RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780215|ref|YP_003064628.1| hypothetical protein CLIBASIA_00500 [Candidatus Liberibacter asiaticus str. psy62] (262 letters) >gnl|CDD|161662 TIGR00010, TIGR00010, hydrolase, TatD family. Several genomes have multiple paralogs related to this family. However, a set of 17 proteins can be found, one each from 17 of the first 20 genomes, such that each member forms a bidirectional best hit across genomes with all other members of the set. This core set (and one other near-perfect member), but not the other paralogs, form the seed for this model. Additionally, members of the seed alignment and all trusted hits, but not all paralogs, have a conserved motif DxHxH near the amino end. The member from E. coli was recently shown to have DNase activity. Length = 252 Score = 251 bits (644), Expect = 1e-67 Identities = 110/254 (43%), Positives = 165/254 (64%), Gaps = 3/254 (1%) Query: 2 LIDTHCHLLLPDFDEDRHDVIMRAHQANVLKMIAIAIKVKDFVPLIKLCQDYPSSIFCSV 61 LID HCHL DF+ED +VI RA A V ++A+ ++DF+ ++L + YP+ ++ +V Sbjct: 1 LIDAHCHLDFLDFEEDVEEVIERAKAAGVTAVVAVGTDLEDFLRALELAEKYPN-VYAAV 59 Query: 62 GTHPCHAHEENEVLVDELVCLASHPRVVAIGETGLDRYHNAHTIEEQKVVFLRHIEASRI 121 G HP ++ + + EL LA+HP+VVAIGETGLD Y Q+ VF ++ + Sbjct: 60 GVHPLDVDDDTKEDIKELERLAAHPKVVAIGETGLDYYKADEYKRRQEEVFRAQLQLAEE 119 Query: 122 TGIPLVIHSRSADDDMAAILQEEMKKGPFPFVIHCFSSSQKLADICLELGGYISFTGMIT 181 +P++IH+R A++D+ IL+EE K V+HCF+ +LA L+LG YIS +G++T Sbjct: 120 LNLPVIIHARDAEEDVLDILREE--KPKVGGVLHCFTGDAELAKKLLDLGFYISISGIVT 177 Query: 182 FPKYDALRAIARGIPMDRVLVETDSPYIVPVSCQGKRNEPAYVVNTAKALAKEKDVSYED 241 F +LR + R IP++R+LVETDSPY+ PV +GKRNEPA+V T +A+A+ K + E+ Sbjct: 178 FKNAKSLREVVRKIPLERLLVETDSPYLAPVPYRGKRNEPAFVRYTVEAIAEIKGMDVEE 237 Query: 242 LMEETTKNALKLFS 255 L + TTKNA +LF Sbjct: 238 LAQITTKNAKRLFG 251 >gnl|CDD|182752 PRK10812, PRK10812, putative DNAse; Provisional. Length = 265 Score = 197 bits (503), Expect = 2e-51 Identities = 103/257 (40%), Positives = 152/257 (59%), Gaps = 7/257 (2%) Query: 1 MLIDTHCHLLLPDFD---EDRHDVIMRAHQANVLKMIAIAIKVKDFVPLIKLCQDYPSSI 57 L+D+HCHL D+ +D DV+ +A +V +A+A + + + L + + + Sbjct: 2 FLVDSHCHLDGLDYQSLHKDVDDVLAKAAARDVKFCLAVATTLPGYRHMRDLVGERDNVV 61 Query: 58 FCSVGTHPCHAHEENEVLVDELVCLASHPRVVAIGETGLDRYHNAHTIEEQKVVFLRHIE 117 F S G HP + E +V +EL LA+ VVA+GETGLD Y+ T Q+ F HI+ Sbjct: 62 F-SCGVHPLNQDEPYDV--EELRRLAAEEGVVAMGETGLDYYYTPETKVRQQESFRHHIQ 118 Query: 118 ASRITGIPLVIHSRSADDDMAAILQEEMKKGPFPFVIHCFSSSQKLADICLELGGYISFT 177 R P+++H+R A D AIL+EE K V+HCF+ ++ A L+LG