RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780583|ref|YP_003064996.1| glyoxalase II [Candidatus Liberibacter asiaticus str. psy62] (256 letters) >gnl|CDD|36031 KOG0813, KOG0813, KOG0813, Glyoxylase [General function prediction only]. Length = 265 Score = 180 bits (458), Expect = 3e-46 Identities = 89/253 (35%), Positives = 127/253 (50%), Gaps = 9/253 (3%) Query: 13 DNFCILIH-NHKYRLTAAID---APDTYIISKMLREKGWFLTHIFNTHHHIDHTRANLNL 68 DN+ L+ K +D K L ++ LT I THHH DH+ N ++ Sbjct: 12 DNYMYLLGDGDKTIDADLVDPAEPEYVIPSLKKLDDENRRLTAILTTHHHYDHSGGNEDI 71 Query: 69 KKFFNCTIFGPLEESSKIPGIDHGLSDGDTFDFGSHPIKIIATPGHTIGHICYHF---MN 125 K+ I +IPGI GL DG+T G ++ + TPGHT GHICY+ Sbjct: 72 KREIPYDIKVIGGADDRIPGITRGLKDGETVTVGGLEVRCLHTPGHTAGHICYYVTESTG 131 Query: 126 DHFLCVGDTLFSLGCGRIFEDSYAEMFESLEKIKSFSDKTHIYFGHEYTENNAYFALSCD 185 + + GDTLF GCGR FE + +M SL ++ + D T IY GHEYT++N FA + Sbjct: 132 ERAIFTGDTLFGAGCGRFFEGTAEQMDSSLNELIALPDDTRIYPGHEYTKSNLKFARYVE 191 Query: 186 PHNLELQKYCSKVKSMRSQNLYTN-PSTISLEKKVNPFLRIENTSLRKNLNM-ENASNLA 243 P N Q+ + RS+ T PST+ EK NPF+R++ ++K L + E A + Sbjct: 192 PRNEVEQEKLDWLVERRSKEKPTMVPSTLGEEKLYNPFMRLKKEKVQKALGLTETADRIV 251 Query: 244 VFTELRIRKNQSK 256 V +LR KN+ Sbjct: 252 VMGKLRELKNRFS 264 >gnl|CDD|30837 COG0491, GloB, Zn-dependent hydrolases, including glyoxylases [General function prediction only]. Length = 252 Score = 93.4 bits (230), Expect = 6e-20 Identities = 59/257 (22%), Positives = 92/257 (35%), Gaps = 49/257 (19%) Query: 1 MTSLNIAISLYHDNFCILIHNHKYRLT---AAIDAPDTYIISKMLREKGWFLTHIFNTHH 57 +T+ I + N L+ + + + D + + L G + I TH Sbjct: 12 ITAFPIGVGPLSGNSVYLLVDGEGGAVLIDTGLGDADAEALLEALAALGLDVDAILLTHG 71 Query: 58 HIDHTRANLNLKKFFNC-TIFGPLEESSKIPG-------------------IDHGLSDGD 97 H DH LK+ F + P E + L DGD Sbjct: 72 HFDHIGGAAVLKEAFGAAPVIAPAEVPLLLREEILRKAGVTAEAYAAPGASPLRALEDGD 131 Query: 98 TFDFGSHPIKIIATPGHTIGHICYHFMNDHFLCVGDTLFS--LGCGR--IFEDSYAEMFE 153 D G ++++ TPGHT GHI + + L GDTLF+ G GR + A++ Sbjct: 132 ELDLGGLELEVLHTPGHTPGHIVFLLEDGGVLFTGDTLFAGDTGVGRLDLPGGDAAQLLA 191 Query: 154 SLEKIKSFS-DKTHIYFGH---EYTENNAYFALSCDPHNLELQKYCSKVKSMRSQNLYTN 209 SL ++ T + GH EY AL+ L Sbjct: 192 SLRRLLLLLLPDTLVLPGHGPDEYDPAARALALTAPRL------------------LEVA 233 Query: 210 PSTISLEKKVNPFLRIE 226 +T+ E+++NPFLR+ Sbjct: 234 ETTLGDERRLNPFLRLF 250 >gnl|CDD|36032 KOG0814, KOG0814, KOG0814, Glyoxylase [General function prediction only]. Length = 237 Score = 70.4 bits (172), Expect = 4e-13 Identities = 56/200 (28%), Positives = 83/200 (41%), Gaps = 12/200 (6%) Query: 15 FCILIHNHKYRLTAAIDAPDTYII--SKMLREKGWFLTHIFNTHHHIDHTRANLNLKKFF 72 + L+ +HK ID + ++++++ G L + NTH H DH LK Sbjct: 22 YTYLLGDHKTGKAVIIDPVLETVSRDAQLIKDLGLDLIYALNTHVHADHITGTGLLKTLL 81 Query: 73 NCTIFGPLEESSKIPG--IDHGLSDGDTFDFGSHPIKIIATPGHTIGHICYHFMNDHFLC 130 G S G D L DGD + G +++ ATPGHT G + Y + Sbjct: 82 P----GCKSVISSASGAKADLHLEDGDIIEIGGLKLEVRATPGHTNGCVTYVEHDLRMAF 137 Query: 131 VGDTLFSLGCGR--IFEDSYAEMFESL-EKIKSFSDKTHIYFGHEYTENNAYFALSCDPH 187 GD L GCGR + A ++ES+ KI + + IY H+Y Sbjct: 138 