RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780909|ref|YP_003065322.1| hypothetical protein
CLIBASIA_04040 [Candidatus Liberibacter asiaticus str. psy62]
         (159 letters)



>gnl|CDD|149519 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal.
          This domain is found to the N-terminus of bacterial
          signal peptidases of the S49 family (pfam01343).
          Length = 154

 Score = 34.0 bits (79), Expect = 0.019
 Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 7/45 (15%)

Query: 41 ALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPK 85
          ALLD+   KA EKA + A K       A  KA +K   K++ KP+
Sbjct: 61 ALLDKKELKAWEKAEKKAEK-------AKAKAEKKKAKKEEPKPR 98


>gnl|CDD|179899 PRK04950, PRK04950, ProP expression regulator; Provisional.
          Length = 213

 Score = 33.4 bits (77), Expect = 0.027
 Identities = 16/62 (25%), Positives = 23/62 (37%)

Query: 36  AERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVPV 95
            E  +  L+EA  K   + AE   K  E A E  K    +   K K   K+ +   + P 
Sbjct: 96  VEHARKQLEEAKAKVQAQRAEQQAKKREAAGEKEKAPRRERKPKPKAPRKKRKPRAQKPE 155

Query: 96  AA 97
             
Sbjct: 156 PQ 157



 Score = 26.8 bits (60), Expect = 2.3
 Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 1/69 (1%)

Query: 50  AAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVPVAANIEPESQETQQQ 109
           A ++  EA  K   Q AE   K  E    + +K P+  ++          +P +Q+ + Q
Sbjct: 99  ARKQLEEAKAKVQAQRAEQQAKKREAA-GEKEKAPRRERKPKPKAPRKKRKPRAQKPEPQ 157

Query: 110 VINKTTTSQ 118
               +  S+
Sbjct: 158 HTPVSDISE 166


>gnl|CDD|179009 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
           protein; Reviewed.
          Length = 782

 Score = 33.3 bits (77), Expect = 0.032
 Identities = 23/88 (26%), Positives = 43/88 (48%), Gaps = 9/88 (10%)

Query: 45  EATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVPVAANIEPESQ 104
           E  Q+  +K  E A K A+QA + AKK A++II       KE +++ +   A+    E  
Sbjct: 558 EKLQEEEDKLLEEAEKEAQQAIKEAKKEADEII-------KELRQLQKGGYASVKAHELI 610

Query: 105 ETQQQV--INKTTTSQTDAEKTPNEKRQ 130
           E ++++   N+    +   +K   E+ +
Sbjct: 611 EARKRLNKANEKKEKKKKKQKEKQEELK 638


>gnl|CDD|171865 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase;
           Reviewed.
          Length = 460

 Score = 33.0 bits (75), Expect = 0.035
 Identities = 12/83 (14%), Positives = 22/83 (26%), Gaps = 7/83 (8%)

Query: 23  QADPVAPPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKK 82
           +AD     P     +   A   +A   +A     AA  +        +         +K 
Sbjct: 368 EADIEREQPGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEPEVP-------EKA 420

Query: 83  KPKENQEVNEVPVAANIEPESQE 105
            P  +    +    A    +  E
Sbjct: 421 APIPDPAKPDELAVAGPGDDPAE 443



 Score = 29.9 bits (67), Expect = 0.28
 Identities = 11/93 (11%), Positives = 28/93 (30%), Gaps = 3/93 (3%)

Query: 44  DEATQKAAEKAAE---AARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVPVAANIE 100
           +E ++   E+      A +  A    +A   +A             ++   EVP  A   
Sbjct: 364 EETSEADIEREQPGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEPEVPEKAAPI 423

Query: 101 PESQETQQQVINKTTTSQTDAEKTPNEKRQGTT 133
           P+  +  +  +        + +    +    + 
Sbjct: 424 PDPAKPDELAVAGPGDDPAEPDGIRRQDDFSSR 456


>gnl|CDD|178947 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
          Length = 865

 Score = 32.4 bits (75), Expect = 0.051
 Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 3/47 (6%)

Query: 31  PPQTLAERGKALLDEATQKAAEKAAEAAR-KAAEQAAEAAKKAAEKI 76
            P  L ER +ALL+E   K  EK  E  + K A  AA      A+++
Sbjct: 713 KPSELPERVEALLEE--LKELEKELEQLKAKLAAAAAGDLLAQAKEV 757


>gnl|CDD|184805 PRK14724, PRK14724, DNA topoisomerase III; Provisional.
          Length = 987

 Score = 32.6 bits (74), Expect = 0.052
 Identities = 25/94 (26%), Positives = 39/94 (41%), Gaps = 10/94 (10%)

Query: 30  PPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQE 89
           PP +T A +  A         A KAA+ A+KAA +   A   AA        K P++  +
Sbjct: 855 PPRKTAAAKAGAASAAFGGTVAVKAAKPAKKAAAKKVAAKTAAA--------KTPRKAAK 906

Query: 90  VNEVPVAANIEPESQETQQQVINKTTTSQTDAEK 123
               P AA ++P +      VI     ++ +  K
Sbjct: 907 KKAAPPAAGLKPSAALA--AVIGAEPVARPEVIK 938


>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
          Length = 2084

 Score = 32.0 bits (72), Expect = 0.076
 Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 36   AERGKALLDEATQKAAE--KAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEV 93
            AE  K   D A +KA E  KAAEAA+  AE AA+ A+ A EK    +KKK +  ++ +  
Sbjct: 1324 AEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAA 1383

Query: 94   PVAANIEPESQETQQQ 109
               A  + ++ E +++
Sbjct: 1384 KKKAEEKKKADEAKKK 1399



 Score = 27.8 bits (61), Expect = 1.2
 Identities = 30/98 (30%), Positives = 47/98 (47%), Gaps = 3/98 (3%)

Query: 36   AERGKALLDEATQKAAE--KAAEAARKAAE-QAAEAAKKAAEKIIHKDKKKPKENQEVNE 92
            A+  K   +EA +KA E  KAAEA +KA E + AE AKKA E    ++ KK  E ++  E
Sbjct: 1485 ADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEE 1544

Query: 93   VPVAANIEPESQETQQQVINKTTTSQTDAEKTPNEKRQ 130
               A  ++   +  + +   K   ++   E      R+
Sbjct: 1545 KKKADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRK 1582



 Score = 27.0 bits (59), Expect = 2.2
 Identities = 26/97 (26%), Positives = 47/97 (48%), Gaps = 2/97 (2%)

Query: 36   AERGKALLDEATQKA--AEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEV 93
            A+  K   +EA +KA  A+K AE A+KAAE A   A+ AA++    ++K     ++  E 
Sbjct: 1317 ADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEA 1376

Query: 94   PVAANIEPESQETQQQVINKTTTSQTDAEKTPNEKRQ 130
               A+   +  E +++       ++ D +K    K+ 
Sbjct: 1377 KKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKA 1413



 Score = 27.0 bits (59), Expect = 2.4
 Identities = 34/119 (28%), Positives = 51/119 (42%), Gaps = 8/119 (6%)

Query: 44   DEATQKAAE--KAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVPVAANIEP 101
            DEA +KA E  K A+AA+K AE+    AKKAAE    + +    E +   E   AA  + 
Sbjct: 1318 DEAKKKAEEAKKKADAAKKKAEE----AKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKK 1373

Query: 102  ESQETQQQVINKTTTSQTDAE--KTPNEKRQGTTDGINNQSNATNDPSSKDKIAENTKE 158
            E  + +     K    +  A+  K   E+ +   D +   + A        K AE  K+
Sbjct: 1374 EEAKKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKK 1432



 Score = 26.6 bits (58), Expect = 2.8
 Identities = 30/102 (29%), Positives = 44/102 (43%), Gaps = 8/102 (7%)

Query: 36   AERGKALLDEATQKAAEKA-------AEAARKAAE-QAAEAAKKAAEKIIHKDKKKPKEN 87
            AE  K   DEA + A  K        AE A+KA E + AE AKKA E    ++KKK  E 
Sbjct: 1492 AEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADEL 1551

Query: 88   QEVNEVPVAANIEPESQETQQQVINKTTTSQTDAEKTPNEKR 129
            ++  E+  A   +   +  + +        + +  K   E R
Sbjct: 1552 KKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEAR 1593



