RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780229|ref|YP_003064642.1| hypothetical protein
CLIBASIA_00570 [Candidatus Liberibacter asiaticus str. psy62]
         (1775 letters)



>gnl|CDD|161845 TIGR00376, TIGR00376, DNA helicase, putative.  The gene product may
            represent a DNA helicase. Eukaryotic members of this
            family have been characterized as binding certain
            single-stranded G-rich DNA sequences (GGGGT and GGGCT). A
            number of related proteins are characterized as
            helicases.
          Length = 637

 Score = 66.4 bits (162), Expect = 6e-11
 Identities = 65/297 (21%), Positives = 116/297 (39%), Gaps = 69/297 (23%)

Query: 1358 KDVKFDLVIMDESSQIKPEDALGVIARGKQIVVVGDPKQLPPTRFFDHDNDQEDYDEEVA 1417
            K  +FD+ ++DE+SQ      L  + + +++++ GD KQLPPT    HD ++        
Sbjct: 358  KGWEFDVAVIDEASQAMEPSCLIPLLKARKLILAGDHKQLPPT-ILSHDAEE-------- 408

Query: 1418 AVSQTESILDALLPLFSMRR--LQWHYRSLNENLIACSNYYFYDNSLIVFPS-------- 1467
                  ++ + L+  +  R   L   YR +N+ ++   +  FY+  L    S        
Sbjct: 409  ---LELTLFERLIKEYPERSRTLNVQYR-MNQKIMEFPSREFYNGKLTAHESVANILLRD 464

Query: 1468 -----------------PYTSVDRYGVGFTHVKNGVVVDQGNPEEARVIALAVKDHALRY 1510
                             P   +D  G     +K      + NP EA +++  ++   ++ 
Sbjct: 465  LPKVEATDSEDDLETEIPLLFIDTSGCELFELKEADSTSKYNPGEAELVSEIIQA-LVKM 523

Query: 1511 --PEESLGVIAMNAKQRDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENVQGDE 1568
              P   +GVI     Q DL+   +     +  ++E              + +++  QG E
Sbjct: 524  GVPANDIGVITPYDAQVDLLRQLLEH---RHIDIE--------------VSSVDGFQGRE 566

Query: 1569 RDRIFISFTYGPHEPGGRVFQRFGPINSDIGWRRLNVLFTRSRRRIEVFSTMRYLDV 1625
            ++ I ISF             R G +      RRLNV  TR+RR++ V    R L  
Sbjct: 567  KEVIIISFVRS---------NRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSN 614



 Score = 60.6 bits (147), Expect = 4e-09
 Identities = 67/296 (22%), Positives = 119/296 (40%), Gaps = 43/296 (14%)

Query: 316 IEESKSHWAVRRYGVLGLLNFSKMLMYLDLDHLRWPEGEDNIL-NHDIIQRLFIAQSCDH 374
           +EES   W+++R  +    N        D+   R  E    +  NH  +    + +    
Sbjct: 92  LEESVPQWSLKRVRIDLYAN--------DVTFKRMKEALRALTENHSRLLEFILGREAPS 143

Query: 375 DKDNASSNQNIEYKIDEIEDIHQRCPLIDDSDSSQHSAVIDVINGKNL-IIEGPPGTGKS 433
                   Q  +  ++E                SQ  AV   ++ K+L +I GPPGTGK+
Sbjct: 144 KASEIHDFQFFDPNLNE----------------SQKEAVSFALSSKDLFLIHGPPGTGKT 187

Query: 434 QTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLGEFCLEL-HSHKVHKRAILDD 492
           +T+  +I   +  G ++L  A    A++ +  RL  A   +  + L H  ++ K      
Sbjct: 188 RTLVELIRQLVKRGLRVLVTAPSNIAVDNLLERL--ALCDQKIVRLGHPARLLKSNKQHS 245

Query: 493 LRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQIWKNTELSIHQILMGAAR-- 550
           L   I+N     +  +I  +I   +EL  + N+  +   Q  +   LS  +IL  A +  
Sbjct: 246 LDYLIENHPKYQIVADIREKI---DELIEERNKKLKPSPQKRRG--LSDIKILRKALKKR 300

Query: 551 -YRHNLPLDPVQLHVEGLSGENADRLLRS------RLEDQIKAFKDVIVEFHKQAG 599
             R    L    +     + ++ DRLL+       R+E++I A  DV+   +  AG
Sbjct: 301 EARGIESLKIASMAEWIETNKSIDRLLKLLPEIEERIENEILAESDVVQSTNSSAG 356


>gnl|CDD|162366 TIGR01448, recD_rel, helicase, putative, RecD/TraA family.  This
           model describes a family similar to RecD, the
           exodeoxyribonuclease V alpha chain of TIGR01447. Members
           of this family, however, are not found in a context of
           RecB and RecC and are longer by about 200 amino acids at
           the amino end. Chlamydia muridarum has both a member of
           this family and a RecD.
          Length = 720

 Score = 39.8 bits (93), Expect = 0.006
 Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 2/51 (3%)

Query: 406 DSSQHSAVIDVINGKNLIIEGPPGTGKSQTITNIIA-AAMLHG-KKILFCA 454
              Q  A+   I  K +I+ G PGTGK+     II  A  L G   +   A
Sbjct: 325 SEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAA 375



