RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780661|ref|YP_003065074.1| exonuclease I [Candidatus Liberibacter asiaticus str. psy62] (471 letters) >gnl|CDD|183310 PRK11779, sbcB, exonuclease I; Provisional. Length = 476 Score = 723 bits (1868), Expect = 0.0 Identities = 265/467 (56%), Positives = 339/467 (72%), Gaps = 2/467 (0%) Query: 1 MTNHFVIYDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFI 60 M F+ +DYETFG + ALDRPAQFAG+R D I VF+CKPADDYLP PEAV I Sbjct: 4 MQPTFLWHDYETFGANPALDRPAQFAGIRTDADLNIIGEPLVFYCKPADDYLPSPEAVLI 63 Query: 61 TGITPQKALRDGVVEAEFSRRIHQFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYDSYRW 120 TGITPQ+AL G+ EAEF+ RIH FS P TCI+GYNNIRFDD +R IFYRNFYD Y Sbjct: 64 TGITPQEALEKGLPEAEFAARIHAEFSQPGTCILGYNNIRFDDEVTRYIFYRNFYDPYAR 123 Query: 121 SWDNGNSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHVNAHDAKAD 180 W NGNSRWDLLDV+RA YA P+GI WP +DG SFKL+ L ANGIEH NAHDA +D Sbjct: 124 EWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLEHLTKANGIEHENAHDAMSD 183 Query: 181 VYATLALVWLIREKKPKLFEYLYDYRNKNQLRKLIDIQNMTPLVHVSGMFGASRSNTALI 240 VYAT+A+ LI++K+PKLF+YL+ RNK ++ LID+ M PLVHVSGMFGA R T+ + Sbjct: 184 VYATIAMAKLIKQKQPKLFDYLFQLRNKRKVAALIDVPAMKPLVHVSGMFGAERGCTSWV 243 Query: 241 APVAWHPRYKDSVIGCNLSGDMRVFQDLDSVQLAKRLFTSHDELK-GLVPVPIKEVHLNK 299 AP+AWHP K++VI C+L+GD +LD+ L +RL+T +L G +PVP+K VHLNK Sbjct: 244 APLAWHPTNKNAVIVCDLAGDPSPLLELDADTLRERLYTRRADLAEGELPVPLKLVHLNK 303 Query: 300 CPILMPIDYCKKEHFERWGIDHKRCLENLTLLRQQTNLRDRFKAIYNKPYT-SSSQDVDS 358 CP+L P + E ER GID ++CL+NL LLRQ +LR++ A++ + + S DVD+ Sbjct: 304 CPVLAPAKTLRPEDAERLGIDRQQCLDNLALLRQNPDLREKVVAVFAEAEPFAPSDDVDA 363 Query: 359 QLYDGFFADVDRQIMDRILRTAPEQLSTLNLPFSDRRLPELFFRYRARNFPHTLSEKEKQ 418 QLYDGFF+D DR++M+ I T PE L+ L+L F D RL EL FRYRARNFP TL ++E+Q Sbjct: 364 QLYDGFFSDADRRLMEIIRETEPENLAALDLTFDDPRLEELLFRYRARNFPETLDDEEQQ 423 Query: 419 DWLEHRKKMLTRSRIEEYKNKLQSLSGEYKGDEGKEGLINALYEYLQ 465 WLEHR++ LT R+++Y +L+ L+ EY+ DE K+ L+ ALY+Y + Sbjct: 424 RWLEHRRQRLTPERLQQYAAELEQLAQEYEDDEEKQALLKALYDYAE 470 >gnl|CDD|149465 pfam08411, Exonuc_X-T_C, Exonuclease C-terminal. This bacterial domain is found at the C-terminus of Exodeoxyribonuclease I/Exonuclease I (pfam00929), which is a single-strand specific DNA nuclease affecting recombination and expression pathways. The exonuclease I protein in E. coli is associated with DNA deoxyribophosphodiesterase (dRPase). Length = 268 Score = 328 bits (844), Expect = 1e-90 Identities = 132/268 (49%), Positives = 183/268 (68%), Gaps = 10/268 (3%) Query: 206 RNKNQLRKLIDIQNMTPLVHVSGMFGASRSNTALIAPVAWHPRYKDSVIGCNLSGDMRVF 265 R+K + KLID+ M PLVHVSGMFGA R T+ + P+AWHP K++VI C+L+ D Sbjct: 1 RSKKAVAKLIDLVAMKPLVHVSGMFGAERGCTSWVLPLAWHPTNKNAVIVCDLAQDPSPL 60 Query: 266 