 Score = 25.1 bits (54), Expect = 8.9
 Identities = 29/79 (36%), Positives = 44/79 (55%), Gaps = 5/79 (6%)

Query: 36   AERGKALLDEATQKAAE-KAAEAARKAAEQA--AEAAKKAAE--KIIHKDKKKPKENQEV 90
            A   K   DEA +KA E K A+ A+K AE+A  A+ AKK AE  K   + KKK +E ++ 
Sbjct: 1413 AAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKA 1472

Query: 91   NEVPVAANIEPESQETQQQ 109
            +E    A    ++ E +++
Sbjct: 1473 DEAKKKAEEAKKADEAKKK 1491


>gnl|CDD|183309 PRK11778, PRK11778, putative inner membrane peptidase;
          Provisional.
          Length = 330

 Score = 31.7 bits (73), Expect = 0.091
 Identities = 13/32 (40%), Positives = 17/32 (53%)

Query: 41 ALLDEATQKAAEKAAEAARKAAEQAAEAAKKA 72
          ALLD+   KA  KA +   K   +AA+A  K 
Sbjct: 59 ALLDKKELKAWHKAQKKKEKQEAKAAKAKSKP 90


>gnl|CDD|179919 PRK05035, PRK05035, electron transport complex protein RnfC;
           Provisional.
          Length = 695

 Score = 31.1 bits (71), Expect = 0.15
 Identities = 21/73 (28%), Positives = 30/73 (41%)

Query: 37  ERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVPVA 96
            R KA   E    A  +     RKAA  AA A  KA +    +   +P+E ++  +  VA
Sbjct: 622 ARAKAKKAEQQANAEPEEPVDPRKAAVAAAIARAKARKAAQQQANAEPEEAEDPKKAAVA 681

Query: 97  ANIEPESQETQQQ 109
           A I     +   Q
Sbjct: 682 AAIARAKAKKAAQ 694



 Score = 27.6 bits (62), Expect = 1.6
 Identities = 25/95 (26%), Positives = 35/95 (36%), Gaps = 6/95 (6%)

Query: 34  TLAERGKALLDEATQKAAEKAAEAARKAAEQAAEA---AKKAAEKIIHKDKKKPKENQEV 90
              E  KA       +    AA   +KAA  AA A   AKKAA++       + +E  + 
Sbjct: 521 AAREARKAQARARQAEKQAAAAADPKKAAVAAAIARAKAKKAAQQ---AANAEAEEEVDP 577

Query: 91  NEVPVAANIEPESQETQQQVINKTTTSQTDAEKTP 125
            +  VAA I     +   Q        +  AE  P
Sbjct: 578 KKAAVAAAIARAKAKKAAQQAASAEPEEQVAEVDP 612



 Score = 27.2 bits (61), Expect = 1.9
 Identities = 15/89 (16%), Positives = 29/89 (32%), Gaps = 5/89 (5%)

Query: 40  KALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDK-----KKPKENQEVNEVP 94
           +A L+        +  +AA   A +  +A   A  ++  K          K     +   
Sbjct: 459 QARLEREKAAREARHKKAAEARAAKDKDAVAAALARVKAKKAAATQPIVIKAGARPDNSA 518

Query: 95  VAANIEPESQETQQQVINKTTTSQTDAEK 123
           V A  E    + + +   K   +  D +K
Sbjct: 519 VIAAREARKAQARARQAEKQAAAAADPKK 547


>gnl|CDD|185412 PTZ00046, PTZ00046, rifin; Provisional.
          Length = 358

 Score = 30.7 bits (70), Expect = 0.16
 Identities = 12/37 (32%), Positives = 19/37 (51%)

Query: 39  GKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEK 75
            + ++++  +    KAA+AA  AAE A  A   A E 
Sbjct: 264 PEEVIEKTVETIVSKAADAAEAAAEAATAAETAALEA 300



 Score = 26.1 bits (58), Expect = 4.4
 Identities = 11/29 (37%), Positives = 13/29 (44%)

Query: 46  ATQKAAEKAAEAARKAAEQAAEAAKKAAE 74
           A   A + A +A   A E A  AA K A 
Sbjct: 169 ALAAAIKAAIKAGAAAGEAAGIAAGKKAV 197


>gnl|CDD|178893 PRK00137, rplI, 50S ribosomal protein L9; Reviewed.
          Length = 147

 Score = 30.4 bits (70), Expect = 0.19
 Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 3/39 (7%)

Query: 38 RGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKI 76
          +GKA+   AT K   K  EA R   E  A      AE +
Sbjct: 33 QGKAV--RAT-KGNLKQLEARRAELEAKAAEELAEAEAL 68


>gnl|CDD|183545 PRK12472, PRK12472, hypothetical protein; Provisional.
          Length = 508

 Score = 30.6 bits (69), Expect = 0.20
 Identities = 19/60 (31%), Positives = 28/60 (46%)

Query: 37  ERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVPVA 96
           +  KA  +E  QKAA++AAEAA +     A+A  K A     K+  K    ++      A
Sbjct: 254 DEAKARAEERQQKAAQQAAEAATQLDTAKADAEAKRAAAAATKEAAKAAAAKKAETAKAA 313



 Score = 27.9 bits (62), Expect = 1.2
 Identities = 17/37 (45%), Positives = 22/37 (59%)

Query: 35  LAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKK 71
           L    KAL    T +A  +A E  +KAA+QAAEAA +
Sbjct: 241 LKRADKALAAAKTDEAKARAEERQQKAAQQAAEAATQ 277


>gnl|CDD|179088 PRK00696, sucC, succinyl-CoA synthetase subunit beta; Provisional.
          Length = 388

 Score = 30.4 bits (70), Expect = 0.21
 Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 2/35 (5%)

Query: 36  AERGKALLDEATQK--AAEKAAEAARKAAEQAAEA 68
            E GK +L E+     AA+   +AA+KA E A   
Sbjct: 354 VELGKKILAESGLNIIAADTLDDAAQKAVEAAKGK 388


>gnl|CDD|150232 pfam09487, HrpB2, Bacterial type III secretion protein (HrpB2).
          This entry represents proteins encoded by genes which
          are found in type III secretion operons in a narrow
          group of species including Xanthomonas, Burkholderia
          and Ralstonia.
          Length = 117

 Score = 30.1 bits (68), Expect = 0.27
 Identities = 21/62 (33%), Positives = 28/62 (45%), Gaps = 4/62 (6%)

Query: 19 ASCGQADPVAPPPPQTLAERGKALLDEATQKA----AEKAAEAARKAAEQAAEAAKKAAE 74
          A  G A PVAP PPQ L ER +AL+  A        A +   A  +  E    A +K  +
Sbjct: 2  AGTGAAPPVAPAPPQELVERFQALMASAPPAPPAAQASEGPSAVSRLVETQDAAVRKVLD 61

Query: 75 KI 76
           +
Sbjct: 62 DV 63


>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 = 30.2 bits (68), Expect = 0.27
 Identities = 19/91 (20%), Positives = 36/91 (39%), Gaps = 1/91 (1%)

Query: 48  QKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDK-KKPKENQEVNEVPVAANIEPESQET 106
           ++          K A++A +A KK  E II + K KK  + +E+  +     ++   Q+ 
Sbjct: 556 KERERNKKLELEKEAQEALKALKKEVESIIRELKEKKIHKAKEIKSIEDLVKLKETKQKI 615

Query: 107 QQQVINKTTTSQTDAEKTPNEKRQGTTDGIN 137
            Q+  N       D  +     ++G    I 
Sbjct: 616 PQKPTNFQADKIGDKVRIRYFGQKGKIVQIL 646


>gnl|CDD|183692 PRK12704, PRK12704, phosphodiesterase; Provisional.
          Length = 520

 Score = 29.7 bits (68), Expect = 0.34
 Identities = 12/36 (33%), Positives = 23/36 (63%)

Query: 42  LLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKII 77
           LL++  ++A  +AA   ++  E+A E A K A++I+
Sbjct: 159 LLEKVEEEARHEAAVLIKEIEEEAKEEADKKAKEIL 194



 Score = 25.1 bits (56), Expect = 8.4
 Identities = 15/47 (31%), Positives = 24/47 (51%)

Query: 43 LDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQE 89
          + EA  K AE+ A+   + A++ AEA KK A     ++  K +   E
Sbjct: 28 IAEAKIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFE 74


