RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780847|ref|YP_003065260.1| hypothetical protein CLIBASIA_03710 [Candidatus Liberibacter asiaticus str. psy62] (282 letters) >gnl|CDD|30992 COG0647, NagD, Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism]. Length = 269 Score = 195 bits (497), Expect = 1e-50 Identities = 79/248 (31%), Positives = 119/248 (47%), Gaps = 10/248 (4%) Query: 8 LRTILPYYDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVIS-Q 66 L ++ YD L D+ GVL+ G + +PG ALK + G VI TN+ S V++ + Sbjct: 1 LFDVMDKYDGFLFDLDGVLYRGNEAIPGAAEALKRLKAAGKPVIFLTNNSTRSREVVAAR 60 Query: 67 IQSLGSSSQFWDDIITSGDLTHHLLVEESHN--IFFIGPQRDYALLEKLNIKIVNEQHAE 124 + SLG DDI+TSGD T L ++ ++ IG + LE ++V+E+ Sbjct: 61 LSSLGGVDVTPDDIVTSGDATADYLAKQKPGKKVYVIGEEGLKEELEGAGFELVDEEEPA 120 Query: 125 TILCTGLYDDEKDKTEDYRMLLERFAHRHIPLICANPDIVANRGNKIIPCAGALALIYQQ 184 + + D E L A P I NPD+ + P AGA+A + +Q Sbjct: 121 RVDAVVVGLDRTLTYEKLAEALLAIAAG-APFIATNPDLTVPTERGLRPGAGAIAALLEQ 179 Query: 185 LNGIV-KMIGKPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDALYV 243 G +IGKP IYE A +K+ ++ +L +GD +DTDI GA +G+D L V Sbjct: 180 ATGREPTVIGKPSPAIYEAALEKL-----GLDRSEVLMVGDRLDTDILGAKAAGLDTLLV 234 Query: 244 SDGIHRHE 251 G+ E Sbjct: 235 LTGVSSAE 242 >gnl|CDD|38093 KOG2882, KOG2882, KOG2882, p-Nitrophenyl phosphatase [Inorganic ion transport and metabolism]. Length = 306 Score = 71.8 bits (176), Expect = 2e-13 Identities = 61/288 (21%), Positives = 109/288 (37%), Gaps = 32/288 (11%) Query: 8 LRTILPYYDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTN-SPRPSASVISQ 66 R +L +D + D GVL G+K +PG+ AL + G ++I TN S + + + Sbjct: 15 ARELLDSFDTFIFDCDGVLWLGEKPIPGSPEALNLLKSLGKQIIFVTNNSTKSREQYMKK 74 Query: 67 IQSLGSSSQFWDDIITSGD-----LTHHLLVEESHNIFFIGPQRDYALLEKLNIK----- 116 LG +S ++I +S L + ++ IG + L++ + Sbjct: 75 FAKLGFNSVKEENIFSSAYAIADYLKKRKPFGKK--VYVIGEEGIREELDEAGFEYFGGG 132 Query: 117 ---IVNEQHAETILCTGLYDDEK------DKTEDYRMLLERFAHRHIP---LICANPD-I 163 + +L GL D D+ Y L++ + P + N D Sbjct: 133 PDGKDTDGAKSFVLSIGLDPDVGAVVVGYDEHFSYPKLMKALNYLQNPGCLFLATNRDAT 192 Query: 164 VANRGNKIIPCAGALALIYQQLNG-IVKMIGKPHLPIYEMAFKKISSLCNSFNKKRILAI 222 IP AG+ + G ++GKP ++E +K + + R + Sbjct: 193 TPPTPGVEIPGAGSFVAAVKFATGRQPIVLGKPSTFMFEYLLEKFN-----IDPSRTCMV 247 Query: 223 GDGMDTDIKGALQSGIDALYVSDGIHRHEYLFNDNIDAQMLQNFFTKK 270 GD +DTDI G L V G+ E + D +M+ +++ Sbjct: 248 GDRLDTDILFGKNCGFKTLLVLSGVTTLEDILEAQGDNKMVPDYYADS 295 >gnl|CDD|119389 cd01427, HAD_like, Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.. Length = 139 Score = 53.1 bits (128), Expect = 8e-08 Identities = 31/115 (26%), Positives = 45/115 (39%), Gaps = 18/115 (15%) Query: 17 VILCDVWGVLHNGQKFL---------PGTIPALKEARENGLKVILFTNSPRPSASVISQI 67 +L D+ G L + + + PG ALKE +E G+K+ L TN R V+ + Sbjct: 1 AVLFDLDGTLLDSEPGIAEIEELELYPGVKEALKELKEKGIKLALATNKSR--REVLELL 58 Query: 68 QSLGSSSQFWDDIITSGDLT----HHLLVEESHNIFFIGPQRD--YALLEKLNIK 116 + LG F D +ITS L P D A L+ L + Sbjct: 59 EELGLDDYF-DPVITSNGAAIYYPKEGLFLGGGPFDIGKPNPDKLLAALKLLGVD 112 >gnl|CDD|38250 KOG3040, KOG3040, KOG3040, Predicted sugar phosphatase (HAD superfamily) [General function prediction only]. Length = 262 Score = 51.8 bits (124), Expect = 2e-07 Identities = 57/235 (24%), Positives = 