RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780856|ref|YP_003065269.1| NADH-quinone oxidoreductase, E
subunit [Candidatus Liberibacter asiaticus str. psy62]
(218 letters)
>gnl|CDD|144740 pfam01257, Complex1_24kDa, Respiratory-chain NADH dehydrogenase 24
Kd subunit.
Length = 145
Score = 221 bits (567), Expect = 1e-58
Identities = 73/147 (49%), Positives = 101/147 (68%), Gaps = 3/147 (2%)
Query: 26 VNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQF 85
++E+I++YP R +SA+IPLL AQEQ G++ AIE +A +L + RV E+ATFY+ F
Sbjct: 1 IDEIIAKYP--RKRSALIPLLHLAQEQYGYLPDEAIEYIAELLGIPPARVYEVATFYSMF 58
Query: 86 QLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACV 145
L PVG + H+QVC TTPC LRG ++L+E K+ KP DG + EEVEC GAC
Sbjct: 59 NLKPVG-KYHIQVCTTTPCHLRGSDELLEALEEKLGIKPGETTPDGKFTLEEVECLGACG 117
Query: 146 NAPMVMIGKDTYEDLTPERLEEIIDAF 172
NAP++ I D Y DLTPE+++EI++A
Sbjct: 118 NAPVMQINDDYYGDLTPEKVDEILEAL 144
>gnl|CDD|32089 COG1905, NuoE, NADH:ubiquinone oxidoreductase 24 kD subunit [Energy
production and conversion].
Length = 160
Score = 205 bits (522), Expect = 1e-53
Identities = 74/163 (45%), Positives = 103/163 (63%), Gaps = 3/163 (1%)
Query: 14 SSFSFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYI 73
++F+FS E+ + +I++YP +SA+IPLL AQEQ GW+ AIE +A++L +
Sbjct: 1 ATFAFSAENLELIEAIIAKYP--DKRSALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRA 58
Query: 74 RVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTL 133
RV +ATFYTQF L PVG R H++VC T C L+G E L++ K+ KP +DG
Sbjct: 59 RVYGVATFYTQFFLKPVG-RHHIRVCTGTACHLKGSEALLKALEKKLGIKPGETTADGKF 117
Query: 134 SWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQ 176
+ E VEC GAC AP+VMI D Y LTPE+LEEI++ +
Sbjct: 118 TLEPVECLGACGQAPVVMINDDVYGRLTPEKLEEILEKLKAKK 160
>gnl|CDD|38406 KOG3196, KOG3196, KOG3196, NADH:ubiquinone oxidoreductase,
NDUFV2/24 kD subunit [Energy production and conversion].
Length = 233
Score = 173 bits (439), Expect = 3e-44
Identities = 89/201 (44%), Positives = 119/201 (59%), Gaps = 3/201 (1%)
Query: 1 MSVRRLAEEEFQPSSFSFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAA 60
+ V R E F F+ E+ V +++ YP A+IPLL AQ Q GW+ +A
Sbjct: 22 LFVHRDTPENNPDLPFEFTPENQKRVKAILAIYPEGHKAGALIPLLDLAQRQHGWLPISA 81
Query: 61 IEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKI 120
+ VA +L++ +RV E+ATFYT F PVG + HVQVC TTPCMLRG + ++E C+ ++
Sbjct: 82 MNEVAEVLEVPPMRVYEVATFYTMFFRKPVG-KYHVQVCTTTPCMLRGSDDILEACKKQL 140
Query: 121 HQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTI 180
K DG + EEVEC GACVNAPM+ I D YEDLTP++L EI++ G
Sbjct: 141 GIKVGETTKDGLFTLEEVECLGACVNAPMIAINDDYYEDLTPKKLVEILEDLK--AGKKP 198
Query: 181 RPGPQIDRISSAPAGGLTSLL 201
GP+ R +S P GGLTSL
Sbjct: 199 PAGPRNGRFASEPKGGLTSLK 219
>gnl|CDD|48613 cd03064, TRX_Fd_NuoE, TRX-like [2Fe-2S] Ferredoxin (Fd) family,
NADH:ubiquinone oxidoreductase (Nuo) subunit E
subfamily; Nuo, also called respiratory chain Complex 1,
is the entry point for electrons into the respiratory
chains of bacteria and the mitochondria of eukaryotes.
