RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780791|ref|YP_003065204.1| exodeoxyribonuclease VII large
subunit [Candidatus Liberibacter asiaticus str. psy62]
         (529 letters)



>gnl|CDD|31758 COG1570, XseA, Exonuclease VII, large subunit [DNA replication,
           recombination, and repair].
          Length = 440

 Score =  418 bits (1075), Expect = e-117
 Identities = 180/496 (36%), Positives = 260/496 (52%), Gaps = 62/496 (12%)

Query: 13  PEYSVSELSYHLKHIVESNLSHVCVRGEISGYRGIHSSGHAYFSLKDNHSRIDAIIWKGT 72
              SVSEL+ ++K ++E +L  V VRGEIS +    +SGH YF+LKD  ++I  +++KG 
Sbjct: 4   KILSVSELNDYIKRLLERDLGQVWVRGEISNFTR-PASGHLYFTLKDERAQIRCVMFKGN 62

Query: 73  LNKIEFLPEEGIEFLVIGKITTFPGSSKYQIIIESLIPSGSGTLLTALEKRKKKLLEEGL 132
             +++F PEEG++ LV GKI+ +     YQI+ ES+ P+G G L  A E+ K KL  EGL
Sbjct: 63  NRRLKFRPEEGMQVLVRGKISLYEPRGDYQIVAESMEPAGLGALYLAFEQLKAKLAAEGL 122

Query: 133 FSDQHKNPIPFIPKIIAVITSPTGAVIRDILQRISCRFP-LRVIIFPVKVQGDECPKEIA 191
           F  + K P+PF PK I VITSPTGA +RDIL  +S RFP + VI++P  VQG+   +EI 
Sbjct: 123 FDPERKKPLPFFPKKIGVITSPTGAALRDILHTLSRRFPSVEVIVYPTLVQGEGAAEEIV 182

Query: 192 NAILQLNTLKEGRTCPRPDIIILARGGGSIEDLWHFNDEMIVRAIANSSIPIISAIGHET 251
            AI + N   +       D++I+ARGGGSIEDLW FNDE++ RAIA S IP+ISA+GHET
Sbjct: 183 EAIERANQRGD------VDVLIVARGGGSIEDLWAFNDEIVARAIAASRIPVISAVGHET 236

Query: 252 DWTLADYAADLRAPTPTGAAEMAVPVKEHLQSSLINLEARLNNIIIRLIKYKINTLNSLL 311
           D+TLAD+ ADLRAPTPT AAE+ VP    L   L  L+ RL+  + RL+  K   L  L 
Sbjct: 237 DFTLADFVADLRAPTPTAAAELVVPDSAELLQQLDQLQRRLHRALRRLLDQKKQRLEHLA 296

Query: 312 KALP--NSDQTLSCSRYRLDRLPRELEHNLEIIIFRKYRHFNHIINRIKSDFLIHNIQKN 369
           + L   + ++ LS  + RLD L   L   LE                       + +   
Sbjct: 297 RRLQFRSPERLLSEQQQRLDELAIRLRRALE-----------------------NQLALK 333

Query: 370 RQHILEKQQHIEQIVKQHLRYIFLEKKEKIAILHMLREQTKNRIFYLHTHIKKLITRIEF 429
           +Q +    Q +   +++                                 +++L  R++ 
Sbjct: 334 KQRLERLTQRLNPQIQRQQ-----------------------------QRLQQLERRLDK 364

Query: 430 ILSHKIKSCHTSVSITTRILQSFAYKNTLKRGYTSIQDTNNNFITQKRNLATKTRILINF 489
            L  ++K     +      L+S +   TL RGY  ++  N   I    +L    R+ +  
Sbjct: 365 ALRRQLKRKRERLEALVEQLESLSPLATLARGYAVVRKENGQVIKSVADLKAGDRLTLRL 424

Query: 490 FDGQANAIVINKAPPK 505
            DG+ +A V      K
Sbjct: 425 ADGEVDAEVKGVQTEK 440


>gnl|CDD|145640 pfam02601, Exonuc_VII_L, Exonuclease VII, large subunit.  This
           family consist of exonuclease VII, large subunit
           EC:3.1.11.6 This enzyme catalyses exonucleolytic
           cleavage in either 5'->3' or 3'->5' direction to yield
           5'-phosphomononucleotides. This exonuclease VII enzyme
           is composed of one large subunit and 4 small ones.
          Length = 295

