RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780836|ref|YP_003065249.1| putative type I restriction-modification system DNA methylase [Candidatus Liberibacter asiaticus str. psy62] (674 letters) >gnl|CDD|30634 COG0286, HsdM, Type I restriction-modification system methyltransferase subunit [Defense mechanisms]. Length = 489 Score = 197 bits (503), Expect = 7e-51 Identities = 128/469 (27%), Positives = 203/469 (43%), Gaps = 48/469 (10%) Query: 9 ASLANFIWKNAEDLWGDFKHTDFGKVILPFTLLRRLECALEPTRSAVREKYLAFGGSNID 68 L++ +WK A+ L GD + + IL L+ L E A E+ Sbjct: 5 KELSDKLWKIADILRGDIDVSGYKDYILGLLFLKYLSDKFELEFEAELEEDNEAK-YAYP 63 Query: 69 LESFVKVAGYSFYNTSEYSLSTLGSTNTRNNLESYIASFSDNAKAIFEDFDFSSTIARLE 128 + F Y F + + + LG +N I + + K +F D DF+ + Sbjct: 64 AKGFFIPERYRFDDLKKNAEENLGDFL--DNALRKIEEKNPDLKGVFADLDFNDALKLGS 121 Query: 129 KAGLLYKICKNFSGIELHPDTVPDRVMSNIYEHLIRRFGSEVSEGAEDFMTPRDVVHLAT 188 LL K+ F I+ + + YE+L+R+F + A +F TPR+V L Sbjct: 122 LLKLLNKVILKFDEIDGRALD--RDLFGDAYEYLLRKFAEAEGKEAGEFYTPREVSEL-I 178 Query: 189 ALLLDPDDALFKESPGMIRTLYDPTCGTGGFLTDAMNHVADCGSHHKIPPILVPHGQELE 248 LLDP+ ++YDP CG+GG L A ++ I +GQE+ Sbjct: 179 VELLDPEP---------RNSIYDPACGSGGMLLQAAKYLKRHQDEIFI------YGQEIN 223 Query: 249 PETHAVCVAGMLIRRLESDPRRDLSKNIQQGSTLSKDLFTGK----RFHYCLSNPPF-GK 303 T+ + +++ +E D NI+ G TLS K +F + ++NPPF GK Sbjct: 224 DTTYRLAKMNLILHGIEGD------ANIRHGDTLSNPKHDDKDDKGKFDFVIANPPFSGK 277 Query: 304 KWEKDKDAVEKEHKNGELGRFGPGLPKISDGSMLFLMHLANKLELPPNGGGRAAIVLSSS 363 W D E++ + G F + + FL H+ KL GGRAAIVL Sbjct: 278 GWGGDLLESEQDERFFFYGVFPTK----NSADLAFLQHILYKL----KPGGRAAIVLPDG 329 Query: 364 PLFNGRAGSGESEIRRWLLENDLIEAIVALPTDLFFRTNIATYLWILSNRKTEERRGKVQ 423 LF G E +IR+ LLE++L+EAI+ LPT LF+ T I T + L+ K ER V Sbjct: 330 VLF---RGGAEKDIRKDLLEDNLLEAIIGLPTGLFYNTGIPTNILFLTKNKPAERN-DVL 385 Query: 424 LINATDLWTSIRNEGKKRRIINDDQRRQILDIYVSRENG-KFSRMLDYR 471 I+A+ + ++ + ++ +I+D Y + FS+ + Sbjct: 386 FIDASKEHF---EKPLNKKRLTEENIEKIVDTYREFKEIEGFSKSVSLE 431 >gnl|CDD|111293 pfam02384, N6_Mtase, N-6 DNA Methylase. Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The R-M system is a complex containing three polypeptides: M (this family), S (pfam01420), and R. This family consists of N-6 adenine-specific DNA methylase EC:2.1.1.72 from Type I and Type IC restriction systems. These methylases have the same sequence specificity as their corresponding restriction enzymes. Length = 312 Score = 180 bits (459), Expect = 1e-45 Identities = 98/319 (30%), Positives = 156/319 (48%), Gaps = 39/319 (12%) Query: 154 VMSNIYEHLIRRFGSEVSEGAEDFMTPRDVVHLATALLLDPDDALFKESPGMIRTLYDPT 213 + + YE+L+ +F +E + +F TPR+V L LL+P ++YDP