor protein [Candidatus Liberibacter asiaticus str. psy62]
(201 letters)
>gnl|CDD|48517 cd02968, SCO, SCO (an acronym for Synthesis of Cytochrome c
Oxidase) family; composed of proteins similar to Sco1, a
membrane-anchored protein possessing a soluble domain
with a TRX fold. Members of this family are required for
the proper assembly of cytochrome c oxidase (COX). They
contain a metal binding motif, typically CXXXC, which is
located in a flexible loop. COX, the terminal enzyme in
the respiratory chain, is imbedded in the inner
mitochondrial membrane of all eukaryotes and in the
plasma membrane of some prokaryotes. It is composed of
two subunits, COX I and COX II. It has been proposed
that Sco1 specifically delivers copper to the CuA site,
a dinuclear copper center, of the COX II subunit.
Mutations in human Sco1 and Sco2 cause fatal infantile
hepatoencephalomyopathy and cardioencephalomyopathy,
respectively. Both disorders are associated with severe
COX deficiency in affected tissues. More recently, it
has been argued that the redox sensitivity of the copper
binding properties of Sco1 implies that it participates
in signaling events rather than functioning as a
chaperone that transfers copper to COX II..
Length = 142
Score = 132 bits (334), Expect = 5e-32
Identities = 57/143 (39%), Positives = 81/143 (56%), Gaps = 5/143 (3%)
Query: 38 DVHLVAQDGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTL-LNAY 96
D L QDG +LS L KP +V+FG+T+C VCPTTL+ L + LKQ+ G +
Sbjct: 4 DFTLTDQDGRPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLGADGGDDVQVV 63
Query: 97 FITVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDVMRVAKNFRIYVNNVLAEKSGVEEKY 156
FI+VDP+RDTPEV+K + + F IG++G P ++ +AK F +Y V + Y
Sbjct: 64 FISVDPERDTPEVLKAYAKAFGPGWIGLTGTPEEIEALAKAFGVYYEKV----PEDDGDY 119
Query: 157 FVDHTTALLLFDTAGSIVGVIPY 179
VDH+ A+ L D G +V
Sbjct: 120 LVDHSAAIYLVDPDGKLVRYYGG 142
>gnl|CDD|32182 COG1999, COG1999, Uncharacterized protein SCO1/SenC/PrrC, involved
in biogenesis of respiratory and photosynthetic systems
[General function prediction only].
Length = 207
Score = 126 bits (318), Expect = 3e-30
Identities = 70/199 (35%), Positives = 101/199 (50%), Gaps = 10/199 (5%)
Query: 3 ALGIILGTILLAVLGSIAYVSFSSKFVDGNRRFNS-----DVHLVAQDGTDFSLSSLYIK 57
AL ++L LL +L S K N + D L QDG F+L L K
Sbjct: 9 ALSLLLLLALLFLLLVGLAAEASDKGDRFNLDAAAVYIGGDFELTDQDGKPFTLKDLKGK 68
Query: 58 PSIVFFGFTNCSAVCPTTLSRLDRLLKQVD-PTGTLLNAYFITVDPKRDTPEVMKKFV-Q 115
PS+VFFG+T+C VCPTTL+ L LLK++ G + FITVDP+RDTPEV+KK+
Sbjct: 69 PSLVFFGYTHCPDVCPTTLAELKALLKKLGEGEGDDVQVVFITVDPERDTPEVLKKYAEL 128
Query: 116 RFSDRIIGISGDPIDVMRVAKNFRIYVNNVLAEKSGVEEKYFVDHTTALLLFDTAGSIVG 175
F R IG++G P + VAK + ++ + V + Y +DH+ L D G +G
Sbjct: 129 NFDPRWIGLTGTPEQIEEVAKAYGVFYSKV---PLDDSQNYTIDHSAGFYLIDADGRFLG 185
Query: 176 VIPYKDDSDSAIEKINRLI 194
Y + + + +L+
Sbjct: 186 TYDYGEPPEEIAADLKKLL 204
>gnl|CDD|38003 KOG2792, KOG2792, KOG2792, Putative cytochrome C oxidase assembly
protein [Energy production and conversion].
