RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780847|ref|YP_003065260.1| hypothetical protein CLIBASIA_03710 [Candidatus Liberibacter asiaticus str. psy62] (282 letters) >gnl|CDD|162373 TIGR01460, HAD-SF-IIA, Haloacid Dehalogenase Superfamily Class (subfamily) IIA. Many of the genes in this subfamily have been annotated as "pNPPase" "4-nitrophenyl phosphatase" or "NPPase". These all refer to the same activity versus a common lab test compound used to determine phosphatase activity. There is no evidence that this activity is physiologically relevant. Length = 236 Score = 146 bits (370), Expect = 7e-36 Identities = 70/240 (29%), Positives = 102/240 (42%), Gaps = 15/240 (6%) Query: 18 ILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSP-RPSASVISQIQSLGSSSQF 76 L D+ GVL G K +PG AL R G V+ TN+ R ++ SL Sbjct: 1 FLFDIDGVLWLGHKPIPGAAEALNRLRAKGKPVVFLTNNSSRSEEDYAEKLSSLLGVDVS 60 Query: 77 WDDIITSGDLTHHLLVEESHN--IFFIGPQRDYALLEKLNIK-----IVNEQHAETILCT 129 D IITSG +T LL + ++ IG LE L + ++ E I Sbjct: 61 PDQIITSGSVTKDLLRQRFEGEKVYVIGVGELRESLEGLGFRNDFFDDIDHLAIEKIPAA 120 Query: 130 GLYDDEKDKTEDYRMLLERFAHR-HIPLICAN-PDIVANRGNKIIPCAGALALIYQQLNG 187 + + D + D +P I AN D+V + P AGA+A ++L+G Sbjct: 121 VIVGEPSDFSYDELAKAAYLLAEGDVPFIAANRDDLVRLGDGRFRPGAGAIAAGIKELSG 180 Query: 188 IVKMI-GKPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDALYVSDG 246 + GKP IY A +L + ++R + +GD + TDI GA +G D L V G Sbjct: 181 REPTVVGKPSPAIYRAA----LNLLQARPERRDVMVGDNLRTDILGAKNAGFDTLLVLTG 236 >gnl|CDD|130526 TIGR01459, HAD-SF-IIA-hyp4, HAD-superfamily class IIA hydrolase, TIGR01459. This hypothetical equivalog is a member of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this equivalog are all gram negative and primarily alpha proteobacteria. Only one sequence hase been annotated as other than "hypothetical." That one, from Brucella, is annotated as related to NagD, but only by sequence similarity and should be treated with some skepticism. (See comments for Class IIA subfamily). Length = 242 Score = 136 bits (343), Expect = 7e-33 Identities = 78/239 (32%), Positives = 109/239 (45%), Gaps = 16/239 (6%) Query: 15 YDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSS 74 YDV L D+WGV+ +G PG + L + G V +NSPR S+ ++SLG ++ Sbjct: 8 YDVFLLDLWGVIIDGNHTYPGAVQNLNKIIAQGKPVYFVSNSPRNIFSLHKTLKSLGINA 67 Query: 75 QFWDDIITSGDLTHHLLVEESHNIFFIGPQRDYALLEKLNIKI----------VNEQHAE 124 + II+SG++ ++ ES F I Y L N I N+ +A Sbjct: 68 DLPEMIISSGEIA-VQMILESKKRFDIRNGIIYLLGHLENDIINLMQCYTTDDENKANAS 126 Query: 125 TILCTGLYDDEKDKTEDYRMLLERFAHRHIPLICANPDIVANRGNKIIPCAGALALIYQQ 184 I +++ D E + L R IP ICANPD N+ AG A + +Q Sbjct: 127 LITIYRSENEKLDLDE-FDELFAPIVARKIPNICANPDRGINQHGIYRYGAGYYAELIKQ 185 Query: 185 LNGIVKMIGKPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDALYV 243 L G V GKP Y F K C++ K R+L +GD TDI GA + GID V Sbjct: 186 LGGKVIYSGKP----YPAIFHKALKECSNIPKNRMLMVGDSFYTDILGANRLGIDTALV 240 >gnl|CDD|162369 TIGR01452, PGP_euk, phosphoglycolate/pyridoxal phosphate phosphatase family. This model is closely related to a family of bacterial sequences including the E. coli NagD and B. subtilus AraL genes which are characterized by the ability to hydrolyze para-nitrophenylphosphate (pNPPases or NPPases). The chlamydomonas PGPase does not catalyze this reaction and so presumably these two groups have different functions and substrate specificities. Many of the genes in this alignment have been annotated as pNPPases due to this association. Length = 279 Score = 53.3 bits (128), Expect = 7e-08 Identities = 60/290 (20%), Positives = 105/290 (36%), Gaps = 40/290 (13%) Query: 16 DVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPS-ASVISQIQSLG--- 