93/235 (39%), Gaps = 16/235 (6%) Query: 18 ILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPS-ASVISQIQSLGSSSQF 76 +L D+ G LH +PG + ALK R+ +KV TN+ + S ++ ++Q LG Sbjct: 10 VLLDLSGTLHIEDAAVPGAVEALKRLRDQHVKVKFVTNTTKESKRNLHERLQRLGFDVS- 68 Query: 77 WDDIITSGDLTHHLLVEESHNIFFIGPQRDYALLEKLNIKIVNEQHAETILCTGLYDDEK 136 ++I TS L E + I D AL + I + L + ++ Sbjct: 69 EEEIFTSLPAARQYLEENQLRPYLI--VDDDALEDFDGIDTSDPNCVVIGLAPEGFSYQR 126 Query: 137 DKTEDYRMLLERFAHRHIPLICANPDIVANR--GNKIIPCAGALALIYQQLNGIVKMIGK 194 +R+LLE LI R G + P AL Y ++GK Sbjct: 127 -LNRAFRVLLEMKKP---LLIAIGKGRYYKRVDGLCLGPGPFVAALEYAT-GCEATVVGK 181 Query: 195 PHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDALYVSDGIHR 249 P +E A + + + + + IGD ++ D+ GA G+ + V G R Sbjct: 182 PSPFFFESALQALG-----VDPEEAVMIGDDLNDDVGGAQACGMRGILVKTGKFR 231 >gnl|CDD|31215 COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]. Length = 229 Score = 38.3 bits (88), Expect = 0.002 Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 5/53 (9%) Query: 194 KPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDALYVSDG 246 KP I+E A +K+ + L +GD ++ DI GA G+ ++++ G Sbjct: 154 KPDPEIFEYALEKLG-----VPPEEALFVGDSLENDILGARALGMKTVWINRG 201 >gnl|CDD|30907 COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]. Length = 264 Score = 35.5 bits (81), Expect = 0.018 Identities = 42/207 (20%), Positives = 70/207 (33%), Gaps = 40/207 (19%) Query: 14 YYDVILCDVWG-VLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSL-- 70 ++ D+ G +L + + P T AL RE G+KV+L T RP V+S ++ L Sbjct: 2 MIKLLAFDLDGTLLDSNKTISPETKEALARLREKGVKVVLATG--RPLPDVLSILEELGL 59 Query: 71 --------GSSSQFWDDIITSGDLTHHL------LVEESHNIFFIGPQRDYALLEK---- 112 G+ +++ L+ L+E+ I + D L K Sbjct: 60 DGPLITFNGALIYNGGELLFQKPLSREDVEELLELLEDFQGIALVLYTDDGIYLTKKRGT 119 Query: 113 ----------LNIKIVNEQHAETILCTGLYDDEKDKTEDYRMLLERFAHRHIPLICANP- 161 L+ E L D + E L +RF + + + P Sbjct: 120 FAEARIGFANLSPVGREAAELEDNKIIALDKDHEILEELVEALRKRFPDLGLTVSSSGPI 179 Query: 162 --DIVANRGNKIIPCAGALALIYQQLN 186 DI +K AL + + L Sbjct: 180 SLDITPKGVSK----GYALQRLAKLLG 202 >gnl|CDD|144342 pfam00702, Hydrolase, haloacid dehalogenase-like hydrolase. This family are structurally different from the alpha/ beta hydrolase family (pfam00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of (S)-2-haloacid dehalogenase from Pseudomonas sp. CBS3. The rest of the fold is composed of the core alpha/beta domain. Length = 190 Score = 35.3 bits (81), Expect = 0.020 Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 3/57 (5%) Query: 33 LPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQFWDDIITSGDLTHH 89 PG ALK +E G+KV + TN R +A + + L +D I+ S D+ Sbjct: 99 YPGAREALKALKERGIKVAILTNGDRANAEAVLEALGLAD---LFDVIVDSDDVGPV 152 Score = 31.5 bits (71), Expect = 0.29 Identities = 36/222 (16%), Positives = 65/222 (29%), Gaps = 38/222 (17%) Query: 15 YDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSS 74 ++ D G L +G+ + I L + + LG Sbjct: 1 IKAVVFDKDGTLTDGEPPIAEAIVEAAAELGLPLL-----------LPLEEVEKLLGRGV 49 Query: 75 QFWDDIITSGDLTHHLLVEESHNIFFIGPQRDYALLEKLNIKIVNEQHAETILCTGLYDD 134 + + I+ G LT LL+E + AL ++ I Sbjct: 50 EGIERILLEGGLTAELLLELEGELAAGKTAVLVALDGEVLGLIA---------------- 93 Query: 135 EKDKT-EDYRMLLERFAHRHIPLICA--NPDIVANRGNKIIPCAGALALIYQQLNGIVKM 