YISF+ Sbjct: 119 IGRELNKPVIVHTRDARADTLAILREE-KVTDCGGVLHCFTEDRETAGKLLDLGFYISFS 177 Query: 178 GMITFPKYDALRAIARGIPMDRVLVETDSPYIVPVSCQGKRNEPAYVVNTAKALAKEKDV 237 G++TF + LR AR +P+DR+LVETDSPY+ PV +GK N+PA V + A+ +A K V Sbjct: 178 GIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGV 237 Query: 238 SYEDLMEETTKNALKLF 254 S E+L + TT N +LF Sbjct: 238 SVEELAQVTTDNFARLF 254 >gnl|CDD|182449 PRK10425, PRK10425, DNase TatD; Provisional. Length = 258 Score = 138 bits (349), Expect = 2e-33 Identities = 81/252 (32%), Positives = 126/252 (50%), Gaps = 15/252 (5%) Query: 12 PDFDEDRHDVIMRAHQANVLKMIAIAIKVKDFVPLIKLCQDYPSSIFCSVGTHPCHAHEE 71 F +DR DV+ RA A V M+ +++ KL + YPS + + G HP + + Sbjct: 11 SQFAKDRDDVVARAFAAGVNGMLITGTNLRESQQAQKLARQYPSC-WSTAGVHPHDSSQW 69 Query: 72 NEVLVDELVCLASHPRVVAIGETGLDRYHNAHTIEEQKVVFLRHIEASRITGIPLVIHSR 131 + ++ LA+ P VVAIGE GLD N T EEQ+ F+ + + +P+ +H R Sbjct: 70 QAATEEAIIELAAQPEVVAIGECGLDFNRNFSTPEEQERAFVAQLAIAAELNMPVFMHCR 129 Query: 132 SADDDMAAILQEEMKKGPFPFVIHCFSSSQKLADICLELGGYISFTGMITFPKYD----- 186 A + A+L+ + K P V+HCF+ +++ CL G YI TG + D Sbjct: 130 DAHERFMALLEPWLDKLPGA-VLHCFTGTREEMQACLARGLYIGITGWVC----DERRGL 184 Query: 187 ALRAIARGIPMDRVLVETDSPYIVPVSCQGK----RNEPAYVVNTAKALAKEKDVSYEDL 242 LR + IP +R+L+ETD+PY++P K RNEPA++ + + +A + L Sbjct: 185 ELRELLPLIPAERLLLETDAPYLLPRDLTPKPASRRNEPAFLPHILQRIAHWRGEDAAWL 244 Query: 243 MEETTKNALKLF 254 T NA LF Sbjct: 245 AATTDANARTLF 256 >gnl|CDD|171118 PRK11449, PRK11449, putative deoxyribonuclease YjjV; Provisional. Length = 258 Score = 123 bits (309), Expect = 6e-29 Identities = 75/255 (29%), Positives = 128/255 (50%), Gaps = 5/255 (1%) Query: 2 LIDTHCHLLLPDFDEDRHDVIMRAHQANVLKMIAIAIKVKDFVPLIKLCQDYPSSIFCSV 61 IDTHCH P F D + RA QA V K+I A + ++F ++ L + Y ++ ++ Sbjct: 5 FIDTHCHFDFPPFSGDEEASLQRAAQAGVGKIIVPATEAENFARVLALAERYQP-LYAAL 63 Query: 62 GTHPCHAHEENEVLVDELV-CLASHP-RVVAIGETGLDRYHNAHTIEEQKVVFLRHIEAS 119 G HP + ++V +D+L L P +VVA+GE GLD + + E Q+ + ++ + Sbjct: 64 GLHPGMLEKHSDVSLDQLQQALERRPAKVVAVGEIGLDLFGDDPQFERQQWLLDEQLKLA 123 Query: 120 RITGIPLVIHSRSADDDMAAILQEEMKKGPFPFVIHCFSSSQKLADICLELGGYISFTGM 179 + +P+++HSR D +A L+ P V+H FS S + A+ ++LG I G Sbjct: 124 KRYDLPVILHSRRTHDKLAMHLKRH--DLPRTGVVHGFSGSLQQAERFVQLGYKIGVGGT 181 Query: 180 ITFPKYDALRAIARGIPMDRVLVETDSPYIVPVSCQGKRNEPAYVVNTAKALAKEKDVSY 239 IT+P+ R + +P+ +L+ETD+P + QG+ N P L + + Sbjct: 182 ITYPRASKTRDVIAKLPLASLLLETDAPDMPLNGFQGQPNRPEQAARVFDVLCELRPEPA 241 Query: 240 EDLMEETTKNALKLF 254 +++ E N LF Sbjct: 242 DEIAEVLLNNTYTLF 256 >gnl|CDD|180280 PRK05835, PRK05835, fructose-bisphosphate