71 + D GVL G++ +PG L G + TN+ S A + LG Sbjct: 3 QGFIFDCDGVLWLGERVVPGAPELLDRLARAGKAALFVTNNSTKSRAEYALKFARLGFNG 62 Query: 72 SSSQFWDDIITSGDLTHHLLVEESHNIFFIGPQRDYALLEKLNIKIVNE----QHAETIL 127 + Q + + + L + ++ IG + A L+ I++ + A Sbjct: 63 LAEQLFSSALCAARLLRQP-PDAPKAVYVIGEEGLRAELDAAGIRLAGDPSAGDGAAPRG 121 Query: 128 CTGLYDDEK---------DKTEDYRMLLERFAHRHIP---LICANPDIVANRGN-KIIPC 174 E+ D+ Y L E AH P + N D + P Sbjct: 122 SGAFMKLEENVGAVVVGYDEHFSYAKLREACAHLREPGCLFVATNRDPWHPLSDGSRTPG 181 Query: 175 AGALALIYQQLNG---IVKMIGKPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIK 231 G+L + +G +V +GKP F+ I+ + + R L +GD ++TDI Sbjct: 182 TGSLVAAIETASGRQPLV--VGKPSPY----MFECITENFS-IDPARTLMVGDRLETDIL 234 Query: 232 GALQSGIDALYVSDGIHRHEYLFNDNIDAQMLQNFFTKKNLYPHWWIQQL 281 + G+ + V G+ R E +AQ + +L P + ++ L Sbjct: 235 FGHRCGMTTVLVLSGVSRLE-------EAQEYLA-AGQHDLVPDYVVESL 276 >gnl|CDD|130524 TIGR01457, HAD-SF-IIA-hyp2, HAD-superfamily subfamily IIA hydrolase, TIGR01457. This hypothetical equivalog is a member of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this equivalog are all gram positive (low-GC) bacteria. Sequences found in this model are annotated variously as related to NagD or 4-nitrophenyl phosphatase, and this hypothetical equivalog, of all of those within the Class IIA subfamily, is most closely related to the E. coli NagD enzyme and the PGP_euk equivalog (TIGR01452). However, there is presently no evidence that this hypothetical equivalog has the same function of either those. Length = 249 Score = 52.9 bits (127), Expect = 8e-08 Identities = 53/255 (20%), Positives = 109/255 (42%), Gaps = 29/255 (11%) Query: 15 YDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTN----SPRPSASVISQIQSL 70 Y L D+ G ++ G++ +P + E ++ + + TN +P A +++ Sbjct: 1 YKGYLIDLDGTMYKGKERIPEAETFVHELQKRDIPYLFVTNNSTRTPESVAEMLASFDIP 60 Query: 71 GSSSQFWDDIITSGDLTHHLLVEESHNIFFIGPQRDYALLEKLNIKIVNEQHAETILCTG 130 + + + + D + L +E++ ++ IG + +++ E+ ++ G Sbjct: 61 ATLETVFTASMATADYMNDLKLEKT--VYVIGEEGLKEAIKEAGYVEDKEKPDYVVV--G 116 Query: 131 LYDDEKDKTEDYRMLLERFA------HRHIPLICANPDIVANRGNKIIPCAGALALIYQQ 184 L D+ DY E+FA + I N D+ ++P G+L + + Sbjct: 117 L-----DRQIDY----EKFATATLAIRKGAHFIGTNGDLAIPTERGLLPGNGSLITVLEV 167 Query: 185 LNGIVKM-IGKPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDALYV 243 G+ + IGKP+ I E A + + + ++ L +GD TDI+ + +GID L V Sbjct: 168 ATGVKPVYIGKPNAIIMEKAVEHLGT-----EREETLMVGDNYLTDIRAGIDAGIDTLLV 222 Query: 244 SDGIHRHEYLFNDNI 258 G+ + E + I Sbjct: 223 HTGVTKAEEVAGLPI 237 >gnl|CDD|182466 PRK10444, PRK10444, UMP phosphatase; Provisional. Length = 248 Score = 44.0 bits (104), Expect = 4e-05 Identities = 55/247 (22%), Positives = 101/247 (40%), Gaps = 45/247 (18%) Query: 18 ILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSA-SVISQIQSLG---SS 73 ++CD+ GVL + +PG L + GL ++L TN P + + ++ + G Sbjct: 4 VICDIDGVLMHDNVAVPGAAEFLHRILDKGLPLVLLTNYPSQTGQDLANRFATAGVDVPD 63 Query: 74 SQFWDDIITSGDLTHHLLVEESHNIFFIGPQRDYALLEKL-----NIKIVNEQH---AET 125 S F+ + + D +E + IG + AL+ +L I +N ET Sbjct: 64 SVFYTSAMATADFLRR---QEGKKAYVIG---EGALIHELYKAGFTITDINPDFVIVGET 117 Query: 126 ILCTGLYDDEKDKTEDYRMLLE--RFAHRHIPLICANPDIVANRGNKIIPCAGALALIYQ 183 ++ ++ M+ + F I NPD G P GAL + Sbjct: 118 ------------RSYNWDMMHKAAYFVANGARFIATNPD---THGRGFYPACGALCAGIE 162 Query: 184 QLNGIVKM---IGKPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDA 240 +++G + +GKP I A K+ + + + + +GD + TDI Q+G++ Sbjct: 163 KISG--RKPFYVGKPSPWIIRAALNKMQA-----HSEETVIVGDNLRTDILAGFQAGLET 215 Query: 241 LYVSDGI 247 + V G+ Sbjct: 216 ILVLSGV 222 >gnl|CDD|178475 PLN02887, PLN02887, hydrolase family protein. Length = 580 Score = 41.0 bits (96), Expect = 3e-04 Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 1/60 (1%) Query: 3 KEITSLRTILPYYDVILCDVWGVLHNGQKFLPGT-IPALKEARENGLKVILFTNSPRPSA 61 K+ SLR P + I CD+ G L N + + T ALKEA G+KV++ T RP+ Sbjct: 296 KKEGSLRFYKPKFSYIFCDMDGTLLNSKSQISETNAKALKEALSRGVKVVIATGKARPAV 355 >gnl|CDD|181865 PRK09449, PRK09449, dUMP phosphatase; Provisional. Length = 224 Score = 39.9 bits (94), Expect = 8e-04 Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 4/48 (8%) Query: 192 IGKPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGID 239 + KP + I++ A + ++ R+L +GD + +DI G + +GID Sbjct: 148 VAKPDVAIFDYAL----EQMGNPDRSRVLMVGDNLHSDILGGINAGID 191 >gnl|CDD|162787 TIGR02253, CTE7, HAD superfamily (subfamily IA) hydrolase, TIGR02253. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterized by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA (TIGR01549). Length = 221 Score = 39.3 bits (92), Expect = 0.001 Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 17/88 (19%) Query: 31 KFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSS--QFWDDIITSGDLTH 88 + PG L E RE+G ++ + T+ + Q + L F+D +ITS + Sbjct: 94 RVYPGVRDTLMELRESGYRLGIITDGLP-----VKQWEKLERLGVRDFFDAVITSEEEG- 147 Query: 89 HLLVEESHNIFFIGPQRDYALLEKLNIK 116 VE+ H F YA L++L +K Sbjct: 148 ---VEKPHPKIF------YAALKRLGVK 166 Score = 32.4 bits (74), Expect = 0.14 Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 9/48 (18%) Query: 193 GKPHLPIYEMAFKKISSLCNSFNKK--RILAIGDGMDTDIKGALQSGI 238 KPH I+ A K + +GD +D DIKGA G+ Sbjct: 149 EKPHPKIFYAA-------LKRLGVKPEEAVMVGDRLDKDIKGAKNLGM 189 >gnl|CDD|162395 TIGR01509, HAD-SF-IA-v3, haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED. HAD subfamilies caused by an overly broad single model. Length = 183 Score = 39.0 bits (91), Expect = 0.002 Identities = 25/59 (42%), Positives = 31/59 (52%), Gaps = 4/59 (6%) Query: 31 KFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQFWDDIITSGDLTHH 89 K LPG P L+ R G K+ L TNSPR A + +Q LG F D +I SGD+ Sbjct: 85 KPLPGVEPLLEALRARGKKLALLTNSPRDHAVL---VQELGLRDLF-DVVIFSGDVGRG 139 >gnl|CDD|162788 TIGR02254, YjjG/YfnB, HAD superfamily (subfamily IA) hydrolase, TIGR02254. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterized by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA (TIGR01549). Most likely, these enzymes are phosphatases. Length = 224 Score = 37.9 bits (88), Expect = 0.003 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 6/59 (10%) Query: 192 IGKPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDALYVSDGIHRH 250 I KP I+ A +++ F+K+ +L IGD + DIKG +G+D +++ H Sbjct: 150 IQKPDKEIFNYALERMPK----FSKEEVLMIGDSLTADIKGGQNAGLDTCWMN--PDMH 202 >gnl|CDD|182523 PRK10530, PRK10530, pyridoxal phosphate (PLP) phosphatase; Provisional. Length = 272 Score = 37.7 bits (88), Expect = 0.003 Identities = 19/41 (46%), Positives = 24/41 (58%), Gaps = 1/41 (2%) Query: 15 YDVILCDVWGVLHNGQK-FLPGTIPALKEARENGLKVILFT 54 Y VI D+ G L +K LP ++ AL ARE G KVI+ T Sbjct: 3 YRVIALDLDGTLLTPKKTILPESLEALARAREAGYKVIIVT 43 >gnl|CDD|162372 TIGR01458, HAD-SF-IIA-hyp3, HAD-superfamily subfamily IIA hydrolase, TIGR01458. This hypothetical equivalog is a member of the IIA subfamily (TIGR01460) of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. One sequence (GP|10716807) has been annotated as a "phospholysine phosphohistidine inorganic pyrophosphatase," probably in reference to studies on similarly described (but unsequenced) enzymes from bovine and rat tissues. However, the supporting information for this annotation has never been published. Length = 257 Score = 34.5 bits (79), Expect = 0.036 Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 6/81 (7%) Query: 18 ILCDVWGVLHN----GQKFLPGTIPALKEARENGLKVILFTNSPRPS-ASVISQIQSLGS 