Length = 280
Score = 106 bits (267), Expect = 3e-24
Identities = 50/198 (25%), Positives = 92/198 (46%), Gaps = 15/198 (7%)
Query: 5 GIILGTILLAVLGSIAYVSFSSKFVDGNRR-----------FNSDVHLVAQDGTDFSLSS 53
+ + L + G++AY+ + R LV DG +
Sbjct: 77 LLATFALGLGLGGALAYLKKEKARLLEKERESANRTAGKPAIGGPFSLVDHDGKRVTEKD 136
Query: 54 LYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDP-TGTLLNAYFITVDPKRDTPEVMKK 112
K S+++FGFT+C +CP L ++ ++ +++ G FI+VDP+RD+ EV+ +
Sbjct: 137 FLGKWSLIYFGFTHCPDICPDELEKMSAVVDEIEAKPGLPPVPLFISVDPERDSVEVVAE 196
Query: 113 FVQRFSDRIIGISGDPIDVMRVAKNFRIYVNNVLAEKSGVEEKYFVDHTTALLLFDTAGS 172
+V F +++G++G V +VAK +R+Y + + ++ Y VDH+ + L D G
Sbjct: 197 YVSEFHPKLLGLTGTTEQVKQVAKKYRVYFSTGPKD---EDQDYLVDHSIFMYLIDPEGE 253
Query: 173 IVGVIPYKDDSDSAIEKI 190
V D+D + I
Sbjct: 254 FVDYYGRNYDADELADSI 271
>gnl|CDD|145666 pfam02630, SCO1-SenC, SCO1/SenC. This family is involved in
biogenesis of respiratory and photosynthetic systems.
SCO1 is required for a post-translational step in the
accumulation of subunits COXI and COXII of cytochrome c
oxidase. SenC is required for optimal cytochrome c
oxidase activity and maximal induction of genes encoding
the light-harvesting and reaction centre complexes of R.
capsulatus.
Length = 159
Score = 105 bits (265), Expect = 7e-24
Identities = 48/136 (35%), Positives = 84/136 (61%), Gaps = 2/136 (1%)
Query: 39 VHLVAQDGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTLLNAYFI 98
L+ Q+G +F+ +L K S+++FGFTNC +CP L RL ++K++ + FI
Sbjct: 20 FTLIDQNGKNFTSENLKGKLSLIYFGFTNCPDICPPALDRLTDIIKKLKAENIDVQPVFI 79
Query: 99 TVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDVMRVAKNFRIYVNNVLAEKSGVEEKYFV 158
+VDP+RDTP+V+K++++ F IG++G ++ VAK F+++ + V+ +K + Y V
Sbjct: 80 SVDPERDTPKVLKEYLKNFHPSFIGLTGTTDEIKSVAKKFKVFYSKVIVDKPEQD--YLV 137
Query: 159 DHTTALLLFDTAGSIV 174
DH++ L D G I+
Sbjct: 138 DHSSFFYLIDPDGKIL 153
>gnl|CDD|48515 cd02966, TlpA_like_family, TlpA-like family; composed of TlpA,
ResA, DsbE and similar proteins. TlpA, ResA and DsbE are
bacterial protein disulfide reductases with important
roles in cytochrome maturation. They are
membrane-anchored proteins with a soluble TRX domain
containing a CXXC motif located in the periplasm. The
TRX domains of this family contain an insert,
approximately 25 residues in length, which correspond to
an extra alpha helix and a beta strand when compared
with TRX. TlpA catalyzes an essential reaction in the
biogenesis of cytochrome aa3, while ResA and DsbE are
essential proteins in cytochrome c maturation. Also
included in this family are proteins containing a
TlpA-like TRX domain with domain architectures similar
to E. coli DipZ protein, and the N-terminal TRX domain
of PilB protein from Neisseria which acts as a disulfide
reductase that can recylce methionine sulfoxide
reductases..
