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)