RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780834|ref|YP_003065247.1| DNA primase [Candidatus
Liberibacter asiaticus str. psy62]
         (648 letters)



>gnl|CDD|180189 PRK05667, dnaG, DNA primase; Validated.
          Length = 580

 Score =  565 bits (1458), Expect = e-161
 Identities = 212/618 (34%), Positives = 315/618 (50%), Gaps = 61/618 (9%)

Query: 1   MNYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKG 60
              P +FI++L   + I ++IG+YV   +        +Y   CPFHDEKTPSF  +  K 
Sbjct: 2   GRIPPEFIEELRARVDIVDVIGEYVKLKKAG-----RNYKGLCPFHDEKTPSFTVSPDKQ 56

Query: 61  FYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRL 120
           FY+CF C   GD + FL    G SF+E+V+ LA  AG+ LP  D   +++   +  L  +
Sbjct: 57  FYHCFGCGAGGDVIKFLMEYEGLSFVEAVEELADRAGIELPYED---QQERSRRQRLYEI 113

Query: 121 IEVATDFFHHSL-----KNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQ 175
           +E+A  F+   L       AR      YL +RG+    IE F +GYAPD   +L +HL  
Sbjct: 114 MELAAKFYQQQLRTPEGAEARQ-----YLYKRGLSEETIERFGIGYAPDGWDALLKHLGG 168

Query: 176 KGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLN 235
           KGFSE+++ EAGLLI  ++    YDRFRNR++FPIR  RG+VI FGGR L   +  KYLN
Sbjct: 169 KGFSEKELEEAGLLIKNEDGGGPYDRFRNRIMFPIRDLRGRVIGFGGRVLGDDKP-KYLN 227

Query: 236 SPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVV 295
           SPET LFHKG+ LY    A    +K+I K  +      +I+VEGYMDV++L QAG+ N V
Sbjct: 228 SPETPLFHKGRVLYGLDEA----RKAIAKKKQ------VIVVEGYMDVIALHQAGITNAV 277

Query: 296 SSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSR 355
           +SLGTALTE  L+LL +L+  ++LCFDGD  G +AA +A++L L  L  G +V    L  
Sbjct: 278 ASLGTALTEEHLKLLRRLTDEVILCFDGDKAGRKAALRALELALPLLKDGRQVRVAFLPD 337

Query: 356 GEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHI 415
           G+DPD  +R  G  AF  L+ +++PL + L +R    +  +TP+ RA L       I  I
Sbjct: 338 GKDPDDLVRKEGPEAFRALLEQAIPLSEFLIRRLIPGKDLDTPEGRAALLERAAPLIAKI 397

Query: 416 KDQKLRYYYSQAIRDRLQQLFQKYITEHSGYGRYWKKNARHRDQKGPSQRLMQSSLVKGK 475
            D  LR  Y + + +RL  L                      +Q  P  +  Q       
Sbjct: 398 PDPTLRDSYRRKLAERLGILDD-----------------AQLEQLVPKAQEPQLK----- 435

Query: 476 LSKKPSLREAALLLTLINHPAILQEQYQELADIRYDNNEL-QKLWSFLFSDFVEQKYFLP 534
            +++P   E  LL  L+ HP + +E    L +  ++   L + L   + +          
Sbjct: 436 -AERPRTAERELLALLLQHPELAEEVRDALDEEDFEGLPLFRALLEAILAQ---PGLTTG 491

Query: 535 EEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSRQ 594
            ++ + L + G  EL   L+       +     E +I  + +  + AL   +  +LL  +
Sbjct: 492 SQLLEHLRDAGLEELAALLESLAVWEEIS----EEDIAALEKELKDALEKLRD-QLLEER 546

Query: 595 KEEIEKQIAQVTAKGEAE 612
            EE+  +   +   G + 
Sbjct: 547 LEELIAKERLLEGHGLSS 564


>gnl|CDD|162334 TIGR01391, dnaG, DNA primase, catalytic core.  This protein
           contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim
           domain (Pfam:PF01751).
          Length = 415

