RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780935|ref|YP_003065348.1| rare lipoprotein A [Candidatus Liberibacter asiaticus str. psy62] (276 letters) >gnl|CDD|31140 COG0797, RlpA, Lipoproteins [Cell envelope biogenesis, outer membrane]. Length = 233 Score = 168 bits (426), Expect = 1e-42 Identities = 86/186 (46%), Positives = 108/186 (58%), Gaps = 9/186 (4%) Query: 13 SVVCVVVLGMSSCFFSSTYKDDKL--EYFPESMYGVTASDRIVSGKRVPRGGGRYFLGKP 70 V ++ L + C F E +YGV A R K G GR KP Sbjct: 9 CVAALLALLAACCSTKKVPSGMTRSKYNFNEQVYGVKADPRDNPLK----GSGRLTANKP 64 Query: 71 YQIMGRWYVPRQYTA-YAAVGMASWYGKAFHGRLTANGEVYGTEYITAAHPTLPLPSYVR 129 YQ+ G+ Y P+ A + VG ASWYG+ FHGR TANGE Y +TAAH TLPLP+YVR Sbjct: 65 YQVKGKSYYPKAEPASFEQVGYASWYGEKFHGRKTANGERYDMNALTAAHKTLPLPTYVR 124 Query: 130 VTNMENGISLVVRVNDRGPYHSNRLIDLSNAAAKILRVEERGVSKVHVEYLGMA--LLNG 187 VTN++NG S+VVR+NDRGP+ S R+IDLS AAA L + GV+KV +E LG+A L G Sbjct: 125 VTNLDNGRSVVVRINDRGPFVSGRIIDLSKAAADKLGMIRSGVAKVRIEVLGVASASLPG 184 Query: 188 MDQEYL 193 + L Sbjct: 185 NASKTL 190 >gnl|CDD|146125 pfam03330, DPBB_1, Rare lipoprotein A (RlpA)-like double-psi beta-barrel. Rare lipoprotein A (RlpA) contains a conserved region that has the double-psi beta-barrel (DPBB) fold. The function of RlpA is not well understood, but it has been shown to act as a prc mutant suppressor in Escherichia coli. The DPBB fold is often an enzymatic domain. The members of this family are quite diverse, and if catalytic this family may contain several different functions. Another example of this domain is found in the N terminus of pollen allergen. Length = 76 Score = 64.9 bits (159), Expect = 2e-11 Identities = 34/92 (36%), Positives = 42/92 (45%), Gaps = 17/92 (18%) Query: 88 AVGMASWYGKAFHGRLTANGEVYGTEYITAAHPTLPLPSYVRVTNMENGISLVVRVNDRG 147 A G AS Y TA GE Y + +TAA P+Y RVT S+ V + DR Sbjct: 2 AAGSASLYNDG-----TACGECYQVKCLTAA-----FPTYCRVTR-----SVTVTITDRC 46 Query: 148 PYHSNRLIDLSNAAAKILRVEERGVSKVHVEY 179 P+ R DLS A + L G+ V VEY Sbjct: 47 PFPPRRHFDLSGPAFEALAKPRAGI--VPVEY 76 >gnl|CDD|146739 pfam04257, Exonuc_V_gamma, Exodeoxyribonuclease V, gamma subunit. The Exodeoxyribonuclease V enzyme is a multi-subunit enzyme comprised of the proteins RecB, RecC (this family) and RecD. This enzyme plays an important role in homologous genetic recombination, repair of double strand DNA breaks resistance to UV irradiation and chemical DNA-damage. The enzyme (EC:3.1.11.5) catalyses ssDNA or dsDNA-dependent ATP hydrolysis, hydrolysis of ssDNA or dsDNA and unwinding of dsDNA. This family consists of two AAA domains. Length = 1008 Score = 29.9 bits (68), Expect = 0.79 Identities = 12/20 (60%), Positives = 16/20 (80%) Query: 149 YHSNRLIDLSNAAAKILRVE 168 YHSNRL L++ AK+LR+E Sbjct: 5 YHSNRLEVLADLLAKLLRLE 24 >gnl|CDD|110355 pfam01347, Vitellogenin_N, Lipoprotein amino terminal region. This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100. These proteins are all involved in lipid transport. This family contains the LV1n chain from lipovitellin, that contains two structural domains. Length = 579 Score = 28.8 bits (65), Expect = 1.9 Identities = 7/40 (17%), Positives = 17/40 (42%), Gaps = 6/40 (15%) Query: 188 MDQEYLRSTVMVNSATVLPLGCQYREEIV------VIPYL 221 +Q YL ++ ++ +++ C + +IP L Sbjct: 413 QNQPYLNTSALLAYGSLVRRYCVNNNKHTPACPEELIPPL 452 >gnl|CDD|146350 pfam03665, UPF0172, Uncharacterized protein family (UPF0172). In Chlamydomonas reinhardtii the protein TLA1 (truncated light-harvesting chlorophyll antenna size) apparently regulates genes