Length = 116
Score = 39.5 bits (92), Expect = 7e-04
Identities = 30/140 (21%), Positives = 45/140 (32%), Gaps = 26/140 (18%)
Query: 38 DVHLVAQDGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTLLNAYF 97
D L DG SLS L K +V F + C C + L+ L K+ G
Sbjct: 1 DFSLPDLDGKPVSLSDLKGKVVLVNFWASWC-PPCRAEMPELEALAKEYKDDGVE----V 55
Query: 98 ITVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDVMRVAKNFRIYVNNVLAEKSGVEEKYF 157
+ V+ D P +K F+++ + I +L + + Y
Sbjct: 56 VGVNVDDDDPAAVKAFLKK---------------------YGITFPVLLDPDGELAKAYG 94
Query: 158 VDHTTALLLFDTAGSIVGVI 177
V L D G I
Sbjct: 95 VRGLPTTFLIDRDGRIRARH 114
>gnl|CDD|144244 pfam00578, AhpC-TSA, AhpC/TSA family. This family contains
proteins related to alkyl hydroperoxide reductase (AhpC)
and thiol specific antioxidant (TSA).
Length = 124
Score = 33.0 bits (76), Expect = 0.059
Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 6/78 (7%)
Query: 41 LVAQDGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTLLNAYFITV 100
L DG + SLS K ++FF + + VC T L L L ++ L + V
Sbjct: 10 LPDLDGKEVSLSDYKGKWVVLFFYPKDFTPVCTTELPALADLYEEFKK----LGVEVLGV 65
Query: 101 DPKRDTPEVMKKFVQRFS 118
D+PE KKF ++
Sbjct: 66 SV--DSPESHKKFAEKLG 81
>gnl|CDD|30799 COG0450, AhpC, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 194
Score = 32.1 bits (73), Expect = 0.095
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 47 TDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTLLNAYFITVDP 102
+ +LS Y K ++FF + + VCPT + + ++ G ++ D
Sbjct: 24 EEITLSDYYGKWVVLFFYPADFTFVCPTEIIAFAKRYEEFQKRGV--EVIGVSTDS 77
>gnl|CDD|48520 cd02971, PRX_family, Peroxiredoxin (PRX) family; composed of the
different classes of PRXs including many proteins
originally known as bacterioferritin comigratory
proteins (BCP), based on their electrophoretic mobility
before their function was identified. PRXs are
thiol-specific antioxidant (TSA) proteins also known as
TRX peroxidases and alkyl hydroperoxide reductase C22
(AhpC) proteins. They confer a protective antioxidant
role in cells through their peroxidase activity in which
hydrogen peroxide, peroxynitrate, and organic
hydroperoxides are reduced and detoxified using reducing
equivalents derived from either TRX, glutathione,
trypanothione and AhpF. They are distinct from other
peroxidases in that they have no cofactors such as
metals or prosthetic groups. The first step of
catalysis, common to all PRXs, is the nucleophilic
attack by the catalytic cysteine (also known as the
peroxidatic cysteine) on the peroxide leading to
cleavage of the oxygen-oxygen bond and the formation of
a cysteine sulfenic acid intermediate. The second step
of the reaction, the resolution of the intermediate,
distinguishes the different types of PRXs. The presence
or absence of a second cysteine (the resolving cysteine)
classifies PRXs as either belonging to the 2-cys or
1-cys type. The resolving cysteine of 2-cys PRXs is
either on the same chain (atypical) or on the second
chain (typical) of a functional homodimer. Structural
and motif analysis of this growing family supports the
need for a new classification system. The peroxidase
activity of PRXs is regulated in vivo by irreversible
cysteine over-oxidation into a sulfinic acid,
phosphorylation and limited proteolysis..
Length = 140
Score = 31.0 bits (70), Expect = 0.23
Identities = 23/82 (28%), Positives = 33/82 (40%), Gaps = 12/82 (14%)
Query: 38 DVHLVAQDGTDFSLSSLYIKPSIVFF---GFTNCSAVCPTTLSRLDRLLKQVDPTGTLLN 94
D L A DG + SLS K ++FF FT VC T L L ++
Sbjct: 4 DFTLPATDGGEVSLSDFKGKWVVLFFYPKDFT---PVCTTELCAFRDLAEEFA----KGG 56
Query: 95 AYFITVDPKRDTPEVMKKFVQR 116
A + V D+P K + ++
Sbjct: 57 AEVLGVSV--DSPFSHKAWAEK 76
>gnl|CDD|38979 KOG3775, KOG3775, KOG3775, Mitogen-activated protein kinase
scaffold protein JIP [Signal transduction mechanisms].