It is a multisubunit complex with at least 14 core
subunits. It catalyzes the electron transfer of NADH to
quinone coupled with the transfer of protons across the
membrane, providing the proton motive force required for
energy-consuming processes. Electrons are transferred
from NADH to quinone through a chain of iron-sulfur
clusters in Nuo, including the [2Fe-2S] cluster present
in NuoE core subunit, also called the 24 kD subunit of
Complex 1. This subfamily also include formate
dehydrogenases, NiFe hydrogenases and NAD-reducing
hydrogenases, that contain a NuoE domain. A subset of
these proteins contain both NuoE and NuoF in a single
chain. NuoF, also called the 51 kD subunit of Complex 1,
contains one [4Fe-4S] cluster and also binds the NADH
substrate and FMN..
Length = 80
Score = 102 bits (256), Expect = 8e-23
Identities = 35/80 (43%), Positives = 48/80 (60%)
Query: 93 RAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMI 152
+ ++VC T C LRG E L+E K+ KP DG + EEVEC GAC AP++MI
Sbjct: 1 KHVIRVCTGTACHLRGAEALLEALEKKLGIKPGETTPDGRFTLEEVECLGACDLAPVMMI 60
Query: 153 GKDTYEDLTPERLEEIIDAF 172
D Y LTPE+++ I++A
Sbjct: 61 NDDVYGRLTPEKVDAILEAL 80
>gnl|CDD|48529 cd02980, TRX_Fd_family, Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin
(Fd) family; composed of [2Fe-2S] Fds with a TRX fold
(TRX-like Fds) and proteins containing domains similar
to TRX-like Fd including formate dehydrogenases,
NAD-reducing hydrogenases and the subunit E of
NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are
soluble low-potential electron carriers containing a
single [2Fe-2S] cluster. The exact role of TRX-like Fd
is still unclear. It has been suggested that it may be
involved in nitrogen fixation. Its homologous domains in
large redox enzymes (such as Nuo and hydrogenases)
function as electron carriers..
Length = 77
Score = 74.2 bits (182), Expect = 2e-14
Identities = 29/80 (36%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 94 AHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMI- 152
H+ VC T C LRG E+L+E ++ + DG ++ E V C GAC AP+V++
Sbjct: 1 HHILVCTGTACGLRGAEELLEALEKELGIRGG----DGRVTVERVGCLGACGLAPVVVVY 56
Query: 153 -GKDTYEDLTPERLEEIIDA 171
Y +TPE +EEI++
Sbjct: 57 PDGVWYGRVTPEDVEEIVEE 76
>gnl|CDD|48630 cd03081, TRX_Fd_NuoE_FDH_gamma, TRX-like [2Fe-2S] Ferredoxin (Fd)
family, NADH:ubiquinone oxidoreductase (Nuo) subunit E
subfamily, NAD-dependent formate dehydrogenase (FDH)
gamma subunit; composed of proteins similar to the gamma
subunit of NAD-linked FDH of Ralstonia eutropha, a
soluble enzyme that catalyzes the irreversible oxidation
of formate to carbon dioxide accompanied by the
reduction of NAD+ to NADH. FDH is a heteromeric enzyme
composed of four nonidentical subunits (alpha, beta,
gamma and delta). The FDH gamma subunit is closely
related to NuoE, which is part of a multisubunit complex
(Nuo) catalyzing the electron transfer of NADH to
quinone coupled with the transfer of protons across the
membrane. Electrons are transferred from NADH to quinone
through a chain of iron-sulfur clusters in Nuo,
including the [2Fe-2S] cluster present in NuoE.