aldolase; Provisional. Length = 307 Score = 30.3 bits (68), Expect = 0.48 Identities = 23/54 (42%), Positives = 30/54 (55%), Gaps = 7/54 (12%) Query: 107 EQKVVFLRHIEASRITGIPLVIHSRSA--DDDMAAILQE--EMK--KG-PFPFV 153 E K+ F R E R+T IPLV+H SA DD + L ++K KG PF F+ Sbjct: 188 EPKLDFERLQEVKRLTNIPLVLHGASAIPDDVRKSYLDAGGDLKGSKGVPFEFL 241 >gnl|CDD|180713 PRK06826, dnaE, DNA polymerase III DnaE; Reviewed. Length = 1151 Score = 29.9 bits (68), Expect = 0.76 Identities = 12/25 (48%), Positives = 15/25 (60%) Query: 103 HTIEEQKVVFLRHIEASRITGIPLV 127 H I EQ+ V I+ S+ GIPLV Sbjct: 179 HGIPEQRKVNEELIKLSKELGIPLV 203 >gnl|CDD|132639 TIGR03600, phage_DnaB, phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model. Length = 421 Score = 28.5 bits (64), Expect = 1.8 Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 8/58 (13%) Query: 186 DALRAIARGI-----PMDRVLVETDSPYIVPVSCQGKRNEP-AYVVNTAKALAKEKDV 237 +R+IAR I +D ++V D ++ + RNE + KALAKE DV Sbjct: 290 AQIRSIARRIKRKKGGLDLIVV--DYIQLMAPTRGRDRNEELGGISRGLKALAKELDV 345 >gnl|CDD|182210 PRK10050, PRK10050, curli assembly protein CsgF; Provisional. Length = 138 Score = 28.0 bits (62), Expect = 2.3 Identities = 15/41 (36%), Positives = 23/41 (56%) Query: 216 GKRNEPAYVVNTAKALAKEKDVSYEDLMEETTKNALKLFSK 256 G N A+++N+A+A KD SY D T +AL F++ Sbjct: 33 GNPNNGAFLLNSAQAQNSYKDPSYNDDFGIETPSALDNFTQ 73 >gnl|CDD|179185 PRK00962, PRK00962, hypothetical protein; Provisional. Length = 165 Score = 28.1 bits (63), Expect = 2.4 Identities = 13/33 (39%), Positives = 15/33 (45%) Query: 220 EPAYVVNTAKALAKEKDVSYEDLMEETTKNALK 252 EP YV KA +E D+ LM E KN Sbjct: 66 EPDYVYKYIKAYNEENDLLVAKLMAEALKNKTN 98 >gnl|CDD|182623 PRK10657, PRK10657, isoaspartyl dipeptidase; Provisional. Length = 388 Score = 27.5 bits (62), Expect = 3.7 Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 11/57 (19%) Query: 160 SQKLADICLEL---GGYISFTGMITF-------PKYDAL-RAIARGIPMDRVLVETD 205 ++ L + LE GG I T +AL RA+ G+P+ RV + +D Sbjct: 229 NEPLFEQALEFAKKGGVIDLTTSDPDFLGEGEVAPAEALKRALEAGVPLSRVTLSSD 285 >gnl|CDD|180822 PRK07069, PRK07069, short chain dehydrogenase; Validated. Length = 251 Score = 27.0 bits (60), Expect = 4.7 Identities = 7/20 (35%), Positives = 13/20 (65%) Query: 181 TFPKYDALRAIARGIPMDRV 200 + +A R +ARG+P+ R+ Sbjct: 197 RLGEEEATRKLARGVPLGRL 216 >gnl|CDD|180765 PRK06939, PRK06939, 2-amino-3-ketobutyrate coenzyme A ligase; Provisional. Length = 397 Score = 27.1 bits (61), Expect = 4.7 Identities = 7/18 (38%), Positives = 12/18 (66%) Query: 82 LASHPRVVAIGETGLDRY 99 LA+HP ++A + LD + Sbjct: 55 LANHPELIAAAKAALDSH 72 >gnl|CDD|115893 pfam07268, EppA_BapA, Exported protein precursor (EppA/BapA). This family consists of a number of exported protein precursor (EppA and BapA) sequences which seem to be specific to Borrelia burgdorferi (Lyme disease spirochete). bapA gene sequences are quite stable but the encoded proteins do not provoke a strong immune response in most individuals. Conversely, EppA proteins are much more antigenic but are more variable in sequence. It is thought that BapA and EppA play important roles during the Borrelia burgdorferi infectious cycle. Length = 163 Score = 26.6 bits (59), Expect = 5.7 Identities = 10/27 (37%), Positives = 15/27 (55%) Query: 32 KMIAIAIKVKDFVPLIKLCQDYPSSIF 58 K+I +I + D + L + YP SIF Sbjct: 99 KIITDSIFLSDIDNINNLIEGYPDSIF 125 >gnl|CDD|161739 TIGR00167, cbbA, ketose-bisphosphate aldolases. fructose-bisphosphate and tagatose-bisphosphate aldolase. Length = 288 Score = 26.9 bits (60), Expect = 5.9 Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 11/60 (18%) Query: 89 VAIGETGLDRYHNAHTIEEQKVVFLRHIEASRITGIPLVIHSRSADDDMAAILQEEMKKG 148 AIG H + E + + F R E + +PLV+H S I EE+KK Sbjct: 177 AAIGNV-----HGVYKGEPKGLDFERLEEIQKYVNLPLVLHGGS------GIPDEEIKKA 225 >gnl|CDD|183417 PRK12299, obgE, GTPase CgtA; Reviewed. Length = 335 Score = 26.6 bits (60), Expect = 6.0 Identities = 11/40 (27%), Positives = 21/40 (52%), Gaps = 9/40 (22%) Query: 112 FLRHIEASRITGIPLVIH--SRSADDDMAA--ILQEEMKK 147 FL+HIE +R+ ++H A D + ++ E++K Sbjct: 230 FLKHIERTRL-----LLHLVDIEAVDPVEDYKTIRNELEK 264 >gnl|CDD|162608 TIGR01928, menC_lowGC/arch, o-succinylbenzoic acid (OSB) synthetase. This model describes the enzyme o-succinylbenzoic acid synthetase (menC) that is involved in one of the steps of the menaquinone biosynthesis pathway. It takes SHCHC and makes it into 2-succinylbenzoate. Included in this model are low GC gram positive bacteria and archaea. Also included in the seed and in the model are enzymes with the com-name of N-acylamino acid racemase (or the more general term, racemase / racemase family), which refers to the enzyme's industrial application as racemases, and not to its biological function as o-succinylbenzoic acid synthetase. Length = 324 Score = 26.7 bits (59), Expect = 6.1 Identities = 25/90 (27%), Positives = 33/90 (36%), Gaps = 6/90 (6%) Query: 96 LDRYHNAHTIEE----QKVVFLRHIEASRITGIPLVIHSRSADDDMAAI-LQEEMKKGPF 150 LDRY + IEE + L + IT I L S DD I L Sbjct: 195 LDRYQLLY-IEEPFKIDDLSMLDELAKGTITPICLDESITSLDDARNLIELGNVKVINIK 253 