 Score = 30.9 bits (70), Expect = 3.0
 Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 4/53 (7%)

Query: 1350 SVANYLEPKDVKFDLVIMDESSQIKPEDA---LGVIARGKQIVVVGDPKQLPP 1399
               N+LE   +  DL+I+DESS +    A   L  +    ++++VGD  QLP 
Sbjct: 406  FRHNHLEDP-IDCDLLIVDESSMMDTWLALSLLAALPDHARLLLVGDTDQLPS 457


>gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular
           activities.  AAA - ATPases associated with a variety of
           cellular activities. This profile/alignment only detects
           a fraction of this vast family. The poorly conserved
           N-terminal helix is missing from the alignment.
          Length = 148

 Score = 37.0 bits (85), Expect = 0.042
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 25/166 (15%)

Query: 419 GKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLGEFCLE 478
           G+ ++I GPPG+GK+     +       G  +++   +    EV+   L     G+    
Sbjct: 2   GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKK--- 58

Query: 479 LHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQIWKNTE 538
                      L              +   +D EIT   + + +      E  ++    +
Sbjct: 59  ---ASGSGELRLRLALALARKLKPDVLI--LD-EITSLLDAEQEALLLLLEELRLLLLLK 112

Query: 539 LSIHQILMGAARYRHNLPLDPVQLHVEGLSGENADRLLRSRLEDQI 584
              +  ++       +L                   LLR R + +I
Sbjct: 113 SEKNLTVILTTNDEKDL----------------GPALLRRRFDRRI 142


>gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown
           domain fusion protein; Reviewed.
          Length = 725

 Score = 36.6 bits (85), Expect = 0.065
 Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 16/62 (25%)

Query: 421 NLIIEGPPGTGKSQTITNIIA----------AAMLHGKKILFCAQKMAAIEVVRHRLEKA 470
           +LI+ GPPG GK+ T+  IIA           A+L G K L      A ++  + RLE+ 
Sbjct: 54  SLILYGPPGVGKT-TLARIIANHTRAHFSSLNAVLAGVKDL-----RAEVDRAKERLERH 107

Query: 471 GL 472
           G 
Sbjct: 108 GK 109


>gnl|CDD|184869 PRK14867, PRK14867, DNA topoisomerase VI subunit B; Provisional.
          Length = 659

 Score = 34.8 bits (80), Expect = 0.22
 Identities = 47/199 (23%), Positives = 90/199 (45%), Gaps = 33/199 (16%)

Query: 979  FKRIQKLHCDELSKKITKVFGRIQELEQFLPKQKELQN-RSALFVGEGNVFDSLIQ-RLS 1036
              ++  +   ELS+  TK   RI+ELE+++ +   L+N R ++F      +D+++   L+
Sbjct: 251  SSKVSSMLNSELSRVTTK---RIKELEEYVLRDLLLENYRDSVF------WDTVVSCYLN 301

Query: 1037 HN----FDPWQNWFKEDEI-----LLQEAQEFSAKLHKIREKNIVLAEESLIKKFFGEEI 1087
             +    FD + ++F + EI     L+    E   +L     K +V+  E L  K   EEI
Sbjct: 302  FDFTKYFDKYGHYFDKKEIEDVKMLINGLPESLGELKTYCLKYLVM--EYLFNKLDEEEI 359

Query: 1088 KLSVFDSNTKESNKSLAVINSTLEFAH-SIRERVLFDELIQGINHIDDHTIYNSFIKDLK 1146
            K        +  N       + +E+A  +     L DE  + + +I        F+K+LK
Sbjct: 360  K--------EIKNHFKKKPENFMEWAEKNYLNASLLDEFRKKVKNITKSP--EEFVKELK 409

Query: 1147 NLRMIWQQQVKTQEDFIED 1165
            +  M+  ++++     I+D
Sbjct: 410  DKAMVSDEELEKYRKEIKD 428


>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
            beta/beta'; Reviewed.
          Length = 2890

 Score = 33.4 bits (76), Expect = 0.50
 Identities = 22/102 (21%), Positives = 48/102 (47%), Gaps = 15/102 (14%)

Query: 1060 SAKLHKIREKNIVLAE---ESLIKKFFGEEI---KLSVFDSNTKESNKSLAVINSTLEFA 1113
            S K+ +++E ++   E   + L+ +   E +   K  + D  T+     L  I+      
Sbjct: 273  SRKIKELKENHLEWVEYPMDILLNRHLAEPVMVGKEVLLDMLTQLDKNKLEKIHD----- 327

Query: 1114 HSIRERVLFDELIQGINHIDDHTIYNSFIKDLKNLRMIWQQQ 1155
              ++E V+ ++L  G     D +I +SF  D ++L+++ Q +
Sbjct: 328  LGVQEFVIINDLALGH----DASIIHSFSADSESLKLLKQTE 365


>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
          Length = 319

 Score = 33.2 bits (76), Expect = 0.62
 Identities = 28/85 (32%), Positives = 42/85 (49%), Gaps = 20/85 (23%)

Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQKMA----------AIEVVRHRL 467
           N  NLI+ GPPGTGK+   T+I+A A     ++L    K A           I+VVR+++
Sbjct: 33  NMPNLILSGPPGTGKT---TSILALA----HELLGPNYKEAVLELNASDDRGIDVVRNKI 85