QDLDSVQLAKRLFTSHDEL-KGLVPVPIKEVHLNKCPILMPIDYCKKEHFERWGIDHKRC 324 DL + +L +RL+T ++L +G + VP+K VHLNKCPIL P + E ER GID ++C Sbjct: 61 LDLSAEELRQRLYTKREDLAEGELRVPLKLVHLNKCPILAPAKTLRPEDAERLGIDREQC 120 Query: 325 LENLTLLRQQTNLRDRFKAIYN--KPYTSSSQDVDSQLYDGFFADVDRQIMDRILRTAPE 382 L+NL LLRQ LR++ K ++ + + S+ DVD QLYDGFF+D D+++M+ I T+PE Sbjct: 121 LKNLALLRQNPELREKLKEVFEEEREFPPST-DVDQQLYDGFFSDADKRLMEIIRETSPE 179 Query: 383 QLSTLNLPFSDRRLPELFFRYRARNFPHTLSEKEKQDWLEHRKKMLTRSR-----IEEYK 437 QL+ L L F D+RLPEL FRYRARNFP TLSE+E+Q W E+ ++ L +E+Y+ Sbjct: 180 QLAELELNFDDKRLPELLFRYRARNFPETLSEEEQQRWQEYCQQRLLDPAGGALTLEDYE 239 Query: 438 NKLQSLSGEYKGDEGKEGLINALYEYLQ 465 KL+ L+ EY DE K+ L+ ALY+Y Q Sbjct: 240 QKLEQLAAEYSDDE-KQALLQALYDYAQ 266 >gnl|CDD|162341 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. Length = 850 Score = 53.7 bits (129), Expect = 9e-08 Identities = 46/197 (23%), Positives = 82/197 (41%), Gaps = 33/197 (16%) Query: 5 FVIYDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLP-DPEAVFITGI 63 + + D ET G ++ D+ Q G+ V E +++ F + P P +TGI Sbjct: 2 YAVVDLETTGTQLSFDKIIQI-GIVVVEDGEIVDT----FHTDVNPNEPIPPFIQELTGI 56 Query: 64 TPQKALRDGVVEA-EFSRRIHQFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYD-SYRWS 121 + + +A FS+ + + + I +N+ FD N + D Y Sbjct: 57 SDNM-----LQQAPYFSQVAQEIYDLLEDGIFVAHNVHFD----LNFLAKALKDCGYEP- 106 Query: 122 WDNGNSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHVNAHDAKADV 181 R D +++ + + P+ + S++L +L+ A G+ H N H A +D Sbjct: 107 --LPKPRIDTVELAQIFF---------PTEE----SYQLSELSEALGLTHENPHRADSDA 151 Query: 182 YATLALVWLIREKKPKL 198 AT L+ L+ EK KL Sbjct: 152 QATAELLLLLFEKMEKL 168 >gnl|CDD|128755 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases. Length = 169 Score = 44.2 bits (105), Expect = 7e-05 Identities = 47/194 (24%), Positives = 68/194 (35%), Gaps = 27/194 (13%) Query: 5 FVIYDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFITGIT 64 V+ D ET G D D + A V VD +I + KP D A I GIT Sbjct: 2 LVVIDCETTGLDPGKDEIIEIAAVDVDG--GRIIVVFDTYVKP--DRPITDYATEIHGIT 57 Query: 65 PQKALRDGVVEAEFSRRIHQFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYDSYRWSWDN 124 P+ L D E + +F ++ N + FD F + + Sbjct: 58 PEM-LDDAPTFEEVLEELLEFLK--GKILVAGNALNFD--LR---FLKLEHPRLGIKDPP 109 Query: 125 GNSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHV-NAHDAKADVYA 183 N D L + RA+ + L+ LA G+E + AH A D A Sbjct: 110 KNPVIDTLKLARALN--------------PGRKYSLKKLAERLGLEVIGRAHRALDDARA 155 Query: 184 TLALVWLIREKKPK 197 T L + E+ + Sbjct: 156 TAKLFKKLVERLLE 169 >gnl|CDD|162340 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model. Length = 1213 Score = 42.4 bits (100), Expect = 2e-04 Identities = 45/192 (23%), Positives = 73/192 (38%), Gaps = 33/192 (17%) Query: 5 