 Score =  430 bits (1108), Expect = e-121
 Identities = 184/435 (42%), Positives = 254/435 (58%), Gaps = 24/435 (5%)

Query: 2   NYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGF 61
             P +FI +L   + I ++I +YV   ++  N     Y   CPFH EKTPSF  +  K F
Sbjct: 1   MIPEEFIDELKERVDIVDVISEYVKLKKKGRN-----YVGLCPFHHEKTPSFSVSPEKQF 55

Query: 62  YYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTD--LIR 119
           Y+CF C   GD + FL  + G SF+E+V+ LA  AG+ LP    + EKKE+      L  
Sbjct: 56  YHCFGCGAGGDAIKFLMEIEGISFVEAVEELAKRAGIDLPFEKDQQEKKEQKSKRKKLYE 115

Query: 120 LIEVATDFFHHSLKNARDKRLHY-YLDERGIDSHAIEMFKLGYAPDSRYSLREHL-RQKG 177
           L+E+A  FF + LK+  + R    YL  RG+    I+ F+LGYAP++   L + L  +KG
Sbjct: 116 LLELAAKFFKNQLKHTPENRAALDYLQSRGLSDETIDRFELGYAPNNWDFLFDFLQNKKG 175

Query: 178 FSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSP 237
           F  E + EAGLL+  +N    YDRFRNR++FPI   +G+V+ FGGR L   E  KYLNSP
Sbjct: 176 FDLELLAEAGLLVKKENGKY-YDRFRNRIMFPIHDPKGRVVGFGGRAL-GDEKPKYLNSP 233

Query: 238 ETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSS 297
           ET LF K + LY    A    +K IRK+        +ILVEGYMDV++L QAG++N V+S
Sbjct: 234 ETPLFKKSELLYGLHKA----RKEIRKEKE------LILVEGYMDVIALHQAGIKNAVAS 283

Query: 298 LGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGE 357
           LGTALTE  ++LL + +  I+LCFDGD  G +AA +AI+L+L   I    V  + L  G+
Sbjct: 284 LGTALTEEHIKLLKRYADEIILCFDGDKAGRKAALRAIELLLPLGI---NVKVIKLPGGK 340

Query: 358 DPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKD 417
           DPD ++R  G  A +KL+  S  L++ L  R   N + +TP+E+A+L   L   I  I D
Sbjct: 341 DPDEYLRKEGVEALKKLLENSKSLIEFLIARLLSNYNLDTPEEKAKLVEELLPLIKKIPD 400

Query: 418 QKLRYYYSQAIRDRL 432
             LR YY Q +   L
Sbjct: 401 PILRDYYLQKLAQLL 415


>gnl|CDD|149368 pfam08275, Toprim_N, DNA primase catalytic core, N-terminal domain.
           
          Length = 128

 Score =  164 bits (418), Expect = 6e-41
 Identities = 63/129 (48%), Positives = 77/129 (59%), Gaps = 1/129 (0%)

Query: 127 FFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEA 186
           F+H  LK         YL  RG+    I+ F LGYAPD   +L  HL +KGF  E ++EA
Sbjct: 1   FYHELLKTKEGAAARDYLKSRGLSPETIKRFGLGYAPDGWDNLLNHLEKKGFDLELLLEA 60

Query: 187 GLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGK 246
           GLL+  ++    YDRFRNR++FPIR   G+V+ FGGR L   E  KYLNSPET LF KGK
Sbjct: 61  GLLVKREDGG-YYDRFRNRIMFPIRDESGRVVGFGGRALDDEEPPKYLNSPETPLFKKGK 119

Query: 247 NLYNFFGAL 255
            LY    A 
Sbjct: 120 VLYGLDEAK 128


>gnl|CDD|128681 smart00400, ZnF_CHCC, zinc finger. 
          Length = 55

 Score = 85.4 bits (212), Expect = 4e-17
 Identities = 26/55 (47%), Positives = 35/55 (63%)