>gnl|CDD|177950 PLN02316, PLN02316, synthase/transferase.
          Length = 1036

 Score = 29.5 bits (66), Expect = 0.39
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 6/75 (8%)

Query: 35  LAERGKALLDEATQKAAEK---AAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVN 91
           L E  +  L++  ++ AE+   A E  R+  E+AA  A +A  K   + +++  +N    
Sbjct: 250 LLEEKRRELEKLAKEEAERERQAEEQRRREEEKAAMEADRAQAKAEVEKRREKLQNLLKK 309

Query: 92  EVPVAAN---IEPES 103
               A N   IEP  
Sbjct: 310 ASRSADNVWYIEPSE 324


>gnl|CDD|178558 PLN02976, PLN02976, amine oxidase.
          Length = 1713

 Score = 29.4 bits (66), Expect = 0.39
 Identities = 15/21 (71%), Positives = 17/21 (80%)

Query: 48   QKAAEKAAEAARKAAEQAAEA 68
            +KAA  AAEAAR AAE AA+A
Sbjct: 1432 EKAAFAAAEAARAAAEAAAQA 1452


>gnl|CDD|178945 PRK00247, PRK00247, putative inner membrane protein translocase
           component YidC; Validated.
          Length = 429

 Score = 29.4 bits (66), Expect = 0.42
 Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 35  LAERGKALLDEAT-QKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEV 93
           +A++ +A   E   +   E+AA  AR  A +AA  AKK        ++  P EN+E    
Sbjct: 350 IAQKRRAAEREINREARQERAAAMARARARRAAVKAKKKGLIDASPNEDTPSENEESKGS 409

Query: 94  P 94
           P
Sbjct: 410 P 410


>gnl|CDD|177568 PHA03248, PHA03248, DNA packaging tegument protein UL25;
           Provisional.
          Length = 583

 Score = 29.2 bits (66), Expect = 0.46
 Identities = 22/76 (28%), Positives = 29/76 (38%), Gaps = 10/76 (13%)

Query: 35  LAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVP 94
           L E   AL D     AA + A+AA    + AA             D +   E+ E  EV 
Sbjct: 94  LEEVADALADLEEAAAAAEEADAAADERKAAAGD----------GDGRAAGEDDEAREVQ 143

Query: 95  VAANIEPESQETQQQV 110
           +  N  P   +T  QV
Sbjct: 144 IVKNDPPLRYDTNLQV 159


>gnl|CDD|177542 PHA03144, PHA03144, helicase-primase primase subunit; Provisional.
          Length = 746

 Score = 28.9 bits (65), Expect = 0.60
 Identities = 12/25 (48%), Positives = 14/25 (56%)

Query: 45  EATQKAAEKAAEAARKAAEQAAEAA 69
           +A    A  AAE AR A + AAEA 
Sbjct: 513 DAVSADALAAAERARAACQAAAEAV 537


>gnl|CDD|150639 pfam09989, DUF2229, CoA enzyme activase uncharacterized domain
           (DUF2229).  Members of this family include various
           bacterial hypothetical proteins, as well as CoA enzyme
           activases. The exact function of this domain has not, as
           yet, been defined.
          Length = 218

 Score = 28.7 bits (65), Expect = 0.69
 Identities = 13/55 (23%), Positives = 27/55 (49%), Gaps = 2/55 (3%)

Query: 33  QTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKEN 87
           + L E GK L    +++  +KA E A +  E   +  +K  E+ +   +++ K+ 
Sbjct: 130 KRLYELGKKL--GISKEEIKKAVEKALEEQEAFKKDLRKKGEEALAYLEEEGKKG 182


>gnl|CDD|162889 TIGR02499, HrpE_YscL_not, type III secretion apparatus protein,
          HrpE/YscL family.  This model is related to Pfam model
          pfam06188, but is broader. pfam06188 describes
          HrpE-like proteins, components of bacterial type III
          secretion systems primarily in bacteria that infect
          plants. This model includes also the homologous
          proteins of animal pathogens, such as YscL of Yersinia
          pestis. This model excludes the related protein FliH of
          the bacterial flagellar apparatus (see pfam02108).
          Length = 166

 Score = 28.8 bits (65), Expect = 0.71
 Identities = 11/50 (22%), Positives = 20/50 (40%)

Query: 26 PVAPPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEK 75
          PV          + +A+L  A Q+A    A+A  +A        ++  E+
Sbjct: 2  PVLRAEDLAALAQAQAILAAARQRAEAILADAEEEAEASRQLGYEQGLEQ 51


>gnl|CDD|184903 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
          Length = 756

 Score = 28.5 bits (65), Expect = 0.81
 Identities = 11/24 (45%), Positives = 13/24 (54%), Gaps = 5/24 (20%)

Query: 51  AEKAAEAARKAAEQAAEAAKKAAE 74
             K  +AAR     A EAA+KA E
Sbjct: 373 VGKIIDAAR-----AREAARKARE 391


>gnl|CDD|178640 PLN03091, PLN03091, hypothetical protein; Provisional.
          Length = 459

 Score = 28.4 bits (63), Expect = 0.84
 Identities = 11/71 (15%), Positives = 27/71 (38%)

Query: 80  DKKKPKENQEVNEVPVAANIEPESQETQQQVINKTTTSQTDAEKTPNEKRQGTTDGINNQ 139
           DK     + E+N +    +    + + ++         Q + E + + K   + +  ++ 
Sbjct: 147 DKASSVVSNELNLLKADNSKPLAALQEKRSSSISPAGYQLEVESSSSSKINNSNNNNHSN 206

Query: 140 SNATNDPSSKD 150
           SN      +KD
Sbjct: 207 SNLMTPTPNKD 217


>gnl|CDD|181031 PRK07562, PRK07562, ribonucleotide-diphosphate reductase subunit
            alpha; Validated.
          Length = 1220

 Score = 28.4 bits (64), Expect = 0.86
 Identities = 18/59 (30%), Positives = 23/59 (38%)

Query: 10   LLSLLSTTMASCGQADPVAPPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEA 68
              +L+  T         VA  P  + A         A   AA  AAEA +  AE+ AEA
Sbjct: 1125 KPTLVVVTGGGAAAGAAVAAAPAASAATFSDKAAAAAAAAAAAAAAEAKKVEAERRAEA 1183



 Score = 26.9 bits (60), Expect = 2.8
 Identities = 10/38 (26%), Positives = 19/38 (50%), Gaps = 2/38 (5%)

Query: 42  LLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHK 79
           + D+    A E  A     AA +A + A+K  E+++ +
Sbjct: 928 IEDDDDDDALE--ALIEAPAAARAVQVAEKIVERVVER 963


>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional.
          Length = 333

 Score = 28.3 bits (63), Expect = 0.90
 Identities = 24/106 (22%), Positives = 44/106 (41%)

Query: 28  APPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKEN 87
           A    + ++++  A    + +KAA+ AA+AA+KA + A +A KKAA+ +    KK  K  
Sbjct: 219 AKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKALKKAAKAVKKAAKKAAKAA 278

Query: 88  QEVNEVPVAANIEPESQETQQQVINKTTTSQTDAEKTPNEKRQGTT 133
            +  +    A       + +        +      K P    +G  
Sbjct: 279 AKAAKGAAKATKGKAKAKKKAGKKAAAGSKAKATAKAPKRGAKGKK 324



 Score = 28.3 bits (63), Expect = 0.94
 Identities = 18/59 (30%), Positives = 30/59 (50%)

Query: 27  VAPPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPK 85
              P  ++ A++  A    A +K ++K A     +A++AA+ A KAA+K     KK  K
Sbjct: 203 AKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKALK 261



 Score = 27.9 bits (62), Expect = 1.3
 Identities = 23/76 (30%), Positives = 38/76 (50%)

Query: 10  LLSLLSTTMASCGQADPVAPPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAA 69
           +L+ +    A      P A    +  + + K+   + ++K A K A +A+KAA+ AA+AA
Sbjct: 190 VLAAVGAANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAA 249

Query: 70  KKAAEKIIHKDKKKPK 85
           KKA +      KK  K
Sbjct: 250 KKAKKTAKKALKKAAK 265



 Score = 25.6 bits (56), Expect = 5.9
 Identities = 23/59 (38%), Positives = 33/59 (55%)