191 DK R L+ R I + A + + A +I + Sbjct: 94 LADKLYPGAREALKALKERGIKVAILTNGDRANAEAVLEALGLADLFDVIV---DSDDVG 150 Query: 192 IGKPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGA 233 KP I+ A +++ + +L +GDG++ A Sbjct: 151 PVKPKPEIFLKALERLG-----VKPEEVLMVGDGVNDAPALA 187 >gnl|CDD|30982 COG0637, COG0637, Predicted phosphatase/phosphohexomutase [General function prediction only]. Length = 221 Score = 33.9 bits (77), Expect = 0.045 Identities = 15/64 (23%), Positives = 32/64 (50%), Gaps = 3/64 (4%) Query: 26 LHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQFWDDIITSGD 85 G K +PG + L++ + G+ + + ++SPR +A + L ++D I+T+ D Sbjct: 81 ELEGLKPIPGVVELLEQLKARGIPLAVASSSPRRAAERVLARLGL---LDYFDVIVTADD 137 Query: 86 LTHH 89 + Sbjct: 138 VARG 141 >gnl|CDD|38295 KOG3085, KOG3085, KOG3085, Predicted hydrolase (HAD superfamily) [General function prediction only]. Length = 237 Score = 34.2 bits (78), Expect = 0.045 Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 5/62 (8%) Query: 194 KPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDALYVSDGIHRHEYL 253 KP I+++A +++ + + IGD ++ D +GA G A+ V + I + L Sbjct: 168 KPDPRIFQLALERLGV-----KPEECVHIGDLLENDYEGARNLGWHAILVDNSITALKEL 222 Query: 254 FN 255 Sbjct: 223 EY 224 >gnl|CDD|36831 KOG1618, KOG1618, KOG1618, Predicted phosphatase [General function prediction only]. Length = 389 Score = 31.5 bits (71), Expect = 0.27 Identities = 26/106 (24%), Positives = 45/106 (42%), Gaps = 12/106 (11%) Query: 153 HIPLICANPDIV---ANRGNKIIPCAGALAL--IYQQLNGI---VKMIGKPHLPIYEMA- 203 HIP+ +N D++ + + A L L IYQ+L G +GKP Y+ A Sbjct: 222 HIPIYASNMDLLWMAEYKLPRFGHGAFRLCLESIYQKLTGKPLRYTTLGKPTKLTYDYAE 281 Query: 204 ---FKKISSLCNSFNKKRILAIGDGMDTDIKGALQSGIDALYVSDG 246 ++ + K++ +GD +D++GA A + G Sbjct: 282 DVLRRQAKRRGGAAPIKKLYMVGDNPMSDVRGANLFHQYAPELGAG 327 >gnl|CDD|107313 cd06318, PBP1_ABC_sugar_binding_like_9, Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Length = 282 Score = 31.3 bits (71), Expect = 0.34 Identities = 12/35 (34%), Positives = 22/35 (62%) Query: 35 GTIPALKEARENGLKVILFTNSPRPSASVISQIQS 69 G +PA+ A+ G+ V++ +S A V++Q+QS Sbjct: 68 GLVPAVAAAKAAGVPVVVVDSSINLEAGVVTQVQS 102 >gnl|CDD|36583 KOG1369, KOG1369, KOG1369, Hexokinase [Carbohydrate transport and metabolism]. Length = 474 Score = 31.0 bits (70), Expect = 0.35 Identities = 27/185 (14%), Positives = 56/185 (30%), Gaps = 27/185 (14%) Query: 2 TKEITSLRTILPYYDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSA 61 + I + + + WG + LP T V++ S P Sbjct: 250 MRNIEKVEGDAGRGPMCINTEWGAFGDNSLDLPRTE----------YDVVVDEESLNPGK 299 Query: 62 SVISQIQSLGSSSQFWDDIITSGDLTHHLLVEESHNIFFIGPQRDYALLEKLNIKIVNEQ 121 + ++ S G + G++ +L++ G Q K V+ Sbjct: 300 QLFEKMIS-G---------MYLGEIVRLVLLDLLEEGLLFGGQSTKLTPFIFETKYVSAI 349 Query: 122 HAETILCTGLYDDEKDKTEDYRMLLERFAHRHIPLICANPDIVANRGNKIIPCAGALALI 181 + TG + + + + R L+ D+V+ R ++ A +A I Sbjct: 350 EED---DTGALQETEKILDLLGLETTTTEDRK--LVREVCDVVSRRAARL--AAAGIAAI 402 Query: 182 YQQLN 186 + Sbjct: 403 LNKTG 407 >gnl|CDD|34199 COG4555, NatA, ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]. Length = 245 Score = 31.0 bits (70), Expect = 0.35 Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%) Query: 19 