Sbjct: 5 LFGDAYEYLLGKFANEEGKSGGEFYTPREVSKL-IVELLEPKPG---------ESIYDPA 54 Query: 214 CGTGGFLTDAMNHVADCGSHHKIPPILVPHGQELEPETHAVCVAGMLIRRLESDPRRDLS 273 CG+GGFL A V SH + +GQEL P T+ + M++ +E + Sbjct: 55 CGSGGFLIQADKFV---KSHDGDTNDISIYGQELNPTTYRLARMNMILHGIEYN-----D 106 Query: 274 KNIQQGSTLSKDLFTG-KRFHYCLSNPPFGKKWEKDKDAVEKEHKNGELGRFGPGLPKIS 332 I+ G TL F K+F ++NPPF +KW+ + + +N R G+P S Sbjct: 107 FGIRHGDTLLSPKFEEDKKFDVVVANPPFNQKWDANDNL-----ENDPRFRAY-GVPPKS 160 Query: 333 DGSMLFLMHLANKLELPPNGGGRAAIVLSSSPLFNGRAGSGESEIRRWLLENDLIEAIVA 392 + FL H+ L GRAA+VL + LF G E +IR+ L+E DLIEA++A Sbjct: 161 NADFAFLQHIIYHLS----PNGRAAVVLPNGVLF---RGGAEGDIRKALVEKDLIEAVIA 213 Query: 393 LPTDLFFRTNIATYLWILSNRKTEERRGKVQLINATDLWTSIRNEGKKRRIINDDQRRQI 452 LP +LF+ T I T + L K + R+G V I+A++ + +G+K + D+ +I Sbjct: 214 LPPNLFYNTGIPTCILFL--TKNKARKGDVLFIDASNEFEK---KGRKLNPLTDEHIEKI 268 Query: 453 LDIYVSRENG--KFSRMLD 469 +D Y F+++ Sbjct: 269 VDTYGEWPEDVAGFAKVAT 287 >gnl|CDD|31243 COG1041, COG1041, Predicted DNA modification methylase [DNA replication, recombination, and repair]. Length = 347 Score = 32.2 bits (73), Expect = 0.51 Identities = 28/144 (19%), Positives = 46/144 (31%), Gaps = 21/144 (14%) Query: 95 NTRNNLESYIASFSDNAKAIFEDFDFSSTIARLEKAG-------LLYKICKNFSGIELHP 147 + + D ++ FE+ I R E+ + I + L Sbjct: 78 DINEFTVLVLGEAVDWSEYKFEEEKGRVRIRRKEQDVDKGLEKAIGGAIPSEGLRVSL-- 135 Query: 148 DTVPDRVMSNIYEHLIRRFGSEVSEGAEDFMTPRD-----VVHLATALLLDPDDALFKES 202 + PD V+ + G V E RD + +DP A + Sbjct: 136 -SKPDEVVRVVVTEDKVYLGLTVRERDRKAFEKRDPEKRPFFRPGS---MDPRLARAMVN 191 Query: 203 PGMIR---TLYDPTCGTGGFLTDA 223 ++ + DP CGTGG L +A Sbjct: 192 LARVKRGELVLDPFCGTGGILIEA 215 >gnl|CDD|36757 KOG1544, KOG1544, KOG1544, Predicted cysteine proteinase TIN-ag [General function prediction only]. Length = 470 Score = 30.0 bits (67), Expect = 2.4 Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 4/71 (5%) Query: 350 PNGGGRAAIVLSSSPLFNGRAGSGESEIRRWLLENDLIEAIVALPTDLF-FRTNIATYLW 408 PN + + +P + R S E EI + L+EN ++A++ + D F ++ I ++ Sbjct: 331 PNSYVNSNDIYQVTPPY--RVSSNEKEIMKELMENGPVQALMEVHEDFFLYKGGIYSHT- 387 Query: 409 ILSNRKTEERR 419 +S + E R Sbjct: 388 PVSLGRPERYR 398 >gnl|CDD|110191 pfam01170, UPF0020, Putative RNA methylase family UPF0020. This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains. Length = 171 Score = 29.6 bits (67), Expect = 3.2 Identities = 8/17 (47%), Positives = 10/17 (58%) Query: 207 RTLYDPTCGTGGFLTDA 223 L DP CG+G L +A Sbjct: 30 DPLLDPFCGSGTILIEA 46 >gnl|CDD|177098 CHL00207, rpoB, RNA polymerase beta subunit; Provisional. Length = 1077 Score = 29.3 bits (66), Expect = 3.6 Identities = 10/40 (25%), Positives = 18/40 (45%) Query: 437 EGKKRRIINDDQRRQILDIYVSRENGKFSRMLDYRTFGYR 476 EGK R I ++ + + D + NG + R++ F Sbjct: 748 EGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRS 787 >gnl|CDD|133345 cd04145, M_R_Ras_like, M-Ras/R-Ras-like subfamily. This subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells. It interacts with some of the known Ras effectors, but appears to also have its own effectors. Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts. Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum. In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras. TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 164 Score = 29.3 bits (66), Expect = 3.6 Identities = 10/26 (38%), Positives = 15/26 (57%) Query: 599 IQDYFVREVSPHVPDAYIDKIFIDEK 624 IQ YFV + P + D+Y + ID + Sbjct: 23 IQSYFVTDYDPTIEDSYTKQCEIDGQ 48 >gnl|CDD|37143 KOG1932, KOG1932, KOG1932, TATA binding protein associated factor [Transcription]. Length = 1180 Score = 28.8 bits (64), Expect = 5.0 Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 3/61 (4%) Query: 568 DPRADPVTDVNGEWIPDTNLTEYENVPYLESIQDYFVREVSPHVPDAYIDKIFIDEKDKE 627 +P +T +P YL +++ E+S P + +F+DE E Sbjct: 258 EPSMIDITHF---CLPGLEPLVKNTTVYLHKAIEFYEEELSSRYPFSCYKTVFVDEAAVE 314 Query: 628 I 628 I Sbjct: 315 I 315 >gnl|CDD|35956 KOG0737, KOG0737, KOG0737, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 386 Score = 28.3 bits (63), Expect = 6.8 Identities = 31/150 (20%), Positives = 55/150 (36%), Gaps = 22/150 (14%) Query: 419 RGKVQLINAT----DLWTSIRNEGKKRRII---NDDQRRQILDIYVSRENGKFSRMLDYR 471 +V ++ AT DL +I +R + + +QRR+IL + + +E K +D Sbjct: 229 SERVLVLGATNRPFDLDEAIIRRLPRRFHVGLPDAEQRRKILKVILKKE--KLEDDVDLD 286 Query: 472 -----TFGYR--------RIKVLRPLRMSFILDKTGLARLEADITWRKLSPLHQSFWLDI 518 T GY R+ LRP+R + + L +A + S L Sbjct: 287 EIAQMTEGYSGSDLKELCRLAALRPIRELLVSETGLLDLDKAIADLKPTQAAASSCLLRP 346 Query: 519 LKPMMQQIYPYGWAESFVKESIKSNEAKTL 548 L+ + S ++ + N K Sbjct: 347 LEQEDFPKAINRVSASVAMDATRMNALKQW 376 >gnl|CDD|73189 cd00309, chaperonin_type_I_II, chaperonin families, type I and type II. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis.. Length = 464 Score = 28.1 bits (63), Expect = 7.1 Identities = 22/122 (18%), Positives = 43/122 (35%), Gaps = 11/122 (9%) Query: 42 RRLECALEPTRSAVREKYLAFGGSNIDLESFVKVAGYSFYNTSEYSLSTLGSTNTRNNLE 101 R L AL R+AV + + GG ++E + + + LG + LE Sbjct: 330 RSLHDALCAVRAAVEDGGIVPGGGAAEIELSKALEELA---KTLPGKEQLGIEAFADALE 386 Query: 102 SYIASFSDNAKAIFEDFDFSSTIARLEKAGLLYKICKNFSGIELHPDTVPDRVMSNIYEH 161 + ++NA D + +L + +G ++ + D + I + Sbjct: 387 VIPRTLAENAG-----LDPIEVVTKLRAK---HAEGGGNAGGDVETGEIVDMKEAGIIDP 438 Query: 162 