Query: 27  VAPPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPK 85
            A       A++ K    +A +KAA+   +AA+KAA+ AA+AAK AA+    K K K K
Sbjct: 240 KAAKTAAKAAKKAKKTAKKALKKAAKAVKKAAKKAAKAAAKAAKGAAKATKGKAKAKKK 298



 Score = 25.2 bits (55), Expect = 8.2
 Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 2/79 (2%)

Query: 9   ILLSLLSTTMASCGQADPVAPPPPQTLAERGKALLDEATQKAAEKAAEA--ARKAAEQAA 66
           +L ++ +       +         +  A+   A    + +KAA+ A  A  A K A +AA
Sbjct: 190 VLAAVGAANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAA 249

Query: 67  EAAKKAAEKIIHKDKKKPK 85
           + AKK A+K + K  K  K
Sbjct: 250 KKAKKTAKKALKKAAKAVK 268


>gnl|CDD|163397 TIGR03685, L21P_arch, 50S ribosomal protein L12P.  This model
          represents the L12P protein of the large (50S) subunit
          of the archaeal ribosome.
          Length = 105

 Score = 28.1 bits (63), Expect = 0.93
 Identities = 15/44 (34%), Positives = 25/44 (56%)

Query: 43 LDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKE 86
          ++EA +KAA     AA  AA  AA A ++  E+   +++K+  E
Sbjct: 50 IEEAIKKAAAAPVAAAAAAAAAAAAAEEEEEEEEEEEEEKEESE 93


>gnl|CDD|181441 PRK08475, PRK08475, F0F1 ATP synthase subunit B; Validated.
          Length = 167

 Score = 28.1 bits (63), Expect = 1.0
 Identities = 18/64 (28%), Positives = 33/64 (51%)

Query: 49  KAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVPVAANIEPESQETQQ 108
           + A K  E A++ AE   E AKK A  +  K +K+ K++ E         +E E ++ ++
Sbjct: 77  EDALKKLEEAKEKAELIVETAKKEAYILTQKIEKQTKDDIENLIKSFEELMEFEVRKMER 136

Query: 109 QVIN 112
           +V+ 
Sbjct: 137 EVVE 140


>gnl|CDD|180181 PRK05644, gyrB, DNA gyrase subunit B; Validated.
          Length = 638

 Score = 28.1 bits (64), Expect = 1.1
 Identities = 13/23 (56%), Positives = 14/23 (60%), Gaps = 5/23 (21%)

Query: 52  EKAAEAARKAAEQAAEAAKKAAE 74
           EKA  AAR     A EAA+KA E
Sbjct: 376 EKAILAAR-----AREAARKARE 393



 Score = 26.6 bits (60), Expect = 2.7
 Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 2/25 (8%)

Query: 39  GKALLDEATQKAAEKAAEAARKAAE 63
            K ++++A    A +A EAARKA E
Sbjct: 371 AKKIVEKAIL--AARAREAARKARE 393


>gnl|CDD|178775 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
          Length = 1465

 Score = 27.9 bits (62), Expect = 1.1
 Identities = 21/106 (19%), Positives = 43/106 (40%), Gaps = 4/106 (3%)

Query: 41   ALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVPVAANIE 100
            +L +   +K   K A A +KAA+  A A K+    +    +   K   E+ +   A  I 
Sbjct: 1325 SLAERLKKKGGRKPAAANKKAAKPPAAAKKRGPATV----QSGQKLLTEMLKPAEAIGIS 1380

Query: 101  PESQETQQQVINKTTTSQTDAEKTPNEKRQGTTDGINNQSNATNDP 146
            PE +  + +       S +   +    K   +++ ++  S++  D 
Sbjct: 1381 PEKKVRKMRASPFNKKSGSVLGRAATNKETESSENVSGSSSSEKDE 1426



 Score = 26.8 bits (59), Expect = 2.5
 Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 11/90 (12%)

Query: 42   LLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVPVAANIEP 101
             LD+   KA E   +  R AA   + AAKK + +     K  PK+  +            
Sbjct: 1167 KLDKEDAKAEEAREKLQRAAARGESGAAKKVSRQ--APKKPAPKKTTKKAS--------- 1215

Query: 102  ESQETQQQVINKTTTSQTDAEKTPNEKRQG 131
            ES+ T++   +    ++  AE    + R G
Sbjct: 1216 ESETTEETYGSSAMETENVAEVVKPKGRAG 1245


>gnl|CDD|181012 PRK07515, PRK07515, 3-oxoacyl-(acyl carrier protein) synthase III;
           Reviewed.
          Length = 372

 Score = 27.9 bits (63), Expect = 1.2
 Identities = 10/22 (45%), Positives = 11/22 (50%)

Query: 55  AEAARKAAEQAAEAAKKAAEKI 76
           AE    AA QA   A + AE I
Sbjct: 96  AEMGVAAARQALARAGRTAEDI 117


>gnl|CDD|183918 PRK13252, PRK13252, betaine aldehyde dehydrogenase; Provisional.
          Length = 488

 Score = 27.9 bits (63), Expect = 1.3
 Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 2/35 (5%)

Query: 41 ALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEK 75
          A +  AT    E A  +A++   Q   AA  A E+
Sbjct: 36 ATVQAATPADVEAAVASAKQG--QKIWAAMTAMER 68


>gnl|CDD|161969 TIGR00631, uvrb, excinuclease ABC, B subunit.  This family is based
           on the phylogenomic analysis of JA Eisen (1999, Ph.D.
           Thesis, Stanford University).
          Length = 655

 Score = 27.6 bits (62), Expect = 1.3
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 32  PQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVN 91
           PQT+ +  + +LD   +   ++ A   +K  E  ++ +KK  +K+I + +K+ K+     
Sbjct: 582 PQTIRKPIRDILD--IELKEKEDAAKKKKKGEDLSDLSKKELKKLIKQLEKEMKQAARNL 639

Query: 92  EVPVAANIEPESQE 105
           E   AA +  E  E
Sbjct: 640 EFEEAARLRDEILE 653


>gnl|CDD|131724 TIGR02677, TIGR02677, conserved hypothetical protein TIGR02677.
           Members of this protein 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).
          Length = 494

 Score = 27.9 bits (62), Expect = 1.3
 Identities = 14/55 (25%), Positives = 20/55 (36%), Gaps = 4/55 (7%)

Query: 24  ADPVAPPPPQT----LAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAE 74
            DP    PP+     L   G+       +K  ++  E A  A    AE A+ A  
Sbjct: 351 KDPWEEAPPEWVTPRLRVYGEQEPRGRPEKVRDRTEERAELALRARAERARAAQA 405


>gnl|CDD|184893 PRK14900, valS, valyl-tRNA synthetase; Provisional.
          Length = 1052

 Score = 27.7 bits (61), Expect = 1.3
 Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 4/60 (6%)

Query: 28   APPPPQTLAERGKALLDEATQKAAEKAAEA----ARKAAEQAAEAAKKAAEKIIHKDKKK 83
                 +  A    A+  +  +KA  K A A    A+KAA +   A K  A+K+  K   K
Sbjct: 978  VRRSVKKAAATRAAMKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKKAPAKKVARKPAAK 1037



 Score = 25.7 bits (56), Expect = 5.8
 Identities = 16/56 (28%), Positives = 24/56 (42%)

Query: 28  APPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKK 83
             P     A   +   +    ++AEKA  A  +AA+QAA A     EK+    +K 
Sbjct: 922 QKPTQDGPAAEAQPAQENTVVESAEKAVAAVSEAAQQAATAVASGIEKVAEAVRKT 977



 Score = 25.0 bits (54), Expect = 9.7
 Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 3/58 (5%)

Query: 18   MASCGQADPVAPPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEK 75
            +A+  +A   A     +  E+   + +   +       +AA   A    + AKKA  K
Sbjct: 949  VAAVSEAAQQAATAVASGIEK---VAEAVRKTVRRSVKKAAATRAAMKKKVAKKAPAK 1003


>gnl|CDD|182792 PRK10866, PRK10866, outer membrane biogenesis protein BamD;
          Provisional.
          Length = 243

 Score = 27.8 bits (62), Expect = 1.4
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 2/58 (3%)