Query: 39 YWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLA 93
          Y   CPFH EKTPSF  +  K F++CF C   G+ +SFL      SF+E+V++LA
Sbjct: 1  YKGLCPFHGEKTPSFSVSPDKQFFHCFGCGAGGNVISFLMKYDKLSFVEAVKKLA 55


>gnl|CDD|128769 smart00493, TOPRIM, topoisomerases, DnaG-type primases, OLD family
           nucleases and RecR proteins. 
          Length = 76

 Score = 66.5 bits (163), Expect = 2e-11
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 272 SFIILVEGYMDVLSLCQAGV--QNVVSSLGTALTEYQLRLLWKLSPR--IVLCFDGDDPG 327
             +I+VEG  D ++L +AG    NVV+  G  L +  ++LL +L+ +  ++L  D D  G
Sbjct: 1   KVLIIVEGPADAIALEKAGGFGGNVVALGGHLLKKEIIKLLKRLAKKKEVILATDPDREG 60

Query: 328 LRAAYKAIDLVLCH 341
              A+K  +L+   
Sbjct: 61  EAIAWKLAELLKPA 74


>gnl|CDD|129732 TIGR00646, MG010, DNA primase-related protein.  The DNA primase
           DnaG of E. coli and its apparent orthologs in other
           eubacterial species are approximately 600 residues in
           length. Within this set, a conspicuous outlier in
           percent identity, as seen in a UPGMA difference tree, is
           the branch containing the Mycoplasmas. This lineage is
           also unique in containing the small, DNA primase-related
           protein modelled by this alignment, which is homologous
           to the central third of DNA primase. Several small
           regions of sequence similarity specifically to
           Mycoplasma sequences rather than to all DnaG homologs
           suggests that the divergence of this protein from DnaG
           post-dated the separation of bacterial lineages. The
           function of this DNA primase-related protein is unknown.
          Length = 218

 Score = 38.4 bits (89), Expect = 0.005
 Identities = 41/162 (25%), Positives = 72/162 (44%), Gaps = 23/162 (14%)

Query: 171 EHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGES 230
            +L+++GF+ +  ++ G          +Y   +  L  P+ +  G +I F  R +   + 
Sbjct: 32  NYLKKRGFNLQDFLKVG-------GGLAYLGEKEWLNLPLYNFDGNLIGFLNRKVGFEK- 83

Query: 231 VKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAG 290
            ++L  P    F+K  +    F  L  L       +  NS   I LVEG  D L+  +AG
Sbjct: 84  -EFLYLP----FNKPPSKSEAFLGLKELP------IEDNS---IYLVEGDFDWLAFRKAG 129

Query: 291 VQNVVSSLGTALTEYQLRLL-WKLSPRIVLCFDGDDPGLRAA 331
           + N +   G  +++ Q++    K   +I +CFD D  G  AA
Sbjct: 130 ILNCLPLCGLTISDKQMKFFKQKKIEKIFICFDNDFAGKNAA 171


>gnl|CDD|150991 pfam10410, DnaB_bind, DnaB-helicase binding domain of primase.
           This domain is the C-terminal region three-helical
           domain of primase. Primases synthesize short RNA strands
           on single-stranded DNA templates, thereby generating the
           hybrid duplexes required for the initiation of synthesis
           by DNA polymerases. Primases are recruited to
           single-stranded DNA by helicases, and this domain is the
           region of the primase which binds DnaB-helicase. It is
           associated with the Toprim domain (pfam01751) which is
           the central catalytic core.
          Length = 59

 Score = 34.7 bits (81), Expect = 0.064
 Identities = 17/57 (29%), Positives = 25/57 (43%)

Query: 381 LVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQ 437
           L + L++R  E    +TP+ RA L       I  I D  LR  Y Q + + L    +
Sbjct: 1   LSEFLFRRLLEGYDLDTPEGRAALLREALPLIAKIPDPVLRELYLQELAELLGISEE 57


