RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781078|ref|YP_003065491.1| hypothetical protein CLIBASIA_04900 [Candidatus Liberibacter asiaticus str. psy62] (242 letters) >gnl|CDD|110393 pfam01389, OmpA_membrane, OmpA-like transmembrane domain. The structure of OmpA transmembrane domain shows that it consists of an eight stranded beta barrel. This family includes some other distantly related outer membrane proteins with low scores. Length = 175 Score = 39.3 bits (92), Expect = 0.001 Identities = 26/110 (23%), Positives = 48/110 (43%), Gaps = 17/110 (15%) Query: 134 LKAGYSV-DSLLIYGMGGFGGAYVIDSSLEKVESDNSKNAKGRFDGHGSSVVLGIGLDYM 192 LK Y + D L +YG G ++ + + N K G S + +G++Y Sbjct: 81 LKLSYPLTDDLDVYGKVG---GALVRAD---YKFYEDANGKTGNHDTGVSPLFALGVEYA 134 Query: 193 VNYDISLSASYRYIPHHIHSVNNSNAKSDVERVDRKGNAHIASLGINMHF 242 V ++++ Y+Y +NN D+ + ++ + ASLGI+ F Sbjct: 135 VTPELAVRLEYQY-------LNNIG---DLHKQGKRPDNGSASLGISYRF 174 >gnl|CDD|33435 COG3637, COG3637, Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]. Length = 199 Score = 34.2 bits (78), Expect = 0.030 Identities = 24/156 (15%), Positives = 44/156 (28%), Gaps = 20/156 (12%) Query: 93 LGHNIQLEDFVFGI---NCHTTAAKDDSTFYRL--KEKYFIYGDVVLKAGYSVDS-LLIY 146 G+N++ V G+ +T + S + YG + Y ++ Y Sbjct: 58 AGYNLKYRYSVLGVEGSFTYTGQSGRYSGGSGKNQVDNKAWYGSLRAGPDYRINDRFSPY 117 Query: 147 GMGGFGGAYVIDSSLEKVESDNSKNAKGRFDGHGSSVVLGIGLDYMVNYDISLSASYRYI 206 G G V E S + G+ G G+ Y ++++ Y Y Sbjct: 118 GGAGVAYGKV---KTSTDEVGGSADESKTKTGYA----YGAGVQYNPTDNVAIDLGYEYS 170 Query: 207 PHHIHSVNNSNAKSDVERVDRKGNAHIASLGINMHF 242 + H +G+ F Sbjct: 171 -------DFGKKDGVDGGYSGDVKTHTVKVGVGYKF 199 >gnl|CDD|111657 pfam02784, Orn_Arg_deC_N, Pyridoxal-dependent decarboxylase, pyridoxal binding domain. These pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates This domain has a TIM barrel fold. Length = 245 Score = 32.2 bits (74), Expect = 0.12 Identities = 18/89 (20%), Positives = 31/89 (34%), Gaps = 4/89 (4%) Query: 98 QLEDFVFGINCHTTAAKDD-STFYRLKEKYFIYGDVVLKAGYSVDSLLIYGMGGFGGAYV 156 +L V G++ H + D F + D + G+ + L + G GGFG Y Sbjct: 149 ELGLNVVGVHFHVGSGCTDAEAFVKAARDARNVFDQGAELGFELKILDL-G-GGFGVDYT 206 Query: 157 IDSSLEKVESDNSKNAKGRFDGHGSSVVL 185 E+ ++ A H + Sbjct: 207 GAEDFEEY-AEVINAALEEVFPHDPHPTI 234 >gnl|CDD|146513 pfam03922, OmpW, OmpW family. This family includes outer membrane protein W (OmpW) proteins from a variety of bacterial species. This protein may form the receptor for S4 colicins in E. coli. Length = 189 Score = 27.8 bits (62), Expect = 2.5 Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 2/59 (3%) Query: 184 VLGIGLDYMVNYDISLSASYRYIPHHIHSVNNSNAKSDVERVDRKGNAHIASLGINMHF 242 G+DYMVN D ++ Y+ I + + + K + + S+G+ F Sbjct: 133 AGQAGVDYMVNDDWLVNMDVWYM--FIDTTASYKLGGAKLKTKVKLDPWVFSIGLGYRF 189 >gnl|CDD|37417 KOG2206, KOG2206, KOG2206, Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis]. Length = 687 Score = 27.7 bits (61), Expect = 3.1 Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 10/74 (13%) Query: 31 PRKIDLFNEADNNVEYQDDEYGIWSGNYVGLHISRLYETHPLADTI--NRKTYNSLLPNG 