72 +L D+ GVL+ +PG+ A+K R +KV TN+ + S ++ ++Q LG Sbjct: 4 VLLDISGVLYISDAKSGVAVPGSQEAVKRLRGASVKVRFVTNTTKESKQDLLERLQRLGF 63 Query: 73 SSQFWDDIITSGDLTHHLLVE 93 D++ T LL E Sbjct: 64 DIS-EDEVFTPAPAARQLLEE 83 >gnl|CDD|182696 PRK10748, PRK10748, flavin mononucleotide phosphatase; Provisional. Length = 238 Score = 32.4 bits (74), Expect = 0.12 Identities = 10/29 (34%), Positives = 19/29 (65%) Query: 217 KRILAIGDGMDTDIKGALQSGIDALYVSD 245 IL +GD + TD+ GA++ G+ A +++ Sbjct: 181 GEILHVGDDLTTDVAGAIRCGMQACWINP 209 >gnl|CDD|161707 TIGR00099, Cof-subfamily, Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily. The members of this subfamily are restricted almost exclusively to bacteria (one sequences from S. pombe scores above trusted, while another is between trusted and noise). It is notable that no archaea are found in this group, the closest relations to the archaea found here being two Deinococcus sequences. Length = 256 Score = 31.9 bits (73), Expect = 0.19 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 3/56 (5%) Query: 17 VILCDVWG-VLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLG 71 +I D+ G +L++ P T AL + RE G+KV+L T RP V + ++ LG Sbjct: 1 LIFIDLDGTLLNDDHTISPSTKEALAKLREKGIKVVLATG--RPYKEVKNILKELG 54 >gnl|CDD|130231 TIGR01163, rpe, ribulose-phosphate 3-epimerase. This family consists of Ribulose-phosphate 3-epimerase, also known as pentose-5-phosphate 3-epimerase (PPE). PPE converts D-ribulose 5-phosphate into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle. It has been found in a wide range of bacteria, archebacteria, fungi and plants. Length = 210 Score = 31.9 bits (73), Expect = 0.19 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 12/57 (21%) Query: 5 ITSLRTILPYYDVILCDVWGVLHN----GQKFLPGTIPALKEAR----ENGLKVILF 53 + L +LP D++L + V N GQKF+P T+ ++E R ENGL +++ Sbjct: 117 LEFLEYVLPDVDLVL--LMSV--NPGFGGQKFIPDTLEKIREVRKMIDENGLSILIE 169 >gnl|CDD|162371 TIGR01456, CECR5, HAD-superfamily class IIA hydrolase, TIGR01456, CECR5. The Schizosaccharomyces pombe sequence (EGAD|138276) is annotated as "phosphatidyl synthase," however this is due entirely to a C-terminal region of the protein (outside the region of similarity of this model) which is highly homologous to a family of CDP-alcohol phosphatidyltransferases. (Thus, the annotation of GP|4226073 from C. elegans as similar to phosphatidyl synthase, is a mistake as this gene does not contain the C-terminal portion). The physical connection of the phosphatidyl synthase and the HAD-superfamily hydrolase domain in S. pombe may, however, be an important clue to the substrate for the hydrolases in this equivalog. Length = 321 Score = 31.4 bits (71), Expect = 0.27 Identities = 27/119 (22%), Positives = 45/119 (37%), Gaps = 18/119 (15%) Query: 147 ERFAHRHIPLICANPDIVANRGNKIIPCAG------ALALIYQQLNGI---VKMIGKPHL 197 E+ IP+ +N D++ K+ G L IY +LNG +GKP Sbjct: 178 EKSGKPSIPIYFSNQDLLWANEYKL-NRFGQGAFRLLLERIYLELNGKPLQYYTLGKPTK 236 Query: 198 PIYEMAFKKISSLCNSFNKKR--------ILAIGDGMDTDIKGALQSGIDALYVSDGIH 248 Y+ A + + + + +GD +DI GA G + V G++ Sbjct: 237 LTYDFAEDVLIDWEKRLSGTKPSTSPFHALYMVGDNPASDIIGAQNYGWFSCLVKTGVY 295 >gnl|CDD|178251 PLN02645, PLN02645, phosphoglycolate phosphatase. Length = 311 Score = 30.5 bits (69), Expect = 0.52 Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 2/40 (5%) Query: 210 LCNSFN--KKRILAIGDGMDTDIKGALQSGIDALYVSDGI 247 L N F K +I +GD +DTDI G L V G+ Sbjct: 239 LANKFGIEKSQICMVGDRLDTDILFGQNGGCKTLLVLSGV 278 Score = 30.1 bits (68), Expect = 0.59 Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 1/64 (1%) Query: 9 RTILPYYDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPS-ASVISQI 67 ++ + + D GV+ G K + G