Query: 468 EKAGLGEFCLELHSHKVHKRAILDD 492
           +     +  L    HK+    ILD+
Sbjct: 86  KMFAQKKVTLPPGRHKI---VILDE 107


>gnl|CDD|148013 pfam06152, Phage_min_cap2, Phage minor capsid protein 2.  Family of
           related phage minor capsid proteins.
          Length = 361

 Score = 32.0 bits (73), Expect = 1.3
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 140 IREIEKKIEISLQKLTSIIQNYGYADIEDLERAIKE--NKPLKPPHFQNNLSDNQIQTAY 197
           I+ I K   ++ + +T +I+N G   I+D+++ + E  NK L      N  +        
Sbjct: 65  IKLIAKYTGVAEEAITRVIKNAGLKIIKDIDKQLSEALNKGLGADPESNFQTIVDKVLNA 124

Query: 198 FQDKLESILRLIN 210
           +Q +  S L L+N
Sbjct: 125 YQRQAWSDLNLVN 137


>gnl|CDD|163008 TIGR02768, TraA_Ti, Ti-type conjugative transfer relaxase TraA.  This
            protein contains domains distinctive of a single strand
            exonuclease (N-terminus, MobA/MobL, pfam03389) as well as
            a helicase domain (central region, homologous to the
            corresponding region of the F-type relaxase TraI,
            TIGR02760). This protein likely fills the same role as
            TraI(F), nicking (at the oriT site) and unwinding the
            coiled plasmid prior to conjugative transfer.
          Length = 744

 Score = 31.7 bits (72), Expect = 1.5
 Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 4/41 (9%)

Query: 1363 DLVIMDESSQIKPEDALGVIA----RGKQIVVVGDPKQLPP 1399
            D++++DE+  +       V+      G ++V+VGDP+QL P
Sbjct: 441  DVLVIDEAGMVGSRQMARVLKEAEEAGAKVVLVGDPEQLQP 481


>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
          Length = 269

 Score = 31.8 bits (72), Expect = 1.6
 Identities = 15/35 (42%), Positives = 21/35 (60%)

Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452
            G NL++ GPPG GKS     I  A + +G ++LF
Sbjct: 105 KGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLF 139


>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
          Length = 254

 Score = 31.8 bits (72), Expect = 1.7
 Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 406 DSSQHSAVIDVINGK-NLIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452
           D+  H   +D + GK N++  GPPGTGK+     +   A   G ++LF
Sbjct: 84  DTIAHLGTLDFVTGKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLF 131


>gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
          Length = 413

 Score = 31.6 bits (73), Expect = 1.9
 Identities = 13/24 (54%), Positives = 18/24 (75%), Gaps = 1/24 (4%)

Query: 421 NLIIEGPPGTGKSQTITNIIAAAM 444
           ++I+ GPPGTGK+ T+  IIA A 
Sbjct: 38  SMILWGPPGTGKT-TLARIIAGAT 60


>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus.  This family consists of the
           C-terminal region of several eukaryotic and archaeal
           RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
           or TIP49b) proteins. The N-terminal domain contains the
           pfam00004 domain. In zebrafish, the liebeskummer (lik)
           mutation, causes development of hyperplastic embryonic
           hearts. lik encodes Reptin, a component of a
           DNA-stimulated ATPase complex. Beta-catenin and Pontin,
           a DNA-stimulated ATPase that is often part of complexes
           with Reptin, are in the same genetic pathways. The
           Reptin/Pontin ratio serves to regulate heart growth
           during development, at least in part via the
           beta-catenin pathway. TBP-interacting protein 49 (TIP49)
           was originally identified as a TBP-binding protein, and
           two related proteins are encoded by individual genes,
           tip49a and b. Although the function of this gene family
           has not been elucidated, they are supposed to play a
           critical role in nuclear events because they interact
           with various kinds of nuclear factors and have DNA
           helicase activities.TIP49a has been suggested to act as
           an autoantigen in some patients with autoimmune
           diseases.
          Length = 395

 Score = 31.5 bits (72), Expect = 2.0
 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 9/55 (16%)

Query: 417 INGKNLIIEGPPGTGKSQTITNIIAAAMLH--GKKILFCAQKMAAIEVVRHRLEK 469
           I G+ ++I GPPGTGK+      +A A+    G+   FC   ++  EV    ++K
Sbjct: 48  IAGRAVLIAGPPGTGKTA-----LAIAISKELGEDTPFCP--ISGSEVYSLEMKK 95


>gnl|CDD|162341 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
            putative.  This model represents a family of proteins in
            Gram-positive bacteria. The N-terminal region of about
            200 amino acids resembles the epsilon subunit of E. coli
            DNA polymerase III and the homologous region of the
            Gram-positive type DNA polymerase III alpha subunit. The
            epsilon subunit contains an exonuclease domain. The
            remainder of this protein family resembles a predicted
            ATP-dependent helicase, the DNA damage-inducible protein
            DinG of E. coli.
          Length = 850

 Score = 31.3 bits (71), Expect = 2.1
 Identities = 53/246 (21%), Positives = 86/246 (34%), Gaps = 46/246 (18%)

