RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781175|ref|YP_003065588.1| UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase [Candidatus Liberibacter asiaticus str. psy62] (296 letters) >gnl|CDD|31117 COG0774, LpxC, UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]. Length = 300 Score = 331 bits (850), Expect = 1e-91 Identities = 136/287 (47%), Positives = 188/287 (65%), Gaps = 6/287 (2%) Query: 8 RLQHTIADSITITGIGIHSGKRANLKLCPAPEGVGILFKCTQSGGITDSLSALWSNVLRT 67 Q T+ +++TG+G+HSGK+ L L PAP GI+F+ T + + A NV T Sbjct: 2 MKQRTLKRIVSLTGVGLHSGKKVTLTLRPAPANTGIVFRRTDLNPPVE-IPADAENVRDT 60 Query: 68 TLSTTIG-SSSCQVRTIEHLMAALYAYGIDNVIIEIDSTEVPIMDGSAKAFVEVIERIGI 126 LSTT+G ++ T+EHLMAAL GIDN+IIE+D E+PIMDGSA FVE+I+ GI Sbjct: 61 MLSTTLGNDHGVRISTVEHLMAALAGLGIDNLIIEVDGPEIPIMDGSAAPFVELIDEAGI 120 Query: 127 KTLTAKRRYLRIIKSVRITSGESWAEFSPHCSMRFEISIEFKNSIIG--FQKWAGDLTQT 184 K AK++++RI K VR+ G+ WAEF+P+ R +I+F + IG +Q + D + Sbjct: 121 KEQNAKKKFIRIKKPVRVEDGDKWAEFTPYDGFRLSYTIDFDHPAIGRQWQSFEFDFSAE 180 Query: 185 VFRNEIYAARTFGFLRDVERYRKAGCALGASLENSVVISEDDQVMNHGGLRYSGEEFVRH 244 FR EI ARTFGF+RDVE R G ALG SLEN++VI DD+V+N GLR+ +EFVRH Sbjct: 181 SFRKEIARARTFGFMRDVEYLRSKGLALGGSLENAIVID-DDRVLNPEGLRF-EDEFVRH 238 Query: 245 KTLDAIGDIALAGYPVIGCYRSCRGSHEINHMALCTLFADKDSYEIV 291 K LDAIGD+ L G+P+IG + + + H +N+ L + AD+ +YEIV Sbjct: 239 KILDAIGDLYLLGHPIIGAFTAYKSGHALNNALLKAILADQTAYEIV 285 >gnl|CDD|146126 pfam03331, LpxC, UDP-3-O-acyl N-acetylglycosamine deacetylase. The enzymes in this family catalyse the second step in the biosynthetic pathway for lipid A. Length = 276 Score = 270 bits (693), Expect = 3e-73 Identities = 114/277 (41%), Positives = 174/277 (62%), Gaps = 4/277 (1%) Query: 10 QHTIADSITITGIGIHSGKRANLKLCPAPEGVGILFKCTQSGGITDSLSALWSNVLRTTL 69 Q T+ ++++G+G+H+GK++ L L PA E GI+F+ T + A NV T L Sbjct: 3 QRTLKRPVSVSGVGLHTGKKSTLTLEPAKENTGIVFQRTDLSPYPI-IPARPENVRDTML 61 Query: 70 STTIGSSSCQVRTIEHLMAALYAYGIDNVIIEIDSTEVPIMDGSAKAFVEVIERIGIKTL 129 STT+G+ ++ T+EHL+AAL GIDN+IIE+D E+PIMDGSA FVE+I++ GIK Sbjct: 62 STTLGNDGARISTVEHLLAALAGLGIDNLIIEVDGPEIPIMDGSALPFVELIDQAGIKEQ 121 Query: 130 TAKRRYLRIIKSVRITSGESWAEFSPHCSMRFEISIEFKN-SIIGFQKWAGDLTQTVFRN 188 A ++ +RI + V + G+ + P ++ +I+FK+ +I Q ++ +Q FR Sbjct: 122 EAAKKIIRIKEPVYVQDGDKFLAAFPSDGLKISYTIDFKHPAIGKSQWYSFVFSQESFRK 181 Query: 189 EIYAARTFGFLRDVERYRKAGCALGASLENSVVISEDDQVMNHGGLRYSGEEFVRHKTLD 248 EI ARTFGF+R++E R G G SLEN++V +DD+V+N GLR+ +E VRHK LD Sbjct: 182 EIAPARTFGFMREIEYLRSKGLIKGGSLENAIVF-DDDKVLNPPGLRFE-DEPVRHKILD 239 Query: 249 AIGDIALAGYPVIGCYRSCRGSHEINHMALCTLFADK 285 IGD+ L G PVIG + + + H +N+ + + AD+ Sbjct: 240 LIGDLYLLGVPVIGHFIAYKSGHSLNNQLVQKILADQ 276 >gnl|CDD|30814 COG0466, Lon, ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]. Length = 782 Score = 27.4 bits (61), Expect = 5.3 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 4/49 (8%) Query: 90 LYAYGIDNVIIEIDSTEVPIMDGSAKAFVEVIERIGIKTLTAKRRYLRI 138 LY G I++I + + DG+ K VE ++R+ I L+ + + Sbjct: 68 LYEVGTLAKILQI----LKLPDGTVKVLVEGLQRVRISKLSDEEEFFEA 112 >gnl|CDD|37043 KOG1832, KOG1832, KOG1832, HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]. Length = 1516 Score = 27.4 bits (60), Expect = 5.4 Identities = 21/109 (19%), Positives = 39/109 (35%), Gaps = 5/109 (4%) Query: 182 TQTVFRNEIYAARTFGFLRDVERYRKAGCALGASLENSVVISEDDQVMNHGGL---RYSG 238 + + +EI+ RTF L V + CA+ + V+ + + + R Sbjct: 1279 NEVIINSEIWDMRTFKLLHSVPSLDQ--CAVTFNSTGDVMYAMLNIEDVMSDVHTRRVKH 1336 Query: 239 EEFVRHKTLDAIGDIALAGYPVIGCYRSCRGSHEINHMALCTLFADKDS 287 F +T DAI +A PV C + + + + +D Sbjct: 1337 PLFSSFRTFDAIDYSDIATIPVDRCLLDLCTEPTDSFLGVIEMEDQEDM 1385 >gnl|CDD|133288 cd01888, eIF2_gamma, eIF2-gamma (gamma subunit of initiation factor 2). eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits. The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome. The gamma subunit has no intrinsic GTPase activity, but is stimulated by the GTPase activating protein (GAP) eIF5, and GDP/GTP exchange is stimulated by the guanine nucleotide exchange factor (GEF) eIF2B. eIF2B is a heteropentamer, and the epsilon chain binds eIF2. Both eIF5 and eIF2B-epsilon are known to bind strongly to eIF2-beta, but have also been shown to bind directly to eIF2-gamma. It is possible that eIF2-beta serves simply as a high-affinity docking site for eIF5 and eIF2B-epsilon, or that eIF2-beta serves a regulatory role. eIF2-gamma is found only in eukaryotes and archaea. It is closely related to SelB, the selenocysteine-specific elongation factor from eubacteria. The translational factor components of the ternary complex, IF2 in eubacteria and eIF2 in eukaryotes are not the same protein (despite their unfortunately similar names). Both factors are GTPases; however, eubacterial IF-2 is a single polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is a member of the same family as eubacterial IF2, but the two proteins are only distantly related. This family includes translation initiation, elongation, and release factors. Length = 203 Score = 27.2 bits (61), Expect = 6.1 Identities = 21/80 (26%), Positives = 31/80 (38%), Gaps = 26/80 (32%) Query: 74 GSSSC-QVRTIEHLMAALYAYGIDNVII---EIDSTEVPIMDGSAKAFVEVIERIGIKTL 129 + C Q +T EHL AL G+ ++II +ID +K Sbjct: 116 ANEPCPQPQTSEHLA-ALEIMGLKHIIIVQNKIDL---------------------VKEE 153 Query: 130 TAKRRYLRIIKSVRITSGES 149 A Y +I K V+ T E+ Sbjct: 154 QALENYEQIKKFVKGTIAEN 173 >gnl|CDD|34243 COG4623, COG4623, Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]. Length = 473 Score = 27.2 bits (60), Expect = 6.1 Identities = 10/19 (52%), Positives = 15/19 (78%) Query: 1 MEMLQIGRLQHTIADSITI 19 +EM+ G+L +TIADS+ I Sbjct: 169 LEMVAEGKLDYTIADSVEI 187 >gnl|CDD|34398 COG4787, FlgF, Flagellar basal body rod protein [Cell motility and secretion]. Length = 251 Score = 26.8 bits (59), Expect = 6.6 Identities = 24/104 (23%), Positives = 38/104 (36%), Gaps = 24/104 (23%) Query: 183 QTVFRNEIYAARTFGFLRDVERYRKAGCALGASLENSVVISEDDQV-MNHGGLRYSG--- 238 Q V N + A T GF + R + + V++ M+ G L Y+G Sbjct: 19 QAVTANNLANASTTGFRAQLNAARAVQVHGDSLPTRTFVMASTPGTDMSPGSLDYTGRPL 78 Query: 239 ------------------EEFVR--HKTLDAIGDIALAGYPVIG 262 E + R + +DA G + + G+PVIG Sbjct: 79 DVAIQGDGWLAVQDADGSEAYTRNGNIQIDATGQLTIQGHPVIG 122 >gnl|CDD|33033 COG3220, COG3220, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 282 Score = 26.8 bits (59), Expect = 7.8 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 10/61 (16%) Query: 198 FLRDVERYRKAGCALGASLENSVVISEDDQVMNHGGLRYSGEEFVRHKTLDAIGDIALAG 257 FL + R+AGC L + N V + +NHG + EE++ ++ +G+I LAG Sbjct: 157 FLNAL--AREAGCGLLLDVNNIYVNA-----VNHG---FDPEEYLAALPVERVGEIHLAG 206 Query: 258 Y 258 + Sbjct: 207 H 207 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 0.322 0.137 0.404 Gapped Lambda K H 0.267 0.0726 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,532,979 Number of extensions: 183889 Number of successful extensions: 370 Number of sequences better than 10.0: 1 Number of HSP's gapped: 361 Number of HSP's successfully gapped: 12 Length of query: 296 Length of database: 6,263,737 Length adjustment: 93 Effective length of query: 203 Effective length of database: 4,254,100 Effective search space: 863582300 Effective search space used: 863582300 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 (25.7 bits)