RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 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|129588 TIGR00497, hsdM, type I restriction system adenine methylase
           (hsdM).  Function: methylation of specific adenine
           residues; required for both restriction and modification
           activities. The ECOR124/3 I enzyme recognizes
           5'GAA(N7)RTCG. for E.coli see (J. Mol. Biol. 257:
           960-969 (1996)).
          Length = 501

 Score =  103 bits (257), Expect = 2e-22
 Identities = 83/363 (22%), Positives = 155/363 (42%), Gaps = 53/363 (14%)

Query: 109 DNAKAIFEDFDF------SSTIARLEKAGLLYKICKNFSGIELHP-DTVPDRVMSNIYEH 161
           ++ K +F+DF+       S+   R EK   L ++  +   +EL   +        + YE 
Sbjct: 125 ESFKGLFKDFNVSEVKLGSTLTIRTEK---LKELLTSIDTMELDEFEKNSIDAFGDAYEF 181

Query: 162 LIRRFGSEVSEGAEDFMTPRDVVHLATALLLDPDDALFKESPGMIRTLYDPTCGTGGFLT 221
           LI  +     +   +F TP+D+  L   + +   D +          +YD  CG+G  L 
Sbjct: 182 LISMYAQNAGKSGGEFFTPQDISELLARIAIGKKDTVDD--------VYDMACGSGSLLL 233

Query: 222 DAMNHVADCGSHHKIPPILVPHGQELEPETHAVCVAGMLIRRLESDPRRDLSK-NIQQGS 280
             +  + +  S      ++  +GQE+   T+ +C   M++  +      D +  NI    
Sbjct: 234 QVIKVLGEKTS------LVSYYGQEINHTTYNLCRMNMILHNI------DYANFNIINAD 281

Query: 281 TL-SKDLFTGKRFHYCLSNPPFGKKWEKDKDAVEKEHKNGELGRFGPG--LPKISDGSML 337
           TL +K+      F   +SNPP+   W  DK +           RF     L   S   + 
Sbjct: 282 TLTTKEWENENGFEVVVSNPPYSISWAGDKKSNLVSDV-----RFKDAGTLAPNSKADLA 336

Query: 338 FLMHLANKLELPPNGGGRAAIVLSSSPLFNGRAGSGESEIRRWLLENDLIEAIVALPTDL 397
           F++H    L       G AAIV     L+       E  IR++L++ + ++A++ LP++L
Sbjct: 337 FVLHALYVL----GQEGTAAIVCFPGILYREGK---EQTIRKYLVDQNFVDAVIQLPSNL 389

Query: 398 FFRTNIATYLWILSNRKTEERRGKVQLINATDLWTSIRNEGKKRRIINDDQRRQILDIYV 457
           F  T+IAT + +L   K   ++  +  I+ ++ +     E K  R ++     +I+D + 
Sbjct: 390 FSTTSIATSILVL---KKNRKKDPIFFIDGSNEFV---REKKNNR-LSPKNIEKIVDCFN 442

Query: 458 SRE 460
           S++
Sbjct: 443 SKK 445


>gnl|CDD|152596 pfam12161, HsdM_N, HsdM N-terminal domain.  This domain is found at
           the N-terminus of the methylase subunit of Type I DNA
           methyltransferases. This domain family is found in
           bacteria and archaea, and is typically between 123 and
           138 amino acids in length. The family is found in
           association with pfam02384. Mutations in this region of
           EcoKI methyltransferase abolish the normally strong
           preference of this system for methylating hemimethylated
           substrate. The structure of this domain has been shown
           to be all alpha-helical.
          Length = 92

 Score = 54.1 bits (131), Expect = 1e-07
 Identities = 27/126 (21%), Positives = 45/126 (35%), Gaps = 37/126 (29%)

Query: 11  LANFIWKNAEDLWGDFKHTDFGKVILPFTLLRRLECALEPTRSAVREKYLAFGGSNIDLE 70
           L + +W  A+ L GD   +++ + ILP   L+R E          R   L       +L 
Sbjct: 1   LESKLWNIADILRGDVDASEYKEYILPLLFLKR-EY---------RWSNLKANDDGDELG 50

Query: 71  SFVKVAGYSFYNTSEYSLSTLGSTNTRNNLESYIASFSDNAKAIFEDFDFSSTIARLEKA 130
             +                        N+    +   + + K IF D DF++ +   EK 
Sbjct: 51  ENL------------------------NDALPGLEELNPDLKGIFFDADFNTKL---EKP 83

Query: 131 GLLYKI 136
            LL K+
Sbjct: 84  DLLKKV 89


>gnl|CDD|130324 TIGR01257, rim_protein, retinal-specific rim ABC transporter.  This
           model describes the photoreceptor protein (rim protein)
           in eukaryotes. It is the member of ABC transporter
           superfamily. Rim protein is a membrane glycoprotein
           which is localized in the photoreceptor outer segment
           discs. Mutation/s in its genetic loci is implicated in
           the recessive Stargardt's disease.
          Length = 2272

