RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780854|ref|YP_003065267.1| NADH dehydrogenase subunit C
[Candidatus Liberibacter asiaticus str. psy62]
(202 letters)
>gnl|CDD|36925 KOG1713, KOG1713, KOG1713, NADH-ubiquinone oxidoreductase,
NDUFS3/30 kDa subunit [Energy production and
conversion].
Length = 191
Score = 193 bits (492), Expect = 2e-50
Identities = 82/168 (48%), Positives = 114/168 (67%)
Query: 19 SVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHF 78
+ + EL + + ++ + FL+ + F N+ D+ GVD +R NRF+VVY+
Sbjct: 19 VQKVQYQAGDELEILIHPDGVIPVLLFLKGHTYARFQNLYDIAGVDVPTRKNRFEVVYNL 78
Query: 79 LSPKYNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYG 138
LS +YN R+RVK E + S+V ++ ADW EREVWDM+G+ F+ HPDLRRILTDYG
Sbjct: 79 LSVRYNSRIRVKTYTDESTPIDSVVSVFKSADWQEREVWDMFGVTFDNHPDLRRILTDYG 138
Query: 139 FEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRDYDFLSPWE 186
FEGHPLRKD+P++G+VE+ YDD+ K+VV P+EL QE R +D SPWE
Sbjct: 139 FEGHPLRKDYPLSGYVEVRYDDEEKRVVSEPIELAQEFRKFDLNSPWE 186
>gnl|CDD|31193 COG0852, NuoC, NADH:ubiquinone oxidoreductase 27 kD subunit [Energy
production and conversion].
Length = 176
Score = 179 bits (456), Expect = 4e-46
Identities = 84/178 (47%), Positives = 120/178 (67%), Gaps = 4/178 (2%)
Query: 1 MVRKIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDL 60
+ +L + ++ S + V + GEL+L V +L+ + L+D+ F +++DL
Sbjct: 2 DDPVLAELLERLLAELSTVIETVVVAEGELTLKVPPDELIDVLKALKDEG---FDHLLDL 58
Query: 61 CGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAVAEGK-SVPSIVGIYPGADWFEREVWDM 119
GVD+ + RF+VVYH LS K NRR+RVK+ ++E VPS+ I+P A+W+ERE +DM
Sbjct: 59 TGVDYPQETERFEVVYHLLSYKDNRRVRVKVRLSEDDPHVPSVTDIWPAANWYEREAYDM 118
Query: 120 YGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHR 177
+GI FEGHPDLRRIL +EGHPLRKDFP+ G+VE+ YD++ KKVVY PVEL+ E R
Sbjct: 119 FGIVFEGHPDLRRILMPDDWEGHPLRKDFPLRGYVEVRYDEEDKKVVYEPVELIFERR 176
>gnl|CDD|144062 pfam00329, Complex1_30kDa, Respiratory-chain NADH dehydrogenase, 30
Kd subunit.
Length = 103
Score = 138 bits (349), Expect = 1e-33
Identities = 50/107 (46%), Positives = 68/107 (63%), Gaps = 5/107 (4%)
Query: 41 SLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAV-AEGKSV 99
+ FL++D DL GVD+ RF+VVYH S R+R+K+ + + +
Sbjct: 1 EVARFLKEDGFDRLS---DLTGVDYPEE-GRFEVVYHLASIGDGERVRLKVKLPRDDPEI 56
Query: 100 PSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRK 146
PSI I+PGA+W+EREV+DM+GI FEGHPDLRR+L + GHPLRK
Sbjct: 57 PSITDIFPGANWYEREVYDMFGIVFEGHPDLRRLLLPEDWPGHPLRK 103
>gnl|CDD|33073 COG3262, HycE, Ni,Fe-hydrogenase III component G [Energy production
and conversion].
Length = 165
Score = 70.0 bits (171), Expect = 4e-13
Identities = 33/81 (40%), Positives = 45/81 (55%), Gaps = 5/81 (6%)
Query: 73 DVVYHFLSPKYNRRLRVKIAV---AEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPD 129
VY FLS + + V + V A+ PS+ I+P A WFERE+ DMYG+ G PD
Sbjct: 71 FAVYLFLSMEQAPKCWVIVKVSVPADNPEFPSVAPIFPAALWFEREIRDMYGLDPVGAPD 130
Query: 130 LRRIL--TDYGFEGHPLRKDF 148
RR++ D+ +PLRKD
Sbjct: 131 PRRLVLPDDWPEGIYPLRKDA 151
>gnl|CDD|176955 CHL00012, ndhJ, NADH dehydrogenase subunit J.
