RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780288|ref|YP_003064701.1| exodeoxyribonuclease III protein [Candidatus Liberibacter asiaticus str. psy62] (281 letters) >gnl|CDD|161757 TIGR00195, exoDNase_III, exodeoxyribonuclease III. The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family. Length = 254 Score = 226 bits (578), Expect = 5e-60 Identities = 89/256 (34%), Positives = 135/256 (52%), Gaps = 4/256 (1%) Query: 6 VATWNVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSY 65 + +WNVN +RAR+H AW+KEN PD++CLQETK +D+ FP E YH+ GQK Y Sbjct: 3 IISWNVNGLRARLHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFHKEGYHVFFSGQKGY 62 Query: 66 NGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYD 125 +GVAI SK +P+ + ++ D + R I A F + + N Y P+G+ S K Sbjct: 63 SGVAIFSKEEPLSVRRGFGVEEEDAEGRIIMAEF----DSFLVINGYFPNGSRDDSEKLP 118 Query: 126 DKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQK 185 K+ W++ + + ++ ++P++ GD NI P D ++P N F E R+ + Sbjct: 119 YKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEIDLHSPDENRNHTGFLPEEREWLDR 178 Query: 186 LQNMGFTDAIRATHDTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTKP 245 L G D R + YS+WDY + +N+G RID+ ++S ID Sbjct: 179 LLEAGLVDTFRKFNPDEGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDYDI 238 Query: 246 RGWTKPSDHTPVIVSL 261 RG KPSDH PV++ Sbjct: 239 RGSEKPSDHCPVVLEF 254 >gnl|CDD|161970 TIGR00633, xth, exodeoxyribonuclease III (xth). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Length = 255 Score = 221 bits (565), Expect = 2e-58 Identities = 89/261 (34%), Positives = 142/261 (54%), Gaps = 12/261 (4%) Query: 6 VATWNVNSIRARIHNLA-AWIKENNPDIICLQETKTEDKNFPFETLQSLNYH--IETCGQ 62 + +WNVN +RAR+H L W+KE PD++CLQETK D+ FP E + L YH Sbjct: 3 IISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAKS 62 Query: 63 KSYNGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITST 122 K Y+GVAILSK +P+++ G++ D + R I A F + N+Y+P+G Sbjct: 63 KGYSGVAILSKVEPLDVRYGFGGEEHDEEGRVITAEFDG----FTVVNVYVPNGGSRGLE 118 Query: 123 KYDDKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQS 182 + + K+ + ++ + L+ +P+I GD N+ D NP + +A FT E R+ Sbjct: 119 RLEYKLQFWDALFQYYEKELDAGKPVIICGDMNVAHTEIDLGNPKENKGNAGFTPEEREW 178 Query: 183 FQKLQNMGFTDAIRATH-DTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARI 241 F +L G D R + DT Y++WDY + + +N+G RID+ ++S + + I Sbjct: 179 FDELLEAGLVDTFRHFNPDTEGAYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYI 238 Query: 242 DTKPRGWTKPSDHTPVIVSLD 262 D++ RG SDH P+++ LD Sbjct: 239 DSEIRG----SDHCPIVLELD 255 >gnl|CDD|183300 PRK11756, PRK11756, exonuclease III; Provisional. Length = 268 Score = 192 bits (490), Expect = 8e-50 Identities = 90/266 (33%), Positives = 130/266 (48%), Gaps = 16/266 (6%) Query: 10 NVNSIRARIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCGQKSYNGVA 69 N+N +RAR H L A I+++ PD+I LQETK D+ FP E +++L YH+ GQK + GVA Sbjct: 7 NINGLRARPHQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFYHGQKGHYGVA 66 Query: 70 ILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPIT-STKYDDKI 128 +LSK PI + P DD + Q R I AT L + N Y P G TK+ K Sbjct: 67 LLSKQTPIAVRKGFPTDDEEAQRRIIMATIPTPNGNLTVINGYFPQGESRDHPTKFPAKR 126 Query: 129 SWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPI-IWENDA---------CFTLE 178 + + + L + PL+ GD NI P D I I E + F E Sbjct: 127 