TGDALLIRGCGRTDFQQGCPASLYESVHSKIFTLPEDYLIYPAHDYKGFLVSTVWEEKNL 197 Query: 188 NLELQKYCSK-VKSMRSQNL 206 N L K + VK M++ NL Sbjct: 198 NPRLTKSKEEFVKIMKNLNL 217 >gnl|CDD|144377 pfam00753, Lactamase_B, Metallo-beta-lactamase superfamily. Length = 148 Score = 62.4 bits (151), Expect = 1e-10 Identities = 27/126 (21%), Positives = 40/126 (31%), Gaps = 16/126 (12%) Query: 28 AAIDAPDTYIISKMLREKGWFLTHIFNTHHHIDHTRANLNLKKFFNCTIFGPLEES---- 83 + A D ++ L + I TH H DH LK+ + E++ Sbjct: 22 TGLGADDALLLLAALGLDPKDIDAIILTHAHADHIGGLPELKEATPAPVVAAPEDAAALL 81 Query: 84 ------------SKIPGIDHGLSDGDTFDFGSHPIKIIATPGHTIGHICYHFMNDHFLCV 131 + D L GD G + + PGH GH+ + L Sbjct: 82 RLGLDDAELRKLVDVLPPDVDLEGGDGILGGGTLLFVTPHPGHGPGHVVVYLPGGKVLFT 141 Query: 132 GDTLFS 137 GD LF Sbjct: 142 GDLLFG 147 >gnl|CDD|30775 COG0426, FpaA, Uncharacterized flavoproteins [Energy production and conversion]. Length = 388 Score = 33.7 bits (77), Expect = 0.047 Identities = 26/118 (22%), Positives = 41/118 (34%), Gaps = 9/118 (7%) Query: 49 LTHIFNTHHHIDHTRA-NLNLKKFFNCTIFGP------LEESSKIPGIDHGLSDGDTFDF 101 + +I H DH+ + L+ N I L+ P + GDT D Sbjct: 73 IDYIIVNHTEPDHSGSLPELLELAPNAKIICSKLAARFLKGFYHDPEWFKIVKTGDTLDL 132 Query: 102 GSHPIKIIATPG-HTIGHICYHFMNDHFLCVGDTLFSLGCG-RIFEDSYAEMFESLEK 157 G H +K I P H + + D L D + C F++ E+ + K Sbjct: 133 GGHTLKFIPAPFLHWPDTMFTYDPEDKILFSCDAFGAHVCDDYRFDEDIEELLPDMRK 190 >gnl|CDD|111553 pfam02667, SCFA_trans, Short chain fatty acid transporter. This family consists of two sequences annotated as short chain fatty acid transporters, however, there are no references giving details of experimental characterisation of this function. Length = 453 Score = 30.6 bits (69), Expect = 0.48 Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 1/36 (2%) Query: 102 GSHPIKIIATPGHTIGHICYHFMNDHFLCVGDTLFS 137 GS P+ + ATP + + HI + + +T+FS Sbjct: 156 GSMPL-LAATPNNPLKHIFVELFGRETIPLNETIFS 190 >gnl|CDD|31519 COG1328, NrdD, Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]. Length = 700 Score = 30.3 bits (68), Expect = 0.51 Identities = 16/89 (17%), Positives = 34/89 (38%), Gaps = 11/89 (12%) Query: 145 EDSYAEMFESLEKIKSFSDKTHIYFGHEYT------ENNA-YFALSCDPHNLELQKYCSK 197 E++ + +E I+ ++DK G ++ E+ A FA ++ Sbjct: 507 EEAKKFGIKIVEYIREYADKWKKETGLRWSVYQTPAESLADRFARL----DIFEFGEYKV 562 Query: 198 VKSMRSQNLYTNPSTISLEKKVNPFLRIE 226 V+ + YTN + ++ V +I Sbjct: 563 VRGDTDKPYYTNSFHVPVDADVTLGEKIR 591 >gnl|CDD|153084 cd01675, RNR_III, Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit which contains the active and allosteric sites. Length = 555 Score = 28.8 bits (65), Expect = 1.5 Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 9/75 (12%) Query: 155 LEKIKSFSDKTHIYFGHEYT--ENNAY-FALSCDPHNLELQKYCSKVKSMRSQNLYTNPS 211 E+ F ++T + + E T E+ AY FA + +KY + + + YTN Sbjct: 400 RERADEFKEETGLLYSVEATPAESLAYRFA------KKDRKKYGDIIPGVTDKPYYTNSF 453 Query: 212 TISLEKKVNPFLRIE 226 + + + ++PF +I+ Sbjct: 454 HVPVYEDIDPFEKID 468 >gnl|CDD|146396 pfam03735, ENT, ENT domain. This presumed domain is named after Emsy N Terminus (ENT). Emsy is a protein that is amplified