Query: 977  QLFKRIQKLHCDELSKKI----TKVFGRIQELEQFLPKQKELQNRSALFVGEGNVFDSLI 1032
            QL KRIQ+L   E+ +K+    TK   +  +        K LQ  S L        D L 
Sbjct: 483  QLLKRIQQLEKQEILEKLFDFETKDILKDLQAIL-DKLNKLLQIFSELSH---KTVDQLR 538

Query: 1033 ---QRLSHNFDPWQNWFKEDEILLQEAQEFSAKLHKIREKNIVLAEESLIKKFFGEEIKL 1089
                 L  +F   +   KE        +    K             + L K+        
Sbjct: 539  KFDLALKDDFKNIEQSLKEGHTSWISIENLQQKSTIRLYIKDYEVGDVLTKRLL------ 592

Query: 1090 SVFDSNTKESNKSLAVINSTLEFAHSIRERVLFDELIQGINHIDDH--TIYNSFIKDLKN 1147
                       KSL   ++TL+F+HS      F+   Q +   D H  TI  + +   +N
Sbjct: 593  --------PKFKSLIFTSATLKFSHS------FESFPQLLGLTDVHFNTIEPTPLNYAEN 638

Query: 1148 LRMIWQQQVKTQEDFIEDTQLDMAQWAARCNDELVKLISRNSEAIKKPRWLNGWVN--LM 1205
                  Q+V    D        + ++A      ++++      AI  P+ L  + +  ++
Sbjct: 639  ------QRVLIPTDAPAIQNKSLEEYAQEIASYIIEI-----TAITSPKILVLFTSYEML 687

Query: 1206 HMVQDM 1211
            HMV DM
Sbjct: 688  HMVYDM 693


>gnl|CDD|180288 PRK05850, PRK05850, acyl-CoA synthetase; Validated.
          Length = 578

 Score = 31.5 bits (72), Expect = 2.3
 Identities = 34/112 (30%), Positives = 47/112 (41%), Gaps = 29/112 (25%)

Query: 1463 IVFPSPYTSVD---RYG-VGFTH---------VKNGVVVDQGN--PE--EA--------R 1497
            +V PSP T      R G +GF           +K+ ++VD  N  P+  EA        R
Sbjct: 426  LVDPSPGTPEGPWLRTGDLGFISEGELFIVGRIKDLLIVDGRNHYPDDIEATIQEITGGR 485

Query: 1498 VIALAVKDHALRYPEESLGVIAMNAKQRDLIESTINKLCRKDSEVEKAISKL 1549
            V A++V D       E L  I    K+ D  E  +++L     EV  AISK 
Sbjct: 486  VAAISVPDDG----TEKLVAIIELKKRGDSDEEAMDRLRTVKREVTSAISKS 533


>gnl|CDD|128765 smart00489, DEXDc3, DEAD-like helicases superfamily. 
          Length = 289

 Score = 31.2 bits (71), Expect = 2.4
 Identities = 25/119 (21%), Positives = 45/119 (37%), Gaps = 31/119 (26%)

Query: 418 NGKNLIIEGPPGTGKSQT-ITNIIAAAMLHGKKILFCAQKMAAIEVVR--HRLEKAGLGE 474
            GK  I+E P GTGK+ + +   +       ++I    QK+  I + R    +EK     
Sbjct: 26  RGKIGILESPTGTGKTLSLLCLTLTWLRSFPERI----QKIKLIYLSRTVSEIEKR---- 77

Query: 475 FCLELHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQI 533
                          L++LRK +          E D E  +  +L  +L +   ++  +
Sbjct: 78  ---------------LEELRKLMQKV-----EYESDEESEKQAQLLHELGREKPKVLGL 116


>gnl|CDD|128764 smart00488, DEXDc2, DEAD-like helicases superfamily. 
          Length = 289

 Score = 31.2 bits (71), Expect = 2.4
 Identities = 25/119 (21%), Positives = 45/119 (37%), Gaps = 31/119 (26%)

Query: 418 NGKNLIIEGPPGTGKSQT-ITNIIAAAMLHGKKILFCAQKMAAIEVVR--HRLEKAGLGE 474
            GK  I+E P GTGK+ + +   +       ++I    QK+  I + R    +EK     
Sbjct: 26  RGKIGILESPTGTGKTLSLLCLTLTWLRSFPERI----QKIKLIYLSRTVSEIEKR---- 77

Query: 475 FCLELHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQI 533
                          L++LRK +          E D E  +  +L  +L +   ++  +
Sbjct: 78  ---------------LEELRKLMQKV-----EYESDEESEKQAQLLHELGREKPKVLGL 116


>gnl|CDD|184408 PRK13937, PRK13937, phosphoheptose isomerase; Provisional.
          Length = 188

 Score = 31.4 bits (72), Expect = 2.4
 Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 8/42 (19%)

Query: 439 IIAAAMLHGKKILFC--------AQKMAAIEVVRHRLEKAGL 472
            +  A+ +G KIL C        AQ +AA  V R + E+  L
Sbjct: 30  ALIEALANGGKILLCGNGGSAADAQHIAAELVGRFKKERPAL 71


>gnl|CDD|162365 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit.  This
           family describes the exodeoxyribonuclease V alpha
           subunit, RecD. RecD is part of a RecBCD complex. A
           related family in the Gram-positive bacteria separates
           in a phylogenetic tree, has an additional N-terminal
           extension of about 200 residues, and is not supported as
           a member of a RecBCD complex by neighboring genes. The
           related family is consequently described by a different
           model.
          Length = 586