FVIYDYETFGRDVALDRPAQFAGVRV--DRQWEKIESTEVFFCKPADDYLPDPEAVF-IT 61 +V++D ET G D +F V+V R +K + FF KP + P V +T Sbjct: 192 YVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQ----FFIKPHE---PLSAFVTELT 244 Query: 62 GITPQKALRDGVVEAEFSRRIHQFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYDSYRWS 121 GIT Q L + E + +FF I+ +N FD + F + Sbjct: 245 GIT-QDMLENAPEIEEVLEKFKEFF---KDSILVAHNASFDIGFLNTNFEK--VGLEPLE 298 Query: 122 WDNGNSRWDLLDVMRAIYAFSPDGIQWPSRDDGATSFKLQDLALANGIEHVNAHDAKADV 181 N D L++ RA+ S +L ++ G++ + H A D Sbjct: 299 ----NPVIDTLELARALNP-------------EYKSHRLGNICKKLGVDLDDHHRADYDA 341 Query: 182 YATLALVWLIRE 193 AT + ++ E Sbjct: 342 EATAKVFKVMVE 353 >gnl|CDD|181176 PRK07942, PRK07942, DNA polymerase III subunit epsilon; Provisional. Length = 232 Score = 40.0 bits (94), Expect = 0.001 Identities = 28/100 (28%), Positives = 41/100 (41%), Gaps = 20/100 (20%) Query: 8 YDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDP------EAVFIT 61 +D ET G D R A V VD E +ES E +L DP EA + Sbjct: 11 FDLETTGVDPETARIVTAALVVVDADGEVVESRE---------WLADPGVEIPEEASAVH 61 Query: 62 GITPQKALRDG----VVEAEFSRRIHQFFSVPNTCIIGYN 97 GIT + A G V AE + + + ++ ++ +N Sbjct: 62 GITTEYARAHGRPAAEVLAEIADALREAWA-RGVPVVVFN 100 Score = 34.6 bits (80), Expect = 0.050 Identities = 13/40 (32%), Positives = 19/40 (47%) Query: 159 KLQDLALANGIEHVNAHDAKADVYATLALVWLIREKKPKL 198 L L G+ NAH+A AD A + W + + P+L Sbjct: 144 TLTALCEHYGVRLDNAHEATADALAAARVAWALARRFPEL 183 >gnl|CDD|181223 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated. Length = 928 Score = 33.4 bits (77), Expect = 0.13 Identities = 13/31 (41%), Positives = 18/31 (58%) Query: 154 GATSFKLQDLALANGIEHVNAHDAKADVYAT 184 A S+KL+DL+ G+EH H A +D T Sbjct: 128 TAESYKLRDLSEELGLEHDQPHRADSDAEVT 158 >gnl|CDD|162758 TIGR02197, heptose_epim, ADP-L-glycero-D-manno-heptose-6-epimerase. This family consists of examples of ADP-L-glycero-D-mannoheptose-6-epimerase, an enzyme involved in biosynthesis of the inner core of lipopolysaccharide (LPS) for Gram-negative bacteria. This enzyme is homologous to UDP-glucose 4-epimerase (TIGR01179) and belongs to the NAD dependent epimerase/dehydratase family (pfam01370). Length = 314 Score = 28.0 bits (63), Expect = 4.8 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 10/64 (15%) Query: 190 LIREKKPKLFEYLYDYRNKNQLRKLIDIQ-----NMTPLVH-VSGMF----GASRSNTAL 239 + KLF+ +++ QLR + ++ N+ L + VSG+F G +RS L Sbjct: 192 IKAGGNVKLFKSSEGFKDGEQLRDFVYVKDVVDVNLWLLENGVSGIFNLGTGRARSFNDL 251 Query: 240 IAPV 243 V Sbjct: 252 ADAV 255 >gnl|CDD|162870 TIGR02468, sucrsPsyn_pln, sucrose phosphate synthase/possible sucrose phosphate phosphatase, plant. Members of this family are sucrose-phosphate synthases of plants. This enzyme is known to exist in multigene families in several