>gnl|CDD|177375 PHA02540, 61, DNA primase; Provisional.
          Length = 337

 Score = 34.2 bits (79), Expect = 0.11
 Identities = 12/30 (40%), Positives = 18/30 (60%)

Query: 205 RLIFPIRSSRGQVIAFGGRTLSKGESVKYL 234
           RL+ PI +  G++ +F GR L K    KY+
Sbjct: 173 RLVIPIFNKDGKIESFQGRALRKDAPQKYI 202


>gnl|CDD|103511 PRK08624, PRK08624, hypothetical protein; Provisional.
          Length = 373

 Score = 33.4 bits (76), Expect = 0.18
 Identities = 69/305 (22%), Positives = 104/305 (34%), Gaps = 83/305 (27%)

Query: 33  NAVKGDYWACCPFHDEKTPSFHCNDSKGFYY------CFSCHVKGDHLSFLSAL------ 80
           N   G       + +    +FHC    G  +      C    ++G  LSF  A+      
Sbjct: 43  NDGGGSTKLYY-YIEND--NFHCYTRCGDIFDVFELLCKRLKMEGKALSFSKAIRKITKI 99

Query: 81  LGCSFIESVQRLAAIAGVPLPVVD----PKIEKKEKIQTDLIRLIEVATDFFHHSLKNAR 136
           LG S+     +   I    L ++D     K EKKEKIQ  L    E   + F        
Sbjct: 100 LGLSYFYE-PKQQGIKPSFLKILDWVWTGKKEKKEKIQPQLKSFNENILNQF-------- 150

Query: 137 DKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSA 196
            K  +    + GI     + +++ +  D                                
Sbjct: 151 VKIPNRKWLDEGISEKTQKYWEIKFYLDV------------------------------- 179

Query: 197 TSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGE--SVKY--LNSPETILFH-KGKNLYNF 251
                   R+I P R   G++I   GR L K      KY  +   +T   H KGK LY  
Sbjct: 180 -----ISQRIIIPHRDESGELIGIRGRLLDKELVDKNKYFPIYVNDTGYNHPKGKILYGL 234

Query: 252 FGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQA--GVQN-VVSSLGTALTEYQLR 308
           +    Y+++  +K V        I+VE    VL       G  N VV+  G+ ++E Q  
Sbjct: 235 WQNKKYIKE--KKKV--------IIVESEKSVL-FSDKFYGEGNFVVAICGSNISEVQAE 283

Query: 309 LLWKL 313
            L +L
Sbjct: 284 KLLRL 288


>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein.  Function of MutS2 is
           unknown. It should not be considered a DNA mismatch
           repair protein. It is likely a DNA mismatch binding
           protein of unknown cellular function.
          Length = 771

 Score = 32.5 bits (74), Expect = 0.37
 Identities = 27/172 (15%), Positives = 63/172 (36%), Gaps = 20/172 (11%)

Query: 469 SSLVKGKLSKKPSLREAALLLTLINHPAI----LQEQYQELADIRYDNNELQKLWSFLFS 524
           S+L    L     L++ A +L   ++  +       +  E A + +D   L   +  L  
Sbjct: 421 SALAISILEY--LLKQNAQVLITTHYKELKALMYNNEGVENASVLFDEETLSPTYKLLKG 478

Query: 525 D-------FVEQKYFLPEEIHQRLCER--GFGE----LLKQLDRQVRDAGLWSATTEANI 571
                    + Q+Y +P  I ++       F E    L+++L    ++    +   E  +
Sbjct: 479 IPGESYAFEIAQRYGIPHFIIEQAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLL 538

Query: 572 VDVRQGYQQALALYKRFRLLSRQ-KEEIEKQIAQVTAKGEAEKTAILISILH 622
            +  +  ++     +  +   R  K E+EK+  +     + E  +I+  +  
Sbjct: 539 KEQEKLKKELEQEMEELKERERNKKLELEKEAQEALKALKKEVESIIRELKE 590