LCDVWGVLHNGQKFLPGTIPALKEA-RENGLKVILFT 54 LCD VLH G+ L G+I AL L+ I Sbjct: 199 LCDRVIVLHKGEVVLEGSIEALDARTVLRNLEEIFAF 235 >gnl|CDD|147746 pfam05761, 5_nucleotid, 5' nucleotidase family. This family of eukaryotic proteins includes 5' nucleotidase enzymes, such as purine 5'-nucleotidase EC:3.1.3.5. Length = 448 Score = 31.1 bits (71), Expect = 0.37 Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 3/36 (8%) Query: 25 VLHNGQKFL---PGTIPALKEARENGLKVILFTNSP 57 VL + +K++ P PAL RE+G K+ L TNSP Sbjct: 174 VLKDLEKYVIKDPELPPALSRLRESGKKLFLLTNSP 209 >gnl|CDD|88408 cd05013, SIS_RpiR, RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate.. Length = 139 Score = 30.3 bits (68), Expect = 0.65 Identities = 15/57 (26%), Positives = 24/57 (42%) Query: 36 TIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQFWDDIITSGDLTHHLLV 92 T+ A + A+E G KVI T+S + ++ I L SS + L + Sbjct: 76 TVEAAEIAKERGAKVIAITDSANSPLAKLADIVLLVSSEEGDFRSSAFSSRIAQLAL 132 >gnl|CDD|31923 COG1737, RpiR, Transcriptional regulators [Transcription]. Length = 281 Score = 29.9 bits (67), Expect = 0.77 Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 2/50 (4%) Query: 36 TIPALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQ--FWDDIITS 83 + A + A+E G KVI T+S + ++ I L ++ F+ I+S Sbjct: 193 IVEAAELAKERGAKVIAITDSADSPLAKLADIVLLVPVAEESFFRSPISS 242 >gnl|CDD|30590 COG0241, HisB, Histidinol phosphatase and related phosphatases [Amino acid transport and metabolism]. Length = 181 Score = 29.5 bits (66), Expect = 0.98 Identities = 11/25 (44%), Positives = 18/25 (72%) Query: 31 KFLPGTIPALKEARENGLKVILFTN 55 +F+PG IPAL + + G K+++ TN Sbjct: 31 QFIPGVIPALLKLQRAGYKLVVVTN 55 >gnl|CDD|73387 cd04725, OMP_decarboxylase_like, Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two domains: the orotate phosphoribosyltransferase (OPRTase) domain that catalyzes the transfer of phosphoribosyl 5'-pyrophosphate (PRPP) to orotate to form OMP, and the orotidine-5'-phosphate decarboxylase (ODCase) domain that decarboxylates OMP to form UMP.. Length = 216 Score = 28.6 bits (64), Expect = 1.9 Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 7/73 (9%) Query: 177 ALALIYQQLNGIVKMIGKPHLPIYEMAFKKISSLCNSFNKKRIL-----AIGDGMDTDIK 231 ALALI L V + K L ++E A +I L I + + + Sbjct: 13 ALALI-DALGPYVCAV-KVGLELFEAAGPEIVKELRELGFLVFLDLKLGDIPNTVAAAAE 70 Query: 232 GALQSGIDALYVS 244 L G DA+ V Sbjct: 71 ALLGLGADAVTVH 83 >gnl|CDD|100118 cd06167, LabA_like, LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.. Length = 149 Score = 28.4 bits (64), Expect = 2.1 Identities = 7/28 (25%), Positives = 14/28 (50%) Query: 37 IPALKEARENGLKVILFTNSPRPSASVI 64 +P ++ RE G +VI+ + S + Sbjct: 113 VPLVERLRELGKRVIVVGFEAKTSRELR 140 >gnl|CDD|173729 cd06617, PKc_MKK3_6, Catalytic domain of the dual-specificity Protein Kinases, MAP kinase kinases 3 and 6. Protein kinases (PKs), MAP kinase kinase 3 (MKK3) and MKK6 subfamily, catalytic (c) domain. