RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780128|ref|YP_003064541.1| VRR-NUC domain-containing protein [Candidatus Liberibacter asiaticus str. psy62] (103 letters) >gnl|CDD|37354 KOG2143, KOG2143, KOG2143, Uncharacterized conserved protein [Function unknown]. Length = 854 Score = 33.1 bits (75), Expect = 0.017 Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 1/49 (2%) Query: 37 RRGCPDRLIITPNGG-LWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKV 84 R G PD + P +EVK P RLS +Q + L G RV+V Sbjct: 794 RSGFPDLTLWNPETKRFKLVEVKGPNDRLSEKQRLWLALLADSGIRVEV 842 >gnl|CDD|145010 pfam01642, MM_CoA_mutase, Methylmalonyl-CoA mutase. The enzyme methylmalonyl-CoA mutase is a member of a class of enzymes that uses coenzyme B12 (adenosylcobalamin) as a cofactor. The enzyme induces the formation of an adenosyl radical from the cofactor. This radical then initiates a free-radical rearrangement of its substrate, succinyl-CoA, to methylmalonyl-CoA. Length = 517 Score = 28.5 bits (64), Expect = 0.43 Identities = 10/43 (23%), Positives = 21/43 (48%), Gaps = 2/43 (4%) Query: 45 IITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVS 87 +I P GG +++E + T R++ + +E+ G K + Sbjct: 362 VIDPWGGSYYVE--ELTDRIAEEAWKLFQEIEEAGGMAKAIED 402 >gnl|CDD|32093 COG1909, COG1909, Uncharacterized protein conserved in archaea [Function unknown]. Length = 167 Score = 27.5 bits (61), Expect = 0.80 Identities = 12/36 (33%), Positives = 22/36 (61%) Query: 55 IEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEE 90 I+V+ P G ++ + + IE+ G+RV++ V EE Sbjct: 82 IKVRNPPGTITFELIKAIEKALEDGKRVRIFVDGEE 117 >gnl|CDD|146188 pfam03419, Peptidase_U4, Sporulation factor SpoIIGA. Length = 291 Score = 26.8 bits (60), Expect = 1.3 Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 2/34 (5%) Query: 41 PDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEE 74 PDR+ I IEV+K +S +++S E Sbjct: 250 PDRVKIEHEKE--KIEVRKVLIGISDEKLSSDGE 281 >gnl|CDD|146789 pfam04337, DUF480, Protein of unknown function, DUF480. This family consists of several proteins of uncharacterized function. Length = 148 Score = 26.4 bits (59), Expect = 1.7 Identities = 12/26 (46%), Positives = 16/26 (61%) Query: 74 ELRRRGQRVKVLVSMEEVDNFLEELA 99 ELR R +R+ + EV+ LEELA Sbjct: 107 ELRTRSERLHRFADVAEVEAVLEELA 132 >gnl|CDD|146579 pfam04019, DUF359, Protein of unknown function (DUF359). This family of archaebacterial proteins are about 170 amino acids in length. They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function. Length = 121 Score = 26.4 bits (59), Expect = 2.1 Identities = 12/36 (33%), Positives = 19/36 (52%) Query: 55 IEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEE 90 I VK P G ++ + + I+E G+ V + V EE Sbjct: 37 ITVKNPPGTITEELIEAIKEALESGKPVVIFVDGEE 72 >gnl|CDD|146216 pfam03460, NIR_SIR_ferr, Nitrite/Sulfite reductase ferredoxin-like half domain. Sulfite and Nitrite reductases are key to both biosynthetic assimilation of sulfur and nitrogen and dissimilation of oxidized anions for energy transduction. Two copies of this repeat are found in Nitrite and Sulfite reductases and form a single structural domain. Length = 67 Score = 25.2 bits (56), Expect = 3.7 Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 