88 P + +F+ AD ++ IW G+++ L++T + + R + LL Sbjct: 264 PGIVKVFHGADTDI--------IWLQRDFGIYVVNLFDTIQASRLLGLPRPSLAYLLECV 315 Query: 89 LGIELGHNIQLEDF 102 G+ QL D+ Sbjct: 316 CGVLTNKKYQLADW 329 >gnl|CDD|34462 COG4853, COG4853, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 264 Score = 26.8 bits (59), Expect = 5.6 Identities = 11/56 (19%), Positives = 25/56 (44%) Query: 1 MNFNGYGALFFVVFLSIVVPNHSLAVDLYLPRKIDLFNEADNNVEYQDDEYGIWSG 56 M++ ++F VVFL + + S+ + + R E++N + D + + Sbjct: 1 MDWKKTKSIFIVVFLLLNIFLVSIFFNKKVNRSHINLVESNNEENLKADNISVHAS 56 >gnl|CDD|32861 COG3047, OmpW, Outer membrane protein W [Cell envelope biogenesis, outer membrane]. Length = 213 Score = 26.8 bits (59), Expect = 6.1 Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 2/66 (3%) Query: 177 DGHGSSVVLGIGLDYMVNYDISLSASYRYIPHHIHSVNNSNAKSDVERVDRKGNAHIASL 236 D G G+DYM+N D L+ +Y+ + + + K + + + Sbjct: 150 DSWG--AAGQAGVDYMLNDDWLLNMDVKYMFIDTTAKYKAGLGGAKLKSKVKLDPWVFMI 207 Query: 237 GINMHF 242 GI F Sbjct: 208 GIGYRF 213 >gnl|CDD|146437 pfam03797, Autotransporter, Autotransporter beta-domain. Secretion of protein products occurs by a number of different pathways in bacteria. One of these pathways known as the type V pathway was first described for the IgA1 protease. The protein component that mediates secretion through the outer membrane is contained within the secreted protein itself, hence the proteins secreted in this way are called autotransporters. This family corresponds to the presumed integral membrane beta-barrel domain that transports the protein. This domain is found at the C terminus of the proteins it occurs in. The N terminus contains the variable passenger domain that is translocated across the membrane. Once the passenger domain is exported it is cleaved auto-catalytically in some proteins, in others a different protease is used and in some cases no cleavage occurs. Length = 265 Score = 26.3 bits (58), Expect = 7.9 Identities = 26/117 (22%), Positives = 52/117 (44%), Gaps = 15/117 (12%) Query: 90 GIELGHNIQL-EDFVFGIN-CHTTA-AKDDSTFYRLKEKYF---IYGDVVLKAGYSVDSL 143 G +LG + +L D + G+ ++ + +K D + K + +Y G +D + Sbjct: 33 GYQLGADARLGGDLILGLAFGYSFSKSKSDDGGGKGKSDSYGAGLYAQWNFDGGLYLDGV 92 Query: 144 LIYGMGGFGGAYVIDSSLEKVESDNSKNAKGRFDGHGSSVVLGIGLDYMVNYDISLS 200 L YG D+ + K ++ AKG +D HG L G + ++ +++L+ Sbjct: 93 LAYGR--------FDNDV-KRLGTSTGTAKGDYDSHGLGASLEAGYRFKLSGNLTLT 140 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 0.320 0.140 0.414 Gapped Lambda K H 0.267 0.0826 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,970,623 Number of extensions: 156104 Number of successful extensions: 331 Number of sequences better than 10.0: 1 Number of HSP's gapped: 328 Number of HSP's successfully gapped: 14 Length of query: 242 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 151 Effective length of database: 4,297,318 Effective search space: 648895018 Effective search space used: 648895018 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 (21.7 bits) S2: 56 (25.2 bits)