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. The MKK3 and MKK6 subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. The mitogen-activated protein (MAP) kinase signaling pathways are important mediators of cellular responses to extracellular signals. The pathways involve a triple kinase core cascade comprising the MAP kinase (MAPK), which is phosphorylated and activated by a MAPK kinase (MAPKK or MKK), which itself is phosphorylated and activated by a MAPK kinase kinase (MAPKKK or MKKK). MKK3 and MKK6 are dual-specificity PKs that phosphorylate and activate their downstream target, p38 MAPK, on specific threonine and tyrosine residues. MKK3/6 plays roles in the regulation of cell cycle progression, cytokine- and stress-induced apoptosis, oncogenic transformation, and adult tissue regeneration. In addition, MKK6 plays a critical role in osteoclast survival in inflammatory disease while MKK3 is associated with tumor invasion, progression, and poor patient survival in glioma. Length = 283 Score = 28.2 bits (63), Expect = 2.5 Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 8/45 (17%) Query: 187 GIV-KMIGKPHLPIYEMAFKKISSLCNSFNKKRILAIGDGMDTDI 230 G+V KM P I MA K+I + NS +KR+L MD DI Sbjct: 15 GVVDKMRHVPTGTI--MAVKRIRATVNSQEQKRLL-----MDLDI 52 >gnl|CDD|88404 cd05007, SIS_Etherase, N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.. Length = 257 Score = 28.2 bits (63), Expect = 2.8 Identities = 9/34 (26%), Positives = 14/34 (41%) Query: 34 PGTIPALKEARENGLKVILFTNSPRPSASVISQI 67 P + AL+ AR G I +P ++ I Sbjct: 132 PYVLGALRYARARGALTIGIACNPGSPLLQLADI 165 >gnl|CDD|107305 cd06310, PBP1_ABC_sugar_binding_like_2, Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. Length = 273 Score = 28.0 bits (63), Expect = 3.3 Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 3/31 (9%) Query: 36 TIPALKEARENGLKVILF---TNSPRPSASV 63 +P LKEA++ G+ V+L NS + V Sbjct: 71 LVPPLKEAKDAGIPVVLIDSGLNSDIAVSFV 101 >gnl|CDD|88405 cd05008, SIS_GlmS_GlmD_1, SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) contains two SIS domains and catalyzes the deamination and isomerization of glucosamine-6-phosphate into fructose-6-phosphate with the release of ammonia; in presence of high ammonia concentration, GlmD can catalyze the reverse reaction.. Length = 126 Score = 27.8 bits (62), Expect = 3.6 Identities = 9/24 (37%), Positives = 13/24 (54%) Query: 34 PGTIPALKEARENGLKVILFTNSP 57 T+ AL+ A+E G K + TN Sbjct: 60 ADTLAALRLAKEKGAKTVAITNVV 83 >gnl|CDD|144475 pfam00890, FAD_binding_2, FAD binding domain. This family includes members that bind FAD. This family includes the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase. Length = 401 Score = 27.7 bits (62), Expect = 4.3 Identities = 17/65 (26%), Positives = 21/65 (32%), Gaps = 13/65 (20%) Query: 42 EARENGLKVILFTNSPR-PSASVISQ---------IQSLGSSS---QFWDDIITSGDLTH 88 EA E GLKV + A+ S Q G S D + +L Sbjct: 17 EAAEAGLKVAVVEKGQPFGGATAWSSGGIDALGTPPQGAGIDSPDLHPTDTLKGLDELAD 76 Query: 89 HLLVE 93 H VE Sbjct: 77 HPYVE 81 >gnl|CDD|30798 COG0449, GlmS, Glucosamine 6-phosphate synthetase, contains amidotransferase and phosphosugar isomerase domains [Cell envelope biogenesis, outer membrane]. Length = 597 Score = 27.5 bits (61), Expect = 4.5 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 6/58 (10%) Query: 84 GDLTH--HLLVEESHNIFFIGPQRDYALLEKL--NIKIVNEQHAETILCTGLYDDEKD 137 G+L H L++E+ + I P+ D L EK NI+ V + + I+ D +D Sbjct: 491 GELKHGPIALIDENTPVIAIAPKPD--LFEKTKSNIQEVRARGGKIIVIADEGDVAED 546 Score = 27.1 bits (60), Expect = 