 Score =  227 bits (582), Expect = 5e-60
 Identities = 117/368 (31%), Positives = 166/368 (45%), Gaps = 74/368 (20%)

Query: 132 LFSDQHKNPIPFIPKIIAVITSPTGAVIRDILQRISCRFPL-RVIIFPVKVQGDECPKEI 190
           LF    K P+P  PK IAVITS TGA  +D L+    R PL  + I+P  VQGD   + I
Sbjct: 1   LFDPNRKRPLPRFPKRIAVITSATGAAYQDFLRTARRRGPLVEIEIYPTLVQGDGAAESI 60

Query: 191 ANAILQLNTLKEGRTCPRPDIIILARGGGSIEDLWHFNDEMIVRAIANSSIPIISAIGHE 250
            +A+ + N  +   T    D+I++ RGGGS EDLW FNDE + RAIANS IP+I+ IGHE
Sbjct: 61  VSALERANERE---TALDYDVIVIIRGGGSKEDLWVFNDEELARAIANSPIPVITGIGHE 117

Query: 251 TDWTLADYAADLRAPTPTGAAEMAVPVKEHLQSSLINLEARLNNIIIRLIKYKINTLNSL 310
           TD T+AD  AD+RA TPT AAE+ VP +  L   L  LE RL+    R +K ++      
Sbjct: 118 TDTTIADLVADVRAATPTAAAELLVPDRTELLQKLEGLEQRLS----RALKNRLEKEQDR 173

Query: 311 LKALPNSDQTLSCSRYRLDRLPRELEHNLEIIIFRKYRHFNHIINRIKSDFLIHNIQKNR 370
           L  L          R RL  L R                                ++++ 
Sbjct: 174 LNLL----------RERLKSLSRRK------------------------------LEQHE 193

Query: 371 QHILEKQQHIEQIVKQHLRYIFLEKKEKIAILHMLREQTKNRIFYLHTHIKKLITRIEFI 430
           + + E  Q +E  ++  L      K+ ++  L + RE  KN +      ++ L       
Sbjct: 194 ERLAELYQRLESSIQNLLSR----KQSRLERLKLNRELEKNSVLENKLALENL------- 242

Query: 431 LSHKIKSCHTSVSITTRILQSFAYKNTLKRGYTSIQDTNNNFITQKRNLATKTRILINFF 490
                          T  L++ +   TLKRG+  ++  +   +T    L     + I   
Sbjct: 243 ---------------TAQLKALSPLKTLKRGFAIVRRKDGKIVTSAAELKPGDNLEIRLA 287

Query: 491 DGQANAIV 498
           DG A A V
Sbjct: 288 DGSAQAKV 295


>gnl|CDD|72961 cd04489, ExoVII_LU_OBF, ExoVII_LU_OBF: A subfamily of OB folds
           corresponding to the N-terminal OB-fold domain of
           Escherichia coli exodeoxyribonuclease VII (ExoVII) large
           subunit. E. coli ExoVII is composed of two non-identical
           subunits. E. coli ExoVII is a single-strand-specific
           exonuclease which degrades ssDNA from both 3-prime and
           5-prime ends. ExoVII plays a role in methyl-directed
           mismatch repair in vivo. ExoVII may also guard the
           genome from mutagenesis by removing excess ssDNA, since
           the build up of ssDNA would lead to SOS induction and
           PolIV-dependent mutagenesis..
          Length = 78

 Score = 95.2 bits (237), Expect = 4e-20
 Identities = 32/79 (40%), Positives = 48/79 (60%), Gaps = 1/79 (1%)

Query: 34  HVCVRGEISGYRGIHSSGHAYFSLKDNHSRIDAIIWKGTLNKIEFLPEEGIEFLVIGKIT 93
            V V GEIS  +   SSGH YF+LKD  + I  ++W+    ++ F  EEG+E LV GK++
Sbjct: 1   RVWVEGEISNLK-RPSSGHLYFTLKDEDASIRCVMWRSNARRLGFPLEEGMEVLVRGKVS 59