Length = 482
Score = 30.4 bits (68), Expect = 0.37
Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 1/78 (1%)
Query: 97 FITVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDVMRVAKNFRIYVNNVLAEKSGVEEKY 156
+ + + T + +FV R D + GD + V A +F N+ + G+ +
Sbjct: 255 LVNGEEQEQTHRAVFRFVPRHPDELELEIGDAVLVEAEADDFWFEGFNLRTGERGIFPAF 314
Query: 157 FVDHTTALLLFDTAGSIV 174
+ H D GS+
Sbjct: 315 YA-HEVDGPEEDLLGSLR 331
>gnl|CDD|31418 COG1225, Bcp, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 157
Score = 29.0 bits (65), Expect = 0.81
Identities = 38/159 (23%), Positives = 66/159 (41%), Gaps = 18/159 (11%)
Query: 38 DVHLVAQDGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTLLNAYF 97
D L QDG SLS L KP +++F + + C T LL++ + L A
Sbjct: 12 DFELPDQDGETVSLSDLRGKPVVLYFYPKDFTPGCTTEACDFRDLLEEFEK----LGAVV 67
Query: 98 ITVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDVMRVAKNFRIYVNNVLAEKSGVEEKYF 157
+ + P D+P+ KKF ++ +S + VA+ + V EK ++Y
Sbjct: 68 LGISP--DSPKSHKKFAEKHGLTFPLLSDED---GEVAEAY-----GVWGEKKMYGKEYM 117
Query: 158 VDHTTALLLFDTAGSIVGV---IPYKDDSDSAIEKINRL 193
+ ++ D G I V + K +D + + +L
Sbjct: 118 GIERSTFVI-DPDGKIRYVWRKVKVKGHADEVLAALKKL 155
>gnl|CDD|48560 cd03011, TlpA_like_ScsD_MtbDsbE, TlpA-like family, suppressor for
copper sensitivity D protein (ScsD) and actinobacterial
DsbE homolog subfamily; composed of ScsD, the DsbE
homolog of Mycobacterium tuberculosis (MtbDsbE) and
similar proteins, all containing a redox-active CXXC
motif. The Salmonella typhimurium ScsD is a
thioredoxin-like protein which confers copper tolerance
to copper-sensitive mutants of E. coli. MtbDsbE has been
characterized as an oxidase in vitro, catalyzing the
disulfide bond formation of substrates like hirudin. The
reduced form of MtbDsbE is more stable than its oxidized
form, consistent with an oxidase function. This is in
contrast to the function of DsbE from gram-negative
bacteria which is a specific reductase of apocytochrome
c..
Length = 123
Score = 28.7 bits (64), Expect = 1.1
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 10/72 (13%)
Query: 45 DGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTLLNAYFITVDPKR 104
DG F L SL KP +V+F T C VC T +++L ++V +
Sbjct: 9 DGEQFDLESLSGKPVLVYFWATWC-PVCRFTSPTVNQLAADYP---------VVSVALRS 58
Query: 105 DTPEVMKKFVQR 116
+ +F+Q+
Sbjct: 59 GDDGAVARFMQK 70
>gnl|CDD|34137 COG4458, SrfC, Uncharacterized protein conserved in bacteria,
putative virulence factor [Function unknown].
Length = 821
Score = 27.3 bits (60), Expect = 3.0
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 81 RLLKQVDPTGTLLNAYFITVDPKRDTPEVMKKFV 114
RLL + D L NA+F+ +R T + +
Sbjct: 133 RLLSETDIAKILGNAFFLDGPAERRTYLAPESVI 166
>gnl|CDD|34575 COG4968, PilE, Tfp pilus assembly protein PilE [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 139
Score = 27.3 bits (60), Expect = 3.3
Identities = 20/93 (21%), Positives = 32/93 (34%), Gaps = 4/93 (4%)
Query: 11 ILLAVLGSIAYVSFSSKFVDGNRRFNSDVHLVAQDGTDFSLSSLYIKPSIVFFGFTNCSA 70
++ +L IAY S+ + + R S + F ++ T
Sbjct: 18 AIVGILALIAYPSYQNYVLRSRR---SAAKAALLENAQFMERYYALQNGYAGTTSTLAPK 74
Query: 71 VCPTTLSRLDRLLKQVDPTGT-LLNAYFITVDP 102
V P+ D L V P G L A+ +T P
Sbjct: 75 VPPSANEDFDYRLSAVTPAGKATLTAFTLTATP 107
>gnl|CDD|33308 COG3505, VirD4, Type IV secretory pathway, VirD4 components
[Intracellular trafficking and secretion].