 Score = 30.9 bits (70), Expect = 3.1
 Identities = 12/34 (35%), Positives = 18/34 (52%)

Query: 409 QHSAVIDVINGKNLIIEGPPGTGKSQTITNIIAA 442
           Q  AV   +     +I G PGTGK+ T+  ++ A
Sbjct: 150 QKVAVALALKSNFSLITGGPGTGKTTTVARLLLA 183


>gnl|CDD|183903 PRK13230, PRK13230, nitrogenase reductase-like protein; Reviewed.
          Length = 279

 Score = 30.9 bits (70), Expect = 3.4
 Identities = 14/32 (43%), Positives = 17/32 (53%)

Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451
           +     G  G GKS T+ NI AA    GKK+L
Sbjct: 2   RKFCFYGKGGIGKSTTVCNIAAALAESGKKVL 33


>gnl|CDD|181609 PRK09009, PRK09009, C factor cell-cell signaling protein;
            Provisional.
          Length = 235

 Score = 30.8 bits (70), Expect = 3.7
 Identities = 21/105 (20%), Positives = 38/105 (36%), Gaps = 22/105 (20%)

Query: 1135 HTIYNSFIKDLKNLRMIWQQQVKTQEDFIEDTQLDMAQWAARCNDELVKLISRNSEAIKK 1194
            H  Y     D ++  + W               LD+       ++  +K +S     +  
Sbjct: 30   HATYRHHKPDFQHDNVQWHA-------------LDV------TDEAEIKQLSEQFTQLD- 69

Query: 1195 PRWLNGWVNLMHMVQDMQDKGLKEIQAAIFNNSLDVKYLESSLLA 1239
              WL   V ++H      +K L+ + A  F  ++ +  L S LLA
Sbjct: 70   --WLINCVGMLHTQDKGPEKSLQALDADFFLQNITLNTLPSLLLA 112


>gnl|CDD|153048 pfam12614, RRF_GI, Ribosome recycling factor.  This family of
            proteins is found in bacteria and viruses. Proteins in
            this family are approximately 130 amino acids in length.
            There are two conserved sequence motifs: LPS and LKR.
            Overproduction of ribosome recycling factor (RRF) reduces
            tna operon expression and increases the rate of cleavage
            of TnaC-tRNA(2)(Pro), relieving the growth inhibition
            associated with plasmid-mediated tnaC overexpression.
          Length = 128

 Score = 30.4 bits (69), Expect = 3.9
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 2/49 (4%)

Query: 1725 DRLRQEVLERMGWRIRRIWSVDWFSNPDEVIEPIIRELRELISQKSSST 1773
            D+L+ E  E   + IR+I +        + +EP+  +L  LI Q  + T
Sbjct: 58   DQLKTEEYEEFRYLIRKIEAA--LLLHSDKLEPLEDKLIRLIPQNPNIT 104


>gnl|CDD|161955 TIGR00608, radc, DNA repair protein radc.  This family is based on
           the phylogenomic analysis of JA Eisen (1999, Ph.D.
           Thesis, Stanford University).
          Length = 218

 Score = 30.5 bits (69), Expect = 4.2
 Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 15/69 (21%)

Query: 627 SSLENWQSALIKWQKD--HE-------VFLNRYGVQNQRQRLLYWQGQLLAAVDQVPSLP 677
             + + ++A      D  HE       +FL+R      + RL+  +   +  V+ VP  P
Sbjct: 95  PVIRSPEAAAEFLHTDLAHETREHFMVLFLDR------KNRLIAKEVVFIGTVNHVPVHP 148

Query: 678 RVICFKAFK 686
           R I  +A K
Sbjct: 149 REIFKEALK 157


>gnl|CDD|162286 TIGR01287, nifH, nitrogenase iron protein.  This model describes
           nitrogenase (EC 1.18.6.1) iron protein, also called
           nitrogenase reductase or nitrogenase component II. This
           model includes molybdenum-iron nitrogenase reductase
           (nifH), vanadium-iron nitrogenase reductase (vnfH), and
           iron-iron nitrogenase reductase (anfH). The model
           excludes the homologous protein from the
           light-independent protochlorophyllide reductase.
          Length = 275

 Score = 30.4 bits (69), Expect = 4.3
 Identities = 14/32 (43%), Positives = 18/32 (56%)

Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451
           + + I G  G GKS T  NI AA    GKK++
Sbjct: 1   RQIAIYGKGGIGKSTTTQNIAAALAEMGKKVM 32


>gnl|CDD|183073 PRK11281, PRK11281, hypothetical protein; Provisional.
          Length = 1113

 Score = 30.3 bits (69), Expect = 4.4
 Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 12/50 (24%)

Query: 15  DMRRKLLDCSVQ-NKLL--------NFRMDQQSVLRIFNTSPNQLYQQIF 55
           D RR+LLD   Q NK L        N +++QQ +L + ++  + L QQIF
Sbjct: 410 DERRELLD---QLNKQLNNQLNLAINLQLNQQQLLSVSDSLQSTLTQQIF 456


>gnl|CDD|178717 PLN03173, PLN03173, chalcone synthase; Provisional.
          Length = 391