L R G K++ TN+ S A + Sbjct: 22 DELIDSVETFIFDCDGVIWKGDKLIEGVPETLDMLRSMGKKLVFVTNNSTKSRAQYGKKF 81 Query: 68 QSLG 71 +SLG Sbjct: 82 ESLG 85 >gnl|CDD|116866 pfam08282, Hydrolase_3, haloacid dehalogenase-like hydrolase. This family contains haloacid dehalogenase-like hydrolase enzymes. Length = 254 Score = 30.3 bits (69), Expect = 0.64 Identities = 47/227 (20%), Positives = 92/227 (40%), Gaps = 33/227 (14%) Query: 18 ILCDVWG-VLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQF 76 I D+ G +L++ +K T A+K+ +E G+KV++ T RP + ++ LG Sbjct: 1 IASDLDGTLLNSDKKISERTKEAIKKLQEKGIKVVIATG--RPYRGALPVLEELG----L 54 Query: 77 WDDIITS-GDLTHHLLVEESHNIFFIGPQRDYALLEKLNIKIVNEQHAETILCT--GLYD 133 +I G + E+ I + P ++++ I+ + E + +L T G Y Sbjct: 55 DLPVICFNGAYIYD----ENGKILYKNPI-SKEDVKEI-IEYLKENNLSILLYTDDGAY- 107 Query: 134 DEKDKTEDYRMLLERFAHRHIPLICANPDIVANRG-NKIIPCA-----GALALIYQQLNG 187 D +E + E + L+ + +++ + NKI+ L ++L G Sbjct: 108 ILNDVSEKI--VREERYVKSFVLVIDDFELLEDEDINKILIVTDPEDLDELEKELKELFG 165 Query: 188 IVKMIGKPHLPIYEMAFKKIS------SLCNSFN--KKRILAIGDGM 226 + I E+ K +S +L + ++A GDG Sbjct: 166 SLITITSSGPGYLEIMPKGVSKGTALKALAKHLGIDLEEVIAFGDGE 212 >gnl|CDD|180083 PRK05441, murQ, N-acetylmuramic acid-6-phosphate etherase; Reviewed. Length = 299 Score = 29.4 bits (67), Expect = 1.0 Identities = 12/34 (35%), Positives = 16/34 (47%) Query: 34 PGTIPALKEARENGLKVILFTNSPRPSASVISQI 67 P I AL+ ARE G I + +P S + I Sbjct: 145 PYVIGALEYARERGALTIGISCNPGSPLSKEADI 178 >gnl|CDD|183089 PRK11337, PRK11337, DNA-binding transcriptional repressor RpiR; Provisional. Length = 292 Score = 29.3 bits (66), Expect = 1.1 Identities = 30/107 (28%), Positives = 44/107 (41%), Gaps = 28/107 (26%) Query: 16 DVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQ 75 DV+L V H+G+ I A++ A++NG K+I TN S S I ++ Sbjct: 189 DVVL----VVSHSGRT--SDVIEAVELAKKNGAKIICITN------SYHSPI------AK 230 Query: 76 FWDDIITSGDLTHHLLVEESH------NI---FFIG-PQRDYALLEK 112 D +I S LL E + NI FF+ Q + E Sbjct: 231 LADYVICSTAQGSPLLGENAAARIAQLNILDAFFVSVAQLNIEQAEI 277 >gnl|CDD|162473 TIGR01662, HAD-SF-IIIA, HAD-superfamily hydrolase, subfamily IIIA. In the case of histidinol phosphatase and PNK-3'-phosphatase, this model represents a domain of a bifunctional system. In the histidinol phosphatase HisB, a C-terminal domain is an imidazoleglycerol-phosphate dehydratase which catalyzes a related step in histidine biosynthesis. In PNK-3'-phosphatase, N- and C-terminal domains constitute the polynucleotide kinase and DNA-binding components of the enzyme. Length = 132 Score = 29.3 bits (66), Expect = 1.2 Identities = 10/26 (38%), Positives = 13/26 (50%) Query: 31 KFLPGTIPALKEARENGLKVILFTNS 56 P AL E +E G KV++ TN Sbjct: 25 ILYPEVPDALAELKEAGYKVVIVTNQ 50 >gnl|CDD|182760 PRK10826, PRK10826, 2-deoxyglucose-6-phosphatase; Provisional. Length = 222 Score = 29.1 bits (66), Expect = 1.2 Identities = 11/25 (44%), Positives = 14/25 (56%) Query: 33 LPGTIPALKEARENGLKVILFTNSP 57 LPG AL + GLK+ L + SP Sbjct: 94 LPGVREALALCKAQGLKIGLASASP 118 >gnl|CDD|182512 PRK10518, PRK10518, alkaline phosphatase; Provisional. Length = 476 Score = 28.5 bits (64), Expect = 1.8 Identities = 20/44 (45%), Positives = 23/44 (52%), Gaps = 10/44 (22%) Query: 208 SSLCNSFNKKRILAIGDGM-DTDI-------KGA--LQSGIDAL 241 SL N K IL IGDGM D++I +GA GIDAL Sbjct: 62 DSLSNKPAKNVILLIGDGMGDSEITAARNYAEGAGGFFKGIDAL 105 >gnl|CDD|163226 TIGR03351, PhnX-like, phosphonatase-like hydrolase. This clade of sequences are the closest homologs to the PhnX enzyme, phosphonoacetaldehyde (Pald) hydrolase (phosphonatase, TIGR01422). This phosphonatase-like enzyme and PhnX itself are members of the haloacid dehalogenase (HAD) superfamily (pfam00702) having a a