in breast cancer and interacts with BRCA2. The N terminus of this protein is found to be similar to other vertebrate and plant proteins of unknown function. This domain has a completely conserved histidine residue that may be functionally important. Length = 74 Score = 28.0 bits (63), Expect = 2.5 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 11/57 (19%) Query: 187 HNLELQKYCSKVKSMRSQNLYTNPSTISLEKKVNPFLRIENTSLRKNLNMENASNLA 243 H LEL+ Y + +++ R+Q +S EK+ L T LRK L + + + Sbjct: 6 HRLELEAYAAVLRAFRAQG-----DALSWEKEE--LL----TELRKELRISDEEHRE 51 >gnl|CDD|133286 cd01886, EF-G, Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group contains both eukaryotic and bacterial members. Length = 270 Score = 27.8 bits (63), Expect = 2.6 Identities = 9/17 (52%), Positives = 10/17 (58%) Query: 98 TFDFGSHPIKIIATPGH 114 T + H I II TPGH Sbjct: 58 TCFWKDHRINIIDTPGH 74 >gnl|CDD|31428 COG1235, PhnP, Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]. Length = 269 Score = 27.4 bits (60), Expect = 4.4 Identities = 11/43 (25%), Positives = 19/43 (44%) Query: 35 TYIISKMLREKGWFLTHIFNTHHHIDHTRANLNLKKFFNCTIF 77 + + LR L I TH H DH + +L++ + I+ Sbjct: 49 PDLRDQGLRLGVSDLDAILLTHEHSDHIQGLDDLRRAYTLPIY 91 >gnl|CDD|38842 KOG3636, KOG3636, KOG3636, Uncharacterized conserved protein, contains TBC and Rhodanese domains [General function prediction only]. Length = 669 Score = 26.6 bits (58), Expect = 7.3 Identities = 27/100 (27%), Positives = 42/100 (42%), Gaps = 13/100 (13%) Query: 132 GDTLFSLGCGRIFEDSYAEMFES--LEKIKSFSD-------KTHIYFGHEYTE----NNA 178 G+ L +G GR ED+Y M + L+K K + K H YFG + + +NA Sbjct: 384 GEHLCFMGSGRDEEDNYMNMVIAMFLQKNKLYVSFVQGGYKKLHDYFGDQMADCIEDHNA 443 Query: 179 YFALSCDPHNLELQKYCSKVKSMRSQNLYTNPSTISLEKK 218 L C HN + K S S + + +++ K Sbjct: 444 RKCLVCQQHNAQQTKSAPLKTSTPSSTDLFSKFSAAMKSK 483 >gnl|CDD|32402 COG2220, COG2220, Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]. Length = 258 Score = 26.3 bits (57), Expect = 8.1 Identities = 21/110 (19%), Positives = 31/110 (28%), Gaps = 26/110 (23%) Query: 49 LTHIFNTHHHIDHTRANLNLKKFFN--CTIFGPLEESSKIPGID--------HGLSDGDT 98 + +I TH H DH + N + P + I H L GD Sbjct: 53 IDYILITHDHYDHLDDETLIALRTNKAPVVVVP--LGAGDLLIRDGVEAERVHELGWGDV 110 Query: 99 FDFG--------SHPIKIIATPGHTI----GHICYHFMND--HFLCVGDT 134 + G ++ + PG I + Y GDT Sbjct: 111 IELGDLEITAVPAYHVSARHLPGRGIRPTGLWVGYVIETPGGRVYHAGDT 160 >gnl|CDD|31427 COG1234, ElaC, Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]. Length = 292 Score = 26.2 bits (57), Expect = 8.4 Identities = 7/13 (53%), Positives = 8/13 (61%) Query: 49 LTHIFNTHHHIDH 61 + IF TH H DH Sbjct: 54 IDAIFITHLHGDH 66 >gnl|CDD|133430 cd05294, LDH-like_MDH_nadp, A lactate dehydrogenases-like structure with malate dehydrogenase enzymatic activity. The LDH-like MDH proteins have a lactate dehyhydrogenase-like (LDH-like) structure and malate dehydrogenase (MDH) enzymatic activity. This subgroup is composed of some archaeal LDH-like MDHs that prefer NADP(H) rather than NAD(H) as a cofactor. One member, MJ0490 from