 Score = 30.4 bits (68), Expect = 4.5
 Identities = 13/36 (36%), Positives = 20/36 (55%)

Query: 1234 ESSLLAAIYHQLSQEILTEKPHLMHYSAVQFTAKQE 1269
            E S++   Y  L++EIL E P +  Y A    A+Q+
Sbjct: 61   EKSMIKKRYMHLTEEILKENPSVCEYMAPSLDARQD 96


>gnl|CDD|182067 PRK09767, PRK09767, hypothetical protein; Provisional.
          Length = 117

 Score = 30.4 bits (68), Expect = 4.6
 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 1708 IECDGAMYNSAKSARDRDRLRQEVLERMGWRIRRIWSVDWFSNPDEVIEPIIREL 1762
            +E DG  ++ A +   R   R   LE  GW + R W+ +   N + V+E I++EL
Sbjct: 59   VELDGGQHDLAVAYDTR---RTSWLESQGWTVLRFWNNEIDCNEEAVLEIILQEL 110


>gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional.
          Length = 880

 Score = 30.0 bits (68), Expect = 5.0
 Identities = 19/91 (20%), Positives = 47/91 (51%), Gaps = 17/91 (18%)

Query: 107 EYDSDDEKKNYQVLQKVRDL----------IVEDIKTSNDLV-DIREIEKKI---EISLQ 152
           +Y+ ++ +K  +  +K+++           + ++++   +L   + E+EKK+   E  L 
Sbjct: 514 KYNLEELEKKAEEYEKLKEKLIKLKGEIKSLKKELEKLEELKKKLAELEKKLDELEEELA 573

Query: 153 KLTSIIQNYGYADIEDLERAIKENKPLKPPH 183
           +L   ++  G+  +E+LE  +KE   L+P +
Sbjct: 574 ELLKELEELGFESVEELEERLKE---LEPFY 601


>gnl|CDD|185348 PRK15451, PRK15451, tRNA cmo(5)U34 methyltransferase; Provisional.
          Length = 247

 Score = 30.0 bits (67), Expect = 5.6
 Identities = 12/31 (38%), Positives = 19/31 (61%)

Query: 1100 NKSLAVINSTLEFAHSIRERVLFDELIQGIN 1130
            N S+ V+N TL+F      + L D++ QG+N
Sbjct: 125  NASMVVLNFTLQFLEPSERQALLDKIYQGLN 155


>gnl|CDD|150993 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling protein
           DNA-binding domain.  The plasmid conjugative coupling
           protein TrwB forms hexamers from six structurally very
           similar protomers. This hexamer contains a central
           channel running from the cytosolic pole (made up by the
           AADs) to the membrane pole ending at the transmembrane
           pore shaped by 12 transmembrane helices, rendering an
           overall mushroom-like structure. The TrwB_AAD (all-alpha
           domain) domain appears to be the DNA-binding domain of
           the structure. TrwB, a basic integral inner-membrane
           nucleoside-triphosphate-binding protein, is the
           structural prototype for the type IV secretion system
           coupling proteins, a family of proteins essential for
           macromolecular transport between cells and export.
          Length = 386

 Score = 29.9 bits (68), Expect = 5.7
 Identities = 8/32 (25%), Positives = 18/32 (56%)

Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451
           ++++I G  GTGK+Q +  ++      G + +
Sbjct: 16  QHILIVGTTGTGKTQALRELLDQIRARGDRAI 47


>gnl|CDD|130348 TIGR01281, DPOR_bchL, light-independent protochlorophyllide
           reductase, iron-sulfur ATP-binding protein.  The BchL
           peptide (ChlL in chloroplast and cyanobacteria) is an
           ATP-binding iron-sulfur protein of the dark form
           protochlorophyllide reductase, an enzyme similar to
           nitrogenase. This subunit resembles the nitrogenase NifH
           subunit.
          Length = 268

 Score = 29.8 bits (67), Expect = 5.9
 Identities = 12/30 (40%), Positives = 17/30 (56%)

Query: 422 LIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451
           L + G  G GKS T +N+  A    GK++L
Sbjct: 3   LAVYGKGGIGKSTTSSNLSVAFAKLGKRVL 32


>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC.  This family is based on the
           phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
           Stanford University).
          Length = 1042

 Score = 29.9 bits (67), Expect = 6.0
 Identities = 24/176 (13%), Positives = 51/176 (28%), Gaps = 8/176 (4%)

Query: 515 RYEELKGQLNQYAQEINQIWKNTELSIHQILMGAARYRHNLPLDPVQLHVEGLSGENADR 574
                K Q  Q  Q++    +     +   L      +  L  + V+ H        + R
Sbjct: 615 HALLRKLQPEQDLQDVRLHLQQCSQELALKLTALHALQLTLTQERVREHAL------SIR 668

Query: 575 LLRSRLEDQIKAFKDVIVEFHKQAGESMELMNHPWYGVHSSDIHILNYNKALSSLENWQS 634
           +L   L    +     +    +Q     E++      +   + HI  Y++  + +EN  S
Sbjct: 669 VLPKELLASRQLALQKMQSEKEQLTYWKEMLAQCQTLLRELETHIEEYDREFNEIENASS 728