Length = 158
Score = 68.6 bits (168), Expect = 1e-12
Identities = 31/87 (35%), Positives = 48/87 (55%), Gaps = 5/87 (5%)
Query: 75 VYHFLSPKYN----RRLRVKIAVA-EGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPD 129
VYH +Y + +K+ V + +PS+ ++ AD+ ERE +DM GI ++ HP
Sbjct: 68 VYHLTRIQYGVDQPEEVCIKVFVPRKNPRIPSVFWVWKSADFQERESYDMLGISYDNHPR 127
Query: 130 LRRILTDYGFEGHPLRKDFPVTGFVEL 156
L+RIL + G PLRKD+ F E+
Sbjct: 128 LKRILMPESWIGWPLRKDYIAPNFYEI 154
>gnl|CDD|32353 COG2170, COG2170, Uncharacterized conserved protein [Function
unknown].
Length = 369
Score = 26.8 bits (59), Expect = 4.1
Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 8/57 (14%)
Query: 86 RLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGH 142
R + A ++ G +P ADW +EV D +P +R++ G+ G
Sbjct: 71 RDYLVQAASDHGLRICGGGTHPFADWRRQEVPD--------NPRYQRLIERTGYLGR 119
>gnl|CDD|31719 COG1530, CafA, Ribonucleases G and E [Translation, ribosomal
structure and biogenesis].
Length = 487
Score = 26.8 bits (59), Expect = 4.3
Identities = 19/87 (21%), Positives = 30/87 (34%), Gaps = 13/87 (14%)
Query: 83 YNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGH 142
Y RRL I + K P+ +Y R + D G D+ I+ D G E +
Sbjct: 181 YLRRLWEAI-LERAKKRPAPGLLYEETSLVVRVIRDYVG------KDITEIVVD-GKEAY 232
Query: 143 PLRKDFPVTGFVELHYDDKVKKVVYRP 169
K+F + + K+
Sbjct: 233 LEAKEFILEI-----MPELRSKLKLYR 254
>gnl|CDD|30168 cd01713, PAPS_reductase, This domain is found in phosphoadenosine
phosphosulphate (PAPS) reductase enzymes or PAPS
sulphotransferase. PAPS reductase is part of the adenine
nucleotide alpha hydrolases superfamily also including N
type ATP PPases and ATP sulphurylases. A highly modified
version of the P loop, the fingerprint peptide of
mononucleotide-binding proteins, is present in the
active site of the protein, which appears to be a
positively charged cleft containing a number of
conserved arginine and lysine residues. Although PAPS
reductase has no ATPase activity, it shows a striking
similarity to the structure of the ATP pyrophosphatase
(ATP PPase) domain of GMP synthetase, indicating that
both enzyme families have evolved from a common
ancestral nucleotide-binding fold. The enzyme uses
thioredoxin as an electron donor for the reduction of
PAPS to phospho-adenosine-phosphate (PAP) . It is also
found in NodP nodulation protein P from Rhizobium
meliloti which has ATP sulphurylase activity (sulphate
adenylate transferase) ..
Length = 173
Score = 26.6 bits (58), Expect = 5.0
Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 6/57 (10%)
Query: 83 YNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGF 139
R L + +GK I+ + P DW +VW + H L D G+
Sbjct: 119 ARRALLPVVWTDDGK--GGILKVNPLLDWTYEDVWA----YLARHGLPYNPLYDQGY 169
>gnl|CDD|72886 cd03428, Ap4A_hydrolase_human_like, Diadenosine tetraphosphate
(Ap4A) hydrolase is a member of the Nudix hydrolase
superfamily. Ap4A hydrolases are well represented in a
variety of prokaryotic and eukaryotic organisms.
Phylogenetic analysis reveals two distinct subgroups
where plant enzymes fall into one subfamily and
fungi/animals/archaea enzymes, represented by this
subfamily, fall into another. Bacterial enzymes are
found in both subfamilies. Ap4A is a potential
by-product of aminoacyl tRNA synthesis, and accumulation
of Ap4A has been implicated in a range of biological
events, such as DNA replication, cellular
differentiation, heat shock, metabolic stress, and
apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically
into ATP and AMP. It is important in the invasive
properties of bacteria and thus presents a potential
target for inhibition of such invasive bacteria. Besides
the signature nudix motif (G[X5]E[X7]REUXEEXGU, where U
is Ile, Leu, or Val) that functions as a metal binding
and catalytic site, and a required divalent cation, Ap4A
hydrolase is structurally similar to the other members
of the nudix superfamily with some degree of variation.
