RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780563|ref|YP_003064976.1| extracellular solute-binding protein [Candidatus Liberibacter asiaticus str. psy62] (195 letters) >gnl|CDD|31069 COG0725, ModA, ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]. Length = 258 Score = 42.2 bits (99), Expect = 8e-05 Identities = 35/144 (24%), Positives = 58/144 (40%), Gaps = 5/144 (3%) Query: 1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQN-QSVMLPIIHSFEERTGVKISPIY 59 M K L+LL A S +T++ + + I FE+ TGVK+ + Sbjct: 4 MKKILALLLLVLLALGCAAGSAAQEAATITVFAAASLTDALEEIAKQFEKETGVKVEVEF 63 Query: 60 TSSIQ-RPPITQGSPVDVIITKDETSL--ALNEDLLHKLPAHLIKKNSFVLKNENKKLMR 116 S I QG+P D+ I+ D+ + ++ L++ + N VL + Sbjct: 64 GGSGALARQIEQGAPADLFISADDAYMDKLEDKGLIYADSRIVFAGNRLVLAVPKGSKKK 123 Query: 117 ISFDTQVLAYSTKRIKIADLPKSV 140 I +L R+ I D PK+V Sbjct: 124 IESLEDLLERPDVRLAIGD-PKTV 146 >gnl|CDD|31031 COG0687, PotD, Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]. Length = 363 Score = 36.6 bits (84), Expect = 0.005 Identities = 32/159 (20%), Positives = 53/159 (33%), Gaps = 22/159 (13%) Query: 10 LLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPI- 68 L A + E T + + +L FE+ TG+K+ S + Sbjct: 17 ALAALAGAAAAAAEGKTLNVYNWGGYIDPALLK---PFEKETGIKVVYDTFDSNEEMLAK 73 Query: 69 --TQGSPVDVII-TKDETSLALNEDLLHKLPAHLIKKNSFVLKNENKKLMRISFD----- 120 G DV++ + + + E LL L + + L FD Sbjct: 74 LKAGGGGYDVVVPSGYFVARLIKEGLLQPLDKSKLPNWKNLDPE---FLNPPKFDPGNKY 130 Query: 121 -------TQVLAYSTKRIKIADLPKSVFDLTNAQWKKRL 152 T +AY+T ++K A P S DL + + L Sbjct: 131 SVPYFWGTTGIAYNTDKVKDAPPPTSWADLFDPEKFPGL 169 >gnl|CDD|32025 COG1840, AfuA, ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]. Length = 299 Score = 35.8 bits (82), Expect = 0.007 Identities = 23/122 (18%), Positives = 44/122 (36%), Gaps = 9/122 (7%) Query: 43 IIHSFEERTGVKISPIYTSSI-----QRPPITQGSPVDVIITKDETSL--ALNEDLLHKL 95 +I +FE++ G+K+ + S DV+ SL LL Sbjct: 1 LIKAFEKKPGIKVEFVDAGSGELLARIIAEKGNPQAADVLWGGAPVSLDQLKEAGLLQPY 60 Query: 96 PAHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIK--IADLPKSVFDLTNAQWKKRLS 153 + + + + + V A +T K + +PKS DL ++K ++ Sbjct: 61 KSPELDEIPAWAPDPDGAYGGGYVGPLVFAVNTDYNKDLLKPVPKSWADLAKPEYKGKVQ 120 Query: 154 IA 155 +A Sbjct: 121 MA 122 >gnl|CDD|37919 KOG2708, KOG2708, KOG2708, Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [Posttranslational modification, protein turnover, chaperones]. Length = 336 Score = 30.3 bits (68), Expect = 0.34 Identities = 26/108 (24%), Positives = 46/108 (42%), Gaps = 16/108 (14%) Query: 35 QNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQGSPVDVIITKDETSLALNEDLLHK 94 +++ +L ++ E GV I + P G+P+ V+ +A LL Sbjct: 48 HHRAWILGLVKQALEEAGVTSDDIDCICYTKGP-GMGAPLSVVAI-----VARTLSLLWN 101 Query: 95 LP--------AHLIKKNSFVLKNENKKLMRISF-DTQVLAYSTKRIKI 133 P H I+ + +N ++ +S +TQV+AYS KR +I Sbjct: 102 KPLVGVNHCIGH-IEMGREITGAQNPVVLYVSGGNTQVIAYSEKRYRI 148 >gnl|CDD|28891 cd00007, 35EXOc, 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).. Length = 155 Score = 29.2 bits (65), Expect = 0.81 Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 