>gnl|CDD|179719 PRK04031, PRK04031, DNA primase; Provisional.
          Length = 408

 Score = 32.1 bits (74), Expect = 0.52
 Identities = 13/27 (48%), Positives = 20/27 (74%)

Query: 274 IILVEGYMDVLSLCQAGVQNVVSSLGT 300
           II+VEG  DVL+L + G++N ++  GT
Sbjct: 172 IIVVEGRADVLNLLRYGIKNAIAVEGT 198


>gnl|CDD|132284 TIGR03240, arg_catab_astD, succinylglutamic semialdehyde
           dehydrogenase.  Members of this protein family are
           succinylglutamic semialdehyde dehydrogenase (EC
           1.2.1.71), the fourth enzyme in the arginine
           succinyltransferase (AST) pathway for arginine
           catabolism.
          Length = 484

 Score = 30.8 bits (70), Expect = 1.2
 Identities = 24/100 (24%), Positives = 37/100 (37%), Gaps = 18/100 (18%)

Query: 545 GFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQA---------------LALYKRFR 589
           G GE     +       LW     A+   V      A               +A+ +RF 
Sbjct: 10  GQGESFSSTN-PATQEVLWQGAA-ASAAQVEAAVAAARAAFPAWARLSLEERIAVVQRFA 67

Query: 590 -LLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQI 628
            LL  +KE + + IA+ T K   E    + S++ +V I I
Sbjct: 68  ALLEERKEALARVIARETGKPLWETRTEVASMIGKVAISI 107


>gnl|CDD|148601 pfam07087, DUF1353, Protein of unknown function (DUF1353).  This
           family consists of several hypothetical bacterial
           proteins of around 100 residues in length. The function
           of this family is unknown.
          Length = 92

 Score = 29.5 bits (67), Expect = 2.9
 Identities = 15/43 (34%), Positives = 18/43 (41%), Gaps = 2/43 (4%)

Query: 518 LWSFLFSDFVEQKYFLPEEIHQRLCERGFGELLKQLDRQVRDA 560
           LWS     F + KY     IH  L  RG G   K+ D    +A
Sbjct: 34  LWSI-IPPF-DGKYLKAAVIHDYLYSRGIGRTRKEADAIFYEA 74


>gnl|CDD|184625 PRK14328, PRK14328, (dimethylallyl)adenosine tRNA
           methylthiotransferase; Provisional.
          Length = 439

 Score = 29.2 bits (66), Expect = 3.6
 Identities = 11/30 (36%), Positives = 18/30 (60%)

Query: 585 YKRFRLLSRQKEEIEKQIAQVTAKGEAEKT 614
           Y R R  SR+ E+I  +I ++ ++G  E T
Sbjct: 168 YVRGRERSRKPEDIIAEIKELVSEGYKEVT 197


>gnl|CDD|178531 PLN02945, PLN02945, nicotinamide-nucleotide
           adenylyltransferase/nicotinate-nucleotide
           adenylyltransferase.
          Length = 236

 Score = 28.9 bits (65), Expect = 4.0
 Identities = 24/94 (25%), Positives = 37/94 (39%), Gaps = 16/94 (17%)

Query: 163 PDSRYSLREH----LRQKGFSEEKIIEAG--LLIDGDNSATSYDRFRNRLIFPIRSSRGQ 216
              R   R++    +R++G   EK++     L  +  N     D   N     I S+R +
Sbjct: 153 DQVRTICRDYGVVCIRREGQDVEKLVSQDEILNENRGNILVVDDLVPNS----ISSTRVR 208

Query: 217 VIAFGGRTLSKGESVKYLNSPETILFHKGKNLYN 250
                   +S+G SVKYL     I + K   LY 
Sbjct: 209 ------ECISRGLSVKYLTPDGVIDYIKEHGLYM 236