Query: 94  TFPGSSKYQIIIESLIPSG 112
            +     YQ+I+E + P+G
Sbjct: 60  FYEPRGGYQLIVEEIEPAG 78


>gnl|CDD|144799 pfam01336, tRNA_anti, OB-fold nucleic acid binding domain.  This
           family contains OB-fold domains that bind to nucleic
           acids. The family includes the anti-codon binding domain
           of lysyl, aspartyl, and asparaginyl -tRNA synthetases
           (See pfam00152). Aminoacyl-tRNA synthetases catalyse the
           addition of an amino acid to the appropriate tRNA
           molecule EC:6.1.1.-. This family also includes part of
           RecG helicase involved in DNA repair. Replication factor
           A is a heterotrimeric complex, that contains a subunit
           in this family. This domain is also found at the
           C-terminus of bacterial DNA polymerase III alpha chain.
          Length = 75

 Score = 47.3 bits (113), Expect = 1e-05
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 35  VCVRGEISGYRGIHSSGHAYFSLKDNHSRIDAIIWKGTLNKIEFLPEEGIEFLVIGKITT 94
           V V G ++  R       A+ +L+D    I  +++K    K+    +EG   LV GK+  
Sbjct: 1   VTVAGRVTSVRR-SGGKVAFLTLRDGTGSIQVVLFKEEAEKLAKKLKEGDVVLVTGKVKK 59

Query: 95  FPGSSKYQIIIESLIP 110
            PG  + ++++E +  
Sbjct: 60  RPG-GELELVVEEIEV 74


>gnl|CDD|72945 cd03524, RPA2_OBF_family, RPA2_OBF_family: A family of
           oligonucleotide binding (OB) folds with similarity to
           the OB fold of the single strand (ss) DNA-binding domain
           (DBD)-D of human RPA2 (also called RPA32). RPA2 is a
           subunit of Replication protein A (RPA). RPA is a nuclear
           ssDNA-binding protein (SSB) which appears to be involved
           in all aspects of DNA metabolism including replication,
           recombination, and repair. RPA also mediates specific
           interactions of various nuclear proteins. In animals,
           plants, and fungi, RPA is a heterotrimer with subunits
           of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA
           contains six OB folds, which are involved in ssDNA
           binding and in trimerization. The ssDNA binding
           mechanism is believed to be multistep and to involve
           conformational change. This family also includes OB
           folds similar to those found in Escherichia coli SSB,
           the wedge domain of E. coli RecG (a
           branched-DNA-specific helicase), E. coli ssDNA specific
           exodeoxyribonuclease VII large subunit, Pyrococcus
           abyssi DNA polymerase II (Pol II) small subunit,
           Sulfolobus solfataricus SSB, and Bacillus subtilis YhaM
           (a 3'-to-5'exoribonuclease). It also includes the OB
           folds of breast cancer susceptibility gene 2 protein
           (BRCA2), Oxytricha nova telomere end binding protein
           (TEBP), Saccharomyces cerevisiae telomere-binding
           protein (Cdc13), and human protection of telomeres 1
           protein (POT1)..
          Length = 75

 Score = 32.2 bits (73), Expect = 0.32
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 4/77 (5%)

Query: 36  CVRGEISGYRGIHSSG-HAYFSLKD-NHSRIDAIIWKGTLNKIEFLPEEGIEFLVIGKIT 93
            + G +     I + G    F+L D     I   ++     ++E L +EG    + GK+ 
Sbjct: 1   TIVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIKGKVK 60

Query: 94  TFPGSSKYQIIIESLIP 110
            F G  + Q+I+ES+  
Sbjct: 61  KFRG--RLQLIVESIEL 75


>gnl|CDD|119339 cd06558, crotonase-like, Crotonase/Enoyl-Coenzyme A (CoA) hydratase
           superfamily. This superfamily contains a diverse set of
           enzymes including enoyl-CoA hydratase, napthoate
           synthase, methylmalonyl-CoA decarboxylase,
           3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA
           isomerase. Many of these play important roles in fatty
           acid metabolism. In addition to a conserved structural
           core and the formation of trimers (or dimers of
           trimers), a common feature in this superfamily is the
           stabilization of an enolate anion intermediate derived
           from an acyl-CoA substrate. This is accomplished by two
           conserved backbone NH groups in active sites that form
           an oxyanion hole..
          Length = 195