LI 163 L Sbjct: 439 LK 440 >gnl|CDD|34113 COG4412, COG4412, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 760 Score = 28.1 bits (62), Expect = 7.3 Identities = 20/71 (28%), Positives = 27/71 (38%), Gaps = 13/71 (18%) Query: 562 NAFGRKDPRADPVTDVNGEWIPDTNLTEYENVPYL---------ESIQDYFVREVSPHVP 612 N K P P T +GE + D NLT N P L +++ S H Sbjct: 114 NNDKWKVPSTGPNTAADGEKVYDKNLTNLINFPDLPLVMNPLTAPDTGMLYLQYKSSH-- 171 Query: 613 DAYIDKIFIDE 623 Y D +F+ E Sbjct: 172 --YQDYVFVPE 180 >gnl|CDD|113851 pfam05096, Glu_cyclase_2, Glutamine cyclotransferase. This family of enzymes EC:2.3.2.5 catalyse the cyclization of free L-glutamine and N-terminal glutaminyl residues in proteins to pyroglutamate (5-oxoproline) and pyroglutamyl residues respectively. This family includes plant and bacterial enzymes and seems unrelated to the mammalian enzymes. Length = 264 Score = 28.0 bits (62), Expect = 7.9 Identities = 10/41 (24%), Positives = 22/41 (53%), Gaps = 2/41 (4%) Query: 373 GESEIRRWLLENDLIEAIVALPTDLFFR--TNIATYLWILS 411 G S++R + L ++ +A P +F T + Y+++L+ Sbjct: 66 GFSKVRVYDLTQEIFSEKIAFPDTVFGEGLTVVEDYVYLLT 106 >gnl|CDD|133338 cd04138, H_N_K_Ras_like, H-Ras/N-Ras/K-Ras subfamily. H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1. Others are proposed to play negative regulatory roles in oncogenesis, including RASSF and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 162 Score = 27.8 bits (62), Expect = 9.2 Identities = 10/25 (40%), Positives = 16/25 (64%) Query: 599 IQDYFVREVSPHVPDAYIDKIFIDE 623 IQ++FV E P + D+Y ++ ID Sbjct: 22 IQNHFVDEYDPTIEDSYRKQVVIDG 46 >gnl|CDD|32766 COG2943, MdoH, Membrane glycosyltransferase [Cell envelope biogenesis, outer membrane]. Length = 736 Score = 28.0 bits (62), Expect = 9.3 Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 6/54 (11%) Query: 163 IRRFGSEVSE----GAEDFMTPRDVVHLATALLLDPDDALFKESPGMI--RTLY 210 RR+GS S A+ MT +V L + +PD L + SP TLY Sbjct: 234 CRRWGSAYSYMLVLDADSVMTGDCLVRLVRLMEANPDAGLIQTSPKASGGDTLY 287 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 0.320 0.137 0.409 Gapped Lambda K H 0.267 0.0586 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 8,568,408 Number of extensions: 477210 Number of successful extensions: 1116 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1103 Number of HSP's successfully gapped: 20 Length of query: 674 Length of database: 6,263,737 Length adjustment: 100 Effective length of query: 574 Effective length of database: 4,102,837 Effective search space: 2355028438 Effective search space used: 2355028438 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 (21.8 bits) S2: 61 (27.6 bits)