11/60 (18%) Query: 51 GLWWIEVKKPTGRLSHQQMSEIEEL-RRRG---------QRVKVL-VSMEEVDNFLEELA 99 G + + V+ P GRL+ +Q+ + ++ + G Q +++ V E++ LEELA Sbjct: 6 GDYMVRVRVPGGRLTAEQLRALADIAEKYGDGEIRLTTRQNLELHGVPEEDLPELLEELA 65 >gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems. Length = 267 Score = 25.0 bits (55), Expect = 4.2 Identities = 10/14 (71%), Positives = 10/14 (71%) Query: 72 IEELRRRGQRVKVL 85 ELRRRG RV VL Sbjct: 50 GMELRRRGHRVAVL 63 >gnl|CDD|31172 COG0830, UreF, Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]. Length = 229 Score = 24.8 bits (54), Expect = 4.6 Identities = 20/103 (19%), Positives = 36/103 (34%), Gaps = 20/103 (19%) Query: 4 YSFHYQTEKDVEKRLVTGAKKLDCWVRKASFVG------------RRGCPDRLIITPNGG 51 +S+ + E ++ +VT A L+ W++ G R D Sbjct: 23 FSYSFGLETAIQAGIVTDAATLEAWLKTQLNQGLLYNDALLLALAYRALLDDDAEALLEA 82 Query: 52 LWWIEVKKPTGRLSHQQMSEIEELRRRGQR-VKVLVSMEEVDN 93 + +K R EE RR G+ +K+ ++ E D Sbjct: 83 DELLFAQKLA-RELR------EESRRMGRALLKLARALWEDDP 118 >gnl|CDD|31678 COG1489, SfsA, DNA-binding protein, stimulates sugar fermentation [General function prediction only]. Length = 235 Score = 24.8 bits (54), Expect = 4.9 Identities = 17/69 (24%), Positives = 26/69 (37%), Gaps = 17/69 (24%) Query: 42 DRLIITPNGGLWWIEVKK--------------PTGRLSHQQMSEIEELRRRGQRVKVL-- 85 D L+ ++EVK PT R + + E+E L + G R VL Sbjct: 117 DFLLDDDERPDCYVEVKSVTLVENGVAMFPDAPTAR-GQKHLRELERLAKEGYRAVVLFL 175 Query: 86 VSMEEVDNF 94 V ++ F Sbjct: 176 VLRSDITRF 184 >gnl|CDD|119349 cd00598, GH18_chitinase-like, The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel. The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins. The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model.. Length = 210 Score = 25.0 bits (55), Expect = 5.1 Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 5/45 (11%) Query: 44 LIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSM 88 I+ +G L K +EEL + +KVL+S+ Sbjct: 32 AEISSDGSLNLFGDKSEE-----PLKGALEELASKKPGLKVLISI 71 >gnl|CDD|88453 cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.. Length = 70 Score = 24.7 bits (54), Expect = 6.1 Identities = 12/27 (44%), Positives = 14/27 (51%) Query: 60 PTGRLSHQQMSEIEELRRRGQRVKVLV 86 P LS + + EE R GQ VKV V Sbjct: 29 PKSELSEAFIKDPEEHFRVGQVVKVKV 55 >gnl|CDD|114509 pfam05787, DUF839, Bacterial protein of unknown function (DUF839). This family consists of several bacterial proteins of unknown function that contain a predicted beta-propeller repeats. Length = 515 Score = 24.4 bits (53), Expect = 6.3 Identities = 6/15 (40%), Positives = 7/15 (46%) Query: 39 GCPDRLIITPNGGLW 53 PD + P G LW Sbjct: 429 ESPDNITFDPAGRLW 443 >gnl|CDD|145596 pfam02540, NAD_synthase, NAD synthase. NAD synthase (EC:6.3.5.1) is involved in the de novo synthesis of NAD and is induced by stress factors such as heat shock and glucose limitation. Length = 243 Score = 24.6 bits (54), Expect = 6.6 Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 23/71 (32%) Query: 28 WVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVS 87 V + + R P+R+I K P+ L Q E +EL ++ Sbjct: 158 QVYELA--KRLNVPERII-----------KKPPSADLWPGQTDE-DELG---------IT 194 Query: 88 MEEVDNFLEEL 98 +E+D L+ L Sbjct: 195 YDELDQILKGL 205 >gnl|CDD|34143 COG4465, CodY, Pleiotropic