 Score = 30.6 bits (70), Expect = 0.98
 Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 3/43 (6%)

Query: 210 DIIILARGGGSIEDLWHFNDEM--IVRAIANSSIPIISAI-GH 249
           D+  LA    + E+   F  E+  ++RA+     P+I+A+ G 
Sbjct: 61  DLKELAALSDAGEEARAFIRELQELLRALLRLPKPVIAAVNGA 103


>gnl|CDD|30932 COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication,
            recombination, and repair].
          Length = 1139

 Score = 30.6 bits (69), Expect = 0.99
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 5/75 (6%)

Query: 53   AYFSLKDNHSRIDAIIWKGTLNKIEFLPEEGIEFLVIGKITTFPGSSKYQIIIESLIPSG 112
            A+ +L+D    ++ +++     +   L  EG   +V GK+        + +I+E L P  
Sbjct: 1001 AFLTLEDETGILEVVVFPSEYERYRRLLLEGRLLIVKGKVQRREDGVGHALILEDLSP-- 1058

Query: 113  SGTLLTALEKRKKKL 127
               L  A E+    L
Sbjct: 1059 ---LEEARERVADFL 1070


>gnl|CDD|38965 KOG3761, KOG3761, KOG3761, Choline transporter [Lipid transport and
           metabolism].
          Length = 591

 Score = 30.4 bits (68), Expect = 1.3
 Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 6/44 (13%)

Query: 240 SIP--IISAIGHETDWTLADYA----ADLRAPTPTGAAEMAVPV 277
           +IP  +I AI   TDW +  Y            P   A+M +P+
Sbjct: 289 AIPAALIGAIAANTDWNMTAYGLPDNGTKVESIPPDEADMILPI 332


>gnl|CDD|35216 COG5657, CSE1, CAS/CSE protein involved in chromosome segregation
           [Cell division and chromosome partitioning].
          Length = 947

 Score = 29.9 bits (67), Expect = 1.8
 Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 1/68 (1%)

Query: 143 FIPKIIAVITSPTGAVIRDILQRISCRFPLRVIIFPVKVQGDECPKEIANAILQL-NTLK 201
           F+  +  ++T+ T   IRD L   S    + VI +P++   +       N I  L + L 
Sbjct: 283 FVEIVWNLLTTITRPYIRDYLVSKSLTVLINVIKYPIRKTAEVLSNVSENLINNLVDLLI 342

Query: 202 EGRTCPRP 209
                 R 
Sbjct: 343 LPNLILRE 350


>gnl|CDD|32144 COG1961, PinR, Site-specific recombinases, DNA invertase Pin
           homologs [DNA replication, recombination, and repair].
          Length = 222

 Score = 29.7 bits (66), Expect = 1.9
 Identities = 19/143 (13%), Positives = 46/143 (32%), Gaps = 5/143 (3%)

Query: 307 LNSLLKALPNSDQTLSCSRYRLDRLPRELEHNLEII-IFRKYRHFNHIINRIKSDFLIHN 365
           L  LL+ +     TL    Y+LDRL R L   L+++ +  +       +     D     
Sbjct: 53  LQRLLEDIEEGKDTLVV--YKLDRLGRSLSDLLQLLELLAEKGITLISLAENIFDTSSPM 110

Query: 366 IQKNRQHILEKQQHIEQIVKQHLRYIFLEKKEKIAILHMLREQTKNRIFYLHTHIKKLIT 425
            +     +    +   +++ +  R      ++              +           + 
Sbjct: 111 GRLMLMILAALAEFERELISERTRAGIEAARKAGKEGGRPPGYKIKKGRKKAEEQAAAVR 170

Query: 426 RI--EFILSHKIKSCHTSVSITT 446
           R+  + + S+   +    +S +T
Sbjct: 171 RLLADGLGSYSEIARALGISRST 193


>gnl|CDD|73023 cd03264, ABC_drug_resistance_like, ABC-type multidrug transport
           system, ATPase component.  The biological function of
           this family is not well characterized, but display ABC
           domains similar to members of ABCA subfamily.  ABC
           transporters are a large family of proteins involved in
           the transport of a wide variety of different compounds,
           like sugars, ions, peptides, and more complex organic
           molecules.  The nucleotide binding domain shows the
           highest similarity between all members of the family.
           ABC transporters are a subset of nucleotide hydrolases
           that contain a signature motif, Q-loop, and
           H-loop/switch region, in addition to, the Walker A
           motif/P-loop and Walker B motif commonly found in a
           number of ATP- and GTP-binding and hydrolyzing
           proteins..
          Length = 211

