RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780807|ref|YP_003065220.1| glucose-inhibited division protein B [Candidatus Liberibacter asiaticus str. psy62] (168 letters) >gnl|CDD|30706 COG0357, GidB, Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]. Length = 215 Score = 133 bits (336), Expect = 2e-32 Identities = 56/146 (38%), Positives = 80/146 (54%), Gaps = 5/146 (3%) Query: 21 VSRETLEKLEYFYFLFLKWSKKINLVSSSTVEDFWIRHVEDSLRVFQ-LHPYPSIWIDLG 79 V+ E LEKLE + L LKW+K NL + E+ W RH+ DSL + L +D+G Sbjct: 16 VTEEQLEKLEAYVELLLKWNKAYNLTAIRDPEELWQRHILDSLVLLPYLDGKAKRVLDIG 75 Query: 80 SGGGFPGIITSIQLSSIEGGLVNLIESKNKKASFLRYVVQKTAARG-KVFACRIQEAPQM 138 SG GFPGI +I ++ V L+ES KK +FLR V ++ ++ R +E Q Sbjct: 76 SGAGFPGIPLAIAFPDLK---VTLLESLGKKIAFLREVKKELGLENVEIVHGRAEEFGQE 132 Query: 139 ITTCDVISARALADLDTLLEYSFPWL 164 DV+++RA+A L+ LLE P L Sbjct: 133 KKQYDVVTSRAVASLNVLLELCLPLL 158 >gnl|CDD|111429 pfam02527, GidB, rRNA small subunit methyltransferase G. This is a family of bacterial glucose inhibited division proteins these are probably involved in the regulation of cell devision. GidB has been shown to be a methyltransferase G specific to the rRNA small subunit. Previously identified as a glucose-inhibited division protein B that appears to be present and in a single copy in all complete eubacterial genomes so far sequenced. GidB specifically methylates the N7 position of a guanosine in 16S rRNA. Length = 184 Score = 112 bits (282), Expect = 5e-26 Identities = 49/140 (35%), Positives = 72/140 (51%), Gaps = 4/140 (2%) Query: 26 LEKLEYFYFLFLKWSKKINLVSSSTVEDFWIRHVEDSLRVFQ-LHPYPSIWIDLGSGGGF 84 LEKLE + L L+W+K+ NL S + + RH+ DSL V + L D+GSG GF Sbjct: 2 LEKLELYVQLLLEWNKRYNLTSITEPNELLERHLLDSLVVLEYLDNIRIKVADVGSGAGF 61 Query: 85 PGIITSIQLSSIEGGLVNLIESKNKKASFLRYVVQKTAARGKVFACRIQEAPQMITTCDV 144 PGI +I + + L+ES KK +FL + ++ E Q DV Sbjct: 62 PGIPLAIAFPDKK---LTLLESLLKKINFLEELKKELNLENVTIVHARAEEYQHEEQYDV 118 Query: 145 ISARALADLDTLLEYSFPWL 164 I++RA+A L+ L E++ P L Sbjct: 119 ITSRAVASLNELTEWALPLL 138 >gnl|CDD|36352 KOG1137, KOG1137, KOG1137, mRNA cleavage and polyadenylation factor II complex, BRR5 (CPSF subunit) [RNA processing and modification]. Length = 668 Score = 27.2 bits (60), Expect = 2.1 Identities = 11/43 (25%), Positives = 18/43 (41%) Query: 114 LRYVVQKTAARGKVFACRIQEAPQMITTCDVISARALADLDTL 156 L + +QKT+ G+VF +A D + + D L Sbjct: 82 LPFTLQKTSFIGRVFMTHPTKAIYKWLLSDYVRVSNRSGDDRL 124 >gnl|CDD|38004 KOG2793, KOG2793, KOG2793, Putative N2,N2-dimethylguanosine tRNA methyltransferase [RNA processing and modification]. Length = 248 Score = 26.9 bits (59), Expect = 2.5 Identities = 23/127 (18%), Positives = 36/127 (28%), Gaps = 12/127 (9%) Query: 45 LVSSSTVEDFWIRHVEDSLRVFQLHPYPSIWIDLGSGGGFPGIITSIQLSSIEGGLVNLI 104 + + R E + + ++LGSG G GI+ ++ L G V L Sbjct: 60 ATTLAQPLWERRRDSELTATLIGFKTKYINVLELGSGTGLVGILAALLL----GAEVVL- 114 Query: 105 ESKNKKASFLRYVVQKTAARGKVFACRIQ-------EAPQMITTCDVISARALADLDTLL 157 K L++ K + A + LA Sbjct: 115 TDLPKVVENLKFNRDKNNIALNQLGGSVIVAILVWGNALDVSFRLPNPFDLILASDVVYE 174 Query: 158 EYSFPWL 164 E SF L Sbjct: 175 EESFEGL 181 >gnl|CDD|38897 KOG3693, KOG3693, KOG3693, Uncharacterized conserved protein [Function unknown]. Length = 1117 Score = 26.7 bits (58), Expect = 3.0 Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 1/48 (2%) Query: 37 LKWSKKINLVSSSTVEDF-WIRHVEDSLRVFQLHPYPSIWIDLGSGGG 83 L W ++ +T + F +RH+ + Q HPY +W LG G Sbjct: 432 LGWVTTVSRSIMTTPKAFSRVRHISITFGEAQHHPYNDLWAQLGDLYG 479 >gnl|CDD|35630 KOG0409, KOG0409, KOG0409, Predicted dehydrogenase [General function prediction only]. Length = 327 Score = 26.8 bits (59), Expect = 3.1 Identities = 23/117 (19%), Positives = 47/117 (40%), Gaps = 23/117 (19%) Query: 6 SNSILRANYLLNTYNVSRETLEKLEYFYFLFLKWSKKINLVSSSTVEDFWIRHVEDSLRV 65 +++++A Y + Y+ +++ ++ + + V++S E EDS V Sbjct: 51 VSNLIKAGYKVTVYDRTKDKCKEFQ----------EAGARVANSPAE-----VAEDSDVV 95 Query: 66 FQLHPYPSIWIDLGSG------GGFPGIITSIQLSSIEGGLVNLI--ESKNKKASFL 114 + P P D+ G G PG ++ +S+I+ I NK F+ Sbjct: 96 ITMVPNPKDVKDVLLGKSGVLSGIRPGKKATVDMSTIDPDTSLEIAKAISNKGGRFV 152 >gnl|CDD|143381 cd07876, STKc_JNK2, Catalytic domain of the Serine/Threonine Kinase, c-Jun N-terminal Kinase 2. Serine/Threonine Kinases (STKs), c-Jun N-terminal kinase 2 (JNK2) subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The