Query: 151 PFVIHCFSSSQKLADICLELGGYISFTGMI 180 P + + QK + C E G + GM+ Sbjct: 254 PGRLGGLTEVQKAIETCREHGAKVWIGGML 283 >gnl|CDD|148409 pfam06787, UPF0254, Uncharacterized protein family (UPF0254). Length = 160 Score = 26.6 bits (59), Expect = 6.4 Identities = 11/33 (33%), Positives = 15/33 (45%) Query: 220 EPAYVVNTAKALAKEKDVSYEDLMEETTKNALK 252 EP YV+ KA +E D+ +M E K Sbjct: 66 EPDYVIKYIKAYNEENDLKVAKMMAEAVKEKTN 98 >gnl|CDD|162204 TIGR01107, Na_K_ATPase_bet, Sodium Potassium ATPase beta subunit. This model describes the Na+/K+ ATPase beta subunit in eukaryotes. Na+/K+ ATPase(also called Sodium-Potassium pump) is intimately associated with the plasma membrane. It couples the energy released by the hydrolysis of ATP to extrude 3 Na+ ions, with the concomitant uptake of 2K+ ions, against their ionic gradients. Length = 289 Score = 26.2 bits (58), Expect = 8.3 Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 1/29 (3%) Query: 195 IPMDRVL-VETDSPYIVPVSCQGKRNEPA 222 I M+R++ + +P + PV C GKR+E Sbjct: 180 IKMNRIIGFKPKNPGVPPVDCTGKRDEDD 208 >gnl|CDD|182483 PRK10468, PRK10468, hydrogenase 2 small subunit; Provisional. Length = 371 Score = 26.3 bits (58), Expect = 9.2 Identities = 26/90 (28%), Positives = 39/90 (43%), Gaps = 18/90 (20%) Query: 63 THPCHAHEENEVLVDELVCLASHPRV-VAIGETGLDRYHNAHTIEEQKVVFLRHIEAS-- 119 THP E LV E + L H + A G + HNA +E+ K ++ ++ S Sbjct: 70 THP-----TVENLVLETISLEYHEVLSAAFGHQVEENKHNA--LEKYKGQYVLVVDGSIP 122 Query: 120 --------RITGIPLVIHSRSADDDMAAIL 141 + G P+V H R A + AAI+ Sbjct: 123 LKDNGIYCMVAGEPIVDHIRKAAEGAAAII 152 >gnl|CDD|179353 PRK01917, PRK01917, cation-binding hemerythrin HHE family protein; Provisional. Length = 139 Score = 26.3 bits (58), Expect = 9.2 Identities = 11/33 (33%), Positives = 14/33 (42%), Gaps = 3/33 (9%) Query: 66 CHAHEENEVLVDELVCLASHPRVVAIGETGLDR 98 CH E +EVL V +V G+ L R Sbjct: 71 CHRAEHDEVLA---VAADVREKVARDGDFELGR 100 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 0.323 0.137 0.409 Gapped Lambda K H 0.267 0.0761 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,319,627 Number of extensions: 278471 Number of successful extensions: 672 Number of sequences better than 10.0: 1 Number of HSP's gapped: 663 Number of HSP's successfully gapped: 32 Length of query: 262 Length of database: 5,994,473 Length adjustment: 92 Effective length of query: 170 Effective length of database: 4,006,537 Effective search space: 681111290 Effective search space used: 681111290 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 56 (25.3 bits)