transcriptional repressor [Transcription]. Length = 261 Score = 24.4 bits (53), Expect = 6.8 Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 6/41 (14%) Query: 64 LSHQQMSEIEELRRRGQRVKVLVS------MEEVDNFLEEL 98 + +++ EIEE R+ V++ +S +E V++ EEL Sbjct: 158 ILREKLEEIEEEARKRTVVQMAISTLSYSELEAVEHIFEEL 198 >gnl|CDD|144562 pfam01019, G_glu_transpept, Gamma-glutamyltranspeptidase. Length = 506 Score = 24.5 bits (54), Expect = 6.9 Identities = 7/22 (31%), Positives = 10/22 (45%) Query: 70 SEIEELRRRGQRVKVLVSMEEV 91 + EL RG +VKV+ Sbjct: 462 EVLAELEARGHKVKVVPVSSGG 483 >gnl|CDD|38935 KOG3731, KOG3731, KOG3731, Sulfatases [Carbohydrate transport and metabolism]. Length = 541 Score = 24.2 bits (52), Expect = 8.2 Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 1/46 (2%) Query: 53 WWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEEVDNFLEEL 98 W + P H + I +R V S+E + N L EL Sbjct: 252 WILRTTGPMSN-IHIPFTNILPRKRLQTLQSVDDSVERLYNLLGEL 296 >gnl|CDD|36071 KOG0853, KOG0853, KOG0853, Glycosyltransferase [Cell wall/membrane/envelope biogenesis]. Length = 495 Score = 24.1 bits (52), Expect = 8.3 Identities = 10/47 (21%), Positives = 16/47 (34%) Query: 43 RLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSME 89 I P+ G+ E + ++ L G +V L S E Sbjct: 37 VTFIHPDLGIGGAERLVVDAAVHLLSGQDVLGLPDTGGQVVYLTSHE 83 >gnl|CDD|145985 pfam03129, HGTP_anticodon, Anticodon binding domain. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases it is probably the anticodon binding domain. Length = 93 Score = 24.1 bits (53), Expect = 8.7 Identities = 10/25 (40%), Positives = 14/25 (56%) Query: 74 ELRRRGQRVKVLVSMEEVDNFLEEL 98 +R R K VS+EE+ L+EL Sbjct: 69 TVRDRDTGEKETVSLEELVEKLKEL 93 >gnl|CDD|30902 COG0556, UvrB, Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]. Length = 663 Score = 24.0 bits (52), Expect = 8.9 Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 5/48 (10%) Query: 55 IEVKKPTGRLSHQQMSEIEELRRRGQRVKVLV---SM-EEVDNFLEEL 98 IEV+ G++ +SEI + + +RV V M E++ +L+EL Sbjct: 423 IEVRPTKGQVD-DLLSEIRKRVAKNERVLVTTLTKKMAEDLTEYLKEL 469 >gnl|CDD|31663 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]. Length = 366 Score = 24.2 bits (52), Expect = 9.0 Identities = 13/94 (13%), Positives = 30/94 (31%), Gaps = 2/94 (2%) Query: 10 TEKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQM 69 T K + V + + ++ + + K P S ++ Sbjct: 53 TGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSK--ILNKLGKVPLTGDSSLEI 110 Query: 70 SEIEELRRRGQRVKVLVSMEEVDNFLEELACTLY 103 + + V+V ++EVD +++ LY Sbjct: 111 LKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLY 144 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 0.137 0.428 Gapped Lambda K H 0.267 0.0612 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,304,629 Number of extensions: 61921 Number of successful extensions: 219 Number of sequences better than 10.0: 1 Number of HSP's gapped: 219 Number of HSP's successfully gapped: 25 Length of query: 103 Length of database: 6,263,737 Length adjustment: 70 Effective length of query: 33 Effective length of database: 4,751,107 Effective search space: 156786531 Effective search space used: 156786531 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: 51 (23.7 bits)