JNK2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. JNKs are mitogen-activated protein kinases (MAPKs) that are involved in many stress-activated responses including those during inflammation, neurodegeneration, apoptosis, and persistent pain sensitization, among others. Vetebrates harbor three different JNK genes (Jnk1, Jnk2, and Jnk3). JNK1, like JNK2, is expressed in every cell and tissue type. Initially it was thought that JNK1 and JNK2 were functionally redundant as mice deficient in either genes (Jnk1 or Jnk2) could survive but disruption of both genes resulted in lethality. However, recent studies have shown that JNK1 and JNK2 perform distinct functions through specific binding partners and substrates. JNK2 is specifically translocated to the mitochondria during dopaminergic cell death. Specific substrates include the microtubule-associated proteins DCX and Tau, as well as TIF-IA which is involved in ribosomal RNA synthesis regulation. Mice deficient in Jnk2 show protection against arthritis, type 1 diabetes, atherosclerosis, abdominal aortic aneurysm, cardiac cell death, TNF-induced liver damage, and tumor growth, indicating that JNK2 may play roles in the pathogenesis of these diseases. Length = 359 Score = 26.1 bits (57), Expect = 4.7 Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 5/62 (8%) Query: 37 LKWSKKINLVSSSTVEDFWIR-HVEDSLRVFQLHPYPSIWIDLGSGGGFPGIITSIQLSS 95 LK S+ +L+S V D R V+++LR HPY ++W D P I QL Sbjct: 286 LKTSQARDLLSKMLVIDPDKRISVDEALR----HPYITVWYDPAEAEAPPPQIYDAQLEE 341 Query: 96 IE 97 E Sbjct: 342 RE 343 >gnl|CDD|132840 cd07201, cPLA2_Grp-IVB-IVD-IVE-IVF, Group IVB, IVD, IVE, and IVF cytosolic phospholipase A2; catalytic domain; Ca-dependent. Group IVB, IVD, IVE, and IVF cPLA2 consists of two domains: the regulatory C2 domain and alpha/beta hydrolase PLA2 domain. Group IVB, IVD, IVE, and IVF cPLA2 are also referred to as cPLA2-beta, -delta, -epsilon, and -zeta respectively. cPLA2-beta is approximately 30% identical to cPLA2-alpha and it shows low enzymatic activity compared to cPLA2alpha. cPLA2-beta hydrolyzes palmitic acid from 1-[14C]palmitoyl-2-arachidonoyl-PC and arachidonic acid from 1-palmitoyl-2[14C]arachidonoyl-PC, but not from 1-O-alkyl-2[3H]arachidonoyl-PC. cPLA2-delta, -epsilon, and -zeta are approximately 45-50% identical to cPLA2-beta and 31-37% identical to cPLA2-alpha. It's possible that cPLA2-beta, -delta, -epsilon, and -zeta may have arisen by gene duplication from an ancestral gene. The catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms. Movement of the cPLA2 lid possibly exposes a greater hydrophobic surface and the active site. cPLA2 belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Calcium is required for cPLA2 to bind with membranes or phospholipids. The calcium-dependent phospholipid binding domain resides in the N-terminal region of cPLA2; it is homologous to the C2 domain superfamily which is not included in this hierarchy. It includes PLA2G4B, PLA2G4D, PLA2G4E, and PLA2G4F from humans. Length = 541 Score = 25.4 bits (56), Expect = 8.6 Identities = 10/51 (19%), Positives = 14/51 (27%), Gaps = 6/51 (11%) Query: 47 SSSTVEDFWIRHVEDSLRV------FQLHPYPSIWIDLGSGGGFPGIITSI 91 ++ EDFW R D + P + L GG Sbjct: 272 LATGSEDFWHRWTRDKVNDIEDEPPLPPRPPERLTTLLTPGGPLSQAFRDF 322 >gnl|CDD|144488 pfam00909, Ammonium_transp, Ammonium Transporter Family. Length = 399 Score = 24.9 bits (55), Expect = 9.7 Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 7/46 (15%) Query: 58 HVEDSLRVFQLHPYPSIWIDLGSGGGFPGII--TSIQLSSIEGGLV 101 ++D L VF +H IW GG GI + S I GGL+ Sbjct: 300 GIDDPLDVFPVHGVGGIW-----GGIAVGIFAAPYVPPSGIYGGLL 340 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 0.412 Gapped Lambda K H 0.267 0.0752 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,023,167 Number of extensions: 97376 Number of successful extensions: 227 Number of sequences better than 10.0: 1 Number of HSP's gapped: 221 Number of HSP's successfully gapped: 16 Length of query: 168 Length of database: 6,263,737 Length adjustment: 87 Effective length of query: 81 Effective length of database: 4,383,754 Effective search space: 355084074 Effective search space used: 355084074 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)