Query: 635 ALIKWQKDHEVFLNRYGVQNQRQRLLYWQGQLLAAVDQVPSLPRVICFKAFKKLED 690
           +L       E  LN+     +         +         +       +   +L  
Sbjct: 729 SLGSDLAAREDALNQ--SLKELMHQARTVLKARTEAHFNNNEEVTAALQTGAELSH 782


>gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily).  This Pfam
           entry includes some of the AAA proteins not detected by
           the pfam00004 model.
          Length = 139

 Score = 30.0 bits (68), Expect = 6.0
 Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 1/24 (4%)

Query: 421 NLIIEGPPGTGKSQTITNIIAAAM 444
            +++ GPPGTGKS  +   +AAA+
Sbjct: 1   GVLLVGPPGTGKS-ELAERLAAAL 23


>gnl|CDD|181743 PRK09270, PRK09270, nucleoside triphosphate hydrolase
           domain-containing protein; Reviewed.
          Length = 229

 Score = 29.9 bits (68), Expect = 6.8
 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 11/60 (18%)

Query: 386 EYKIDEIEDIHQRCPLIDDSDSSQHSAVIDVINGKNLI--IEGPPGTGKSQTITNIIAAA 443
           +Y+ +EIE +H+  PL+      +  A +     +  I  I GPPG GKS T+   + A 
Sbjct: 6   QYRDEEIEAVHK--PLL------RRLAALQAEPQRRTIVGIAGPPGAGKS-TLAEFLEAL 56


>gnl|CDD|182715 PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA;
           Provisional.
          Length = 413

 Score = 29.7 bits (67), Expect = 7.0
 Identities = 34/133 (25%), Positives = 54/133 (40%), Gaps = 38/133 (28%)

Query: 434 QTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLGEFCLELHSHKVHKRAILDDL 493
           Q I NI              AQ    ++ +R RL   GL       + +++ K  I+ ++
Sbjct: 80  QAIANI-------------AAQNNMTLDQMRSRLAYDGLN---YNTYRNQIRKEMIISEV 123

Query: 494 RKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEI-NQIWKNTELSIHQILMGAARYR 552
           R     R I  +PQE+D                A++I NQ   +TEL++  IL+      
Sbjct: 124 RNNEVRRRITILPQEVD--------------SLAKQIGNQNDASTELNLSHILI------ 163

Query: 553 HNLPLDPVQLHVE 565
             LP +P Q  V+
Sbjct: 164 -PLPENPTQDQVD 175


>gnl|CDD|181881 PRK09466, metL, bifunctional aspartate kinase II/homoserine
            dehydrogenase II; Provisional.
          Length = 810

 Score = 29.5 bits (67), Expect = 7.1
 Identities = 25/115 (21%), Positives = 39/115 (33%), Gaps = 25/115 (21%)

Query: 950  YRKVHQIWKDNSSLDDALINGFLMLDS-------QLFKRIQKLHCDELSKKITKVFGRIQ 1002
            YR+V  I  + S  DD      L++ S       QL   ++    D LS          Q
Sbjct: 28   YRRVAGILAEYSQPDD------LVVVSAAGKTTNQLISWLKLSQTDRLSAHQV-----QQ 76

Query: 1003 ELEQFLPKQKELQNRSALFVGEGNVFDSLIQRLSHNFDPWQNWFKEDEILLQEAQ 1057
             L ++   Q++L     L         SL+ RL  + +             Q A+
Sbjct: 77   TLRRY---QQDLI--EGLL--PAEQARSLLSRLISDLERLAALLDGGINDAQYAE 124


>gnl|CDD|163318 TIGR03545, TIGR03545, conserved hypothetical protein TIGR03545.  This
            model represents a relatively rare but broadly
            distributed uncharacterized protein family, distributed
            in 1-2 percent of bacterial genomes, all of which have
            outer membranes. In many of these genomes, it is part of
            a two-gene pair.
          Length = 555

 Score = 29.7 bits (67), Expect = 7.7
 Identities = 23/125 (18%), Positives = 42/125 (33%), Gaps = 16/125 (12%)

Query: 900  WKKLYAQLPNAYQFAVEKEKLEKRNFGNTLGEHYRGLSTDIVALKNIREWYRKVHQIWKD 959
            WKK    LPN       K++LE       + +       DI     +++   +  ++ K+
Sbjct: 180  WKKRKKDLPNKQDLEEYKKRLE------AIKK------KDIKNPLELQKIKEEFDKLKKE 227

Query: 960  NSSLDDALINGFLMLDSQLFKRIQKLHCDELSKKITKVFGRIQELEQFLPKQKELQNRSA 1019
                D   I           K+++     EL K       R++       K  +L+N + 
Sbjct: 228  -GKADKQKIKSAKNDLQNDKKQLKAD-LAELKKAPQNDLKRLENKYAI--KSGDLKNFAV 283

Query: 1020 LFVGE 1024
               G 
Sbjct: 284  DLFGP 288


>gnl|CDD|183503 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
          Length = 337

 Score = 29.6 bits (67), Expect = 7.8
 Identities = 8/19 (42%), Positives = 15/19 (78%)

Query: 418 NGKNLIIEGPPGTGKSQTI 436
           N  +L+++GPPG+GK+  +
Sbjct: 35  NLPHLLVQGPPGSGKTAAV 53


>gnl|CDD|140295 PTZ00269, PTZ00269, variant surface glycoprotein; Provisional.
          Length = 472

