RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780796|ref|YP_003065209.1| ribonuclease H [Candidatus Liberibacter asiaticus str. psy62] (152 letters) >gnl|CDD|30676 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and repair]. Length = 154 Score = 170 bits (431), Expect = 2e-43 Identities = 84/146 (57%), Positives = 105/146 (71%), Gaps = 3/146 (2%) Query: 7 REVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKY- 65 ++V +TDGAC GNPGPGGWG +LRY EK +SGGE TTNNR EL A I+AL ALK Sbjct: 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKEL 61 Query: 66 -PCKVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQH-KVDLY 123 C+V LYTDS YV +G ++WI KW++NGWKT+DKK VKN DLW + E +H V Sbjct: 62 GACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWE 121 Query: 124 WIKGHAGNQENEKVDRIARNAAVSFK 149 W+KGHAG+ ENE+ D++AR AA + K Sbjct: 122 WVKGHAGHPENERADQLAREAARAAK 147 >gnl|CDD|119393 cd06222, RnaseH, RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.. Length = 130 Score = 132 bits (333), Expect = 6e-32 Identities = 60/141 (42%), Positives = 79/141 (56%), Gaps = 16/141 (11%) Query: 10 HAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGE--KETTNNRMELMAAIKALTALKY-- 65 YTDG+C GNPGP G GV+LR G E ++SGG TTNNR EL+A I+AL Sbjct: 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELG 60 Query: 66 PCKVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQ-HKVDLYW 124 KV +YTDS YV + W + K VKN+DLW + + + HKV W Sbjct: 61 GKKVNIYTDSQYVINALTGWYE-----------GKPVKNVDLWQRLLALLKRFHKVRFEW 109 Query: 125 IKGHAGNQENEKVDRIARNAA 145 + GH+G + NE+ D +A+ AA Sbjct: 110 VPGHSGIEGNERADALAKEAA 130 >gnl|CDD|143857 pfam00075, RnaseH, RNase H. RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. Length = 126 Score = 119 bits (300), Expect = 3e-28 Identities = 52/134 (38%), Positives = 72/134 (53%), Gaps = 15/134 (11%) Query: 12 YTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPCKVLL 71 YTDG+C+GNPG GG G + GK++ TTN R EL+A I+AL AL KV + Sbjct: 7 YTDGSCNGNPGTGGAGYVT-DGGKQRSKPLPG--TTNQRAELLALIEALEALS-GQKVNI 62 Query: 72 YTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKGHAGN 131 YTDS YV G + W S+ K +KN ++W +H V + W+ GH+G Sbjct: 63 YTDSQYVIGGI---LNGWP----TKSESKPIKN-EIWE---LLLKKHAVYIQWVPGHSGI 111 Query: 132 QENEKVDRIARNAA 145 NE D++A+ A Sbjct: 112 PGNELADKLAKQGA 125 >gnl|CDD|38956 KOG3752, KOG3752, KOG3752, Ribonuclease H [Replication, recombination and repair]. Length = 371 Score = 75.5 bits (185), Expect = 5e-15 Identities = 55/155 (35%), Positives = 76/155 (49%), Gaps = 16/155 (10%) Query: 12 YTDGACSGNPGPG---GWGVLLRYKGKEKIISG--GEKETTNNRMELMAAIKAL-TALKY 65 YTDG+ SGN G+GV G E +SG TNNR EL+AAI+AL A Sbjct: 216 YTDGSSSGNGRKSSRAGYGVYWG-PGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSK 274 Query: 66 PC-KVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKT-----VKNIDLWMKFVEASAQH- 118 KV++ TDS Y + W++ W++NGWKTS+ VKN D + + E + Sbjct: 275 NINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEIS 334 Query: 119 --KVDLYWIKGHAGNQENEKVDRIARNAAVSFKNK 151 KV ++ GH+G NE D +AR + Sbjct: 335 NKKVQQEYVGGHSGILGNEMADALARKGSTLASRS 369 >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 = 27.7 bits (62), Expect = 1.5 Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 4/62 (6%) Query: 24 GGWGVLLRYKGKEKIISGGEKE----TTNNRMELMAAIKALTALKYPCKVLLYTDSSYVH 79 R E++ + ++ R EL+ I+ L A + P L Y VH Sbjct: 402 SNTKKSARGYDNEELNALLRQQLQEMDPEKRKELVFEIQELYAEELPMIPLYYPTMYTVH 461 Query: 80 KG 81 +G Sbjct: 462 RG 463 >gnl|CDD|145449 pfam02301, HORMA, HORMA domain. The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognize chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity. Length = 189 Score = 26.5 bits (59), Expect = 3.3 Identities = 19/85 (22%), Positives = 26/85 (30%), Gaps = 11/85 (12%) Query: 30 LRYKGKEKIISGGEKETTNNRMELMAAIKALTAL---------KYPC--KVLLYTDSSYV 78 Y S EK R E+ A ++ L AL C K+L YT Y Sbjct: 96 FSYFPSGGNSSDSEKTEDETRQEIRALLRQLIALVTFLPPLPEDRTCTFKLLYYTPPDYE 155 Query: 79 HKGFSQWIKKWQQNGWKTSDKKTVK 103 GF + + + V Sbjct: 156 PPGFKWADSDSDVKLIENGEPEEVS 180 >gnl|CDD|31961 COG1775, HgdB, Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Amino acid transport and metabolism]. Length = 379 Score = 26.0 bits (57), Expect = 4.6 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 5/75 (6%) Query: 45 ETTNNRM----ELMAAIKALTALKYPCKVLLYTDSSYVHKGFSQWIKKWQQ-NGWKTSDK 99 E T N E+MA IK + + P Y H ++ + ++ G + +++ Sbjct: 104 ENTCNGKKKMYEVMARIKPVHVMDLPFHRKDEPSVKYWHNELDKFKELLEELTGNEITEE 163 Query: 100 KTVKNIDLWMKFVEA 114 K I + + EA Sbjct: 164 KLRDAIARYNRLREA 178 >gnl|CDD|31521 COG1330, RecC, Exonuclease V gamma subunit [DNA replication, recombination, and repair]. Length = 1078 Score = 25.7 bits (56), Expect = 5.8 Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 4/46 (8%) Query: 82 FSQWIKKWQQNGWKTSDKKTVKNIDLWMKFV----EASAQHKVDLY 123 WI W+ + +LW V E S H+ +L+ Sbjct: 142 RPDWIAAWEDGLFLGLGDNEKWQAELWRALVADTTELSQPHRANLH 187 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 0.315 0.131 0.408 Gapped Lambda K H 0.267 0.0773 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,821,792 Number of extensions: 83078 Number of successful extensions: 202 Number of sequences better than 10.0: 1 Number of HSP's gapped: 191 Number of HSP's successfully gapped: 13 Length of query: 152 Length of database: 6,263,737 Length adjustment: 85 Effective length of query: 67 Effective length of database: 4,426,972 Effective search space: 296607124 Effective search space used: 296607124 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 (21.6 bits) S2: 53 (24.1 bits)