RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780712|ref|YP_003065125.1| 30S ribosomal protein S16 [Candidatus Liberibacter asiaticus str. psy62] (116 letters) >gnl|CDD|30577 COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]. Length = 87 Score = 106 bits (265), Expect = 2e-24 Identities = 51/83 (61%), Positives = 64/83 (77%), Gaps = 2/83 (2%) Query: 3 LKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHW 62 +KIRLA GGSK R YRIVVA+SRSPRDG+FIE+LGT+NP L KE R ++ ERI +W Sbjct: 2 VKIRLARGGSKKRPFYRIVVADSRSPRDGRFIERLGTYNPLLGKEE--RVKLDEERILYW 59 Query: 63 MSKGAQPTDRILFFLDKAGLIKR 85 +S+GAQP+D + L KAGL K+ Sbjct: 60 LSQGAQPSDTVRRLLKKAGLAKK 82 >gnl|CDD|144471 pfam00886, Ribosomal_S16, Ribosomal protein S16. Length = 58 Score = 92.9 bits (232), Expect = 2e-20 Identities = 36/61 (59%), Positives = 45/61 (73%), Gaps = 4/61 (6%) Query: 10 GGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQP 69 GG K R YRIVVA+SRSPRDG+FIE+LGT+NP E ++ ERI++W+ KGAQP Sbjct: 2 GGRKKRPFYRIVVADSRSPRDGRFIEELGTYNPIANGE----VKLDVERIKYWLGKGAQP 57 Query: 70 T 70 T Sbjct: 58 T 58 >gnl|CDD|38629 KOG3419, KOG3419, KOG3419, Mitochondrial/chloroplast ribosomal protein S16 [Translation, ribosomal structure and biogenesis]. Length = 112 Score = 90.0 bits (223), Expect = 1e-19 Identities = 45/106 (42%), Positives = 65/106 (61%) Query: 1 MTLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQ 60 M +KIRLA G K+R YRIVVA+SR RDGK IE+LGT++P ++N +NF+RI+ Sbjct: 1 MVVKIRLARFGCKNRPFYRIVVADSRKRRDGKPIEQLGTYDPLPNQDNEKLVALNFDRIK 60 Query: 61 HWMSKGAQPTDRILFFLDKAGLIKRSPQNNPKKSQPKKKALERLAS 106 +W+ GAQP+D + L KAGL P + ++ E++ Sbjct: 61 YWLGVGAQPSDTVEELLGKAGLFPIHPMTFMNAKRNRRLTAEQVLP 106 >gnl|CDD|176950 CHL00005, rps16, ribosomal protein S16. Length = 82 Score = 68.5 bits (168), Expect = 4e-13 Identities = 29/82 (35%), Positives = 47/82 (57%), Gaps = 5/82 (6%) Query: 3 LKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHW 62 +K+RL G K + YRIV + RS R+G+ +EK+G ++P + +N I ++ Sbjct: 2 VKLRLKRCGRKQQAVYRIVAIDVRSRREGRDLEKVGFYDPIKNQ-----TYLNVPAILYF 56 Query: 63 MSKGAQPTDRILFFLDKAGLIK 84 + KGAQPT+ + L KA + K Sbjct: 57 LEKGAQPTETVYDILKKAEVFK 78 >gnl|CDD|36240 KOG1022, KOG1022, KOG1022, Acetylglucosaminyltransferase EXT2/exostosin 2 [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis, Extracellular structures]. Length = 691 Score = 28.1 bits (62), Expect = 0.55 Identities = 13/39 (33%), Positives = 13/39 (33%), Gaps = 3/39 (7%) Query: 20 IVVANSRSPRDGKFIEK---LGTWNPTLPKENPLRFTMN 55 I S SP K IEK W T P P T Sbjct: 42 IGWFYSDSPFSLKPIEKRNISDAWPVTNPAITPASETGL 80 >gnl|CDD|107386 cd06391, PBP1_iGluR_delta_2, N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 are closer related to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq and tumor necrosis factor family that is secreted from cerebellar granule cells. Length = 400 Score = 26.9 bits (59), Expect = 1.3 Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 1/42 (2%) Query: 1 MTLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNP 42 +T ++ G H+ I+ N G+ + KLG WNP Sbjct: 354 LTGELEFNENGGNPNVHFEILGTNYGEDL-GRGVRKLGCWNP 394 >gnl|CDD|34757 COG5156, DOC1, Anaphase-promoting complex (APC), subunit 10 [Cell division and chromosome partitioning / Posttranslational modification, protein turnover, chaperones]. Length = 189 Score = 25.8 bits (56), Expect = 2.8 Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 1/37 (2%) Query: 34 IEKLGTWNPTLPK-ENPLRFTMNFERIQHWMSKGAQP 69 + L W + K +PLR ++ +W S G QP Sbjct: 26 VTHLAEWRLSSFKRGHPLRELLDDNMDTYWQSDGVQP 62 >gnl|CDD|146017 pfam03180, Lipoprotein_9, NLPA lipoprotein. This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to pfam00497 which are solute binding proteins. Length = 236 Score = 24.9 bits (55), Expect = 5.1 Identities = 9/13 (69%), Positives = 10/13 (76%) Query: 72 RILFFLDKAGLIK 84 R L L+KAGLIK Sbjct: 111 RALLLLEKAGLIK 123 >gnl|CDD|31574 COG1384, LysS, Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]. Length = 521 Score = 24.4 bits (53), Expect = 7.1 Identities = 9/22 (40%), Positives = 13/22 (59%) Query: 18 YRIVVANSRSPRDGKFIEKLGT 39 YR+++ R PR G F+ LG Sbjct: 489 YRVLIGKERGPRLGSFLALLGV 510 >gnl|CDD|37740 KOG2529, KOG2529, KOG2529, Pseudouridine synthase [Translation, ribosomal structure and biogenesis]. Length = 395 Score = 24.2 bits (52), Expect = 7.6 Identities = 21/113 (18%), Positives = 37/113 (32%), Gaps = 13/113 (11%) Query: 17 HYRIVVANS--RSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRIL 74 + R+VV +S +P G + G + + P + + SK A+ + R + Sbjct: 275 YKRVVVKDSTVNAPCYGAKLLVPGLLRYSDDIDGPFEVVDMTTKGEAIASKIAEMSLRQV 334 Query: 75 FFLDKAGLIKRSPQNNPK-----------KSQPKKKALERLASKKNADEHATT 116 D + K K+ P K+A K + TT Sbjct: 335 ASCDHGVVAKTKRVIMEADVYERCWGLGPKASPGKEAKAEGKLDKFGKGNETT 387 >gnl|CDD|99782 cd06185, PDR_like, Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur [2Fe-2S] cluster domain. Although structurally homologous to FNR, PDR binds FMN rather than FAD in it's FNR-like domain. Electron transfer between pyrimidines and iron-sulfur clusters (Rieske center [2Fe-2S]) or heme groups is mediated by flavins in respiration, photosynthesis, and oxygenase systems. Type I dioxygenase systems, including the hydroxylate phthalate system, have 2 components, a monomeric reductase consisting of a flavin and a 2Fe-2S center and a multimeric oxygenase. In contrast to other Rieske dioxygenases the ferredoxin like domain is C-, not N-terminal.. Length = 211 Score = 24.4 bits (54), Expect = 7.8 Identities = 9/21 (42%), Positives = 9/21 (42%), Gaps = 3/21 (14%) Query: 9 CGGSKSRHHYRIVV---ANSR 26 CG R YRI V SR Sbjct: 47 CGDPADRDRYRIAVLREPASR 67 >gnl|CDD|173885 cd08520, PBP2_NikA_DppA_OppA_like_21, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 468 Score = 24.2 bits (53), Expect = 7.9 Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 10/44 (22%) Query: 16 HHYRIVVANSRSPRDGKFIEKLGTWNPTLPK------ENPLRFT 53 + +I + +P F+EK+ T P LPK E+P +FT Sbjct: 113 YTVKITLKRPYAP----FLEKIATTVPILPKHIWEKVEDPEKFT 152 >gnl|CDD|34137 COG4458, SrfC, Uncharacterized protein conserved in bacteria, putative virulence factor [Function unknown]. Length = 821 Score = 24.2 bits (52), Expect = 8.2 Identities = 19/90 (21%), Positives = 32/90 (35%), Gaps = 3/90 (3%) Query: 27 SPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKAGLIKRS 86 +P D +F EKLG + P ++ + +Q + +L LD G + R Sbjct: 438 TPFDMRFSEKLGLFKPFDLQDKVAKIKKQDSEVQQHFGDPGKAWGTLL-ALDDGG-VSRL 495 Query: 87 PQNNPKKSQPKKKALERLASKKNADEHATT 116 + P+ K RL + H Sbjct: 496 AEYLSAICLPEIKY-GRLQEQLGELAHEIR 524 >gnl|CDD|38681 KOG3471, KOG3471, KOG3471, RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription, Replication, recombination and repair]. Length = 465 Score = 24.1 bits (52), Expect = 8.4 Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 19/82 (23%) Query: 8 ACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMN-FERIQHWM--- 63 GG K +V+ + RD F++K + +E I H+M Sbjct: 118 LTGGGKQNSFGSLVLGEDKHNRDVDFLDK---------------YASERWECILHFMVGT 162 Query: 64 SKGAQPTDRILFFLDKAGLIKR 85 + ++ +L L AGL+ R Sbjct: 163 PEAKAVSEGVLNLLKHAGLMSR 184 >gnl|CDD|36447 KOG1233, KOG1233, KOG1233, Alkyl-dihydroxyacetonephosphate synthase [General function prediction only]. Length = 613 Score = 24.2 bits (52), Expect = 8.9 Identities = 9/11 (81%), Positives = 9/11 (81%) Query: 7 LACGGSKSRHH 17 LACGGS S HH Sbjct: 562 LACGGSLSHHH 572 >gnl|CDD|31653 COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]. Length = 268 Score = 24.0 bits (52), Expect = 9.0 Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 2/28 (7%) Query: 69 PTD--RILFFLDKAGLIKRSPQNNPKKS 94 PT+ R L L KAGLIK N + Sbjct: 137 PTNEGRALLLLQKAGLIKLKDGVNLLAT 164 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 0.317 0.131 0.396 Gapped Lambda K H 0.267 0.0767 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,428,883 Number of extensions: 68040 Number of successful extensions: 161 Number of sequences better than 10.0: 1 Number of HSP's gapped: 158 Number of HSP's successfully gapped: 20 Length of query: 116 Length of database: 6,263,737 Length adjustment: 81 Effective length of query: 35 Effective length of database: 4,513,408 Effective search space: 157969280 Effective search space used: 157969280 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 (21.7 bits) S2: 51 (23.4 bits)