RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780745|ref|YP_003065158.1| OstA family protein [Candidatus Liberibacter asiaticus str. psy62] (181 letters) >gnl|CDD|163098 TIGR03002, outer_YhbN_LptA, lipopolysaccharide transport periplasmic protein LptA. Members of this protein family include LptA (previously called YhbN). It was shown to be an essential protein in E. coli, implicated in cell envelope integrity, and to play a role in the delivery of LPS to the outer leaflet of the outer membrane. It works with LptB (formerly yhbG), a homolog of ABC transporter ATP-binding proteins, encoded by an adjacent gene. Numerous homologs in other Proteobacteria are found in a conserved location near lipopolysaccharide inner core biosynthesis genes. This family is related to organic solvent tolerance protein (OstA), though distantly. Length = 142 Score = 45.3 bits (108), Expect = 8e-06 Identities = 16/49 (32%), Positives = 25/49 (51%) Query: 42 NEKIHIKADMLEVKDAVQKAFFKGNVFMTQEDFSLQADKMTIDYNNTNR 90 + IHI+AD + D F GNV +TQ ++ADK+ + N+ Sbjct: 7 EQPIHIEADSQTLDDKKGVVTFTGNVVITQGTLKIRADKVVVTRNDAGG 55 >gnl|CDD|179645 PRK03761, PRK03761, LPS assembly outer membrane complex protein LptD; Provisional. Length = 778 Score = 33.0 bits (76), Expect = 0.043 Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 2/78 (2%) Query: 45 IHIKADMLEVKDAVQKAFFKGNVFMTQEDFSLQADKMTIDYNNTNRDVSNKINRMDVERN 104 + I+AD E A + GNV + Q + L AD++ + N + + +D N Sbjct: 51 VTIEADHAEANYP-DDAVYTGNVDIKQGNSRLTADEVQLHQQE-NPGQAEPVRTVDALGN 108 Query: 105 IFIQSGEINVIASNGYVD 122 + +I + + + Sbjct: 109 VHYDDNQIILKGPKAWSN 126 >gnl|CDD|132313 TIGR03269, met_CoM_red_A2, methyl coenzyme M reductase system, component A2. The enzyme that catalyzes the final step in methanogenesis, methyl coenzyme M reductase, contains alpha, beta, and gamma chains. In older literature, the complex of alpha, beta, and gamma chains was termed component C, while this single chain protein was termed methyl coenzyme M reductase system component A2. Length = 520 Score = 28.6 bits (64), Expect = 0.87 Identities = 11/47 (23%), Positives = 18/47 (38%) Query: 38 KVLGNEKIHIKADMLEVKDAVQKAFFKGNVFMTQEDFSLQADKMTID 84 V G + D + D +++ K M Q F+L D +D Sbjct: 83 PVCGGTLEPEEVDFWNLSDKLRRRIRKRIAIMLQRTFALYGDDTVLD 129 >gnl|CDD|129282 TIGR00178, monomer_idh, isocitrate dehydrogenase, NADP-dependent, monomeric type. The monomeric type of isocitrate dehydrogenase has been found so far in a small number of species, including Azotobacter vinelandii, Corynebacterium glutamicum, Rhodomicrobium vannielii, and Neisseria meningitidis. It is NADP-specific. Length = 741 Score = 27.2 bits (60), Expect = 2.8 Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 9/61 (14%) Query: 45 IHIKADMLEVKDAVQ-----KAFFKGNVFMTQEDFSLQADKMTIDYNNTNRDVSNKINRM 99 +H+KA M++V D + + F+K E ++ +D NN D+ KI + Sbjct: 252 LHLKATMMKVSDPIMFGHAVREFYKDAFAKHAEVL----KQLGVDVNNGIGDLYAKIESL 307 Query: 100 D 100 Sbjct: 308 P 308 >gnl|CDD|184326 PRK13788, PRK13788, adenylosuccinate synthetase; Provisional. Length = 404 Score = 27.1 bits (60), Expect = 2.9 Identities = 10/32 (31%), Positives = 18/32 (56%) Query: 120 YVDFQKRILVLNGDRADKVILKEKLNTFLGCK 151 Y D +R+ + GD D+ +L+E++ L K Sbjct: 129 YSDRARRVGIRFGDLLDEAVLRERVERLLEAK 160 >gnl|CDD|162017 TIGR00744, ROK_glcA_fam, ROK family protein (putative glucokinase). This alignment models one branch of the ROK superfamily of proteins. The three members of the seed alignment for this model all have experimental evidence for activity as glucokinase, but the set of related proteins is crowded with paralogs of different or unknown function. Proteins scoring above the trusted_cutoff will show strong similarity to at least one known glucokinase and may be designated as putative glucokinases. However, definitive identification of glucokinases should be done only with extreme caution. Length = 318 Score = 26.8 bits (59), Expect = 3.0 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 7/74 (9%) Query: 92 VSNKINRMDVERNIFIQSGEINVIASNGYVDFQKRIL--VLNGDRADKVILKEKLNTFLG 149 V + I + + + G I + G V+ Q+ + +N D + LKEK+ +G Sbjct: 44 VDSFIQHIAKVGHEIVAIG----IGAPGPVNRQRGTVYFAVNLDWKQEP-LKEKVEARVG 98 Query: 150 CKLIVNIDTSFASL 163 ++V D + A+L Sbjct: 99 LPVVVENDANAAAL 112 >gnl|CDD|184881 PRK14887, PRK14887, KEOPS complex Pcc1-like subunit; Provisional. Length = 84 Score = 26.0 bits (58), Expect = 5.7 Identities = 9/48 (18%), Positives = 21/48 (43%) Query: 101 VERNIFIQSGEINVIASNGYVDFQKRILVLNGDRADKVILKEKLNTFL 148 + R++ + G+ S + +V+ + D L+ LN++L Sbjct: 21 IYRSVLPEHGDSQGERSKADLSLDGNTIVITIEAEDLSALRASLNSWL 68 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.323 0.137 0.378 Gapped Lambda K H 0.267 0.0731 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,752,174 Number of extensions: 164695 Number of successful extensions: 320 Number of sequences better than 10.0: 1 Number of HSP's gapped: 320 Number of HSP's successfully gapped: 22 Length of query: 181 Length of database: 5,994,473 Length adjustment: 87 Effective length of query: 94 Effective length of database: 4,114,577 Effective search space: 386770238 Effective search space used: 386770238 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 54 (24.6 bits)