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)