RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780547|ref|YP_003064960.1| OmpA/MotB [Candidatus Liberibacter asiaticus str. psy62] (160 letters) >gnl|CDD|32711 COG2885, OmpA, Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]. Length = 190 Score = 102 bits (256), Expect = 3e-23 Identities = 38/110 (34%), Positives = 55/110 (50%), Gaps = 1/110 (0%) Query: 41 QEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSI 99 ++ + V FD S ++P L L +L+K+ L+EGH D GS + Sbjct: 74 ARDIILNLPNDVLFDFDSSVLKPKAQATLDELAKYLKKNPITRILVEGHTDSTGSDEYNQ 133 Query: 100 ALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRA 149 AL RRA AV +Y V++G+ A R+ YG+E P E+ AKNRR Sbjct: 134 ALSERRAEAVADYLVSQGVVADRISTVGYGEEKPIASNATEEGRAKNRRV 183 >gnl|CDD|143586 cd07185, OmpA_C-like, Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA. OmpA-like domains (named after the C-terminal domain of Escherichia coli OmpA protein) have been shown to non-covalently associate with peptidoglycan, a network of glycan chains composed of disaccharides, which are crosslinked via short peptide bridges. Well-studied members of this family include the Escherichia coli outer membrane protein OmpA, the Escherichia coli lipoprotein PAL, Neisseria meningitdis RmpM, which interact with the outer membrane, as well as the Escherichia coli motor protein MotB, and the Vibrio flagellar motor proteins PomB and MotY, which interact with the inner membrane. Length = 106 Score = 101 bits (255), Expect = 7e-23 Identities = 37/104 (35%), Positives = 54/104 (51%), Gaps = 1/104 (0%) Query: 51 SVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRRAYAV 109 +++FD S + P +L L L+K+ D IEGH D GS + L RRA AV Sbjct: 3 TIYFDFGSAELTPEAKPLLDKLAEVLKKNPDAKIRIEGHTDSRGSDAYNQELSERRAEAV 62 Query: 110 FNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFL 153 +Y V++G+ ASR+ YG+ P E+ AKNRR + + Sbjct: 63 ADYLVSKGVDASRITAVGYGESRPIASNDTEEGRAKNRRVEIVI 106 >gnl|CDD|144333 pfam00691, OmpA, OmpA family. The Pfam entry also includes MotB and related proteins which are not included in the Prosite family. Length = 97 Score = 76.3 bits (188), Expect = 3e-15 Identities = 34/97 (35%), Positives = 43/97 (44%), Gaps = 2/97 (2%) Query: 53 FFDTSSYSIRPADIQVLSNLGSWLE--KHDCDFLIEGHADELGSRNSSIALGLRRAYAVF 110 FD S + + L L L+ + IEGH D GS + L RRA AV Sbjct: 1 LFDPGSAELTAEARETLDRLAEVLKAPELKIAIKIEGHTDSRGSAKYNWELSARRAQAVA 60 Query: 111 NYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNR 147 NY V GI SR+ V YG+ P ++ AKNR Sbjct: 61 NYLVNHGIPPSRISVEGYGESQPLASNDSDEGRAKNR 97 >gnl|CDD|31551 COG1360, MotB, Flagellar motor protein [Cell motility and secretion]. Length = 244 Score = 51.9 bits (124), Expect = 8e-08 Identities = 31/111 (27%), Positives = 48/111 (43%), Gaps = 7/111 (6%) Query: 50 DSVFFDTSSYSIRPADIQVLSNLGSWLEKHD-CDFLIEGHADEL---GSRNSSIALGLRR 105 DS+ F + S ++P +L + L + IEGH D + GS S+ L R Sbjct: 132 DSLMFASGSAVVQPEFRDLLLKIAKLLADIPNGNIRIEGHTDNVPIKGSFYSNWELSAAR 191 Query: 106 AYAVFNYFVARG-ISASRMKVTSYGKEMPSVYGHDEDAY-AKNRRAIVFLK 154 A +V + G + A R+ V Y P + +D AKNRR + + Sbjct: 192 AQSVVRVLINGGLVEAKRLSVVGYADTRP-LADNDTAEGRAKNRRVEILIL 241 >gnl|CDD|34136 COG4457, SrfB, Uncharacterized protein conserved in bacteria, putative virulence factor [Function unknown]. Length = 1014 Score = 28.8 bits (64), Expect = 0.68 Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 7/94 (7%) Query: 52 VFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSSIALGLRRAYAVFN 111 V + + ++ + ++ ++G+ C LIE H DE N + L LR Sbjct: 238 VKTVSDTLNVPAVPVDLVLDVGN---SRTCGILIEDHPDENDGLNQTYELELRDLSK--P 292 Query: 112 YFVARGISASRMKVTS--YGKEMPSVYGHDEDAY 143 +V SR++ +GKE SV DA+ Sbjct: 293 EYVYNDPFESRVEFAQAEFGKEHFSVESGRPDAF 326 >gnl|CDD|35801 KOG0581, KOG0581, KOG0581, Mitogen-activated protein kinase kinase (MAP2K) [Signal transduction mechanisms]. Length = 364 Score = 26.8 bits (59), Expect = 2.9 Identities = 14/58 (24%), Positives = 22/58 (37%) Query: 17 SISGIDNLDTKISSPDTVLNESSLQEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGS 74 +S D L + S + N L + SS + I +D++ L LGS Sbjct: 32 ILSARDTLPSTSESLELTDNSPPLSKISLSSSSANSELSEDDNGISLSDLERLGVLGS 89 >gnl|CDD|31696 COG1507, COG1507, Uncharacterized conserved protein [Function unknown]. Length = 167 Score = 26.5 bits (58), Expect = 3.1 Identities = 15/31 (48%), Positives = 19/31 (61%) Query: 119 SASRMKVTSYGKEMPSVYGHDEDAYAKNRRA 149 +ASR++ T Y KEM G DE+ A RRA Sbjct: 62 AASRLESTGYMKEMTERLGQDEELRAFYRRA 92 >gnl|CDD|30609 COG0260, PepB, Leucyl aminopeptidase [Amino acid transport and metabolism]. Length = 485 Score = 26.0 bits (57), Expect = 4.4 Identities = 8/18 (44%), Positives = 11/18 (61%) Query: 48 VGDSVFFDTSSYSIRPAD 65 VG + FD+ SI+PA Sbjct: 251 VGKGITFDSGGISIKPAA 268 >gnl|CDD|163641 cd07398, MPP_YbbF-LpxH, Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain. YbbF/LpxH is an Escherichia coli UDP-2,3-diacylglucosamine hydrolase thought to catalyze the fourth step of lipid A biosynthesis, in which a precursor UDP-2,3-diacylglucosamine is hydrolyzed to yield 2,3-diacylglucosamine 1-phosphate and UMP. YbbF belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. Length = 217 Score = 25.9 bits (57), Expect = 5.3 Identities = 4/14 (28%), Positives = 6/14 (42%) Query: 75 WLEKHDCDFLIEGH 88 + D +I GH Sbjct: 184 LARRKGVDGVICGH 197 >gnl|CDD|144468 pfam00883, Peptidase_M17, Cytosol aminopeptidase family, catalytic domain. The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase. Length = 312 Score = 25.3 bits (56), Expect = 7.3 Identities = 7/18 (38%), Positives = 10/18 (55%) Query: 48 VGDSVFFDTSSYSIRPAD 65 VG + FD+ SI+P Sbjct: 84 VGKGITFDSGGISIKPGA 101 >gnl|CDD|146133 pfam03340, Pox_Rif, Poxvirus rifampicin resistance protein. Length = 541 Score = 25.4 bits (56), Expect = 8.4 Identities = 11/39 (28%), Positives = 18/39 (46%) Query: 28 ISSPDTVLNESSLQEQFSSSVGDSVFFDTSSYSIRPADI 66 I S + ++ E+ +E F S + + S YSI D Sbjct: 93 IESVNGIIWETGGEELFDSCRDNKIASKLSGYSIELNDF 131 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 0.318 0.132 0.372 Gapped Lambda K H 0.267 0.0706 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,800,125 Number of extensions: 84617 Number of successful extensions: 207 Number of sequences better than 10.0: 1 Number of HSP's gapped: 205 Number of HSP's successfully gapped: 16 Length of query: 160 Length of database: 6,263,737 Length adjustment: 86 Effective length of query: 74 Effective length of database: 4,405,363 Effective search space: 325996862 Effective search space used: 325996862 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (24.2 bits)