RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780762|ref|YP_003065175.1| recombination protein RecR [Candidatus Liberibacter asiaticus str. psy62] (201 letters) >gnl|CDD|30702 COG0353, RecR, Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]. Length = 198 Score = 243 bits (623), Expect = 2e-65 Identities = 87/198 (43%), Positives = 129/198 (65%) Query: 4 KITGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSIC 63 + IE LI L ++PG GP+SA+R HL+++ + + LA+A+ + CS+C Sbjct: 1 MMYPPPIEKLIDALKKLPGVGPKSAQRLAFHLLQRDREDVERLAKALLEAKENIKHCSVC 60 Query: 64 GNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPE 123 GN+ +DPC IC D+ RD S + VVE+ D+ ALE++ LYHVLGG LSPLD IGPE Sbjct: 61 GNLTESDPCDICSDESRDKSQLCVVEEPKDVLALEKTGEFRGLYHVLGGLLSPLDGIGPE 120 Query: 124 DIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSEL 183 D+ I L++R+ I+E+I A + T+EG+ TA YI LK + +K+TRLA G+P+G EL Sbjct: 121 DLNIDELLQRLAEGSIKEVILATNPTVEGEATALYIARLLKPLGLKVTRLAQGVPVGGEL 180 Query: 184 DYLDDGTIFEAIRSRTVL 201 +Y+D+GT+ A+ R + Sbjct: 181 EYVDEGTLSRALEGRRKI 198 >gnl|CDD|173775 cd01025, TOPRIM_recR, TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved. Length = 112 Score = 156 bits (396), Expect = 4e-39 Identities = 54/109 (49%), Positives = 75/109 (68%) Query: 83 SVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIREL 142 + + VVE+ D+ A+E S LYHVLGG +SPLD IGP+D+ I L+ERI +++E+ Sbjct: 1 NKLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEV 60 Query: 143 IFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTI 191 I A + T+EG+ TA YI LK VK+TRLA GIP+G EL+Y D+ T+ Sbjct: 61 ILATNPTVEGEATALYIAKLLKDFGVKVTRLAQGIPVGGELEYADEITL 109 >gnl|CDD|145340 pfam02132, RecR, RecR protein. Length = 41 Score = 51.7 bits (125), Expect = 1e-07 Identities = 20/41 (48%), Positives = 25/41 (60%) Query: 41 QLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRD 81 + LAEA+ KV CS+CGN+ TDPC IC D +RD Sbjct: 1 EEAERLAEALLEAKEKVRHCSVCGNLTETDPCEICSDPRRD 41 >gnl|CDD|145089 pfam01751, Toprim, Toprim domain. This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks. Length = 89 Score = 43.1 bits (102), Expect = 5e-05 Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 7/95 (7%) Query: 83 SVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERI-EVKKIRE 141 V+I+VE +D AL ++ L G LS + ++ + ++ K E Sbjct: 1 KVLIIVEGPSDAIALAKAGGYKGNVVALLGHLS------DVIPLTKEQLKLLKKLAKKDE 54 Query: 142 LIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYG 176 +I A EG+ A +++ LK + K+ R+ Sbjct: 55 VILATDPDREGEAIAWKLLELLKPLGKKVRRIFLP 89 >gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. Length = 83 Score = 40.1 bits (94), Expect = 5e-04 Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 10/92 (10%) Query: 83 SVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIREL 142 +I+VE +D AL ++ LGG + L++R+ + +E+ Sbjct: 1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHALNK---------TRELLKRLL-GEAKEV 50 Query: 143 IFAISATIEGQTTAHYIMDKLKGIDVKITRLA 174 I A A EG+ A +++ LK + K+ RL Sbjct: 51 IIATDADREGEAIALRLLELLKSLGKKVRRLL 82 >gnl|CDD|145942 pfam03059, NAS, Nicotianamine synthase protein. Nicotianamine synthase EC:2.5.1.43 catalyses the trimerisation of S-adenosylmethionine to yield one molecule of nicotianamine. Nicotianamine has an important role in plant iron uptake mechanisms. Plants adopt two strategies (termed I and II) of iron acquisition. Strategy I is adopted by all higher plants except graminaceous plants, which adopt strategy II. In strategy I plants, the role of nicotianamine is not fully determined: possible roles include the formation of more