Methanococcus jannaschii, has been observed to form dimers and tetramers during crystalization, although it is believed to exist primarilly as a tetramer in solution. In addition to its MDH activity, MJ0490 also possesses fructose-1,6-bisphosphate-activated LDH activity. Members of this subgroup have a higher sequence similarity to LDHs than to other MDHs. LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)- binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenase, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. Length = 309 Score = 26.2 bits (58), Expect = 8.5 Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 10/61 (16%) Query: 23 KYRLTAAIDAPDTYII----------SKMLREKGWFLTHIFNTHHHIDHTRANLNLKKFF 72 KY A APDT I+ K L+E G+ +F H+D R + + K F Sbjct: 103 KYAKQIAEFAPDTKILVVTNPVDVMTYKALKESGFDKNRVFGLGTHLDSLRFKVAIAKHF 162 Query: 73 N 73 N Sbjct: 163 N 163 >gnl|CDD|133434 cd05298, GH4_GlvA_pagL_like, Glycoside Hydrolases Family 4; GlvA- and pagL-like glycosidases. Bacillus subtilis GlvA and Clostridium acetobutylicum pagL are 6-phospho-alpha-glucosidase, catalyzing the hydrolysis of alpha-glucopyranoside bonds to release glucose from oligosaccharides. The substrate specificities of other members of this subgroup are unknown. Some bacteria simultaneously translocate and phosphorylate disaccharides via the phosphoenolpyruvate-dependent phosphotransferase system (PEP_PTS). After translocation, these phospho-disaccharides may be hydrolyzed by the GH4 glycoside hydrolases, which include 6-phospho-beta-glucosidases, 6-phospho-alpha-glucosidases, alpha-glucosidases/alpha-glucuronidases (only from Thermotoga), and alpha-galactosidases. Members of this subfamily are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. Length = 437 Score = 26.1 bits (58), Expect = 8.8 Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 14/58 (24%) Query: 56 HHHIDHTRANLNL----KKFFNCTIFGPLEESSKIPGIDHGLSDGDTFDFGSHPIKII 109 H + ++TRAN + K+ F EE KI I+ G ++G TF H I+ Sbjct: 273 HSNPNYTRANEVMDGREKRVF--------EECRKI--IETGTAEGSTFHVDVHGEYIV 320 >gnl|CDD|146543 pfam03962, Mnd1, Mnd1 family. This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair. Length = 188 Score = 26.0 bits (58), Expect = 8.9 Identities = 8/21 (38%), Positives = 11/21 (52%), Gaps = 1/21 (4%) Query: 185 DPHNL-ELQKYCSKVKSMRSQ 204 + L EL+K KVK + S Sbjct: 10 TFYTLKELEKLAPKVKGISSM 30 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 0.323 0.137 0.422 Gapped Lambda K H 0.267 0.0716 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,143,677 Number of extensions: 165359 Number of successful extensions: 415 Number of sequences better than 10.0: 1 Number of HSP's gapped: 408 Number of HSP's successfully gapped: 21 Length of query: 256 Length of database: 6,263,737 Length adjustment: 92 Effective length of query: 164 Effective length of database: 4,275,709 Effective search space: 701216276 Effective search space used: 701216276 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 (22.0 bits) S2: 56 (25.4 bits)