number of distinctive features that set them apart from typical HAD enzymes. The typical HAD N-terminal motif DxDx(T/V) here is DxAGT and the usual conserved lysine prior to the C-terminal motif is instead an arginine. Also distinctive of phosphonatase, and particular to its bi-catalytic mechanism is a conserved lysine in the variable "cap" domain. This lysine forms a Schiff base with the aldehyde of phosphonoacetaldehyde, providing, through the resulting positive charge, a polarization of the C-P bond necesary for cleavage as well as a route to the initial product of cleavage, an ene-amine. The conservation of these elements in this phosphonatase-like enzyme suggests that the substrate is also, like Pald, a 2-oxo-ethylphosphonate. Despite this, the genomic context of members of this family are quite distinct from PhnX, which is almost invariably associated with the 2-aminoethylphosphonate transaminase PhnW (TIGR02326), the source of the substrate Pald. Members of this clade are never associated with PhnW, but rather associate with families of FAD-dependent oxidoreductases related to deaminating amino acid oxidases (pfam01266) as well as zinc-dependent dehydrogenases (pfam00107). Notably, family members from Arthrobacter aurescens TC1 and Nocardia farcinica IFM 10152 are adjacent to the PhnCDE ABC cassette phosphonates transporter (GenProp0236) typically found in association with the phosphonates C-P lyase system (GenProp0232). These observations suggest two possibilities. First, the substrate for this enzyme family is also Pald, the non-association with PhnW not withstanding. Alternatively, the substrate is something very closely related such as hydroxyphosphonoacetaldehyde (Hpald). Hpald could come from oxidative deamination of 1-hydroxy-2-aminoethylphosphonate (HAEP) by the associated oxidase. HAEP would not be a substrate for PhnW due to its high specificity for AEP. HAEP has been shown to be a constituent of the sphingophosphonolipid of Bacteriovorax stolpii, and presumably has other natural sources. If Hpald is the substrate, the product would be glycoaldehyde (hydroxyacetaldehyde), and the associated alcohol dehydrogenase may serve to convert this to glycol. Length = 220 Score = 28.6 bits (64), Expect = 1.9 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 3/54 (5%) Query: 33 LPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLG-SSSQFWDDIITSGD 85 LPG A + R +G+KV L T R +A + ++ LG + D ++ D Sbjct: 89 LPGAEEAFRSLRSSGIKVALTTGFDRDTAERL--LEKLGWTVGDDVDAVVCPSD 140 >gnl|CDD|182991 PRK11142, PRK11142, ribokinase; Provisional. Length = 306 Score = 28.3 bits (64), Expect = 2.5 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 10/50 (20%) Query: 33 LPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQFWDDIIT 82 L + A K A+++G KVIL +P P+ + L DIIT Sbjct: 144 LETVLAAAKIAKQHGTKVIL---NPAPA-------RELPDELLALVDIIT 183 >gnl|CDD|162385 TIGR01484, HAD-SF-IIB, HAD-superfamily hydrolase, subfamily IIB. The IIB subfamily consists of Trehalose-6-phosphatase (TIGR00685), plant and cyanobacterial Sucrose-phosphatase and a closely related group of bacterial and archaeal sequences, eukaryotic phosphomannomutase (pfam03332), a large subfamily ("Cof-like hydrolases", TIGR00099) containing many closely related bacterial sequences, a hypothetical equivalog containing the E. coli YedP protein, as well as two small clusters containing sequences whose relationship to the other groups is unclear. Length = 204 Score = 28.1 bits (63), Expect = 2.6 Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 4/59 (6%) Query: 17 VILCDVWGVL--HNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSS 73 ++ D+ G L N + P TI AL+ RE G+KV+L T R A + ++ L Sbjct: 1 LLFFDLDGTLLDPNAHELSPETIEALERLREAGVKVVLVTG--RSLAEIKELLKQLPLP 57 >gnl|CDD|178528 PLN02940, PLN02940, riboflavin kinase. Length = 382 Score = 27.9 bits (62), Expect = 2.8 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 9/58 (15%) Query: 31 KFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQFWDD---IITSGD 85 K LPG +K + +G+ + L +NSPR + I++ S Q W + +I GD Sbjct: 93 KALPGANRLIKHLKSHGVPMALASNSPR------ANIEAKISCHQGWKESFSVIVGGD 144 >gnl|CDD|180145 PRK05581, PRK05581, ribulose-phosphate 3-epimerase; Validated. Length = 220 Score = 27.8 bits (63), Expect = 2.9 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 12/50 (24%) Query: 11 ILPYYDVILCDVWGVLHN----GQKFLPGTIPALKEAR----ENGLKVIL 52 +L D++L + V N GQKF+P + ++E R E GL +++ Sbjct: 128 VLDLLDLVL--LMSV--NPGFGGQKFIPEVLEKIRELRKLIDERGLDILI 173 >gnl|CDD|130205 TIGR01135, glmS, glucosamine--fructose-6-phosphate aminotransferase (isomerizing). The member from Methanococcus jannaschii contains an intein. Length = 607 Score = 28.0 bits (63), Expect = 2.9 Identities = 10/31 (32%), Positives = 15/31 (48%) Query: 36 TIPALKEARENGLKVILFTNSPRPSASVISQ 66 T+ AL+ A+E G K + N P + S Sbjct: 354 TLAALRLAKELGAKTLGICNVPGSTLVRESD 384 >gnl|CDD|162475 TIGR01668, YqeG_hyp_ppase, HAD superfamily (subfamily IIIA) phosphatase, TIGR01668. This family consists of sequences from fungi, plants, cyanobacteria, gram-positive bacteria and Deinococcus. There is presently no characterization of any sequence in this family. Length = 170 Score = 27.8 bits (62), Expect = 3.2 Identities = 8/38 (21%), Positives = 20/38 (52%) Query: 216 KKRILAIGDGMDTDIKGALQSGIDALYVSDGIHRHEYL 253 +++ +GD + TD+ G ++G + V +H ++ Sbjct: 108 SEQVAVVGDRLFTDVMGGNRNGSYTILVEPLVHPDQWF 145 >gnl|CDD|183060 PRK11259, solA, N-methyltryptophan oxidase; Provisional. Length = 376 Score = 27.9 bits (63), Expect = 3.2 Identities = 9/43 (20%), Positives = 14/43 (32%), Gaps = 1/43 (2%) Query: 115 IKIVNEQHAETILCTGLYDDEKDKTEDYRMLLERFAHRHIPLI 157 +KI + I D ED L F ++P + Sbjct: 261 LKIGKHNGGQEITSPDERDRFVTVAEDGAE-LRPFLRNYLPGV 302 >gnl|CDD|179153 PRK00884, PRK00884, Maf-like protein; Reviewed. Length = 194 Score = 28.0 bits (63), Expect = 3.2 Identities = 8/21 (38%), Positives = 12/21 (57%), Gaps = 3/21 (14%) Query: 143 RMLLERFAHRHIPLICANPDI 163 R LLE+ +P CA P++ Sbjct: 14 RALLEKL---QLPFECAAPEV 31 >gnl|CDD|178369 PLN02770, PLN02770, haloacid dehalogenase-like hydrolase family protein. Length = 248 Score = 27.5 bits (61), Expect = 3.8 Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 3/58 (5%) Query: 31 KFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQFWDDIITSGDLTH 88 K L G K + GLK TN+PR +A ++ I LG S F+ +I + H Sbjct: 108 KPLNGLYKLKKWIEDRGLKRAAVTNAPRENAELM--ISLLGLSD-FFQAVIIGSECEH 162 >gnl|CDD|184408 PRK13937, PRK13937, phosphoheptose isomerase; Provisional. Length = 188 Score = 27.5 bits (62), Expect = 4.4 Identities = 10/21 (47%), Positives = 14/21 (66%) Query: 34 PGTIPALKEARENGLKVILFT 54 P + AL++ARE G+K I T Sbjct: 120 PNVLAALEKARELGMKTIGLT 140 >gnl|CDD|185541 PTZ00292, PTZ00292, ribokinase; Provisional. Length = 326 Score = 27.4 bits (61), Expect = 4.8 Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%) Query: 33 LPGTIPALKEARENGLKVILFTNSPRPSASVISQI 67 L T+ ALKEA+E G + F +P P + + I Sbjct: 159 LETTLDALKEAKERGCYTV-FNPAPAPKLAEVEII 192 >gnl|CDD|177968 PLN02334, PLN02334, ribulose-phosphate 3-epimerase. Length = 229 Score = 27.3 bits (61), Expect = 4.8 Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 5/45 (11%) Query: 6 TSLRTILPYYDVILCDVWGVL-----HNGQKFLPGTIPALKEARE 45 T + + P + L D+ V+ GQ F+P + ++ R+ Sbjct: 126 TPVEAVEPVVEKGLVDMVLVMSVEPGFGGQSFIPSMMDKVRALRK 