Length = 596
Score = 26.9 bits (59), Expect = 3.9
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 10/68 (14%)
Query: 17 GSIAYVSFSSKFVDGNRRFNSDVHLVAQDGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTL 76
S + SS + + A G+DF + L K + V+FG P +
Sbjct: 327 TSGVLSTASSAL----TLLMNPLVAAATSGSDFDIRDLRKKKTTVYFGLD------PDRI 376
Query: 77 SRLDRLLK 84
SR+ LL+
Sbjct: 377 SRVKPLLR 384
>gnl|CDD|35096 COG5537, IRR1, Cohesin [Cell division and chromosome partitioning].
Length = 740
Score = 26.5 bits (58), Expect = 4.6
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 96 YFITVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDVMRVAK 136
+ + P D +++FV+RF DRI+ D +R+
Sbjct: 340 FLCSRIPHTDA---IRRFVERFKDRILEFLRTDSDCVRICS 377
>gnl|CDD|143420 cd07102, ALDH_EDX86601, Uncharacterized aldehyde dehydrogenase of
Synechococcus sp. PCC 7335 (EDX86601). Uncharacterized
aldehyde dehydrogenase of Synechococcus sp. PCC 7335
(locus EDX86601) and other similar sequences, are
present in this CD.
Length = 452
Score = 26.4 bits (59), Expect = 5.1
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 158 VDHTTALLLFDTAGSIVGVIPYKDDSDSAIEKIN 191
VDH+ ++ +T G +VG++ K D AI +N
Sbjct: 348 VDHSMRVMREETFGPVVGIMKVKSD-AEAIALMN 380
>gnl|CDD|143417 cd07099, ALDH_DDALDH, Methylomonas sp.
4,4'-diapolycopene-dialdehyde dehydrogenase-like. The
4,4'-diapolycopene-dialdehyde dehydrogenase (DDALDH)
involved in C30 carotenoid synthesis in Methylomonas sp.
strain 16a and other similar sequences are present in
this CD. DDALDH converts 4,4'-diapolycopene-dialdehyde
into 4,4'-diapolycopene-diacid.
Length = 453
Score = 26.4 bits (59), Expect = 5.9
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 158 VDHTTALLLFDTAGSIVGVIPYKDDSDSAIEKIN 191
V H ++ +T G ++ V+P D+ D AI N
Sbjct: 347 VPHDMDVMREETFGPVLPVMPVADE-DEAIALAN 379
>gnl|CDD|143461 cd07143, ALDH_AldA_AN0554, Aspergillus nidulans aldehyde
dehydrogenase, AldA (AN0554)-like. NAD(P)+-dependent
aldehyde dehydrogenase (AldA) of Aspergillus nidulans
(locus AN0554), and other similar sequences, are present
in this CD.
