RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780322|ref|YP_003064735.1| SAM-dependent methyltransferase protein [Candidatus Liberibacter asiaticus str. psy62] (273 letters) >gnl|CDD|162684 TIGR02072, BioC, biotin biosynthesis protein BioC. This enzyme, which is found in biotin biosynthetic gene clusters in proteobacteria, firmicutes, green-sulfur bacteria, fusobacterium and bacteroides, is believed to carry out an enzymatic step prior to the formation of pimeloyl-CoA (although attribution of this annotation is not traceable). The enzyme appears related to methyltransferases by homology. Length = 240 Score = 80.0 bits (198), Expect = 7e-16 Identities = 39/170 (22%), Positives = 76/170 (44%), Gaps = 18/170 (10%) Query: 94 LEEIPSISQSVDLILSPLNLHIINDTLEMFSKINHMLKPGGMFLAAIPGIGTLHELRKAL 153 E++P S DLI+S L L +D + S++ +LKPGG+ + G GTLHELR Sbjct: 89 AEKLPLEDSSFDLIVSNLALQWCDDLSQALSELARVLKPGGLLAFSTFGPGTLHELR--- 145 Query: 154 LKAETELTGGASPRVIPFMDIKSAGTLMEKSGFISPIIDQDTYTVYYKSMLHLMHDLRGM 213 + G + ++ + L++ S F ++++ T+ + L ++ L+ Sbjct: 146 -----QSFG---QHGLRYLSLDELKALLKNS-FELLTLEEELITLSFDDPLDVLRHLKKT 196 Query: 214 GMSNPLIRRSKTPPYKSLFKRASTIYTEENSDLTGNVTASFSIIYVMGWK 263 G + R+ K+ +R Y +E + ++ ++Y + K Sbjct: 197 GANGLSSGRTSRKQLKAFLER----YEQEFQ--PDGLPLTYHVVYGIAKK 240 >gnl|CDD|149353 pfam08241, Methyltransf_11, Methyltransferase domain. Members of this family are SAM dependent methyltransferases. Length = 95 Score = 38.0 bits (89), Expect = 0.002 Identities = 15/50 (30%), Positives = 26/50 (52%) Query: 88 EVISCPLEEIPSISQSVDLILSPLNLHIINDTLEMFSKINHMLKPGGMFL 137 + E++P +S D+++S L LH + D +I +LKPGG + Sbjct: 45 TFVVGDAEDLPFPDESFDVVVSSLVLHHLPDPERALREIARVLKPGGKLV 94 >gnl|CDD|149354 pfam08242, Methyltransf_12, Methyltransferase domain. Members of this family are SAM dependent methyltransferases. Length = 98 Score = 34.7 bits (80), Expect = 0.025 Identities = 12/44 (27%), Positives = 22/44 (50%) Query: 93 PLEEIPSISQSVDLILSPLNLHIINDTLEMFSKINHMLKPGGMF 136 L+ I S D++++ LH + D + + +LKPGG+ Sbjct: 55 VLDAIDLDPGSFDVVVASNVLHHLADPRAVLRNLRRLLKPGGVL 98 >gnl|CDD|183351 PRK11873, arsM, arsenite S-adenosylmethyltransferase; Reviewed. Length = 272 Score = 31.8 bits (73), Expect = 0.18 Identities = 29/112 (25%), Positives = 49/112 (43%), Gaps = 19/112 (16%) Query: 94 LEEIPSISQSVDLILSPLNLHIIN---DTLEMFSKINHMLKPGGMFLAAIPGIGTLHELR 150 +E +P SVD+I+S N +IN D +F + +LKPGG F AI + EL Sbjct: 137 IEALPVADNSVDVIIS--NC-VINLSPDKERVFKEAFRVLKPGGRF--AISDVVLRGELP 191 Query: 151 KALLKAETELTG---GASPRVIPFMDIKSAGTLMEKSGFISPIID-QDTYTV 198 + + G GA + + ++ ++GF+ I + Y + Sbjct: 192 EEIRNDAELYAGCVAGA-------LQEEEYLAMLAEAGFVDITIQPKREYRI 236 >gnl|CDD|181665 PRK09130, PRK09130, NADH dehydrogenase subunit G; Validated. Length = 687 Score = 29.8 bits (68), Expect = 0.71 Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 28/87 (32%) Query: 145 TLHELRKAL------LKAETELTGGASPRVIPFMDIKSAGTLMEKSGFISPIIDQDTYTV 198 +L +LR L A ++T + + + S + K+ F SP+ D Sbjct: 606 SLAQLRAKLAAAYPHFAAIDQITPSKDAKDLAA--LASKKGKLSKAPFTSPVKD------ 657 Query: 199 YYKSMLHLMHDLRGMGMSNPLIRRSKT 225 +Y ++NP+ R S