Query: 1  MKRLKYQIILLSLLSTTMASC-GQADPVAPPPPQTLAERGKALLDEATQKAAEKAAEA 57
          M R+KY ++  + LS  +A C G  + V   PP  +    +  L +   K A    EA
Sbjct: 1  MTRMKY-LVAAATLSLFLAGCSGSKEEVPDNPPSEIYATAQQKLQDGNWKQAITQLEA 57


>gnl|CDD|183478 PRK12372, PRK12372, ribonuclease III; Reviewed.
          Length = 413

 Score = 27.6 bits (61), Expect = 1.5
 Identities = 19/53 (35%), Positives = 26/53 (49%)

Query: 23  QADPVAPPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEK 75
           + +  A P     A    A   +A +KAAEK AEAA +AA++ A  A   A  
Sbjct: 313 KGERAAKPAAADKAADKPADRPDAAEKAAEKPAEAAPRAADKPAGQAADPASS 365


>gnl|CDD|173592 PTZ00401, PTZ00401, aspartyl-tRNA synthetase; Provisional.
          Length = 550

 Score = 27.6 bits (61), Expect = 1.5
 Identities = 14/33 (42%), Positives = 21/33 (63%)

Query: 48 QKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKD 80
          +K ++K A  A + AE+ A AA+KAA    +KD
Sbjct: 15 KKQSDKEARKAARLAEEKARAAEKAALVEKYKD 47


>gnl|CDD|180813 PRK07056, PRK07056, amidase; Provisional.
          Length = 454

 Score = 27.6 bits (62), Expect = 1.6
 Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 7/57 (12%)

Query: 25 DPVAPPPPQTLAER-------GKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAE 74
               P    LA          +AL++ A  + A+ A E AR      A+AA+ AA+
Sbjct: 1  TFTMLPTLAALAADLAAGRTTSRALVEAALARIADPAGEGARVFTHVDADAARAAAD 57


>gnl|CDD|169692 PRK09174, PRK09174, F0F1 ATP synthase subunit B'; Validated.
          Length = 204

 Score = 27.5 bits (61), Expect = 1.6
 Identities = 24/64 (37%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 22  GQADPVAPPPPQTLAE-RGKA-LLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHK 79
            +AD       Q LA+ R KA  + +A ++AA+  AEA R A E + E   K AE  I  
Sbjct: 101 QEADAAVAAYEQELAQARAKAHSIAQAAREAAKAKAEAERAAIEASLEKKLKEAEARIAA 160

Query: 80  DKKK 83
            K K
Sbjct: 161 IKAK 164


>gnl|CDD|178829 PRK00055, PRK00055, ribonuclease Z; Reviewed.
          Length = 270

 Score = 27.5 bits (62), Expect = 1.8
 Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 6/42 (14%)

Query: 35  LAERGKALLDEATQKAAEKAAEAARK----AAEQAAEAAKKA 72
           LA+    L+ EAT    ++  E A++     A QAAE AK+A
Sbjct: 184 LAKGADLLVHEAT--FGDEDEELAKEYGHSTARQAAEIAKEA 223


>gnl|CDD|185012 PRK15052, PRK15052, D-tagatose-1,6-bisphosphate aldolase subunit
           GatZ; Provisional.
          Length = 421

 Score = 27.5 bits (61), Expect = 1.8
 Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 5/42 (11%)

Query: 19  ASCGQADPVAPPPPQTLAERGKALLDEATQKAAEKAAEAARK 60
           AS   AD   P  P+T+AER   L      +AAE  A   ++
Sbjct: 125 ASMSCADDPIPLAPETVAERAAVLC-----QAAESVATDCQR 161


>gnl|CDD|131857 TIGR02810, agaZ_gatZ, D-tagatose-bisphosphate aldolase, class II,
           non-catalytic subunit.  Aldolases specific for
           D-tagatose-bisphosphate occur in distinct pathways in
           Escherichia coli and other bacteria, one for the
           degradation of galactitol (formerly dulcitol) and one
           for degradation of N-acetyl-galactosamine and
           D-galactosamine. This family represents a protein of
           both systems that behaves as a non-catalytic subunit of
           D-tagatose-bisphosphate aldolase, required both for full
           activity and for good stability of the aldolase. Note
           that members of this protein family appear in public
           databases annotated as putative tagatose 6-phosphate
           kinases, possibly in error.
          Length = 420

 Score = 27.4 bits (61), Expect = 1.8
 Identities = 14/39 (35%), Positives = 17/39 (43%)

Query: 19  ASCGQADPVAPPPPQTLAERGKALLDEATQKAAEKAAEA 57
           AS G A   AP    T+AER   L   A   A ++  E 
Sbjct: 124 ASMGCAGDPAPLDDATVAERAARLCAVAEAAATDRRGET 162


>gnl|CDD|181236 PRK08119, PRK08119, flagellar motor switch protein; Validated.
          Length = 382

 Score = 27.1 bits (61), Expect = 1.9
 Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 45  EATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVPVA-ANIEPES 103
           E  ++   +A+ AA  A  QAA A K+  ++   + ++  KE Q VN  P    + +P  
Sbjct: 232 EEVEEEEAQASPAAEPATAQAAPAPKQEQQQAPPQRQEPEKEAQPVNVQPAQFQSFDPPP 291

Query: 104 QETQQQ 109
             T + 
Sbjct: 292 LATTEP 297


>gnl|CDD|128558 smart00262, GEL, Gelsolin homology domain.
          Gelsolin/severin/villin homology domain.
          Calcium-binding and actin-binding. Both intra- and
          extracellular domains.
          Length = 90

 Score = 27.3 bits (61), Expect = 1.9
 Identities = 6/34 (17%), Positives = 17/34 (50%)

Query: 59 RKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNE 92
          +K+++   + A + A ++       P + + V+E
Sbjct: 43 KKSSQDEKKKAAELAVELDDTLGPGPVQVRVVDE 76


>gnl|CDD|177398 PHA02569, 39, DNA topoisomerase II large subunit; Provisional.
          Length = 602

 Score = 27.0 bits (60), Expect = 2.0
 Identities = 15/28 (53%), Positives = 19/28 (67%), Gaps = 2/28 (7%)

Query: 54  AAEAARKAAEQAAE--AAKKAAEKIIHK 79
           AA A + AAE+AAE  AAKKA +  + K
Sbjct: 366 AALARKLAAEKAAETKAAKKAKKAKVAK 393


>gnl|CDD|132362 TIGR03319, YmdA_YtgF, conserved hypothetical protein YmdA/YtgF. 
          Length = 514

 Score = 27.2 bits (61), Expect = 2.0
 Identities = 15/44 (34%), Positives = 27/44 (61%)

Query: 34  TLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKII 77
           T  E  + LL+E  ++A  +AA+  ++  E+A E A K A++I+
Sbjct: 145 TQEEAKEILLEEVEEEARHEAAKLIKEIEEEAKEEADKKAKEIL 188


>gnl|CDD|181026 PRK07550, PRK07550, hypothetical protein; Provisional.
          Length = 386

 Score = 27.2 bits (61), Expect = 2.1
 Identities = 11/25 (44%), Positives = 13/25 (52%)

Query: 23 QADPVAPPPPQTLAERGKALLDEAT 47
          QA P  PPPP+ L    +A  D A 
Sbjct: 36 QAVPGYPPPPELLRALAEAAADPAA 60


>gnl|CDD|181971 PRK09586, murP, PTS system N-acetylmuramic acid transporter
           subunits EIIBC; Reviewed.
          Length = 476

 Score = 26.9 bits (60), Expect = 2.1
 Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 1/51 (1%)

Query: 29  PPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHK 79
           P   Q  A+    LL EA     +  AE A +   Q         ++ + K
Sbjct: 69  PGKAQRAAKAMNELLGEAAAPVQD-LAEIAAQNKRQLKAKQTSGVQQFLAK 118


>gnl|CDD|183479 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provisional.
          Length = 400

 Score = 27.1 bits (60), Expect = 2.2
 Identities = 20/68 (29%), Positives = 23/68 (33%), Gaps = 4/68 (5%)

Query: 22  GQADPVAP----PPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKII 77
           G A PV P     P    AE   AL   AT   A      A +A   +  AA + A K  
Sbjct: 236 GDAAPVPPSEAARPKSADAETNAALKTPATAPKAAAKNAKAPEAQPVSGTAAAEPAPKEA 295