 Score = 33.4 bits (76), Expect = 0.20
 Identities = 38/128 (29%), Positives = 53/128 (41%), Gaps = 30/128 (23%)

Query: 469 DYRTFGYRRIKVL--RPLRMS------FILDKTGLARLEADITWRKLSPLHQS-FWLDIL 519
           D   F +R I  +  R LR++       +LDK      E  +T R LS L ++ FW  ++
Sbjct: 493 DMTNFDWRDIFNITDRFLRLANQYLECLVLDKFESYDDEVQLTQRALSLLEENRFWAGVV 552

Query: 520 KPMMQQIYPYGWAESF---VKESIKSN---EAKTLKVKASKSFIVAFINAFGRKDPRADP 573
            P M     Y W  S    VK  I+ +     KT K+K          + +    PRADP
Sbjct: 553 FPDM-----YPWTSSLPPHVKYKIRMDIDVVEKTNKIK----------DRYWDSGPRADP 597

Query: 574 VTDVNGEW 581
           V D    W
Sbjct: 598 VEDFRYIW 605


>gnl|CDD|181902 PRK09489, rsmC, 16S ribosomal RNA m2G1207 methyltransferase;
           Provisional.
          Length = 342

 Score = 29.5 bits (67), Expect = 2.7
 Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 11/68 (16%)

Query: 264 LESDPRRDLSKNIQQGSTLSKDLFT--GKRFHYCLSNPPFGKKWEKDKDAVE------KE 315
           LES  R  L+ N  +G   + ++F+    RF   +SNPPF    +   DA +        
Sbjct: 233 LESS-RATLAANGLEGEVFASNVFSDIKGRFDMIISNPPFHDGIQTSLDAAQTLIRGAVR 291

Query: 316 HKN--GEL 321
           H N  GEL
Sbjct: 292 HLNSGGEL 299


>gnl|CDD|132696 TIGR03657, IsdB, heme uptake protein IsdB.  Isd proteins are
           iron-regulated surface proteins found in Bacillus,
           Staphylococcus and Listeria species and are responsible
           for heme scavenging from hemoproteins. The IsdB protein
           is only observed in Staphylococcus and consists of an
           N-terminal hydrophobic signal sequence, a pair of tandem
           NEAT (NEAr Transporter, pfam05031) domains which confers
           the ability to bind heme and a C-terminal sortase
           processing signal which targets the protein to the cell
           wall. IsdB is believed to make a direct contact with
           methemoglobin facilitating transfer of heme to IsdB. The
           heme is then transferred to other cell wall-bound NEAT
           domain proteins such as IsdA and IsdC.
          Length = 644

 Score = 29.5 bits (65), Expect = 3.0
 Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 7/88 (7%)

Query: 520 KPMMQQIYPYGWAESFVKESIKSNEAKTLK--VKASKSFIVAFINAFGRKDPRADPVTDV 577
           K + +Q+Y     +  + E +K+   K L+   KA    + + I  F    P  + +TD+
Sbjct: 285 KTLERQVYELNKIQDKLPEKLKAEYKKKLEETKKALDEQVKSAITEFQNVQPTNEKMTDL 344

Query: 578 NGEWIPDTNLTEYENVPYLESIQDYFVR 605
                 DT    YE+V   ES+ D FV+
Sbjct: 345 Q-----DTKYVVYESVENNESMMDTFVK 367


>gnl|CDD|162239 TIGR01177, TIGR01177, conserved hypothetical protein TIGR01177.
           This family is found exclusively in the Archaea.
          Length = 329

 Score = 29.3 bits (66), Expect = 3.4
 Identities = 10/16 (62%), Positives = 12/16 (75%)

Query: 208 TLYDPTCGTGGFLTDA 223
            + DP CGTGGFL +A
Sbjct: 185 RVLDPFCGTGGFLIEA 200


>gnl|CDD|184188 PRK13626, PRK13626, transcriptional regulator SgrR; Provisional.
          Length = 552

 Score = 29.2 bits (66), Expect = 3.8
 Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 24/66 (36%)

Query: 471 RTFGYRRIKVLRP---LRMSFILDKTGLAR---------------LEADIT--WRKLSPL 510
           R   YR ++ L P   LR S    +T +AR               LEADI   W+++SPL
Sbjct: 123 RVLYYRPLRNLLPGSALRRS----ETHIARQIFSSLTRINEENGELEADIAHHWQQISPL 178

Query: 511 HQSFWL 516
           H  F+L
Sbjct: 179 HWRFYL 184


>gnl|CDD|179718 PRK04028, PRK04028, glutamyl-tRNA(Gln) amidotransferase subunit E;
           Validated.
          Length = 630