170 >gnl|CDD|129317 TIGR00213, GmhB_yaeD, D,D-heptose 1,7-bisphosphate phosphatase. This family of proteins formerly designated yaeD resembles the histidinol phosphatase domain of the bifunctional protein HisB. The member from E. coli has been characterized as D,D-heptose 1,7-bisphosphate phosphatase, GmhB, involved in inner core LPS assembly (PubMed:11751812). Length = 176 Score = 27.2 bits (60), Expect = 4.9 Identities = 10/25 (40%), Positives = 17/25 (68%) Query: 31 KFLPGTIPALKEARENGLKVILFTN 55 +F+ G I AL+E ++ G ++L TN Sbjct: 26 EFIDGVIDALRELKKMGYALVLVTN 50 >gnl|CDD|131685 TIGR02637, RhaS, rhamnose ABC transporter, rhamnose-binding protein. This sugar-binding component of ABC transporter complexes is found in rhamnose catabolism operon contexts. Mutation of this gene in Rhizobium leguminosarum abolishes rhamnose transport and prevents growth on rhamnose as a carbon source. Length = 302 Score = 27.1 bits (60), Expect = 5.8 Identities = 9/23 (39%), Positives = 16/23 (69%) Query: 37 IPALKEARENGLKVILFTNSPRP 59 +PALK+A + G+KV+ + + P Sbjct: 71 VPALKKAMKRGIKVVTWDSGVAP 93 >gnl|CDD|115244 pfam06574, FAD_syn, FAD synthetase. This family corresponds to the N terminal domain of the bifunctional enzyme riboflavin kinase / FAD synthetase. These enzymes have both ATP:riboflavin 5'-phospho transferase and ATP:FMN-adenylyltransferase activity. They catalyse the 5'-phosphorylation of riboflavin to FMN and the adenylylation of FMN to FAD. This domain is thought to have the flavin mononucleotide (FMN) adenylyltransferase activity. Length = 158 Score = 26.7 bits (60), Expect = 6.3 Identities = 9/22 (40%), Positives = 12/22 (54%) Query: 39 ALKEARENGLKVILFTNSPRPS 60 A + ARE GL ++ T P P Sbjct: 29 AKEIARELGLPSVVVTFEPHPR 50 >gnl|CDD|130561 TIGR01497, kdpB, K+-transporting ATPase, B subunit. One sequence is apparently mis-annotated in the primary literature, but properly annotated by TIGR. Length = 675 Score = 26.8 bits (59), Expect = 6.8 Identities = 11/45 (24%), Positives = 22/45 (48%) Query: 22 VWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVISQ 66 ++GV++ G + R+ G+K I+ T R +A+ I+ Sbjct: 437 IYGVIYLKDIVKGGIKERFAQLRKMGIKTIMITGDNRLTAAAIAA 481 >gnl|CDD|181350 PRK08279, PRK08279, long-chain-acyl-CoA synthetase; Validated. Length = 600 Score = 26.8 bits (60), Expect = 7.3 Identities = 6/13 (46%), Positives = 9/13 (69%) Query: 72 SSSQFWDDIITSG 84 S+S+FWDD+ Sbjct: 276 SASRFWDDVRRYR 288 >gnl|CDD|180171 PRK05627, PRK05627, bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed. Length = 305 Score = 26.7 bits (60), Expect = 7.4 Identities = 9/23 (39%), Positives = 12/23 (52%) Query: 39 ALKEARENGLKVILFTNSPRPSA 61 A + ARE GL ++ T P P Sbjct: 36 AREIARERGLPSVVMTFEPHPRE 58 >gnl|CDD|183990 PRK13351, PRK13351, elongation factor G; Reviewed. Length = 687 Score = 26.5 bits (59), Expect = 8.3 Identities = 10/36 (27%), Positives = 14/36 (38%), Gaps = 1/36 (2%) Query: 131 LYDDEKDKTEDYRMLLERFAHRHIPLICANP-DIVA 165 LY+ K E L ++ + A DIVA Sbjct: 338 LYNGTGGKREKVGRLFRLQGNKREEVDRAKAGDIVA 373 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 0.140 0.425 Gapped Lambda K H 0.267 0.0642 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,708,244 Number of extensions: 302344 Number of successful extensions: 731 Number of sequences better than 10.0: 1 Number of HSP's gapped: 718 Number of HSP's successfully gapped: 53 Length of query: 282 Length of database: 5,994,473 Length adjustment: 92 Effective length of query: 190 Effective length of database: 4,006,537 Effective search space: 761242030 Effective search space used: 761242030 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: 57 (25.9 bits)