5.1 Identities = 10/22 (45%), Positives = 14/22 (63%) Query: 36 TIPALKEARENGLKVILFTNSP 57 T+ AL+ A+E G K + TN P Sbjct: 346 TLAALRLAKEQGAKTLAITNVP 367 >gnl|CDD|107388 cd06393, PBP1_iGluR_Kainate_GluR5_7, N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR5-7 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR5-7 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMAP receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined. Length = 384 Score = 27.3 bits (60), Expect = 4.6 Identities = 14/49 (28%), Positives = 27/49 (55%) Query: 38 PALKEARENGLKVILFTNSPRPSASVISQIQSLGSSSQFWDDIITSGDL 86 P LKE + I+F S + +A ++ Q ++G ++++ I T+ DL Sbjct: 183 PLLKEMKRGREFRIIFDCSHQMAAQILKQAMAMGMMTEYYHFIFTTLDL 231 >gnl|CDD|107297 cd06302, PBP1_LsrB_Quorum_Sensing, Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily. LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling. Length = 298 Score = 27.2 bits (61), Expect = 4.8 Identities = 9/14 (64%), Positives = 12/14 (85%) Query: 38 PALKEARENGLKVI 51 P LK+ARE G+KV+ Sbjct: 72 PVLKKAREAGIKVV 85 >gnl|CDD|32362 COG2179, COG2179, Predicted hydrolase of the HAD superfamily [General function prediction only]. Length = 175 Score = 27.1 bits (60), Expect = 5.1 Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 9/68 (13%) Query: 214 FNKKRILAIGDGMDTDIKGALQSGIDALYV-----SDGIHRHEYLFNDNIDAQMLQNFFT 268 + ++ +GD + TD+ G ++G+ + V DG N + ++L+ Sbjct: 108 LPPEEVVMVGDQLFTDVLGGNRAGMRTILVEPLVAPDGWITK---INRWRERRVLKK-LG 163 Query: 269 KKNLYPHW 276 KK HW Sbjct: 164 KKYGPIHW 171 >gnl|CDD|30475 COG0126, Pgk, 3-phosphoglycerate kinase [Carbohydrate transport and metabolism]. Length = 395 Score = 27.0 bits (60), Expect = 5.7 Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 13/56 (23%) Query: 37 IPALKEARENGLKVILFT-----------NSPRPSASVISQIQSLGSSSQFWDDII 81 +P +K E G KV+L + S P A +S++ LG +F DD + Sbjct: 42 LPTIKYLLEKGAKVVLLSHLGRPKEYSDKTSLEPVAKRLSEL--LGKEVKFVDDCV 95 >gnl|CDD|144433 pfam00834, Ribul_P_3_epim, Ribulose-phosphate 3 epimerase family. This enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate. Length = 201 Score = 26.9 bits (60), Expect = 6.2 Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 7/43 (16%) Query: 10 TILPYYDVILCDVWGVL-------HNGQKFLPGTIPALKEARE 45 T L + +L D+ VL GQ F+P +P +++ R+ Sbjct: 116 TPLDAIEYLLDDLDLVLLMSVNPGFGGQSFIPSVLPKIRKVRK 158 >gnl|CDD|133291 cd01891, TypA_BipA, TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella typhimurium after exposure to bactericidal/permeability-inducing protein (a cationic antimicrobial protein produced by neutrophils), and has since been identified in E. coli as well. The properties thus far described for BipA are related to its role in the process of pathogenesis by enteropathogenic E. coli. It appears to be involved in the regulation of several processes important for infection, including rearrangements of the cytoskeleton of the host, bacterial resistance to host defense peptides, flagellum-mediated cell motility, and expression of K5 capsular genes. It has been proposed that BipA may utilize a novel mechanism to regulate the expression of target genes. In addition, BipA from enteropathogenic E. coli has been shown to be phosphorylated