Similarly, the FDH gamma subunit is hypothesized to be
involved in an electron transport chain involving other
FDH subunits, upon the oxidation of formate..
Length = 80
Score = 52.2 bits (125), Expect = 1e-07
Identities = 18/79 (22%), Positives = 36/79 (45%)
Query: 93 RAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMI 152
R +++C C G E L + ++ +DG+++ E V C G C +P MI
Sbjct: 1 RHVLKLCRAEACQAMGAEALAAHIKARLGIDFHETTADGSVTLEPVYCLGLCACSPAAMI 60
Query: 153 GKDTYEDLTPERLEEIIDA 171
+ + + PE+ + ++
Sbjct: 61 DGEVHGRVDPEKFDALLAE 79
>gnl|CDD|48632 cd03083, TRX_Fd_NuoE_hoxF, TRX-like [2Fe-2S] Ferredoxin (Fd)
family, NADH:ubiquinone oxidoreductase (Nuo) subunit E
subfamily, hoxF; composed of proteins similar to the
NAD-reducing hydrogenase (hoxS) alpha subunit of
Alcaligenes eutrophus H16. HoxS is a cytoplasmic
hydrogenase catalyzing the oxidation of molecular
hydrogen accompanied by the reduction of NAD. It is
composed of four structural subunits encoded by the
genes hoxF, hoxU, hoxY and hoxH. The hoxF protein (or
alpha subunit) is a fusion protein containing an
N-terminal NuoE-like domain and a C-terminal NuoF
domain. NuoE and NuoF are components of Nuo, a
multisubunit complex catalyzing the electron transfer of
NADH to quinone coupled with the transfer of protons
across the membrane. Electrons are transferred from NADH
to quinone through a chain of iron-sulfur clusters in
Nuo, including the [2Fe-2S] cluster in NuoE and the
[4Fe-4S] cluster in NuoF. In addition, NuoF is also the
NADH- and FMN-binding subunit. HoxF may be involved in
the electron transport chain during the NAD-dependent
oxidation of hydrogen through its NuoF domain. The
NuoE-like domain of hoxF contains only one conserved
cysteine in its putative active site, compared to four
cysteines in NuoE, and may have lost the ability to bind
[2Fe-2S] clusters..
Length = 80
Score = 32.2 bits (73), Expect = 0.12
Identities = 12/42 (28%), Positives = 20/42 (47%)
Query: 129 SDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIID 170
DG + C G C P ++I + LTP R+++I +
Sbjct: 37 EDGMVGLFFTSCTGLCDQGPALLINNRVFTRLTPGRIDQIAE 78
>gnl|CDD|30533 COG0184, RpsO, Ribosomal protein S15P/S13E [Translation, ribosomal
structure and biogenesis].
Length = 89
Score = 28.6 bits (64), Expect = 1.3
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 5/62 (8%)
Query: 160 LTPERLEEIIDAFSTGQGDTIRPGPQIDRISSAPAGGLTSLLDNNSK----KRGKKKKDD 215
LT E +E+ D + + DT Q+ + + LT L + K +RG
Sbjct: 3 LTSEIKQELRDEYGIPEVDTGSGEVQL-ALLTERINNLTEHLKEHKKDHHSRRGLLLLVS 61
Query: 216 KI 217
K
Sbjct: 62 KR 63
>gnl|CDD|48631 cd03082, TRX_Fd_NuoE_W_FDH_beta, TRX-like [2Fe-2S] Ferredoxin (Fd)
family, NADH:ubiquinone oxidoreductase (Nuo) subunit E
family, Tungsten-containing formate dehydrogenase
(W-FDH) beta subunit; composed of proteins similar to
the W-FDH beta subunit of Methylobacterium extorquens.