Query: 78  HKDKKKPK 85
            K      
Sbjct: 296 AKAAAAAA 303


>gnl|CDD|184700 PRK14479, PRK14479, dihydroxyacetone kinase; Provisional.
          Length = 568

 Score = 27.1 bits (61), Expect = 2.3
 Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 6/46 (13%)

Query: 36  AERG-KALLDE-----ATQKAAEKAAEAARKAAEQAAEAAKKAAEK 75
           A+ G K ++D         +AA  A     +A   AAEAA++ AE 
Sbjct: 481 AQVGDKTMVDALVPFADALEAAAAAGADLAEAWAAAAEAAEEGAEA 526



 Score = 25.2 bits (56), Expect = 7.9
 Identities = 9/18 (50%), Positives = 11/18 (61%)

Query: 50  AAEKAAEAARKAAEQAAE 67
           A   AAEAA + AE  A+
Sbjct: 512 AWAAAAEAAEEGAEATAD 529


>gnl|CDD|152163 pfam11727, ISG65-75, Invariant surface glycoprotein.  This family
           is found in Trypanosome species, and appears to be one
           of two invariant surface glycoproteins, ISG65 and ISG75.
           that are found in the mammalian stage of the parasitic
           protozoan. the sequence suggests the two families are
           polypeptides with N-terminal signal sequences,
           hydrophilic extracellular domains, single trans-membrane
           alpha-helices and short cytoplasmic domains. they are
           both expressed in the bloodstream form but not in the
           midgut stage. Both polypeptides are distributed over the
           entire surface of the parasite.
          Length = 289

 Score = 26.7 bits (59), Expect = 2.5
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 6/49 (12%)

Query: 32  PQTLAERGKALLDEATQKA------AEKAAEAARKAAEQAAEAAKKAAE 74
             +  ++ K + ++A  K       A+KA   A K AE+  EAA KA  
Sbjct: 97  SDSDKKKIKEICEKAKDKIDEALPEAKKAGREAEKLAEEVKEAAAKALG 145


>gnl|CDD|138835 PRK12279, PRK12279, 50S ribosomal protein L22/unknown domain fusion
           protein; Provisional.
          Length = 311

 Score = 27.0 bits (59), Expect = 2.5
 Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 8/86 (9%)

Query: 42  LLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPK-ENQEVNEVPVAANIE 100
           L D+  ++  E AA  A+K+ +      K   E      KK  K    EV  V    N++
Sbjct: 108 LSDDVNEREKELAAIKAKKSKKPLPVEPKAKVET-----KKVAKPSKVEVKPVEKDENVD 162

Query: 101 PESQETQQQVIN--KTTTSQTDAEKT 124
           PE  + +QQV+   + T SQ + E T
Sbjct: 163 PELLKREQQVLKVVEKTASQKEEETT 188


>gnl|CDD|172043 PRK13419, PRK13419, F0F1 ATP synthase subunit A; Provisional.
          Length = 342

 Score = 26.6 bits (59), Expect = 2.7
 Identities = 17/71 (23%), Positives = 24/71 (33%), Gaps = 6/71 (8%)

Query: 8  IILLSLLSTTMASCGQADPVAPPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAE 67
           +LL+      AS   A           A         A +  A   AEAA  A +    
Sbjct: 12 PLLLNQNDAAFASAEAAAEAHHASAAAAAAA------PAGEHGAAVHAEAAAHAEQAEGG 65

Query: 68 AAKKAAEKIIH 78
            +KA + I+H
Sbjct: 66 HEEKAGDVIMH 76


>gnl|CDD|184888 PRK14894, PRK14894, glycyl-tRNA synthetase; Provisional.
          Length = 539

 Score = 26.5 bits (58), Expect = 3.0
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 14  LSTTMASCGQADPVAPPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKK 71
           L   + S G+++ +A      +  RG+ALL    ++  E     A   A+Q  E  KK
Sbjct: 353 LEAFLKSVGRSEKLAGEARDAILARGEALLQALPERLPEVEQLLAMPGADQ-IELGKK 409


>gnl|CDD|179070 PRK00571, atpC, F0F1 ATP synthase subunit epsilon; Validated.
          Length = 135

 Score = 26.6 bits (60), Expect = 3.1
 Identities = 10/34 (29%), Positives = 14/34 (41%)

Query: 55  AEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQ 88
           AE A    E  AE AK+ AE+ +          +
Sbjct: 83  AERADDIDEARAEEAKERAEEALENKHDDVDYAR 116


>gnl|CDD|184724 PRK14520, rpsP, 30S ribosomal protein S16; Provisional.
          Length = 155

 Score = 26.6 bits (59), Expect = 3.4
 Identities = 13/65 (20%), Positives = 18/65 (27%)

Query: 45  EATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVPVAANIEPESQ 104
           E T K AE             AEA      +     KKK        E    A     + 
Sbjct: 90  EGTLKVAEPKPSKLELFNAALAEADGGPTAEATTPKKKKAAAEAAAAEAAAPAAEAAAAA 149

Query: 105 ETQQQ 109
             +++
Sbjct: 150 AAEEE 154



 Score = 25.4 bits (56), Expect = 7.0
 Identities = 15/41 (36%), Positives = 16/41 (39%)

Query: 35  LAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEK 75
           LAE       EAT    +KAA  A  A   A  A   AA  
Sbjct: 110 LAEADGGPTAEATTPKKKKAAAEAAAAEAAAPAAEAAAAAA 150


>gnl|CDD|183809 PRK12879, PRK12879, 3-oxoacyl-(acyl carrier protein) synthase
          III; Reviewed.
          Length = 325

 Score = 26.4 bits (59), Expect = 3.5
 Identities = 11/25 (44%), Positives = 14/25 (56%)

Query: 52 EKAAEAARKAAEQAAEAAKKAAEKI 76
          E  ++ A KAAE+A   A   AE I
Sbjct: 51 EYTSDLAIKAAERALARAGLDAEDI 75


>gnl|CDD|183029 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
          Length = 434

 Score = 26.4 bits (59), Expect = 3.6
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 3/49 (6%)

Query: 35  LAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKK 83
           L  + KA  ++ T K ++K      K AE+  +  +K   K  H+D K 
Sbjct: 376 LRPKTKAPSEKKTGKPSKKVLA---KRAEKKEKEKEKPKVKKRHRDTKN 421


>gnl|CDD|180554 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
          Length = 106

 Score = 26.5 bits (59), Expect = 3.7
 Identities = 15/47 (31%), Positives = 27/47 (57%)

Query: 43 LDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQE 89
          ++EA +KAA     AA  AA  AA AA +  ++   ++++K +  +E
Sbjct: 50 IEEAIKKAAAAPVAAAAAAAAAAAAAAAEEKKEEEEEEEEKEESEEE 96


>gnl|CDD|184915 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 618

 Score = 26.2 bits (58), Expect = 3.7
 Identities = 19/58 (32%), Positives = 19/58 (32%)

Query: 17  TMASCGQADPVAPPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAE 74
           T A    A P A P  Q  A    A    A   A      AA  A   A  AA  AA 
Sbjct: 380 TPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAA 437


>gnl|CDD|184048 PRK13428, PRK13428, F0F1 ATP synthase subunit delta; Provisional.
          Length = 445

 Score = 26.2 bits (58), Expect = 3.9
 Identities = 20/46 (43%), Positives = 25/46 (54%), Gaps = 3/46 (6%)

Query: 33 QTLAERGKAL--LDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKI 76
          Q LAE   A   L EA Q A  KA E A+  A +  E A++ AE+I
Sbjct: 39 QQLAESATAADRLAEADQ-AHTKAVEDAKAEAARVVEEAREDAERI 83


>gnl|CDD|181267 PRK08173, PRK08173, DNA topoisomerase III; Validated.
          Length = 862

 Score = 26.2 bits (58), Expect = 4.0
 Identities = 12/36 (33%), Positives = 14/36 (38%)

Query: 40  KALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEK 75
           KA   + T   A  AA    + A      AKK A K
Sbjct: 819 KAAAAKKTAAKATAAAATKAEKAAAKKAPAKKTAAK 854



 Score = 25.8 bits (57), Expect = 5.0
 Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 1/44 (2%)