 Score = 29.7 bits (67), Expect = 2.0
 Identities = 11/28 (39%), Positives = 18/28 (64%)

Query: 393 LEKKEKIAILHMLREQTKNRIFYLHTHI 420
           L+ +E+I   ++L E  ++RI  L THI
Sbjct: 161 LDPEERIRFRNLLSELGEDRIVILSTHI 188


>gnl|CDD|34942 COG5379, BtaA, S-adenosylmethionine:diacylglycerol
           3-amino-3-carboxypropyl transferase [Lipid metabolism].
          Length = 414

 Score = 29.2 bits (65), Expect = 2.5
 Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 7/62 (11%)

Query: 116 LLTALEKRKKKLLEEGLFSDQHKNPIPFIPKIIAVITSPTGAVIRDILQRISCRFPLRVI 175
           +L  L  RK  L   G+   Q         ++ +       +V+RD L++++C FPL+  
Sbjct: 219 VLRWLTSRKSSLFGLGIPPGQF-------DELASSQDGSVASVLRDRLEKLACNFPLKDN 271

Query: 176 IF 177
            F
Sbjct: 272 YF 273


>gnl|CDD|72964 cd04492, YhaM_OBF_like, YhaM_OBF_like: A subfamily of OB folds
           similar to that found in Bacillus subtilis YhaM and
           Staphylococcus aureus cmp-binding factor-1 (SaCBF1).
           Both these proteins are 3'-to-5'exoribonucleases. YhaM
           requires Mn2+ or Co2+ for activity and is inactive in
           the presence of Mg2+. YhaM also has a Mn2+ dependent
           3'-to-5'single-stranded DNA exonuclease activity. SaCBF
           is also a double-stranded DNA binding protein, binding
           specifically to cmp, the replication enhancer found in
           S. aureus plasmid pT181. Proteins in this group combine
           an N-terminal OB fold with a C-terminal HD domain. The
           HD domain is found in metal-dependent
           phosphohydrolases..
          Length = 83

 Score = 29.4 bits (66), Expect = 2.6
 Identities = 12/56 (21%), Positives = 23/56 (41%), Gaps = 3/56 (5%)

Query: 55  FSLKDNHSRIDAIIWKGTLNKIEFLPEEGIEFLVIGKITTFPGSSKYQIIIESLIP 110
            +L+D    I+A +W  +    E      I   V G++  + G    Q+ I+ +  
Sbjct: 23  LTLQDKTGEIEAKLWDASEEDEEKFKPGDI-VHVKGRVEEYRGR--LQLKIQRIRL 75


>gnl|CDD|31394 COG1201, Lhr, Lhr-like helicases [General function prediction
           only].
          Length = 814

 Score = 29.1 bits (65), Expect = 3.0
 Identities = 24/81 (29%), Positives = 32/81 (39%), Gaps = 11/81 (13%)

Query: 110 PSGSGTLLTALEKRKKKLLEEGLFSDQHKNPIPFIPKIIAVITSPTGAVIRDILQRISCR 169
           P+GSG    A      +LL  G               I A+  SP  A+  DI +R+   
Sbjct: 45  PTGSGKTEAAFLPVINELLSLG--------KGKLEDGIYALYISPLKALNNDIRRRL--E 94

Query: 170 FPLRVIIFPVKVQ-GDECPKE 189
            PLR +   V V+ GD    E
Sbjct: 95  EPLRELGIEVAVRHGDTPQSE 115


>gnl|CDD|107206 cd01563, Thr-synth_1, Threonine synthase is a pyridoxal phosphate
           (PLP) dependent enzyme that catalyses the last reaction
           in the synthesis of  threonine from aspartate. It
           proceeds by converting O-phospho-L-homoserine (OPH) into
           threonine and inorganic phosphate. In plants, OPH is an
           intermediate between the methionine and
           threonine/isoleucine pathways. Thus threonine synthase
           competes for OPH with cystathionine-gamma-synthase, the
           first enzyme in the methionine pathway. These enzymes
           are in general dimers. Members of this CD, Thr-synth_1,
           are widely distributed in bacteria, archaea and higher
           plants..
          Length = 324