4/53 (7%) Query: 98 HLIKKNSFVLKNENKKLMRISFDTQVLAY----STKRIKIADLPKSVFDLTNA 146 H K + VL + +L FDT + AY + DL K + Sbjct: 60 HDAKFDLVVLARDGIELPGNIFDTMLAAYLLNPGEGSHSLDDLAKEYLGIELD 112 >gnl|CDD|176649 cd06128, DNA_polA_exo, DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Pol I resemble the fold of the 3'-5' exonuclease domain of KF without the proofreading activity of KF. The four critical metal-binding residues are not conserved in BF Pol I and Taq Pol I, and they are unable to bind metals necessary for exonuclease activity. Length = 151 Score = 28.9 bits (64), Expect = 0.85 Identities = 14/46 (30%), Positives = 20/46 (43%) Query: 81 DETSLALNEDLLHKLPAHLIKKNSFVLKNENKKLMRISFDTQVLAY 126 E L ED +K + +L N +L I+FDT + AY Sbjct: 42 LELLKPLLEDEKALKVGQNLKYDRVILANYGIELRGIAFDTMLEAY 87 >gnl|CDD|133047 cd06425, M1P_guanylylT_B_like_N, N-terminal domain of the M1P-guanylyltransferase B-isoform like proteins. GDP-mannose pyrophosphorylase (GTP: alpha-d-mannose-1-phosphate guanyltransferase) catalyzes the formation of GDP-d-mannose from GTP and alpha-d-mannose-1-Phosphate. It contains an N-terminal catalytic domain and a C-terminal Lefthanded-beta-Helix fold domain. GDP-d-mannose is the activated form of mannose for formation of cell wall lipoarabinomannan and various mannose-containing glycolipids and polysaccharides. The function of GDP-mannose pyrophosphorylase is essential for cell wall integrity, morphogenesis and viability. Repression of GDP-mannose pyrophosphorylase in yeast leads to phenotypes, such as cell lysis, defective cell wall, and failure of polarized growth and cell separation. Length = 233 Score = 27.2 bits (61), Expect = 3.2 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 8/64 (12%) Query: 37 QSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQGSPV----DVIITKDETSLALNEDLL 92 M+P + +E++ G+KI+ SI+ P+ P+ D++ DE LN D++ Sbjct: 57 PEDMVPFLKEYEKKLGIKITF----SIETEPLGTAGPLALARDLLGDDDEPFFVLNSDVI 112 Query: 93 HKLP 96 P Sbjct: 113 CDFP 116 >gnl|CDD|146401 pfam03743, TrbI, Bacterial conjugation TrbI-like protein. Although not essential for conjugation, the TrbI protein greatly increase the conjugational efficiency. Length = 186 Score = 27.1 bits (61), Expect = 3.3 Identities = 13/74 (17%), Positives = 30/74 (40%), Gaps = 9/74 (12%) Query: 12 LLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTS-SIQRPP--- 67 LL G +A + ++ T ++ + + +++ Y +I PP Sbjct: 115 LLSGGGQAAAASASS---TSGNGNTSTLQAGDSGA--GQAASQLAQQYLERAINIPPTIE 169 Query: 68 ITQGSPVDVIITKD 81 I G V++++ +D Sbjct: 170 INPGRRVNIVVARD 183 >gnl|CDD|176652 cd06140, DNA_polA_I_Bacillus_like_exo, inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases. Length = 178 Score = 26.5 bits (59), Expect = 5.0 Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 4/44 (9%) Query: 97 AHLIKKNSFVLKNENKKLMRISFDTQVLAY---STKRI-KIADL 136 H K+ LK +L ++FDT + AY T+ +ADL Sbjct: 61 GHDAKRAYVALKRHGIELAGVAFDTMLAAYLLDPTRSSYDLADL 104 >gnl|CDD|111923 pfam03082, MAGSP, Male accessory gland secretory protein. The accessory gland of male insects