QFYQDLQNYLETELSPDNPLLIMGDMNISPTDLD----IGIGEENRKRWLRTGKCSFLPE 182 Query: 179 VRQSFQKLQNMGFTDAIRATH-DTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLH 237 R+ +L + G D R + D + +S++DY + + N+G+RID I+ + Sbjct: 183 EREWLDRLMDWGLVDTFRQLNPDVNDRFSWFDYRSKGFDDNRGLRIDLILATQPLAERCV 242 Query: 238 SARIDTKPRGWTKPSDHTPVIVSLDI 263 ID RG KPSDH P+ + + Sbjct: 243 ETGIDYDIRGMEKPSDHAPIWATFKL 268 >gnl|CDD|139971 PRK13911, PRK13911, exodeoxyribonuclease III; Provisional. Length = 250 Score = 102 bits (255), Expect = 1e-22 Identities = 74/257 (28%), Positives = 121/257 (47%), Gaps = 15/257 (5%) Query: 8 TWNVNSIRA-RIHNLAAWIKENNPDIICLQETKTEDKNFPFETLQSLNYHIETCG-QKSY 65 +WNVN +RA + + D+ C+QE+K + + FE ++ C +K Y Sbjct: 5 SWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGYFDFW--NCAIKKGY 62 Query: 66 NGVAILSKYQPIEIVTHLPGDDLDVQARFIEATFTINTQTLRIGNLYLPHGNPITSTKYD 125 +GV +K +P+ + + ++ D + R I F ++ + N+Y P+ S + Sbjct: 63 SGVVTFTKKEPLSVSYGINIEEHDKEGRVITCEF----ESFYLVNVYTPNSQQALS-RLS 117 Query: 126 DKISWIKRFLRFASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWENDACFTLEVRQSFQK 185 ++SW F +F + LEL++P+I GD N+ D NP +A F+ E R F + Sbjct: 118 YRMSWEVEFKKFL-KALELKKPVIVCGDLNVAHNEIDLENPKTNRKNAGFSDEERGKFSE 176 Query: 186 LQNMGFTDAIRATH-DTHHLYSFWDYYADSWSKNKGIRIDHIMLSPEATSLLHSARIDTK 244 L N GF D R + + Y++W Y + KN G RID+ + S + L A I Sbjct: 177 LLNAGFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYKD 236 Query: 245 PRGWTKPSDHTPVIVSL 261 G SDH PV + L Sbjct: 237 ILG----SDHCPVGLEL 249 >gnl|CDD|180068 PRK05421, PRK05421, hypothetical protein; Provisional. Length = 263 Score = 31.8 bits (73), Expect = 0.19 Identities = 19/90 (21%), Positives = 32/90 (35%), Gaps = 24/90 (26%) Query: 6 VATWNVNSIRARIH--NLAAWIKE-----NNPDIICLQETKT--EDKNFP----FETLQS 52 + WN I+ A W+ + D++ LQE +T E F Q+ Sbjct: 46 LLVWN-------IYKQQRAGWLSVLKNLGKDADLVLLQEAQTTPELVQFATANYLAADQA 98 Query: 53 LNYHIETCGQKSYNGVAILSKYQPIEIVTH 82 + + + +GV LSK P+ Sbjct: 99 PAFVLP----QHPSGVMTLSKAHPVYCCPL 124 >gnl|CDD|147983 pfam06113, BRE, Brain and reproductive organ-expressed protein (BRE). This family consists of several eukaryotic brain and reproductive organ-expressed (BRE) proteins. BRE is a putative stress-modulating gene, found able to down-regulate TNF-alpha-induced-NF-kappaB activation upon over expression. A total of six isoforms are produced by alternative splicing predominantly at either end of the gene.Compared to normal cells, immortalized human cell lines uniformly express higher levels of BRE. Peripheral blood monocytes respond to LPS by down-regulating the expression of all the BRE isoforms.It is thought that the function of BRE and its isoforms is to regulate peroxisomal activities. Length = 238 Score = 29.7 bits (66), Expect = 0.93 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 2/54 (3%) Query: 137 FASQRLELEEPLIFAGDYNIIPQPHDCYNPIIWE--NDACFTLEVRQSFQKLQN 188 F +Q EL IF D + +P P ++ W+ N C L V++ Q+ N Sbjct: 73 FNAQYPELPPDFIFGEDADFLPDPSALHHLAQWDAGNPECLLLLVKELIQQYHN 126 >gnl|CDD|162065 TIGR00844, c_cpa1, na(+)/h(+) antiporter. This model is specific for the fungal members of this family. Length = 810 Score = 28.0 bits (62), Expect = 2.8 Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 3/53 (5%) Query: 137 FASQRLELEEPLIFAGDYNIIPQPH--DCYNPIIWENDACFTLEVRQSFQKLQ 187 F ++L + E ++ A + +I PH + +NP+ W