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)