on a tyrosine residue, while BipA from Salmonella and from E. coli K12 strains is not phosphorylated under the conditions assayed. The phosphorylation apparently modifies the rate of nucleotide hydrolysis, with the phosphorylated form showing greatly increased GTPase activity. Length = 194 Score = 26.7 bits (60), Expect = 6.8 Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 4/42 (9%) Query: 33 LPGTIPALKEARENGLKVILFTNS-PRPSAS---VISQIQSL 70 +P T LK+A E GLK I+ N RP A V+ ++ L Sbjct: 103 MPQTRFVLKKALELGLKPIVVINKIDRPDARPEEVVDEVFDL 144 >gnl|CDD|32049 COG1864, NUC1, DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism]. Length = 281 Score = 26.5 bits (58), Expect = 7.5 Identities = 7/36 (19%), Positives = 15/36 (41%) Query: 104 QRDYALLEKLNIKIVNEQHAETILCTGLYDDEKDKT 139 ++ + LE + + + I+ TG Y + D Sbjct: 157 RKIWLELEDYCRNLARKYGSVVIVFTGPYFRKDDTF 192 >gnl|CDD|36000 KOG0781, KOG0781, KOG0781, Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]. Length = 587 Score = 26.5 bits (58), Expect = 7.6 Identities = 29/118 (24%), Positives = 47/118 (39%), Gaps = 17/118 (14%) Query: 15 YDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVILFTNSPRPSASVISQIQSL---- 70 +DV+L D G +HN + K + N +ILF + Q++ Sbjct: 467 FDVVLIDTAGRMHNNAPLMT---SLAKLIKVNKPDLILFVGEALVGNDSVDQLKKFNRAL 523 Query: 71 --GSSSQFWDDII-----TSGDLTHHLL--VEESHN-IFFIGPQRDYALLEKLNIKIV 118 S+ + D I+ T D + V + I F+G + Y+ L KLN+K V Sbjct: 524 ADHSTPRLIDGILLTKFDTVDDKVGAAVSMVYITGKPILFVGVGQTYSDLRKLNVKAV 581 >gnl|CDD|119353 cd02874, GH18_CFLE_spore_hydrolase, Cortical fragment-lytic enzyme (CFLE) is a peptidoglycan hydrolase involved in bacterial endospore germination. CFLE is expressed as an inactive preprotein (called SleB) in the forespore compartment of sporulating cells. SleB translocates across the forespore inner membrane and is deposited as a mature enzyme in the cortex layer of the spore. As part of a sensory mechanism capable of initiating germination, CFLE degrades a spore-specific peptidoglycan constituent called muramic-acid delta-lactam that comprises the outer cortex. CFLE has a C-terminal glycosyl hydrolase family 18 (GH18) catalytic domain as well as two N-terminal LysM peptidoglycan-binding domains. In addition to SleB, this family includes YaaH, YdhD, and YvbX from Bacillus subtilis.. Length = 313 Score = 26.8 bits (60), Expect = 7.6 Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 1/52 (1%) Query: 5 ITSLRTILPYYDVILCDVWGVLHNGQKFLPGTIPALKEARENGLKVIL-FTN 55 SLR PY I +GV +G ++ A+ G+K +L TN Sbjct: 16 YESLRANAPYLTYIAPFWYGVDADGTLTGLPDERLIEAAKRRGVKPLLVITN 67 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 0.322 0.140 0.425 Gapped Lambda K H 0.267 0.0760 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,549,850 Number of extensions: 187343 Number of successful extensions: 590 Number of sequences better than 10.0: 1 Number of HSP's gapped: 581 Number of HSP's successfully gapped: 46 Length of query: 282 Length of database: 6,263,737 Length adjustment: 93 Effective length of query: 189 Effective length of database: 4,254,100 Effective search space: 804024900 Effective search space used: 804024900 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 (25.7 bits)