N TLE+ + LQ Sbjct: 31 FVKEKLYIGESMV-ASIFGLIVGPHCLNWFNPLSWGNTDSITLEISRILLCLQ 82 >gnl|CDD|182963 PRK11101, glpA, sn-glycerol-3-phosphate dehydrogenase subunit A; Provisional. Length = 546 Score = 27.7 bits (62), Expect = 3.3 Identities = 10/15 (66%), Positives = 10/15 (66%) Query: 83 LPGDDLDVQARFIEA 97 LP DDL QA FI A Sbjct: 94 LPEDDLAFQATFIRA 108 >gnl|CDD|128433 smart00128, IPPc, Inositol polyphosphate phosphatase, catalytic domain homologues. Mg(2+)-dependent/Li(+)-sensitive enzymes. Length = 310 Score = 27.7 bits (62), Expect = 3.5 Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 10/45 (22%) Query: 4 VTVATWNVNSIRARIHN-LAAWIK-------ENNPDIIC--LQET 38 V V TWNV ++A + +W+ PDI LQE Sbjct: 5 VLVGTWNVGGLKADPKVDVTSWLFQKIDVKQSEKPDIYVIGLQEV 49 >gnl|CDD|129656 TIGR00565, trpE_proteo, anthranilate synthase component I, proteobacterial subset. This enzyme resembles some other chorismate-binding enzymes, including para-aminobenzoate synthase (pabB) and isochorismate synthase. There is a fairly deep split between two sets, seen in the pattern of gaps as well as in amino acid sequence differences. This group includes proteobacteria such as E. coli and Helicobacter pylori but also the gram-positive organism Corynebacterium glutamicum. The second group includes eukaryotes, archaea, and most other bacterial lineages; sequences from the second group may resemble pabB more closely than other trpE from this group. Length = 498 Score = 27.5 bits (61), Expect = 4.2 Identities = 15/81 (18%), Positives = 29/81 (35%), Gaps = 6/81 (7%) Query: 182 SFQKLQNMGFTDAIRATHDTHHLYSFWDYYADSW----SKNKGIRIDHIMLSPEATSLLH 237 S+ + ++A ++ + F Y A++ + K RI + Sbjct: 134 SYDLVAGFEDLPHLKAKNNNCPDFCF--YLAETLIVIDHQKKSTRIQASCFAERFEKQRL 191 Query: 238 SARIDTKPRGWTKPSDHTPVI 258 AR+D + T +D PV Sbjct: 192 QARLDLLEQQKTIKADPVPVK 212 >gnl|CDD|180586 PRK06483, PRK06483, dihydromonapterin reductase; Provisional. Length = 236 Score = 27.2 bits (61), Expect = 5.0 Identities = 7/22 (31%), Positives = 12/22 (54%) Query: 10 NVNSIRARIHNLAAWIKENNPD 31 + + +RA IHN + W+ E Sbjct: 71 HTDGLRAIIHNASDWLAEKPGA 92 >gnl|CDD|181356 PRK08290, PRK08290, enoyl-CoA hydratase; Provisional. Length = 288 Score = 26.8 bits (60), Expect = 5.7 Identities = 9/21 (42%), Positives = 10/21 (47%) Query: 184 QKLQNMGFTDAIRATHDTHHL 204 Q L GF A+ A D H L Sbjct: 235 QTLDAQGFRAALDAVFDLHQL 255 >gnl|CDD|184801 PRK14715, PRK14715, DNA polymerase II large subunit; Provisional. Length = 1627 Score = 26.3 bits (58), Expect = 7.8 Identities = 6/35 (17%), Positives = 13/35 (37%) Query: 45 FPFETLQSLNYHIETCGQKSYNGVAILSKYQPIEI 79 E L+ L + E + N + ++ E+ Sbjct: 581 TDLENLKDLVQNWEEKAKPFKNVIHFINLLSRFEL 615 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 0.319 0.134 0.419 Gapped Lambda K H 0.267 0.0719 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,648,157 Number of extensions: 286039 Number of successful extensions: 545 Number of sequences better than 10.0: 1 Number of HSP's gapped: 533 Number of HSP's successfully gapped: 15 Length of query: 281 Length of database: 5,994,473 Length adjustment: 92 Effective length of query: 189 Effective length of database: 4,006,537 Effective search space: 757235493 Effective search space used: 757235493 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 (21.8 bits) S2: 56 (25.4 bits)