 Score = 29.1 bits (66), Expect = 3.2
 Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 8/42 (19%)

Query: 109 IPSGSGTLLTALEKRKKKLLEEGLFSDQHKNPIPFIPKIIAV 150
           +P G+G  +TA+ K  K+L E GL           +P+++ V
Sbjct: 177 VPVGNGGNITAIWKGFKELKELGLIDR--------LPRMVGV 210


>gnl|CDD|133032 cd04189, G1P_TT_long, G1P_TT_long represents the long form of
           glucose-1-phosphate thymidylyltransferase.  This family
           is the long form of Glucose-1-phosphate
           thymidylyltransferase.  Glucose-1-phosphate
           thymidylyltransferase catalyses the formation of
           dTDP-glucose, from dTTP and glucose 1-phosphate. It is
           the first enzyme in the biosynthesis of dTDP-L-rhamnose,
           a cell wall constituent and a feedback inhibitor of the
           enzyme.There are two forms of   Glucose-1-phosphate
           thymidylyltransferase in bacteria and archeae; short
           form and long form.  The long form, which has an extra
           50 amino acids c-terminal, is found in many species for
           which it serves as a sugar-activating enzyme for
           antibiotic biosynthesis and or other, unknown pathways,
           and in which dTDP-L-rhamnose is not necessarily
           produced.The long from enzymes also have a left-handed
           parallel helix domain at the c-terminus, whereas, th
           eshort form enzymes do not have this domain. The
           homotetrameric, feedback inhibited short form is found
           in numerous bacterial species that produce
           dTDP-L-rhamnose.
          Length = 236

 Score = 29.1 bits (66), Expect = 3.3
 Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 6/48 (12%)

Query: 148 IAVITSPTGAVIRDILQRISCRFPLRVIIFPVKVQGDECPKEIANAIL 195
           I ++  PTG  I++ L   S RF +R+       Q +  P  +A+A+L
Sbjct: 49  IGIVVGPTGEEIKEALGDGS-RFGVRITYIL---QEE--PLGLAHAVL 90


>gnl|CDD|30844 COG0498, ThrC, Threonine synthase [Amino acid transport and
           metabolism].
          Length = 411

 Score = 28.7 bits (64), Expect = 4.3
 Identities = 9/26 (34%), Positives = 13/26 (50%)

Query: 109 IPSGSGTLLTALEKRKKKLLEEGLFS 134
           +P G+G  L A+ K  K+ L  G   
Sbjct: 235 VPVGNGGNLLAIYKGFKEGLPIGKID 260


>gnl|CDD|144097 pfam00378, ECH, Enoyl-CoA hydratase/isomerase family.  This family
           contains a diverse set of enzymes including: Enoyl-CoA
           hydratase. Napthoate synthase. Carnitate racemase.
           3-hydoxybutyryl-CoA dehydratase. Dodecanoyl-CoA
           delta-isomerase.
          Length = 169

 Score = 28.0 bits (63), Expect = 6.8
 Identities = 6/38 (15%), Positives = 16/38 (42%)

Query: 210 DIIILARGGGSIEDLWHFNDEMIVRAIANSSIPIISAI 247
           DI  +A    + +  +      +   + +   P+I+A+
Sbjct: 52  DIKEMAAKRPAQQAQFSLEALDLWSRLEDLPKPVIAAV 89


>gnl|CDD|72954 cd04482, RPA2_OBF_like, RPA2_OBF_like: A subgroup of
           uncharacterized archaeal OB folds with similarity to the
           OB fold of the central ssDNA-binding domain (DBD)-D of
           human RPA2 (also called RPA32). RPA2 is a subunit of
           Replication protein A (RPA). RPA is a nuclear
           ssDNA-binding protein (SSB) which appears to be involved
           in all aspects of DNA metabolism including replication,
           recombination, and repair. RPA also mediates specific
           interactions of various nuclear proteins. In animals,
           plants, and fungi, RPA is a heterotrimer with subunits
           of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The
           major DNA binding activity of RPA is associated with
           RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding
           domain. RPA2 DBD-D is also involved in trimerization.
           The ssDNA binding mechanism is believed to be multistep
           and to involve conformational change. N-terminal to
           human RPA2 DBD-D is a domain containing all the known
           phosphorylation sites of RPA. Human RPA2 is
           phosphorylated in a cell cycle dependent manner in
           response to DNA damage..
          Length = 91