Length = 481
Score = 26.3 bits (58), Expect = 6.4
Identities = 32/119 (26%), Positives = 51/119 (42%), Gaps = 36/119 (30%)
Query: 109 VMKKFVQRFSDRIIGIS-GDPID--------VMRVAKNFRI--YVNNVLAEKSGVE---- 153
+ KFV+RF ++ + GDP V ++ RI Y+ + AE + VE
Sbjct: 300 IYDKFVKRFKEKAKKLKVGDPFAEDTFQGPQVSQIQYE-RIMSYIESGKAEGATVETGGK 358
Query: 154 ----EKYFVDHTTALLLFDTA-----------GSIVGVIPYKDDSDSAIEKINRLITYG 197
E YF++ T + D G +V VI +K + + AI++ N TYG
Sbjct: 359 RHGNEGYFIEPT---IFTDVTEDMKIVKEEIFGPVVAVIKFKTEEE-AIKRAND-STYG 412
>gnl|CDD|48566 cd03017, PRX_BCP, Peroxiredoxin (PRX) family, Bacterioferritin
comigratory protein (BCP) subfamily; composed of
thioredoxin-dependent thiol peroxidases, widely
expressed in pathogenic bacteria, that protect cells
against toxicity from reactive oxygen species by
reducing and detoxifying hydroperoxides. The protein
was named BCP based on its electrophoretic mobility
before its function was known. BCP shows substrate
selectivity toward fatty acid hydroperoxides rather
than hydrogen peroxide or alkyl hydroperoxides. BCP
contains the peroxidatic cysteine but appears not to
possess a resolving cysteine (some sequences, not all,
contain a second cysteine but its role is still
unknown). Unlike other PRXs, BCP exists as a monomer.
The plant homolog of BCP is PRX Q, which is expressed
only in leaves and is cellularly localized in the
chloroplasts and the guard cells of stomata. Also
included in this subfamily is the fungal nuclear
protein, Dot5p (for disrupter of telomere silencing
protein 5), which functions as an alkyl-hydroperoxide
reductase during post-diauxic growth..
Length = 140
Score = 26.3 bits (58), Expect = 6.5
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 38 DVHLVAQDGTDFSLSSLYIKPSIVFF 63
D L QDG SLS L KP +++F
Sbjct: 5 DFTLPDQDGETVSLSDLRGKPVVLYF 30
>gnl|CDD|48564 cd03015, PRX_Typ2cys, Peroxiredoxin (PRX) family, Typical 2-Cys
PRX subfamily; PRXs are thiol-specific antioxidant
(TSA) proteins, which confer a protective role in cells
through its peroxidase activity by reducing hydrogen
peroxide, peroxynitrite, and organic hydroperoxides.
The functional unit of typical 2-cys PRX is a
homodimer. A unique intermolecular redox-active
disulfide center is utilized for its activity. Upon
reaction with peroxides, its peroxidatic cysteine is
oxidized into a sulfenic acid intermediate which is
resolved by bonding with the resolving cysteine from
the other subunit of the homodimer. This intermolecular
disulfide bond is then reduced by thioredoxin,
tryparedoxin or AhpF. Typical 2-cys PRXs, like 1-cys
PRXs, form decamers which are stabilized by reduction
of the active site cysteine. Typical 2-cys PRX
interacts through beta strands at one edge of the
monomer (B-type interface) to form the functional
homodimer, and uses an A-type interface (similar to the
dimeric interface in atypical 2-cys PRX and PRX5) at
the opposite end of the monomer to form the stable
decameric (pentamer of dimers) structure..
Length = 173
Score = 26.2 bits (58), Expect = 6.5
Identities = 11/51 (21%), Positives = 22/51 (43%)
Query: 35 FNSDVHLVAQDGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQ 85
F + + + + SLS K ++FF + + VCPT + ++
Sbjct: 8 FKATAVVPNGEFKEISLSDYKGKWVVLFFYPLDFTFVCPTEIIAFSDRYEE 58
>gnl|CDD|107350 cd06355, PBP1_FmdD_like, Periplasmic component (FmdD) of an active
transport system for short-chain amides and urea
(FmdDEF). This group includes the periplasmic component
(FmdD) of an active transport system for short-chain
amides and urea (FmdDEF), found in Methylophilus
methylotrophus, and its homologs from other bacteria.
FmdD, a type I periplasmic binding protein, is induced
by short-chain amides and urea and repressed by excess
ammonia, while FmdE and FmdF are hydrophobic
transmembrane proteins. FmdDEF is predicted to be an
ATP-dependent transporter and closely resembles the
periplasmic binding protein and the two transmembrane
proteins present in various hydrophobic amino
acid-binding transport systems.
