RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780953|ref|YP_003065366.1| OmpA/MotB [Candidatus Liberibacter asiaticus str. psy62] (190 letters) >gnl|CDD|32711 COG2885, OmpA, Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]. Length = 190 Score = 110 bits (275), Expect = 3e-25 Identities = 51/157 (32%), Positives = 79/157 (50%), Gaps = 2/157 (1%) Query: 30 LHKSNDTDIVNKRFGSSLDKAEDEFQMQLQDTGIVVSRIGDMITCYIPVHVSFVSEVF-L 88 L + + G LD AE E + + G R I +P V F + L Sbjct: 35 LIGAGPGALGGAGAGVPLDVAEAELRAKEAGDGPAERRKARDIILNLPNDVLFDFDSSVL 94 Query: 89 EKKFLPMLQLIATILNKFPSTVIAIQSHTDSIGTLKNNLLISQERADVIKSYLIQRGVSS 148 + K L +A L K P T I ++ HTDS G+ + N +S+ RA+ + YL+ +GV + Sbjct: 95 KPKAQATLDELAKYLKKNPITRILVEGHTDSTGSDEYNQALSERRAEAVADYLVSQGVVA 154 Query: 149 NRFISVRGFAYKYPIDTNDTKVGRQNNQRIEIQIFPR 185 +R IS G+ + PI +N T+ GR N+R+EI+I P+ Sbjct: 155 DR-ISTVGYGEEKPIASNATEEGRAKNRRVEIKISPK 190 >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 = 106 bits (268), Expect = 3e-24 Identities = 37/95 (38%), Positives = 57/95 (60%), Gaps = 1/95 (1%) Query: 88 LEKKFLPMLQLIATILNKFPSTVIAIQSHTDSIGTLKNNLLISQERADVIKSYLIQRGVS 147 L + P+L +A +L K P I I+ HTDS G+ N +S+ RA+ + YL+ +GV Sbjct: 13 LTPEAKPLLDKLAEVLKKNPDAKIRIEGHTDSRGSDAYNQELSERRAEAVADYLVSKGVD 72 Query: 148 SNRFISVRGFAYKYPIDTNDTKVGRQNNQRIEIQI 182 ++R I+ G+ PI +NDT+ GR N+R+EI I Sbjct: 73 ASR-ITAVGYGESRPIASNDTEEGRAKNRRVEIVI 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 = 71.3 bits (175), Expect = 2e-13 Identities = 30/89 (33%), Positives = 45/89 (50%), Gaps = 2/89 (2%) Query: 88 LEKKFLPMLQLIATIL-NKFPSTVIAIQSHTDSIGTLKNNLLISQERADVIKSYLIQRGV 146 L + L +A +L I I+ HTDS G+ K N +S RA + +YL+ G+ Sbjct: 9 LTAEARETLDRLAEVLKAPELKIAIKIEGHTDSRGSAKYNWELSARRAQAVANYLVNHGI 68 Query: 147 SSNRFISVRGFAYKYPIDTNDTKVGRQNN 175 +R ISV G+ P+ +ND+ GR N Sbjct: 69 PPSR-ISVEGYGESQPLASNDSDEGRAKN 96 >gnl|CDD|31551 COG1360, MotB, Flagellar motor protein [Cell motility and secretion]. Length = 244 Score = 68.9 bits (168), Expect = 9e-13 Identities = 39/151 (25%), Positives = 71/151 (47%), Gaps = 4/151 (2%) Query: 40 NKRFGSSLDKAEDEFQMQLQDTGIVVSRIGDMITCYIPVHVSF-VSEVFLEKKFLPMLQL 98 +++ G + E + + + + V + + + I + F ++ +F +L Sbjct: 94 SEKLGDLAKELESKPKDIELEHQLGVDDVEEGLVISISDSLMFASGSAVVQPEFRDLLLK 153 Query: 99 IATILNKFPSTVIAIQSHTDS---IGTLKNNLLISQERADVIKSYLIQRGVSSNRFISVR 155 IA +L P+ I I+ HTD+ G+ +N +S RA + LI G+ + +SV Sbjct: 154 IAKLLADIPNGNIRIEGHTDNVPIKGSFYSNWELSAARAQSVVRVLINGGLVEAKRLSVV 213 Query: 156 GFAYKYPIDTNDTKVGRQNNQRIEIQIFPRG 186 G+A P+ NDT GR N+R+EI I + Sbjct: 214 GYADTRPLADNDTAEGRAKNRRVEILILTKK 244 >gnl|CDD|145708 pfam02698, DUF218, DUF218 domain. This large family of proteins contains several highly conserved charged amino acids, suggesting this may be an enzymatic domain (Bateman A pers. obs). The family includes SanA, which is involved in Vancomycin resistance. This protein may be involved in murein synthesis. Length = 148 Score = 26.5 bits (59), Expect = 4.3 Identities = 6/19 (31%), Positives = 13/19 (68%) Query: 134 ADVIKSYLIQRGVSSNRFI 152 A+V++ YL++ GV + + Sbjct: 49 AEVMRRYLVELGVPAEAIL 67 >gnl|CDD|145728 pfam02729, OTCace_N, Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain. Length = 140 Score = 25.6 bits (57), Expect = 8.6 Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 5/28 (17%) Query: 45 SSLDKAEDEFQMQLQDTGIVVSRIGDMI 72 SSL K E L+DT V+SR D I Sbjct: 74 SSLGKGES-----LKDTARVLSRYVDAI 96 >gnl|CDD|147081 pfam04739, AMPKBI, 5'-AMP-activated protein kinase beta subunit, interation domain. This region is found in the beta subunit of the 5'-AMP-activated protein kinase complex, and its yeast homologues Sip1, Sip2 and Gal83, which are found in the SNF1 kinase complex. This region is sufficient for interaction of this subunit with the kinase complex, but is not solely responsible for the interaction, and the interaction partner is not known. The isoamylase N-terminal domain (pfam02922) is sometimes found in proteins belonging to this family. Length = 94 Score = 25.7 bits (57), Expect = 9.0 Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 2/36 (5%) Query: 76 IPVHVSFVSEVFLEKKFLPML--QLIATILNKFPST 109 IP + + KK P L L+ TILNK ++ Sbjct: 10 IPANFQDLLVAEEFKKEPPSLPPHLLKTILNKPTAS 45 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 0.380 Gapped Lambda K H 0.267 0.0756 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,105,794 Number of extensions: 102847 Number of successful extensions: 219 Number of sequences better than 10.0: 1 Number of HSP's gapped: 216 Number of HSP's successfully gapped: 9 Length of query: 190 Length of database: 6,263,737 Length adjustment: 88 Effective length of query: 102 Effective length of database: 4,362,145 Effective search space: 444938790 Effective search space used: 444938790 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: 54 (24.5 bits)