NCBI Conserved Domain Search
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RPS-BLAST 2.2.9 [May-01-2004]
Query= local sequence: lcl|tmpseq_0 unnamed protein product
         (369 letters)

Database: cdd.v2.00
gnl|CDD|8310 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination gnl|CDD|10913 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair] gnl|CDD|10828 COG1106, COG1106, Predicted ATPases [General function prediction only] gnl|CDD|10293 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair] gnl|CDD|10914 COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning] gnl|CDD|13222 COG3910, COG3910, Predicted ATPase [General function prediction only]
 Domain Relatives
PSSMs producing significant alignments: Score
(bits)		 E
value
 
gnl|CDD|8310 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain... 75.7 9e-15
gnl|CDD|10913 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway... 371 7e-104
gnl|CDD|10828 COG1106, COG1106, Predicted ATPases [General function predicti... 46.2 6e-06
gnl|CDD|10293 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,... 39.3 7e-04
gnl|CDD|10914 COG1196, Smc, Chromosome segregation ATPases [Cell division an... 38.1 0.002
gnl|CDD|13222 COG3910, COG3910, Predicted ATPase [General function predictio... 35.7 0.008

gnl|CDD|8310, pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. 
             CD-Length = 170 residues,  97.1% aligned
             Score = 75.7 bits (186), Expect = 9e-15

Query:  3    LTRVSVTAVRNLHPVTLSP--SPRINILYGDNGSGKTSVLEAIH-LLGL--ARSFRSARL  57
Sbjct:  1    LKRLEIEGFKSYAGKTVIGPFSPGFNAIVGPNGSGKSNVLDAILFVLGERSASSLRAERL  60

Query:  58   QPVIQYEEAACTVFGQ----VMLANGIASNLGISRERQGEFTIR------------IDGQ  101
Sbjct:  61   SDLIHKGSGAKPKLNSAEVTITFDNQNSGPEPLDELN-PEVTIRRRVYRDGKSEYFINGK  119

Query:  102  NARSAAQLAETLPLQLINPDS--FRLLEGA--------PKIRRQFLD  138
Sbjct:  120  RVT-KKEVQELLESAGIDIKMPYFIIAQGEVEDIASMKPKERRELLE  165
gnl|CDD|10913, COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair] 
             CD-Length = 363 residues, 100.0% aligned
             Score =  371 bits (954), Expect = 7e-104

Query:  1    MSLTRVSVTAVRNLHPVTLSPSPRINILYGDNGSGKTSVLEAIHLLGLARSFRSARLQPV  60
Sbjct:  1    MYLLSLLLRNFRNYAELDLDLSPGVNVLVGENGQGKTNLLEAIYLLALGRSHRTSRDKEL  60

Query:  61   IQYEEAACTVFGQVMLANGIASNLGISRERQGEFTIRIDGQNARSAAQLAETLPLQLINP  120
Sbjct:  61   IRTGADEAEISARVQRKGREGT-LGLQISKKGRRRVRINGTKARKLAELAGHLNVVLFTP  119

Query:  121  DSFRLLEGAPKIRRQFLDWGVFHVEPRFLPVWQRLQKALRQRNSWLRHGKLDPASQAAWD  180
Sbjct:  120  EDLGLVKGSPSDRRRFLDWLLFQIEPVYLEALSNYEKLLKQRNALLKQLQGDYAWLDVWD  179

Query:  181  RELSLASDEIDAYRRSYIQALKPVFEETLAELVSLDDLTLSYYRG------WDKDRDLLE  234
Sbjct:  180  QQLAELGAEIAAARAEYLNALAPLAEKIHQLFLPELESLSIFYRGSVDVTAWEIEEDYLE  239

Query:  235  VLASSLLRDQQMGHTQAGPQRADLRIRLAGHNAAEILSRGQQKLVVCALRIAQGHLINRA  294
Sbjct:  240  ALAKRRERDLARGYTLVGPHRDDLLFRLNGKPAADFASQGQQKTLALALRLAEIELLREE  299

Query:  295  KRGQCVYLVDDLPSELDEQHRMALCRLLEDLGCQVFITCVDPQLLKDGWRTDTPVSMFHV  354
Sbjct:  300  TGEYPILLLDDVASELDDGRRAALLDTIE-LGVQVFVTTTDLEDIDDNLDENA--QMFHV  356

Query:  355  EHGKVSQ  361
Sbjct:  357  EDGKITK  363
gnl|CDD|10828, COG1106, COG1106, Predicted ATPases [General function prediction only] 
             CD-Length = 371 residues, only  24.8% aligned
             Score = 46.2 bits (109), Expect = 6e-06

Query:  3    LTRVSVTAVRNLHPVTLSPSPRINILYGDNGSGKTSVLEAIHLLGLARSFRSARLQPVIQ  62
Sbjct:  2    IKSFKIKNFKSFRELELEDFGKINIIYGANGAGKSNLLEALYFLKGLISPGSESPIPFER  61

Query:  63   YEEAACTVFGQVMLANGIASNLGISRERQGEFTIRIDG  100
Sbjct:  62   EINIWNGSYGK------EESNLDIFFEQDKEVEIISKN  93
gnl|CDD|10293, COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair] 
             CD-Length = 908 residues, only   8.1% aligned
             Score = 39.3 bits (91), Expect = 7e-04

Query:  1    MSLTRVSVTAVR---NLHPVTLSPSPRINILYGDNGSGKTSVLEAIH--LLGLARSFRSA  55
Sbjct:  1    MKILRLRLKNFRSFKDIDIEKLFDSG-IFLIVGPNGAGKSSILDAITFALYGKTPRLGAF  59

Query:  56   RLQPVIQYEEAACTV  70
Sbjct:  60   SLDDLIRAGEKSASV  74
gnl|CDD|10914, COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning] 
             CD-Length = 1163 residues, only   8.9% aligned
             Score = 38.1 bits (88), Expect = 0.002

Query:  16    PVTLSPSPRINILYGDNGSGKTSVLEAIHL-LGL--ARSFRSARLQPVI----QYEEAAC  68
Sbjct:  17    PTEINFSPGFTAIVGPNGSGKSNIVDAIRFVLGEQSAKNLRASKMSDLIFAGSGNRKPAN  76

Query:  69    TVFGQVMLAN------GIASNLGISR--ERQGEFTIRIDGQNAR  104
Sbjct:  77    YAEVELTFDNSDNTLPLEYEEISVTRRIYRDGESEYYINGEKVR  120
gnl|CDD|13222, COG3910, COG3910, Predicted ATPase [General function prediction only] 
             CD-Length = 233 residues, only  15.5% aligned
             Score = 35.7 bits (82), Expect = 0.008

Query:  7    SVTAVRNLHPVTLSPSPRINILYGDNGSGKTSVLEAI  43
Sbjct:  22   SLPAFRHLEE-RLEFRAPITFITGENGSGKSTLLEAI  57
Citing CD-Search: Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, and Bryant SH (2003), "CDD: a curated Entrez database of conserved domain alignments", Nucleic Acids Res. 31:383-387.

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