RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780905|ref|YP_003065318.1| glutamate racemase [Candidatus Liberibacter asiaticus str. psy62] (271 letters) >gnl|CDD|31139 COG0796, MurI, Glutamate racemase [Cell envelope biogenesis, outer membrane]. Length = 269 Score = 216 bits (552), Expect = 5e-57 Identities = 80/259 (30%), Positives = 127/259 (49%), Gaps = 8/259 (3%) Query: 13 QNSILIFDSGIGGLIVLQKMRFLMPEYHFIYVADDVGFPYGNWEDHALKKRLMFLFSDIL 72 Q I +FDSG+GGL VL+++R +P+ IYV D FPYG + +++R + + +L Sbjct: 5 QPPIGVFDSGVGGLSVLREIRRQLPDEDIIYVGDTARFPYGEKSEEEIRERTLEIVDFLL 64 Query: 73 DKYQPVLSVIACNTAFTLIKDELRSTFPSMAFLGAVPAIKQAAAYTQSGLISILSTPATL 132 ++ VIACNTA + ++LR F + +G +PAIK A A T++G I +++TPAT+ Sbjct: 65 ERG-IKALVIACNTASAVALEDLREKFD-IPVVGVIPAIKPAVALTRNGRIGVIATPATV 122 Query: 133 RRTYTSNLIHSYVSQCHIHLVSSMILASRVEEYACGIKIKEDEIKKEIEGCFIEKEGKRT 192 + +LI + C + ++ L VEE + ++ + Sbjct: 123 KSNAYRDLIARFAPDCEVESLACPELVPLVEEG----IRGGPVALEVLKEYLPPLQEAGP 178 Query: 193 DVIVLACTHYPLIVHVFRQLSPWPVDWLDNSDSIARRARCLLPRINTH--QTRVFDDHAL 250 D +VL CTHYPL+ +Q+ V +D+ ARR LL DH Sbjct: 179 DTLVLGCTHYPLLKPEIQQVLGEHVALIDSGAETARRLARLLSPEGLLAKGADGGPDHRF 238 Query: 251 FLSGKPDIAMRRLMQGFGL 269 F +G PD + L + GL Sbjct: 239 FTTGDPDEFEQLLKRWLGL 257 >gnl|CDD|144681 pfam01177, Asp_Glu_race, Asp/Glu/Hydantoin racemase. This family contains aspartate racemase, glutamate racemase, hydantoin racemase and arylmalonate decarboxylase. Length = 212 Score = 69.7 bits (171), Expect = 7e-13 Identities = 38/151 (25%), Positives = 65/151 (43%), Gaps = 9/151 (5%) Query: 81 VIACNTAFTLIKDELRSTFPSMAFLGAVPAIKQAAAYTQSGLISILSTPATLRRTYTSNL 140 VIACNTA L ELR + +G V A +A A + + +L+T T+ S L Sbjct: 69 VIACNTAHALA-GELREATD-IPVIGIVEAALKALALLGAKRVGVLATYGTI----VSGL 122 Query: 141 IHSYVSQCHIHLVSSMILASRVEEYACGIKIKEDEIKKEIEGCFIEKEGKRTDVIVLACT 200 +++ I +V+ I VE + E+ + + D ++L CT Sbjct: 123 YQELLAEAGIEVVAPAIRLGIVE--VLELGRIEEASVEALAAALERLAEDGADAVILGCT 180 Query: 201 HYPLIVHVFRQLSPW-PVDWLDNSDSIARRA 230 PL++ + L P V +D++ ++A Sbjct: 181 ELPLLLELIEALEPELGVPVIDSNQALAWAL 211 >gnl|CDD|173782 cd03362, TOPRIM_TopoIA_TopoIII, TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. Length = 151 Score = 29.5 bits (67), Expect = 1.1 Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 1/33 (3%) Query: 167 CGIKIKEDEIKKEIEGCFIEKEGKRTDVIVLAC 199 K+K D+ KK+ ++K KR D IV+A Sbjct: 75 APFKLKVDKGKKKQFK-VLKKLAKRADEIVIAT 106 >gnl|CDD|37659 KOG2448, KOG2448, KOG2448, Dihydroxy-acid dehydratase [Amino acid transport and metabolism]. Length = 596 Score = 28.8 bits (64), Expect = 1.5 Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 3/64 (4%) Query: 79 LSVIACNTAFTLIKDELRSTFPSMAFLGAVPAIKQAAAYTQSGLISILSTPATLRRTYTS 138 L IA + L D+ + + F+ +K + Y L I TP+ L+ Sbjct: 315 LIAIARSVGLELTLDDFQKVSDATPFIAD---LKPSGKYVMEDLHKIGGTPSVLKYLLEL 371 Query: 139 NLIH 142 L+ Sbjct: 372 GLMD 375 >gnl|CDD|173778 cd01028, TOPRIM_TopoIA, TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. Length = 142 Score = 26.8 bits (60), Expect = 6.9 Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 1/33 (3%) Query: 167 CGIKIKEDEIKKEIEGCFIEKEGKRTDVIVLAC 199 K KK+ ++K K+ D IVLA Sbjct: 67 FEPKYVVIPDKKKQLK-ALKKLAKKADEIVLAT 98 >gnl|CDD|29992 cd01126, TraG_VirD4, The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.. Length = 384 Score = 26.1 bits (57), Expect = 9.8 Identities = 23/93 (24%), Positives = 36/93 (38%), Gaps = 10/93 (10%) Query: 67 LFSDILDKYQPVLSVIACNTAFTLIKDELRSTFPSMAFLGAVPAIKQAAAYTQSGLIS-- 124 LF+ I+D+ L + DE FP LG + ++A A I Sbjct: 244 LFNQIIDRLGRSLPGPEEKYRVLFLLDE----FPL---LGKLETFEKAIAIMAGYGIRLL 296 Query: 125 -ILSTPATLRRTYTSNLIHSYVSQCHIHLVSSM 156 I + A L TY S++S C + L ++ Sbjct: 297 LIFQSLAQLEGTYGDAGASSFLSNCGVRLFFAV 329 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 0.326 0.140 0.426 Gapped Lambda K H 0.267 0.0684 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,423,856 Number of extensions: 184016 Number of successful extensions: 528 Number of sequences better than 10.0: 1 Number of HSP's gapped: 523 Number of HSP's successfully gapped: 12 Length of query: 271 Length of database: 6,263,737 Length adjustment: 92 Effective length of query: 179 Effective length of database: 4,275,709 Effective search space: 765351911 Effective search space used: 765351911 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 57 (25.8 bits)