that define the chlorophyll-a antenna size in the photosynthetic apparatus. This family was formerly known as UPF0172. Length = 195 Score = 28.0 bits (63), Expect = 2.7 Identities = 27/103 (26%), Positives = 39/103 (37%), Gaps = 24/103 (23%) Query: 101 GRLTANGEVYGTEYITAAHPTLPLPSYVRVTNM-------ENGISLVVRVNDRGPYHSNR 153 G+ T + V T+ + H TL L + V + G+ +V G YH+N Sbjct: 32 GKSTKSSSVLITDAVPLFHSTLALAPMLEVALAQVESYAKQKGLVIV------GYYHANE 85 Query: 154 LID---LSNAAAKILRVEERGVSKVHVEYLGMALLNGMDQEYL 193 D S A KI K+ E A+L +D E L Sbjct: 86 RFDDSSPSPVAKKIA-------DKIA-ENFNNAVLLLVDNEKL 120 >gnl|CDD|31912 COG1726, NqrA, Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrA [Energy production and conversion]. Length = 447 Score = 27.6 bits (61), Expect = 4.3 Identities = 9/31 (29%), Positives = 13/31 (41%) Query: 101 GRLTANGEVYGTEYITAAHPTLPLPSYVRVT 131 G+L GE+ + A P + P VR Sbjct: 249 GKLFLTGELLTERVVALAGPQVNKPRLVRTV 279 >gnl|CDD|146761 pfam04293, SpoVR, SpoVR like protein. One family member is the Bacillus subtilis stage V sporulation protein R, which is involved in spore cortex formation. Little is known about cortex biosynthesis, except that it depends on several sigma E controlled genes, including spoVR. Length = 427 Score = 27.5 bits (62), Expect = 4.4 Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 13/36 (36%) Query: 70 PYQIMGRWYVPRQYTAYAAVGMAS----W-YGKAFH 100 + M Y AYA+VGM + W +GK F Sbjct: 36 TAEQM--------YDAYASVGMPTRYPHWSFGKHFE 63 >gnl|CDD|163605 pfam04080, Per1, Per1-like. PER1 is required for GPI-phospholipase A2 activity and is involved in lipid remodelling of GPI-anchored proteins. Length = 264 Score = 27.6 bits (62), Expect = 4.4 Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 1/40 (2%) Query: 64 RYFLGKPYQIMGRWYVPRQYTAYAAVGMASWYGKA-FHGR 102 R+ PY + R Y YA VGM +W A FH R Sbjct: 74 RFRRLVPYNLPLRPTRKGNYIIYAIVGMNAWIWSAIFHTR 113 >gnl|CDD|111979 pfam03141, DUF248, Putative methyltransferase. Members of this family of hypothetical plant proteins are probably methyltransferases: several of the aligned sequences either match the methyltransferase profile, or contain a SAM-binding motif. A protein from Arabidopsis thaliana contains both. Several family members are described as ankyrin like. Length = 506 Score = 26.9 bits (60), Expect = 6.2 Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 18/56 (32%) Query: 233 CDDDSLQKQREISL-----RER------KKSN-LIPLPNGYSPPRKMGKIPIP-SR 275 C D+ + +S RER +K L+P P+GY P IP P SR Sbjct: 5 CLDNDRAIKFLLSRERMEHRERHCPPSEEKLRCLVPPPDGYKTP-----IPWPKSR 55 >gnl|CDD|177149 MTH00080, COX2, cytochrome c oxidase subunit II; Provisional. Length = 231 Score = 26.5 bits (59), Expect = 7.4 Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 1/37 (2%) Query: 4 FSCDCLLKGSVV-CVVVLGMSSCFFSSTYKDDKLEYF 39 F+C L V+ VV L + + +K K+EY Sbjct: 25 FNCSLLFGEFVLAFVVFLFLYLISNNFYFKSKKIEYQ 61 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 0.321 0.137 0.415 Gapped Lambda K H 0.267 0.0788 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,463,661 Number of extensions: 180479 Number of successful extensions: 287 Number of sequences better than 10.0: 1 Number of HSP's gapped: 285 Number of HSP's successfully gapped: 11 Length of query: 276 Length of database: 6,263,737 Length adjustment: 92 Effective length of query: 184 Effective length of database: 4,275,709 Effective search space: 786730456 Effective search space used: 786730456 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 (21.9 bits) S2: 57 (25.6 bits)