 Score = 29.0 bits (66), Expect = 4.3
 Identities = 16/64 (25%), Positives = 27/64 (42%), Gaps = 21/64 (32%)

Query: 114 IFEDFDFSSTIAR-LEKAGLLYKI-CKNFSGI---ELHPDTVPDRVMSNIYEHLIRRFGS 168
           +F+D   S  I + L+K G +  I    F G+   E+ P                RR G+
Sbjct: 287 LFKDTK-SKIIKKALKKGGKVLAIKLPGFKGLLGREIQPG---------------RRLGT 330

Query: 169 EVSE 172
           E+++
Sbjct: 331 ELAD 334


>gnl|CDD|129569 TIGR00477, tehB, tellurite resistance protein TehB.  Part of a
           tellurite-reducing operon tehA and tehB.
          Length = 195

 Score = 28.3 bits (63), Expect = 7.2
 Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 10/80 (12%)

Query: 51  TRSAVRE--------KYLAFGGSNIDLESFVKVAGYSF--YNTSEYSLSTLGSTNTRNNL 100
           T SAVRE        K L  G        ++ +AGY    ++ +  S++++     R NL
Sbjct: 18  THSAVREAVKTVAPCKTLDLGCGQGRNSLYLSLAGYDVRAWDHNPASIASVLDMKARENL 77

Query: 101 ESYIASFSDNAKAIFEDFDF 120
                ++  NA A+ ED+DF
Sbjct: 78  PLRTDAYDINAAALNEDYDF 97


>gnl|CDD|177647 PHA03419, PHA03419, E4 protein; Provisional.
          Length = 200

 Score = 28.0 bits (62), Expect = 7.6
 Identities = 16/42 (38%), Positives = 18/42 (42%)

Query: 293 HYCLSNPPFGKKWEKDKDAVEKEHKNGELGRFGPGLPKISDG 334
              L  PP GKK EK K   EK  + GE    GP      +G
Sbjct: 83  DLALQPPPGGKKKEKKKKETEKPAQGGEKPDQGPEAKGEGEG 124


>gnl|CDD|162206 TIGR01110, mdcA, malonate decarboxylase, alpha subunit.  This model
           describes malonate decarboxylase alpha subunit, from
           both the water-soluble form as found in Klebsiella
           pneumoniae and the form couple to sodium ion pumping in
           Malonomonas rubra. Malonate decarboxylase Na+ pump is
           the paradigm of the family of Na+ transport
           decarboxylases. Essentially, it couples the energy
           derived from decarboxylation of a carboxylic acid
           substrate to move Na+ ion across the bilayer. Functional
           malonate decarboylase is a multi subunit protein. The
           alpha subunit enzymatically performs the transfer of
           malonate (substrate) to an acyl carrier protein subunit
           for subsequent decarboxylation, hence the name:
           acetyl-S-acyl carrier protein:malonate carrier
           protein-SH transferase.
          Length = 543

 Score = 27.9 bits (62), Expect = 9.1
 Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 5/54 (9%)

Query: 128 EKAGLLYKICKNFSGIELHPDTVPDRVMSNIYEHLIRRFGSEVSEGAEDFMTPR 181
           E  GL  KICKN++ +  HP  +P   + + +   +  FG E+  G ED++  R
Sbjct: 265 ESLGLKGKICKNWA-LNPHPTLIP--AIESGWVESVHSFGGEL--GMEDYIEAR 313


>gnl|CDD|152369 pfam11934, DUF3452, Domain of unknown function (DUF3452).  This
           presumed domain is functionally uncharacterized. This
           domain is found in bacteria and eukaryotes. This domain
           is typically between 124 to 150 amino acids in length.
           This domain is found associated with pfam01858,
           pfam01857. This domain has a single completely conserved
           residue W that may be functionally important.
          Length = 138

 Score = 27.7 bits (62), Expect = 9.6
 Identities = 18/71 (25%), Positives = 27/71 (38%), Gaps = 6/71 (8%)

Query: 102 SYIASFSDNAKAIFEDFDFSSTIARLEKA----GLLY-KICKNFSGIELHPDTVPDRVMS 156
             +  F     +I E+  F + +  LE+      +LY K  + F  I L P   P    S
Sbjct: 34  KKLKQFDVKMDSILEN-RFGAEVKELERNFVVLSVLYKKYKRIFREIFLEPPEEPPSRSS 92

Query: 157 NIYEHLIRRFG 167
                 + RFG
Sbjct: 93  PCSSSDLFRFG 103


  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
   0.320    0.137    0.409 

Gapped
Lambda     K      H
   0.267   0.0448    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 11,515,080
Number of extensions: 777698
Number of successful extensions: 1473
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1468
Number of HSP's successfully gapped: 23
Length of query: 674
Length of database: 5,994,473
Length adjustment: 100
Effective length of query: 574
Effective length of database: 3,833,673
Effective search space: 2200528302
Effective search space used: 2200528302
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: 60 (27.6 bits)