is a genital tissue that secretes many components of the ejaculatory fluid, some of which affect the female's receptivity to courtship and her rate of oviposition. This protein is expressed exclusively in the male accessory glands of adult Drosophila melanogaster. The proteins are transferred to the female fly during copulation and are rapidly altered in the female genital tract. Length = 267 Score = 26.3 bits (57), Expect = 5.1 Identities = 14/36 (38%), Positives = 22/36 (61%) Query: 131 IKIADLPKSVFDLTNAQWKKRLSIAPNNISFHRLLN 166 I I+DLP + + N++ K SI NNI F++ L+ Sbjct: 75 IDISDLPLDDYPINNSKSLKNSSIDLNNIPFNKGLD 110 >gnl|CDD|38225 KOG3015, KOG3015, KOG3015, F1-ATP synthase assembly protein [Energy production and conversion]. Length = 283 Score = 26.5 bits (58), Expect = 5.3 Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 4/51 (7%) Query: 20 FSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQ 70 FS E+ + L D P+I FE R GVK+ P + +I + Sbjct: 144 FSPES--EDLGRLRDLQVEEWDPLIEWFENRLGVKLQP--SDNILGGKQAE 190 >gnl|CDD|176651 cd06139, DNA_polA_I_Ecoli_like_exo, DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair. Length = 193 Score = 25.9 bits (58), Expect = 7.1 Identities = 8/21 (38%), Positives = 12/21 (57%) Query: 106 VLKNENKKLMRISFDTQVLAY 126 VL N +L +FDT + +Y Sbjct: 81 VLANHGIELRGPAFDTMLASY 101 >gnl|CDD|58176 cd03510, Rhizobitoxine-FADS-like, This CD includes the dihydrorhizobitoxine fatty acid desaturase (RtxC) characterized in Bradyrhizobium japonicum USDA110, and other related proteins. Dihydrorhizobitoxine desaturase is reported to be involved in the final step of rhizobitoxine biosynthesis. This domain family appears to be structurally related to the membrane fatty acid desaturases and the alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXX(X)HH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA desaturase and alkane hydroxylase.. Length = 175 Score = 25.6 bits (56), Expect = 8.6 Identities = 9/19 (47%), Positives = 13/19 (68%) Query: 144 TNAQWKKRLSIAPNNISFH 162 T W +RL AP+NI++H Sbjct: 136 TFGGWIERLLFAPHNINYH 154 >gnl|CDD|37008 KOG1797, KOG1797, KOG1797, Uncharacterized conserved protein (Neuroblastoma-amplified protein) [Function unknown]. Length = 1660 Score = 25.5 bits (55), Expect = 9.5 Identities = 9/31 (29%), Positives = 13/31 (41%) Query: 20 FSTENTTKYLTLYTDQNQSVMLPIIHSFEER 50 E+ L L T+ + M+ I FEE Sbjct: 1017 LDAEDAALELGLCTNCGCADMMNIAIKFEEH 1047 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 0.319 0.133 0.371 Gapped Lambda K H 0.267 0.0631 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,191,613 Number of extensions: 105908 Number of successful extensions: 280 Number of sequences better than 10.0: 1 Number of HSP's gapped: 278 Number of HSP's successfully gapped: 25 Length of query: 195 Length of database: 6,263,737 Length adjustment: 89 Effective length of query: 106 Effective length of database: 4,340,536 Effective search space: 460096816 Effective search space used: 460096816 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 55 (25.2 bits)