Several regions in the sequences are poorly defined and
substrate and metal binding sites are only predicted
based on kinetic studies..
Length = 130
Score = 26.4 bits (58), Expect = 5.1
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 11/58 (18%)
Query: 145 RKDFPVTGF-VELHY--DDKVKKVVY--------RPVELMQEHRDYDFLSPWEGVNSL 191
+ F V GF L+Y K+K V Y V+L +EH+DY +L E + L
Sbjct: 59 EQLFIVLGFKETLNYQVRGKLKTVTYFLAELRPDVEVKLSEEHQDYRWLPYEEALKLL 116
>gnl|CDD|145696 pfam02677, DUF208, Uncharacterized BCR, COG1636.
Length = 176
Score = 26.3 bits (59), Expect = 5.9
Identities = 22/75 (29%), Positives = 27/75 (36%), Gaps = 18/75 (24%)
Query: 51 HCCFVNIIDLCGVD---FLS--RSNRFDVVYHFLSP------KYNRRLRVKIAVAEGKSV 99
H C C L R F+V F +P +Y RRL AE +
Sbjct: 4 HIC-------CAPCSSYPLEYLREYGFEVTGFFYNPNIHPYSEYLRRLEEVKRFAEKLGI 56
Query: 100 PSIVGIYPGADWFER 114
P I G Y +W ER
Sbjct: 57 PLIEGDYDPEEWLER 71
>gnl|CDD|34255 COG4636, Uma2, Uncharacterized protein conserved in cyanobacteria
[Function unknown].
Length = 200
Score = 26.0 bits (56), Expect = 7.5
Identities = 13/67 (19%), Positives = 17/67 (25%), Gaps = 3/67 (4%)
Query: 67 SRSNRFDVVYHFLSPKYNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGI---F 123
R N F L + + L + VP P E
Sbjct: 48 ERINTFLGNDLGLYLEPLQGLGEAFGSPDCFVVPGSAYREPDVSVVCDERLSYLPQIDEE 107
Query: 124 FEGHPDL 130
F+ PDL
Sbjct: 108 FDIAPDL 114
>gnl|CDD|38676 KOG3466, KOG3466, KOG3466, NADH:ubiquinone oxidoreductase,
NDUFB9/B22 subunit [Energy production and conversion].
Length = 157
Score = 25.9 bits (56), Expect = 8.6
Identities = 12/49 (24%), Positives = 18/49 (36%)
Query: 100 PSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDF 148
P I PG +ERE + HP + DY + +K+
Sbjct: 78 PYIFPDSPGGSSYEREPCPPDWCLDDWHPAEKAQYPDYFAKREQRKKER 126
>gnl|CDD|146968 pfam04583, Baculo_p74, Baculoviridae p74 conserved region.
Baculoviruses are distinct from other virus families in
that there are two viral phenotypes: budded virus (BV)
and occlusion-derived virus (ODV). BVs disseminate viral
infection throughout the tissues of the host and ODVs
transmit baculovirus between insect hosts. GFP tagging
experiments implicate p74 as an ODV envelope protein.
Length = 250
Score = 25.7 bits (57), Expect = 8.9
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 112 FEREVWDMYGIFFEGHPDLRRILTDYGFE 140
+ + D+ F E H + ILTD GF+
Sbjct: 5 SDDSLEDIITQFLEDHALISGILTDLGFD 33
>gnl|CDD|32035 COG1850, RbcL, Ribulose 1,5-bisphosphate carboxylase, large subunit
[Carbohydrate transport and metabolism].
Length = 429
Score = 25.6 bits (56), Expect = 8.9
Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 3/80 (3%)
Query: 117 WDMYGIFFEGHPDLRRILT---DYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELM 173
+ G+ H + T ++G L K + G +LH V K+ + +
Sbjct: 270 DEDIGLAIHAHRAMHAAFTRSPNHGISFLVLAKLLRLIGVDQLHIGTVVGKLEGDREDYV 329
Query: 174 QEHRDYDFLSPWEGVNSLFA 193
+ +++ F W + +F
Sbjct: 330 ESDKEFFFEQDWAHIKPVFP 349
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
0.325 0.144 0.457
Gapped
Lambda K H
0.267 0.0764 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,749,582
Number of extensions: 154142
Number of successful extensions: 429
Number of sequences better than 10.0: 1
Number of HSP's gapped: 426
Number of HSP's successfully gapped: 19
Length of query: 202
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 113
Effective length of database: 4,340,536
Effective search space: 490480568
Effective search space used: 490480568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 55 (24.9 bits)