T Sbjct: 658 FY--------------LTNPIARASAT 670 >gnl|CDD|181282 PRK08195, PRK08195, 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated. Length = 337 Score = 29.4 bits (67), Expect = 1.0 Identities = 7/13 (53%), Positives = 11/13 (84%) Query: 140 IPGIGTLHELRKA 152 +PGIGT+ +L+ A Sbjct: 85 LPGIGTVDDLKMA 97 >gnl|CDD|151603 pfam11161, DUF2944, Protein of unknown function (DUF2946). This family of proteins with unknown function appear to be restricted to Proteobacteria. Length = 178 Score = 28.9 bits (65), Expect = 1.5 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 5/61 (8%) Query: 133 GGMFLAAIPGIGTLHELRKALLKAETELTG---GASPRVIPFMDIKSAGTLMEKSGFI-S 188 G ++LA G+G LH+ L +L G G R +P + SA L + GF+ S Sbjct: 116 GRVYLATPAGLGLLHDHDMDLFAEALDLGGDACGGDGRTLPLEPVLSA-ELPRRFGFVRS 174 Query: 189 P 189 P Sbjct: 175 P 175 >gnl|CDD|129061 smart00828, PKS_MT, Methyltransferase in polyketide synthase (PKS) enzymes. Length = 224 Score = 28.5 bits (64), Expect = 1.7 Identities = 13/35 (37%), Positives = 20/35 (57%) Query: 105 DLILSPLNLHIINDTLEMFSKINHMLKPGGMFLAA 139 DL+ +H I D +++FS I+ LK GG + A Sbjct: 69 DLVFGFEVIHHIKDKMDLFSNISRHLKDGGHLVLA 103 >gnl|CDD|132261 TIGR03217, 4OH_2_O_val_ald, 4-hydroxy-2-oxovalerate aldolase. Members of this protein family are 4-hydroxy-2-oxovalerate aldolase, also called 4-hydroxy-2-ketovalerate aldolase and 2-oxo-4-hydroxypentanoate aldolase. This enzyme, part of the pathway for the meta-cleavage of catechol, produces pyruvate and acetaldehyde. Acetaldehyde is then converted by acetaldehyde dehydrogenase (acylating) (DmpF; EC 1.2.1.10) to acetyl-CoA. The two enzymes are tightly associated. Length = 333 Score = 28.5 bits (64), Expect = 2.1 Identities = 8/13 (61%), Positives = 12/13 (92%) Query: 140 IPGIGTLHELRKA 152 +PGIGT+H+L+ A Sbjct: 84 LPGIGTVHDLKAA 96 >gnl|CDD|180713 PRK06826, dnaE, DNA polymerase III DnaE; Reviewed. Length = 1151 Score = 28.3 bits (64), Expect = 2.4 Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 3/24 (12%) Query: 30 DRVAKEIAFRLNMINQTFENALEL 53 DR+AK I L + T + ALEL Sbjct: 454 DRIAKMIPTELGI---TIDKALEL 474 >gnl|CDD|151230 pfam10758, DUF2586, Protein of unknown function (DUF2586). This bacterial family of proteins has no known function. Length = 363 Score = 27.3 bits (61), Expect = 4.5 Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 1/36 (2%) Query: 136 FLAAIPGIGTLHELRKALLKAETELTGG-ASPRVIP 170 FL A+ GI + L A LT G A+ RV Sbjct: 133 FLLAVAGIDAEGQTWSDYLAALAALTDGVAAERVAL 168 >gnl|CDD|149453 pfam08397, IMD, IRSp53/MIM homology domain. The N-terminal predicted helical stretch of the insulin receptor tyrosine kinase substrate p53 (IRSp53) is an evolutionary conserved F-actin bundling domain involved in filopodium formation. The domain has been named IMD after the IRSp53 and missing in metastasis (MIM) proteins in which it occurs. Filopodium-inducing IMD activity is regulated by Cdc42 and Rac1 and is SH3-independent. Length = 218 Score = 27.0 bits (60), Expect = 5.3 Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 2/49 (4%) Query: 48 ENALELHGITGIVGYTCMETKKIHRMIRAEISTEFSTLKREVISCPLEE 96 E A G + +G +HR I +++ F E+I+ PLE+ Sbjct: 45 EMASNSPG-SRELGSVLTRMSMVHRSINSKLEEFFKAFHDELIN-PLEK 91 >gnl|CDD|132559 TIGR03520, GldE, gliding motility-associated protein GldE. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldC is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. GldE was discovered because of its adjacency to GldD in F. johnsonii. Overexpression of GldE partially supresses the effects of a GldB point mutant suggesting that GldB and GldE interact. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility and in fact some do not appear to express the gliding phenotype. Length = 408 Score = 26.9 bits (60), Expect = 5.7 Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 4/54 (7%) Query: 58 GIVGYTCMETKKIHR----MIRAEISTEFSTLKREVISCPLEEIPSISQSVDLI 107 GIV + +TK++ R + +I T FS + ++I IP +++D I Sbjct: 184 GIVSFGNTDTKQVMRPRLDIFALDIETSFSEIIPKIIENGYSRIPVYKETIDNI 237 >gnl|CDD|162355 TIGR01429, AMP_deaminase, AMP deaminase. This model describes AMP deaminase, a large, well-conserved eukaryotic protein involved in energy metabolism. Most members of the family have an additional, poorly alignable region of 150 amino acids or more N-terminal to the region included in the model. Length = 611 Score = 26.7 bits (59), Expect = 6.4 Identities = 25/111 (22%), Positives = 38/111 (34%), Gaps = 29/111 (26%) Query: 63 TCMETKKIHRMIRAEISTE-----------FSTLKREVISCPLEEIPSISQSVDLILSPL 111 M K + R I+ ++ TE TL+ S L+ DL + L Sbjct: 180 ASMNQKHLLRFIKHKLKTEPDETVIERDGKKLTLREVFDSLHLD-------PYDLSVDTL 232 Query: 112 NLHIINDTLEMFSKINHMLKPGGMFLAAIPGIGTLHELRKALLKAETELTG 162 ++H +T F K N P G LR+ LK + + G Sbjct: 233 DVHADRNTFHRFDKFNLKYNPVGE-----------SRLREIFLKTDNYIGG 272 >gnl|CDD|140236 PTZ00209, PTZ00209, retrotransposon hot spot protein; Provisional. Length = 693 Score = 26.1 bits (57), Expect = 9.1 Identities = 17/55 (30%), Positives = 21/55 (38%), Gaps = 13/55 (23%) Query: 229 KSLFKRASTIYTEENSDLTG---NVTAS----------FSIIYVMGWKSTTFKTG 270 K F R I+TEE D+T V A F + MGW S F+ Sbjct: 74 KVFFGRPQHIWTEEEVDITPEHCEVDAELEERPTGLEIFVLTSKMGWPSDRFQCS 128 >gnl|CDD|182457 PRK10434, srlR, DNA-bindng transcriptional repressor SrlR; Provisional. Length = 256 Score = 26.2 bits (58), Expect = 9.9 Identities = 14/46 (30%), Positives = 27/46 (58%), Gaps = 1/46 (2%) Query: 91 SCPLEEIPSISQSVDLILSPLNLHIINDTLEMFSKINHMLKPGGMF 136 S L+ +P +S+ ++ + +LHI+N E+ ++ +L PGG F Sbjct: 101 STVLQMVPLLSRFNNITVMTNSLHIVNALSELDNEQT-ILMPGGTF 145 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.322 0.136 0.389 Gapped Lambda K H 0.267 0.0710 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,429,750 Number of extensions: 281230 Number of successful extensions: 524 Number of sequences better than 10.0: 1 Number of HSP's gapped: 522 Number of HSP's successfully gapped: 27 Length of query: 273 Length of database: 5,994,473 Length adjustment: 92 Effective length of query: 181 Effective length of database: 4,006,537 Effective search space: 725183197 Effective search space used: 725183197 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: 56 (25.4 bits)