>gnl|CDD|162972 TIGR02680, TIGR02680, conserved hypothetical protein TIGR02680.
           Members of this protein family belong to a conserved
           gene four-gene neighborhood found sporadically in a
           phylogenetically broad range of bacteria: Nocardia
           farcinica, Symbiobacterium thermophilum, and
           Streptomyces avermitilis (Actinobacteria), Geobacillus
           kaustophilus (Firmicutes), Azoarcus sp. EbN1 and
           Ralstonia solanacearum (Betaproteobacteria). Proteins in
           this family average over 1400 amino acids in length.
          Length = 1353

 Score = 29.0 bits (65), Expect = 4.2
 Identities = 45/212 (21%), Positives = 75/212 (35%), Gaps = 21/212 (9%)

Query: 418 QKLRYYYSQAIRDRLQQLFQKYITEHSGYGRYWKKNARHRDQKGPSQRLMQSSLVKGKLS 477
           Q+ R Y    +R R      +  +  + Y +  +   R RD+   ++   +    + +  
Sbjct: 254 QRYRRYARTMLRRRAT----RLRSAQTQYDQLSRDLGRARDELETAREEERELDARTEAL 309

Query: 478 KKPSLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEI 537
           ++ +      L  L   PA   +  +EL   R D   LQ   +      + +     EE 
Sbjct: 310 EREADALRTRLEALQGSPAY--QDAEELERARADAEALQAAAADARQA-IREAESRLEEE 366

Query: 538 HQRL---------CERGFGELLKQLDRQVRDAGLWSA-TTEANIVDVRQGYQQALALYKR 587
            +RL          ER      +QL R    AGL  A T E +     Q  Q+  AL  R
Sbjct: 367 RRRLDEEAGRLDDAERELRAAREQLARAAERAGLSPAHTAEPDAALAAQELQELGALDAR 426

Query: 588 FRLLSRQKEEIEKQIA----QVTAKGEAEKTA 615
            +   R   +  +Q+A    +      AE T 
Sbjct: 427 RQDADRVIAQRSEQVALLRRRDDVADRAEATH 458


>gnl|CDD|165993 PLN02352, PLN02352, phospholipase D epsilon.
          Length = 758

 Score = 28.7 bits (64), Expect = 4.6
 Identities = 12/23 (52%), Positives = 15/23 (65%)

Query: 619 SILHEVHIQIHQIESQEAMIEGF 641
           SIL   HIQ HQI ++ + I GF
Sbjct: 85  SILGRFHIQAHQIVTEASFINGF 107


>gnl|CDD|152291 pfam11855, DUF3375, Protein of unknown function (DUF3375).  This
           family of proteins are functionally uncharacterized.
           This protein is found in bacteria. Proteins in this
           family are typically between 479 to 499 amino acids in
           length.
          Length = 471

 Score = 28.5 bits (64), Expect = 5.4
 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 9/79 (11%)

Query: 544 RGFGELLKQLDRQVRDA-GLWSATTEANIVDVRQGY------QQALALYKRFRLL--SRQ 594
           R   +  +QLDRQ+R+    W  +    + ++  GY       Q  +    +  L    +
Sbjct: 192 RRVEDNFRQLDRQLRERIIDWDGSRGEVLEEIFDGYDAIADSDQGRSFRAFWDFLLDPER 251

Query: 595 KEEIEKQIAQVTAKGEAEK 613
           +EE+++ +  V A+  A+ 
Sbjct: 252 QEELDELLRAVLARPPAQG 270


>gnl|CDD|184265 PRK13709, PRK13709, conjugal transfer nickase/helicase TraI;
           Provisional.
          Length = 1747

 Score = 28.6 bits (64), Expect = 5.6
 Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 14/73 (19%)

Query: 545 GFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIAQ 604
            F EL  +++ Q++   L         VDV +GY   L       L+SR   E EK I +
Sbjct: 899 SFTELGGEINAQIKRGDLLY-------VDVAKGYGTGL-------LVSRASYEAEKSILR 944

Query: 605 VTAKGEAEKTAIL 617
              +G+   T ++
Sbjct: 945 HILEGKEAVTPLM 957