Query: 29  PPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKA 72
               +  A +  A      +KAA K A  A+K A +   A K  
Sbjct: 820 AAAAKKTAAKATAAAATKAEKAAAKKA-PAKKTAAKKTAARKTG 862



 Score = 25.4 bits (56), Expect = 7.5
 Identities = 18/46 (39%), Positives = 22/46 (47%)

Query: 30  PPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEK 75
            P +  A   K    +AT  AA KA +AA K A     AAKK A +
Sbjct: 814 EPREPKAAAAKKTAAKATAAAATKAEKAAAKKAPAKKTAAKKTAAR 859


>gnl|CDD|162962 TIGR02651, RNase_Z, ribonuclease Z.  Processing of the 3-prime end
           of tRNA precursors may be the result of endonuclease or
           exonuclease activity, and differs in different species.
           Member of this family are ribonuclease Z, a tRNA 3-prime
           endonuclease that processes tRNAs to prepare for
           addition of CCA. In species where all tRNA sequences
           already have the CCA tail, such as E. coli, the need for
           such an enzyme is unclear. Protein similar to the E.
           coli enzyme, matched by TIGR02649, are designated
           ribonuclease BN.
          Length = 299

 Score = 26.0 bits (58), Expect = 4.0
 Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 2/33 (6%)

Query: 42  LLDEAT--QKAAEKAAEAARKAAEQAAEAAKKA 72
           L+ EAT   +  + A E     A QAAE AK+A
Sbjct: 225 LIHEATFLDEDKKLAKEYGHSTAAQAAEIAKEA 257


>gnl|CDD|179302 PRK01558, PRK01558, V-type ATP synthase subunit E; Provisional.
          Length = 198

 Score = 26.3 bits (58), Expect = 4.1
 Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 6/46 (13%)

Query: 43 LDEATQKAAEKAAEAARKA------AEQAAEAAKKAAEKIIHKDKK 82
          L+EA + A E   EA  +A      AE+ A+  K  AEK  +  K+
Sbjct: 17 LEEAERLANEIILEAKEEAEEIIAKAEEEAKELKAKAEKEANDYKR 62


>gnl|CDD|185454 PTZ00112, PTZ00112, origin recognition complex 1 protein;
           Provisional.
          Length = 1164

 Score = 26.1 bits (57), Expect = 4.1
 Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 79  KDKKKPKENQEVNEVPVAANIEPESQETQQQVINKTT--TSQTDAEKTPNEKRQGTTDGI 136
              K  KENQ    V ++++  P ++E   + + K T  T  T  +K     R  +T   
Sbjct: 158 HSPKVIKENQ-STHVNISSDNSPRNKEISNKQLKKQTNVTHTTCYDKMRRSPRNTSTIKN 216

Query: 137 NNQSNATNDPSSKDKIAENTKED 159
           N           KDK   N K+D
Sbjct: 217 NTNDKNKEKNKEKDK---NIKKD 236


>gnl|CDD|179408 PRK02292, PRK02292, V-type ATP synthase subunit E; Provisional.
          Length = 188

 Score = 26.1 bits (58), Expect = 4.3
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 3/63 (4%)

Query: 40  KALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKEN--QEVNEVPVAA 97
           + + DEA  +A+E  AEA  +A E  AE A+  AE+I+   + + +    Q   +   +A
Sbjct: 8   EDIRDEARARASEIRAEADEEAEEIIAE-AEADAEEILEDREAEAEREIEQLREQELSSA 66

Query: 98  NIE 100
            +E
Sbjct: 67  KLE 69


>gnl|CDD|180856 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
           Validated.
          Length = 725

 Score = 25.9 bits (57), Expect = 4.4
 Identities = 14/87 (16%), Positives = 29/87 (33%), Gaps = 8/87 (9%)

Query: 80  DKKKPKENQEVNEVPVAA--------NIEPESQETQQQVINKTTTSQTDAEKTPNEKRQG 131
              + +E  E                +I+ +  E +  +  K+ T   +      + +  
Sbjct: 354 ALSELEEEDENEIKFKKIEENSIDNLDIKEKKIENENDIEGKSDTKNLEEGFETKDNKNK 413

Query: 132 TTDGINNQSNATNDPSSKDKIAENTKE 158
            +  IN   N   +   KD++ E T E
Sbjct: 414 NSSFINKTENILTNSPLKDELLEKTTE 440


>gnl|CDD|162284 TIGR01282, nifD, nitrogenase molybdenum-iron protein alpha chain.
           Nitrogenase consists of alpha (NifD) and beta (NifK)
           subunits of the molybdenum-iron protein and an
           ATP-binding iron-sulfur protein (NifH). This model
           describes a large clade of NifD proteins, but excludes a
           lineage that contains putative NifD and NifD homologs
           from species with vanadium-dependent nitrogenases.
          Length = 466

 Score = 26.2 bits (58), Expect = 4.4
 Identities = 12/36 (33%), Positives = 18/36 (50%)

Query: 51  AEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKE 86
             K AE+ RK AE   +  K+ AE++I K +     
Sbjct: 289 PTKIAESLRKIAEFFDDEIKEKAEEVIAKYQPAVDA 324


>gnl|CDD|181920 PRK09510, tolA, cell envelope integrity inner membrane protein
           TolA; Provisional.
          Length = 387

 Score = 25.9 bits (57), Expect = 4.4
 Identities = 23/57 (40%), Positives = 30/57 (52%)

Query: 36  AERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNE 92
           AE  K    EA +KAA +A  AA KAA +A  AA+KAA     +     K   EV++
Sbjct: 205 AEAKKKAAAEAKKKAAAEAKAAAAKAAAEAKAAAEKAAAAKAAEKAAAAKAAAEVDD 261


>gnl|CDD|178730 PLN03188, PLN03188, kinesin-12 family protein; Provisional.
          Length = 1320

 Score = 26.1 bits (57), Expect = 4.5
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 6/55 (10%)

Query: 45   EATQKAAE------KAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEV 93
            EA Q A E      +A EA   A ++A +A ++AAE     DK K K   E++ +
Sbjct: 1194 EAVQAAGELLVRLKEAEEALTVAQKRAMDAEQEAAEAYKQIDKLKRKHENEISTL 1248


>gnl|CDD|152489 pfam12054, DUF3535, Domain of unknown function (DUF3535).  This
           presumed domain is functionally uncharacterized. This
           domain is found in eukaryotes. This domain is typically
           between 439 to 459 amino acids in length. This domain is
           found associated with pfam00271, pfam02985, pfam00176.
           This domain has two completely conserved residues (P and
           K) that may be functionally important.
          Length = 442

 Score = 26.1 bits (58), Expect = 4.6
 Identities = 15/42 (35%), Positives = 21/42 (50%)

Query: 34  TLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEK 75
           T  ++ K  L    +  A +A E AR+    A E AK+A EK
Sbjct: 246 TDFDKLKKSLSPKQKLTALQALEDARRRLLAAIEEAKEAKEK 287


>gnl|CDD|180240 PRK05759, PRK05759, F0F1 ATP synthase subunit B; Validated.
          Length = 156

 Score = 25.9 bits (58), Expect = 5.0
 Identities = 27/93 (29%), Positives = 40/93 (43%), Gaps = 14/93 (15%)

Query: 27  VAPPPPQTLAERGKALLD--EATQKAAEKAAEAARKAAEQAAEA----------AKKAAE 74
           V PP  + L ER K + D   A ++A ++   A  K   Q AEA          AKK A 
Sbjct: 25  VWPPIMKALEERQKKIADGLAAAERAKKELELAQAKYEAQLAEARAEAAEIIEQAKKRAA 84

Query: 75  KIIHKDKKKPKENQEVNEVPVAANIEPESQETQ 107
           +II  ++ K +   E   +   A  E E +  +
Sbjct: 85  QII--EEAKAEAEAEAARIKAQAQAEIEQERKR 115


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

 Score = 26.0 bits (58), Expect = 5.0
 Identities = 8/21 (38%), Positives = 12/21 (57%)

Query: 44  DEATQKAAEKAAEAARKAAEQ 64
           D+A +KAA +A E A    + 
Sbjct: 306 DKAGRKAALRALELALPLLKD 326


>gnl|CDD|182708 PRK10763, PRK10763, phospholipase A; Provisional.
          Length = 289

 Score = 25.9 bits (57), Expect = 5.0
 Identities = 8/15 (53%), Positives = 12/15 (80%)