W-FDH is a heterodimeric NAD-dependent enzyme catalyzing
the conversion of formate to carbon dioxide. The beta
subunit is a fusion protein containing an N-terminal
NuoE domain and a C-terminal NuoF domain. NuoE and NuoF
are components of Nuo, a multisubunit complex catalyzing
the electron transfer of NADH to quinone coupled with
the transfer of protons across the membrane. Electrons
are transferred from NADH to quinone through a chain of
iron-sulfur clusters in Nuo, including the [2Fe-2S]
cluster in NuoE and the [4Fe-4S] cluster in NuoF. In
addition, NuoF is also the NADH- and FMN-binding
subunit. Similarly, the beta subunit of W-FDH is most
likely involved in the electron transport chain during
the NAD-dependent oxidation of formate..
Length = 72
Score = 27.6 bits (61), Expect = 3.0
Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 8/76 (10%)
Query: 96 VQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKD 155
V+VC + C + G E+L+ + + C G C AP ++G+
Sbjct: 4 VRVCDSLSCAMAGAEELLAALEAGL--------GPEGVRVVRAPCVGRCERAPAALVGQR 55
Query: 156 TYEDLTPERLEEIIDA 171
+ TP + ++A
Sbjct: 56 PVDGATPAAVAAAVEA 71
>gnl|CDD|35483 KOG0262, KOG0262, KOG0262, RNA polymerase I, large subunit
[Transcription].
Length = 1640
Score = 26.5 bits (58), Expect = 6.4
Identities = 10/41 (24%), Positives = 17/41 (41%)
Query: 134 SWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFST 174
W E++ + AC + + D Y E+ + ID F
Sbjct: 1081 MWFELDKKIACPDPVLAKYNPDKYLGSVSEKFRKKIDDFDD 1121
>gnl|CDD|29278 cd00227, CPT, Chloramphenicol (Cm) phosphotransferase (CPT).
Cm-inactivating enzyme; modifies the primary (C-3)
hydroxyl of the antibiotic. Related structurally to
shikimate kinase II..
Length = 175
Score = 26.5 bits (58), Expect = 6.5
Identities = 8/66 (12%), Positives = 23/66 (34%)
Query: 138 VECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTIRPGPQIDRISSAPAGGL 197
+ + P + G D++ + P + ++ + PGP+ + A +
Sbjct: 19 ARALQSVLAEPWLHFGVDSFIEALPLKCQDAEGGIEFDGDGGVSPGPEFRLLEGAWYEAV 78
Query: 198 TSLLDN 203
++
Sbjct: 79 AAMARA 84
>gnl|CDD|31633 COG1444, COG1444, Predicted P-loop ATPase fused to an
acetyltransferase [General function prediction only].
Length = 758
Score = 26.1 bits (57), Expect = 6.9
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 155 DTYEDLTPERLEEIIDAFSTGQGDTIR-PGPQIDRISSAPAGGLT 198
DTY DL PE +++ + D G Q+DR+ +G +
Sbjct: 635 DTYRDLEPELARLLLENATLSDDDWPELTGFQLDRLELYASGPVL 679
>gnl|CDD|147007 pfam04637, Herpes_pp85, Herpesvirus phosphoprotein 85 (HHV6-7
U14/HCMV UL25). This family includes UL25 proteins from
HCMV, as well as U14 proteins from HHV 6 and HHV7. These
85 kD phosphoproteins appear to act as structural
antigens, but their precise function is otherwise
unknown.
Length = 502
Score = 25.8 bits (57), Expect = 8.6
Identities = 17/59 (28%), Positives = 24/59 (40%), Gaps = 3/59 (5%)
Query: 129 SDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTIRPGPQID 187
+DG ++ E Q +V+ G LTPE+LEE +D G P D
Sbjct: 401 TDGQITVEHYPLQSTYE---LVLEGAARQTGLTPEQLEEYLDRAPLGAEVEDGLEPPAD 456
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
0.317 0.132 0.393
Gapped
Lambda K H
0.267 0.0685 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,656,949
Number of extensions: 132802
Number of successful extensions: 291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 284
Number of HSP's successfully gapped: 17
Length of query: 218
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 128
Effective length of database: 4,318,927
Effective search space: 552822656
Effective search space used: 552822656
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 (21.7 bits)
S2: 55 (25.1 bits)