 Score = 27.9 bits (62), Expect = 6.8
 Identities = 14/74 (18%), Positives = 25/74 (33%), Gaps = 9/74 (12%)

Query: 35  VCVRGEISGYRGIHSSGHAYFSLKDNHSRIDAIIWKGT--LNKIEFLPEEGIEFLVIGKI 92
             V G++         GH +F + D    ID   ++ T     +       +  L+ G  
Sbjct: 1   YRVTGKVVEEPRTIEGGHVFFKISDGTGEIDCAAYEPTKEFRDV-------VRLLIPGDE 53

Query: 93  TTFPGSSKYQIIIE 106
            T  GS +    + 
Sbjct: 54  VTVYGSVRPGTTLN 67


>gnl|CDD|133422 cd01337, MDH_glyoxysomal_mitochondrial, Glyoxysomal and
          mitochondrial malate dehydrogenases.  MDH is one of the
          key enzymes in the citric acid cycle, facilitating both
          the conversion of malate to oxaloacetate and
          replenishing levels of oxalacetate by reductive
          carboxylation of pyruvate. Members of this subfamily
          are localized to the glycosome and mitochondria. MDHs
          are part of the NAD(P)-binding Rossmann fold
          superfamily, which includes a wide variety of protein
          families including the NAD(P)-binding domains of
          alcohol dehydrogenases, tyrosine-dependent
          oxidoreductases, glyceraldehyde-3-phosphate
          dehydrogenases, formate/glycerate dehydrogenases,
          siroheme synthases, 6-phosphogluconate dehydrogenases,
          aminoacid dehydrogenases, repressor rex, and
          NAD-binding potassium channel domains, among others.
          Length = 310

 Score = 27.8 bits (63), Expect = 7.3
 Identities = 12/33 (36%), Positives = 21/33 (63%), Gaps = 3/33 (9%)

Query: 17 VSELS-YHLKHI--VESNLSHVCVRGEISGYRG 46
          VSEL+ Y + +   V ++LSH+    +++GY G
Sbjct: 26 VSELALYDIVNTPGVAADLSHINTPAKVTGYLG 58


>gnl|CDD|32687 COG2860, COG2860, Predicted membrane protein [Function unknown].
          Length = 209

 Score = 27.8 bits (62), Expect = 8.4
 Identities = 9/22 (40%), Positives = 13/22 (59%)

Query: 142 PFIPKIIAVITSPTGAVIRDIL 163
           P I  +  V+T   G V+RD+L
Sbjct: 119 PLIAVVAGVLTGVGGGVLRDVL 140


>gnl|CDD|38808 KOG3602, KOG3602, KOG3602, WD40 repeat-containing protein [General
           function prediction only].
          Length = 1459

 Score = 27.7 bits (61), Expect = 8.6
 Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 4/79 (5%)

Query: 369 NRQHILEKQQHIEQIVKQHLRYIFLEKKEKIAILHMLREQTKNRIFYLHTHIKKLITRIE 428
           N Q    ++QH   +V   L+YI   + E    L  L ++  + ++  H        RI 
Sbjct: 487 NLQLFSRERQHGPWLVSHALKYITASRSESWEDLISLDDKVLDDVWQYHLP----TRRIP 542

Query: 429 FILSHKIKSCHTSVSITTR 447
            +L  +       V ++ R
Sbjct: 543 PLLWLRNIRNLLPVYLSER 561


  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
   0.321    0.137    0.398 

Gapped
Lambda     K      H
   0.267   0.0665    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 6,437,613
Number of extensions: 354937
Number of successful extensions: 990
Number of sequences better than 10.0: 1
Number of HSP's gapped: 981
Number of HSP's successfully gapped: 43
Length of query: 529
Length of database: 6,263,737
Length adjustment: 98
Effective length of query: 431
Effective length of database: 4,146,055
Effective search space: 1786949705
Effective search space used: 1786949705
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 (21.9 bits)
S2: 60 (27.0 bits)