species of both monocots and dicots. The N-terminal domain is the glucosyltransferase domain. Members of this family also have a variable linker region and a C-terminal domain that resembles sucrose phosphate phosphatase (SPP) (EC 3.1.3.24) (see TIGR01485), the next and final enzyme of sucrose biosynthesis. The SPP-like domain likely serves a binding and not a catalytic function, as the reported SPP is always encoded by a distinct protein. Length = 1050 Score = 28.2 bits (63), Expect = 4.8 Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 2/31 (6%) Query: 350 TSSSQDVDSQ--LYDGFFADVDRQIMDRILR 378 TS+ Q+++ Q LYDGF ++R++ R R Sbjct: 387 TSTRQEIEEQWGLYDGFDVILERKLRARARR 417 >gnl|CDD|130365 TIGR01298, RNaseT, ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases. Length = 200 Score = 27.9 bits (62), Expect = 5.8 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 6/86 (6%) Query: 6 VIYDYETFGRDVALDRPAQFAGVRV---DRQWEKIESTEVFFCKPADDYLPDPEAVFITG 62 V+ D ET G + D + A + + ++ W ++T F +P + PEA+ TG Sbjct: 11 VVVDVETGGFNAKTDALLEIAAITLKMDEQGWLFPDTTLHFHVEPFEGANIQPEALEFTG 70 Query: 63 ITPQKALRDGVVEAEFSRRIHQFFSV 88 I LR V E E +H+ F V Sbjct: 71 IDLDHPLRGAVSEYE---ALHEIFKV 93 >gnl|CDD|151027 pfam10453, NUFIP1, Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1). Proteins in this family have been implicated in the assembly of the large subunit of the ribosome and in telomere maintenance. Some proteins in this family contain a CCCH zinc finger. This family contains a protein called human fragile X mental retardation-interacting protein 1, which is known to bind RNA and is phosphorylated upon DNA damage. Length = 57 Score = 27.3 bits (61), Expect = 9.7 Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 1/27 (3%) Query: 413 SEKEKQDWLEHRKKM-LTRSRIEEYKN 438 + +E W+E RKK T++ IE+ K Sbjct: 20 TPEEIAKWIEERKKNYPTKANIEKKKK 46 >gnl|CDD|182476 PRK10458, PRK10458, DNA cytosine methylase; Provisional. Length = 467 Score = 27.3 bits (61), Expect = 9.7 Identities = 8/17 (47%), Positives = 12/17 (70%) Query: 196 PKLFEYLYDYRNKNQLR 212 P L++YLY Y K+Q + Sbjct: 328 PVLWKYLYRYAKKHQAK 344 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 0.322 0.139 0.431 Gapped Lambda K H 0.267 0.0734 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 8,184,521 Number of extensions: 545276 Number of successful extensions: 1123 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1115 Number of HSP's successfully gapped: 27 Length of query: 471 Length of database: 5,994,473 Length adjustment: 97 Effective length of query: 374 Effective length of database: 3,898,497 Effective search space: 1458037878 Effective search space used: 1458037878 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: 59 (26.5 bits)