Length = 348
Score = 26.1 bits (58), Expect = 6.6
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 7/36 (19%)
Query: 96 YFITVDPKRDTPEVMKKFVQRFSDRI--IGISGDPI 129
YF +VD TPE KKFV F R ++ DP+
Sbjct: 247 YFQSVD----TPE-NKKFVAAFKARYGQDRVTNDPM 277
>gnl|CDD|143431 cd07113, ALDH_PADH_NahF, Escherichia coli NAD+-dependent
phenylacetaldehyde dehydrogenase PadA-like.
NAD+-dependent, homodimeric, phenylacetaldehyde
dehydrogenase (PADH, EC=1.2.1.39) PadA of Escherichia
coli involved in the catabolism of 2-phenylethylamine,
and other related sequences, are present in this CD.
Also included is the Pseudomonas fluorescens ST StyD
PADH involved in styrene catabolism, the Sphingomonas
sp. LB126 FldD protein involved in fluorene degradation,
and the Novosphingobium aromaticivorans NahF
salicylaldehyde dehydrogenase involved in the
NAD+-dependent conversion of salicylaldehyde to
salicylate.
Length = 477
Score = 26.3 bits (58), Expect = 6.7
Identities = 25/111 (22%), Positives = 40/111 (36%), Gaps = 33/111 (29%)
Query: 108 EVMKKFVQRFSDRIIGISGDP-------------------IDVMRVAKNFRIYVNNVLAE 148
E++ K Q S +G D +D R + + LA
Sbjct: 299 ELVTKLKQALSSFQVGSPMDESVMFGPLANQPHFDKVCSYLDDARAEGDEIVRGGEALAG 358
Query: 149 KSGVEEKYFVDHT--------TALLLFDTAGSIVGVIPYKDDSDSAIEKIN 191
E YFV T + L+ +T G +V +PY+D+ + I+ IN
Sbjct: 359 -----EGYFVQPTLVLARSADSRLMREETFGPVVSFVPYEDE-EELIQLIN 403
>gnl|CDD|34830 COG5233, GRH1, Peripheral Golgi membrane protein [Intracellular
trafficking and secretion].
Length = 417
Score = 25.9 bits (56), Expect = 7.9
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 110 MKKFVQRFSDRIIGISGDPIDVMRVAKNF 138
+K D I+GI+ DP+ + + +
Sbjct: 76 AEKAGMVVGDYILGINEDPLRFLEMNRRR 104
>gnl|CDD|31437 COG1244, COG1244, Predicted Fe-S oxidoreductase [General function
prediction only].
Length = 358
Score = 25.7 bits (56), Expect = 8.2
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 108 EVMKKFVQRFSDRIIGI--SGDPIDVMRVAKNFRIYVNNVLAEKSGVEE 154
E K+ +F + ++ I SG +D V + R Y+ ++E V+E
Sbjct: 90 EAYSKYEGKFDEFVVKIFTSGSFLDPEEVPREARRYILERISENDNVKE 138
>gnl|CDD|112592 pfam03786, UxuA, D-mannonate dehydratase (UxuA). UxuA (this
family) and UxuB are required for hexuronate
degradation.
Length = 350
Score = 25.8 bits (57), Expect = 8.4
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 74 TTLSRLDRLLKQVD-PTG--TLLNAYFITVDPKRDTPEVMKKFVQR 116
T + RLL+ VD P TL + P D PE++++F R
Sbjct: 221 TNIEDYQRLLELVDSPYNGITLCTGSY-GARPDNDLPEMIREFADR 265
>gnl|CDD|37461 KOG2250, KOG2250, KOG2250, Glutamate/leucine/phenylalanine/valine
dehydrogenases [Amino acid transport and metabolism].
Length = 514
Score = 25.7 bits (56), Expect = 9.2
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 98 ITVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDV 131
I +DPK + +++ +RF+D +I I G DV
Sbjct: 148 ILIDPKGKSDNEIERITRRFTDELIDIIGPDTDV 181
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.323 0.140 0.398
Gapped
Lambda K H
0.267 0.0706 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,412,582
Number of extensions: 127214
Number of successful extensions: 448
Number of sequences better than 10.0: 1
Number of HSP's gapped: 440
Number of HSP's successfully gapped: 37
Length of query: 201
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 112
Effective length of database: 4,340,536
Effective search space: 486140032
Effective search space used: 486140032
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.0 bits)