stable complexes with ferrous than with ferric ion, which might serve as a sensor of the physiological status of iron within a plant, or which might be involved in the transport of iron. In strategy II (graminaceous) plants, nicotianamine is the key intermediate (and nicotianamine synthase the key enzyme) in the synthesis of the mugineic family (the only known family in plants) of phytosiderophores. Phytosiderophores are iron chelators whose secretion by the roots is greatly increased in instances of iron deficiency. Length = 277 Score = 30.4 bits (69), Expect = 0.35 Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 14/80 (17%) Query: 87 VVEDVADLWA-------LERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKI 139 +VE + DL+A L S VNAL+ L + P P I + L I+ +I Sbjct: 9 LVEKILDLYAAISKLESLSPSPDVNALFTQLVTTCIP-----PSPIDVTKLGPEIQ--EI 61 Query: 140 RELIFAISATIEGQTTAHYI 159 R L+ + + EG +HY Sbjct: 62 RSLLIRLCSEAEGLLESHYS 81 >gnl|CDD|33999 COG4277, COG4277, Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]. Length = 404 Score = 28.0 bits (62), Expect = 1.8 Identities = 10/16 (62%), Positives = 12/16 (75%) Query: 15 KILARIPGFGPRSARR 30 K L R+PG G +SARR Sbjct: 330 KELLRVPGIGVKSARR 345 >gnl|CDD|146710 pfam04216, FdhE, Protein involved in formate dehydrogenase formation. The function of these proteins is unknown. They may possibly be involved in the formation of formate dehydrogenase. Length = 287 Score = 27.7 bits (62), Expect = 2.0 Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 24/64 (37%) Query: 60 CSICGN--------VDTTDP------CAIC------IDQQRDASVIIVVEDVA----DLW 95 C+ CG+ ++ +P C C +DQ++D + V +D+A DL Sbjct: 212 CTNCGSTKGLAYWSLEEGEPGVRAETCDTCHSYLKILDQEKDPDLEPVADDLASLALDLL 271 Query: 96 ALER 99 A E+ Sbjct: 272 AREK 275 >gnl|CDD|30977 COG0632, RuvA, Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]. Length = 201 Score = 27.5 bits (61), Expect = 2.4 Identities = 12/31 (38%), Positives = 17/31 (54%) Query: 14 IKILARIPGFGPRSARRATLHLVKKKEQLLG 44 +K L++IPG G ++A R L L K L Sbjct: 107 VKALSKIPGIGKKTAERIVLELKGKLAAFLK 137 >gnl|CDD|36325 KOG1109, KOG1109, KOG1109, Vacuole membrane protein VMP1 [General function prediction only]. Length = 440 Score = 27.7 bits (61), Expect = 2.4 Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%) Query: 10 IENLIKILARIPGFGPRSARRATLHLVKKKEQLL 43 E + IL +PG G R R L++K++QLL Sbjct: 339 FEERVSILDTVPGLGHR-LREPFRWLLEKQKQLL 371 >gnl|CDD|31216 COG1012, PutA, NAD-dependent aldehyde dehydrogenases [Energy production and conversion]. Length = 472 Score = 27.6 bits (61), Expect = 2.6 Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 9/62 (14%) Query: 82 ASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRE 141 AS +IV E V D + +L +G L P +GP LI ++ ++ Sbjct: 279 ASRLIVHESVYDEFVERLVARAASL--KVGDPLDPSTDLGP-------LISEEQLDRVEG 329 Query: 142 LI 143 I Sbjct: 330 YI 331 >gnl|CDD|133359 cd04159, Arl10_like, Arl10-like subfamily. Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved. Length = 159 Score = 26.5 bits (59), Expect = 5.1 Identities = 28/80 (35%), Positives = 41/80 (51%), Gaps = 13/80 (16%) Query: 80 RDASVIIVVEDVADLWALERSKAVNALYHVLGG-SLS--PLDRIG-----PEDIGIQSLI 131 R + I+ V D AD ALE +K N L+ +L SL PL +G P + + LI Sbjct: 66 RGVNAIVYVVDAADRTALEAAK--NELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELI 123 Query: 132 ERIEVKKI--RE-LIFAISA 148 E++ +K I RE ++IS Sbjct: 124 EQMNLKSITDREVSCYSISC 143 >gnl|CDD|112424 pfam03606, DcuC, C4-dicarboxylate anaerobic carrier. Length = 456 Score = 26.5 bits (59), Expect = 5.8 Identities = 11/48 (22%), Positives = 24/48 (50%), Gaps = 1/48 (2%) Query: 109 VLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTA 156 V+GG ++R G D G+++L++ ++ + I ++A T Sbjct: 82 VVGGFAGVMNRTGAIDAGVKALVKPLKGIES-PYILLLAAYFSLGGTV 128 >gnl|CDD|133068 cd03856, M14_Nna1_like, Peptidase M14-like domain of Nna-1 (Nervous system Nuclear protein induced by Axotomy), also known as ATP/GTP binding protein (AGTPBP-1) and cytosolic carboxypeptidase (CCP), and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This subfamily includes the human AGTPBP-1 and AGBL -2, -3, -4, and -5, and the mouse Nna1/CCP-1 and CCP -2 through -6. Nna1-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Nna1 is widely expressed in the developing and adult nervous systems, including cerebellar Purkinje and granule neurons, miral cells of the olfactory bulb and retinal photoreceptors. Nna1 is also induced in axotomized motor neurons. Mutations in Nna1 cause Purkinje cell degeneration (pcd). The Nna1 CP domain is required to prevent the retinal photoreceptor loss and cerebellar ataxia phenotypes of pcd mice, and a functional zinc-binding domain is needed for Nna-1 to support neuron survival in these mice. Nna1-like proteins from the different phyla are highly diverse, but they all contain a characteristic N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal domain might act as a folding domain. Length = 269 Score = 25.9 bits (57), Expect = 7.4 Identities = 15/56 (26%), Positives = 23/56 (41%) Query: 105 ALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIM 160 AL L G+ L I G E + ++ IF I+ G+T A ++M Sbjct: 18 ALCESLQGNSCDLLTITSPPEGNDIKYEHLCSFANKKYIFLIARVHPGETNASWVM 73 >gnl|CDD|143443 cd07125, ALDH_PutA-P5CDH, Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA. The proline catabolic enzymes of the aldehyde dehydrogenase (ALDH) protein superfamily, proline dehydrogenase and Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH, (EC=1.5.1.12 )), catalyze the two-step oxidation of proline to glutamate; P5CDH catalyzes the oxidation of glutamate semialdehyde, utilizing NAD+ as the electron acceptor. In some bacteria, the two enzymes are fused into the bifunctional flavoenzyme, proline utilization A (PutA) These enzymes play important roles in cellular redox control, superoxide generation, and apoptosis. In certain prokaryotes such as Escherichia coli, PutA is also a transcriptional repressor of the proline utilization genes. Length = 518 Score = 25.6 bits (57), Expect = 8.8 Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 1/20 (5%) Query: 126 GIQSLIERIEVKKIRELIFA 145 GI S ER E++ RE + A Sbjct: 440 GIHSRDER-EIEYWRERVEA 458 >gnl|CDD|35317 KOG0094, KOG0094, KOG0094, GTPase Rab6/YPT6/Ryh1, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]. Length = 221 Score = 25.6 bits (56), Expect = 8.8 Identities = 8/22 (36%), Positives = 14/22 (63%) Query: 80 RDASVIIVVEDVADLWALERSK 101 RD+SV ++V D+ D + E + Sbjct: 93 RDSSVAVIVYDITDRNSFENTS 114 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 0.139 0.398 Gapped Lambda K H 0.267 0.0702 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,379,398 Number of extensions: 120659 Number of successful extensions: 285 Number of sequences better than 10.0: 1 Number of HSP's gapped: 284 Number of HSP's successfully gapped: 26 Length of query: 201 Length of database: 6,263,737 Length adjustment: 89 Effective length of query: 112 Effective length of database: 4,340,536 Effective search space: 486140032 Effective search space used: 486140032 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: 55 (25.0 bits)