 Score = 29.5 bits (66), Expect = 7.9
 Identities = 19/44 (43%), Positives = 27/44 (61%), Gaps = 6/44 (13%)

Query: 1041 PW----QNWFKEDEILLQEAQEFSAKLHKIREKNIVLAEESLIK 1080
            PW    +    E E+LLQ+ Q+ SAKL +I+E +  +  ESLIK
Sbjct: 325  PWMKALEKVENEMEVLLQDKQDKSAKLERIKELSQEI--ESLIK 366


>gnl|CDD|180003 PRK05302, PRK05302, 30S ribosomal protein S7; Validated.
          Length = 156

 Score = 29.7 bits (68), Expect = 7.9
 Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 4/43 (9%)

Query: 432 KSQTITNIIAAAMLHGKKILFCAQKM--AAIEVVRHRLEKAGL 472
            S  +T  I   ML GKK +  A+K+   A++++  +  K  L
Sbjct: 19  GSVLVTKFINKLMLDGKKSV--AEKIVYGALDIIEEKTGKDPL 59


>gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
          Length = 328

 Score = 29.3 bits (67), Expect = 8.0
 Identities = 12/19 (63%), Positives = 14/19 (73%), Gaps = 1/19 (5%)

Query: 426 GPPGTGKSQTITNIIAAAM 444
           GPPG GK+ T+ NIIA  M
Sbjct: 58  GPPGLGKT-TLANIIANEM 75


>gnl|CDD|180381 PRK06067, PRK06067, flagellar accessory protein FlaH; Validated.
          Length = 234

 Score = 29.6 bits (67), Expect = 8.3
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 422 LIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452
           ++IEG  GTGKS      +  A+  GKK+  
Sbjct: 28  ILIEGDHGTGKSVLSQQFVYGALKQGKKVYV 58


>gnl|CDD|162859 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit.  A number of
            genomes (actinobacteria, cyanobacteria,
            betaproteobacteria and pseudomonads) which apparently
            biosynthesize B12, encode a cobN gene but are
            demonstrably lacking cobS and cobT. These genomes do,
            however contain a homolog (modelled here) of the
            magnesium chelatase subunits BchI/BchD family. Aside from
            the cyanobacteria (which have a separate magnesium
            chelatase trimer), these species do not make chlorins, so
            do not have any use for a magnesium chelatase.
            Furthermore, in nearly all cases the members of this
            family are proximal to either CobN itself or other genes
            involved in cobalt transport or B12 biosynthesis.
          Length = 633

 Score = 29.3 bits (66), Expect = 8.8
 Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 9/83 (10%)

Query: 1472 VDRYGVGFTHVKNGVVVDQGNPEEARV-------IALAVKDHALRYPEESLGVIAMN-AK 1523
            V+R G+  +H    V++   NPEE  +         L V   A R PEE + +I    A 
Sbjct: 157  VEREGLSVSHPARFVLIGTMNPEEGDLRPQLLDRFGLCVDVAAPRDPEERVEIIRRRLAF 216

Query: 1524 QRDLIESTINKLCRKDSEVEKAI 1546
              D  E+   +   +  E+   I
Sbjct: 217  DADP-EAFAARWAAEQEELRNRI 238


>gnl|CDD|185583 PTZ00375, PTZ00375, dihydroxyacetone kinase-like protein;
           Provisional.
          Length = 584

 Score = 29.4 bits (66), Expect = 9.2
 Identities = 11/46 (23%), Positives = 14/46 (30%), Gaps = 3/46 (6%)

Query: 890 LSLAKNPGISWKKLYAQLPN-AYQFAVEKEKLEKRNFGNTLGEHYR 934
           L     P  SW    A+ P  A Q A  + +   R          R
Sbjct: 336 LLNFHTPQSSWA--TAKGPLSALQLAKPEAEAASRKAATPTNSLLR 379


>gnl|CDD|179887 PRK04863, mukB, cell division protein MukB; Provisional.
          Length = 1486

 Score = 29.2 bits (66), Expect = 9.4
 Identities = 24/100 (24%), Positives = 42/100 (42%), Gaps = 21/100 (21%)

Query: 255  LEKRSSTSQPGLTQYHLRYTGEEIILNLSLKEKLQSDFGIILPAIAEGMWPEDYFLQIQK 314
            L  R S ++    Q   + T  E  ++ +L +KL+           E     DY  ++++
Sbjct: 1065 LHARLSANRSRRNQLEKQLTFCEAEMD-NLTKKLRK---------LE----RDYH-EMRE 1109

Query: 315  IIEESKSHW-----AVRRYGVLGLLNFSKMLMYLDLDHLR 349
             +  +K+ W      V+  GV   L+  + L YL  D LR
Sbjct: 1110 QVVNAKAGWCAVLRLVKDNGVERRLH-RRELAYLSADELR 1148


  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
   0.319    0.136    0.397 

Gapped
Lambda     K      H
   0.267   0.0681    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 29,648,298
Number of extensions: 2032730
Number of successful extensions: 4945
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4932
Number of HSP's successfully gapped: 97
Length of query: 1775
Length of database: 5,994,473
Length adjustment: 107
Effective length of query: 1668
Effective length of database: 3,682,417
Effective search space: 6142271556
Effective search space used: 6142271556
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: 64 (28.5 bits)