>gnl|CDD|135648 PRK05898, dnaE, DNA polymerase III DnaE; Validated.
          Length = 971

 Score = 28.3 bits (63), Expect = 6.0
 Identities = 13/48 (27%), Positives = 23/48 (47%)

Query: 529 QKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQ 576
           Q   +  EI ++LC  G  + L   D QV+   +     E +I++ +Q
Sbjct: 222 QNSIISSEILKQLCISGLNKRLNANDGQVKKIYVKRLKYELDIINEKQ 269


>gnl|CDD|116857 pfam08273, Prim_Zn_Ribbon, Zinc-binding domain of
          primase-helicase. 
          Length = 39

 Score = 28.2 bits (63), Expect = 6.2
 Identities = 8/17 (47%), Positives = 11/17 (64%)

Query: 56 NDSKGFYYCFSCHVKGD 72
           D +G ++CFSC   GD
Sbjct: 21 KDGRGTWFCFSCGYAGD 37


>gnl|CDD|148586 pfam07061, Swi5, Swi5.  Swi5 is involved in meiotic DNA repair
           synthesis and meiotic joint molecule formation. It is
           known to interact with Swi2, Rhp51 and Swi6.
          Length = 81

 Score = 28.0 bits (63), Expect = 6.9
 Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 580 QALALYKRFRLLSRQKEEIEKQIAQVTAKGEAEKT-AILISILHE 623
           +  +L      L  Q +++E  IA++ A+ + EKT    I +LHE
Sbjct: 1   KLSSLLASIAELKAQADQLESLIAELKAEQDPEKTVKRHIRLLHE 45


>gnl|CDD|184853 PRK14851, PRK14851, hypothetical protein; Provisional.
          Length = 679

 Score = 28.3 bits (63), Expect = 7.0
 Identities = 22/96 (22%), Positives = 38/96 (39%), Gaps = 9/96 (9%)

Query: 376 VESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQL 435
               PL D +WKR T  + ++       +   LK  I  I    L +      RD+L++L
Sbjct: 422 HTKDPLADHIWKRCTNRKPYSKRPLPEWVLNDLKTRIRSIPGAHLHFITG---RDQLRKL 478

Query: 436 FQ------KYITEHSGYGRYWKKNARHRDQKGPSQR 465
            +      +  TEH G   ++    R   ++   +R
Sbjct: 479 AKVIYLADRIRTEHQGLHEHFTSMIRFNMKEALQKR 514


>gnl|CDD|172030 PRK13397, PRK13397, 3-deoxy-7-phosphoheptulonate synthase;
           Provisional.
          Length = 250

 Score = 28.1 bits (62), Expect = 7.7
 Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 3/53 (5%)

Query: 217 VIAFGGRTLSKGESVKYLNSPET-ILFHKG--KNLYNFFGALNYLQKSIRKDV 266
           VI  G R +   E +K L+  +  ILF +G    +  + GAL+YLQ + + ++
Sbjct: 101 VIQVGARNMQNFEFLKTLSHIDKPILFKRGLMATIEEYLGALSYLQDTGKSNI 153


>gnl|CDD|183751 PRK12794, flaF, flagellar biosynthesis regulatory protein FlaF;
           Reviewed.
          Length = 122

 Score = 28.0 bits (63), Expect = 8.6
 Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 3/39 (7%)

Query: 503 QELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRL 541
             LA+  + N   +KLWS   SD  +    LP E+  R+
Sbjct: 45  AALAEALHFN---RKLWSIFASDVADPDNPLPIELRARI 80


  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
   0.322    0.139    0.413 

Gapped
Lambda     K      H
   0.267   0.0678    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 10,858,693
Number of extensions: 727589
Number of successful extensions: 1637
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1618
Number of HSP's successfully gapped: 40
Length of query: 648
Length of database: 5,994,473
Length adjustment: 100
Effective length of query: 548
Effective length of database: 3,833,673
Effective search space: 2100852804
Effective search space used: 2100852804
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)