Query: 135 GINNQSNATNDPSSK 149
           G N+QSN  +DP+S+
Sbjct: 159 GYNHQSNGRSDPTSR 173


>gnl|CDD|183749 PRK12792, flhA, flagellar biosynthesis protein FlhA; Reviewed.
          Length = 694

 Score = 25.8 bits (57), Expect = 5.2
 Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 2/25 (8%)

Query: 48  QKAAEKAAEAAR--KAAEQAAEAAK 70
           ++AA  AAEAA+  +  E A   AK
Sbjct: 326 RRAARAAAEAAKVKREEESAQAEAK 350


>gnl|CDD|179543 PRK03137, PRK03137, 1-pyrroline-5-carboxylate dehydrogenase;
           Provisional.
          Length = 514

 Score = 25.7 bits (57), Expect = 5.5
 Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 8/40 (20%)

Query: 45  EATQKAAEKAAEAARKA--------AEQAAEAAKKAAEKI 76
           +AT++ AEKA +AA +A         E  A    +AA  I
Sbjct: 69  KATKELAEKAMQAALEAFETWKKWSPEDRARILLRAAAII 108


>gnl|CDD|182751 PRK10811, rne, ribonuclease E; Reviewed.
          Length = 1068

 Score = 25.8 bits (57), Expect = 5.7
 Identities = 15/112 (13%), Positives = 27/112 (24%), Gaps = 4/112 (3%)

Query: 17   TMASCGQADPVAPPPPQTLAERGKAL---LDEATQKAAEKAAEAARKAAEQAAEAAKKAA 73
                   A+P             + +   + E  Q   E     A++ AE A    +   
Sbjct: 895  VEEPVVVAEPQPEEVVVVETTHPEVIAAPVTEQPQVITESDVAVAQEVAEHAEPVVEPQD 954

Query: 74   EKIIHKDKKKPKENQEVNEVPVAANIEPESQETQQQVINKTTTSQTDAEKTP 125
            E     ++        V E  V A             +   T  + +     
Sbjct: 955  E-TADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVAPAQ 1005


>gnl|CDD|149170 pfam07946, DUF1682, Protein of unknown function (DUF1682).  The
           members of this family are all hypothetical eukaryotic
           proteins of unknown function. One member is described as
           being an adipocyte-specific protein, but no evidence of
           this was found.
          Length = 322

 Score = 25.7 bits (57), Expect = 5.7
 Identities = 12/51 (23%), Positives = 26/51 (50%), Gaps = 2/51 (3%)

Query: 40  KALLDEATQKAAEKAAEAARKA--AEQAAEAAKKAAEKIIHKDKKKPKENQ 88
           + +L  A ++  E+A E   +    E+ A+ AK + E+    ++K+ K+  
Sbjct: 270 EKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKYEEKERKKEA 320


>gnl|CDD|173593 PTZ00402, PTZ00402, glutamyl-tRNA synthetase; Provisional.
          Length = 601

 Score = 25.7 bits (56), Expect = 5.7
 Identities = 13/22 (59%), Positives = 18/22 (81%)

Query: 54  AAEAARKAAEQAAEAAKKAAEK 75
           A+ A   AA++AA+AAKKAA+K
Sbjct: 574 ASAANDLAAKRAAKAAKKAAQK 595



 Score = 24.9 bits (54), Expect = 9.1
 Identities = 15/34 (44%), Positives = 24/34 (70%), Gaps = 2/34 (5%)

Query: 33  QTLAERGKALLDEATQKAAEKAAEAARKAAEQAA 66
           +TL ++G A    A   AA++AA+AA+KAA++ A
Sbjct: 566 KTLPKKGIA--SAANDLAAKRAAKAAKKAAQKQA 597


>gnl|CDD|152176 pfam11740, KfrA_N, Plasmid replication region DNA-binding N-term.
           The broad host-range plasmid RK2 is able to replicate in
           and be inherited in a stable manner in diverse
           Gram-negative bacterial species. It encodes a number of
           co-ordinately regulated operons including a central
           control korF1 operon that represses the kfrA operon. The
           KfrA polypeptide is a site-specific DNA-binding protein
           whose operator overlaps the kfrA promoter. The
           N-terminus, containing an helix-turn-helix motif, is
           essential for function. Downstream from this family is
           an extended coiled-coil domain containing a heptad
           repeat segment which is probably responsible for
           formation of multimers, and may provide an example of a
           bridge to host structures required for plasmid
           partitioning.
          Length = 120

 Score = 25.7 bits (57), Expect = 5.7
 Identities = 18/64 (28%), Positives = 21/64 (32%), Gaps = 10/64 (15%)

Query: 22  GQADPVAPPPPQTLAERGKALLDEATQKA----------AEKAAEAARKAAEQAAEAAKK 71
               P AP  P  L+E    L+    + A          A  AAEA R   E     A  
Sbjct: 50  AALAPAAPELPDALSEALAELVAALWEAAQEEAEERLAAARAAAEAERAELEAELAEAAA 109

Query: 72  AAEK 75
            AE 
Sbjct: 110 EAEA 113


>gnl|CDD|184866 PRK14864, PRK14864, putative biofilm stress and motility protein
          A; Provisional.
          Length = 104

 Score = 25.8 bits (57), Expect = 5.8
 Identities = 8/27 (29%), Positives = 12/27 (44%), Gaps = 2/27 (7%)

Query: 9  ILLSLLSTTMASCG--QADPVAPPPPQ 33
              LL+  +++C   Q  P   PPP 
Sbjct: 8  FASLLLTLLLSACSALQGTPQPAPPPA 34


>gnl|CDD|181844 PRK09424, pntA, NAD(P) transhydrogenase subunit alpha; Provisional.
          Length = 509

 Score = 25.6 bits (57), Expect = 5.9
 Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 11/45 (24%)

Query: 29  PPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAA 73
           PPP Q  A             AA  AA AA++  ++ A   +K A
Sbjct: 370 PPPIQVSA-----------APAAAAAAPAAKEEEKKPASPWRKYA 403


>gnl|CDD|180892 PRK07220, PRK07220, DNA topoisomerase I; Validated.
          Length = 740

 Score = 25.5 bits (56), Expect = 5.9
 Identities = 18/67 (26%), Positives = 24/67 (35%), Gaps = 5/67 (7%)

Query: 23  QADPVAPPPPQTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKK 82
           +A       P+++ +          +K AEK  EA     E  AEA      K      K
Sbjct: 676 KAQQPKKEKPKSIKDIKGI-----GKKTAEKLEEAGITTVEALAEADPVELSKTTKISVK 730

Query: 83  KPKENQE 89
           K K  QE
Sbjct: 731 KIKSWQE 737


>gnl|CDD|148033 pfam06188, HrpE, HrpE protein.  This family consists of several
          bacterial HrpE proteins. The exact function of this
          family is unknown but it is thought that HrpE is
          involved in the secretion of HrpZ (harpinPss).
          Length = 191

 Score = 25.4 bits (56), Expect = 5.9
 Identities = 16/39 (41%), Positives = 24/39 (61%), Gaps = 6/39 (15%)

Query: 37 ERGKALLDEATQKA------AEKAAEAARKAAEQAAEAA 69
             + LL++A Q+A      AE+ AEA ++ AE+ AEAA
Sbjct: 30 LLARTLLEDARQQAEQILDLAEEKAEALQQRAEEQAEAA 68


>gnl|CDD|183398 PRK12280, rplW, 50S ribosomal protein L23; Reviewed.
          Length = 158

 Score = 25.5 bits (56), Expect = 6.1
 Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 2/58 (3%)

Query: 45  EATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVPVAANIEPE 102
           E +++  EK A  A+K  E+  +  KK AEK+  K   K  +N            + E
Sbjct: 101 EVSKETEEKEAIKAKK--EKKEKKEKKVAEKLAKKKSTKTTKNTTKKATKKTTTKKEE 156


>gnl|CDD|162823 TIGR02361, dak_ATP, dihydroxyacetone kinase, ATP-dependent.  This
           family consists of examples of the form of
           dihydroxyacetone kinase (also called glycerone kinase)
           that uses ATP (2.7.1.29) as the phosphate donor, rather
           than a phosphoprotein as in E. coli. This form is
           composed of a single chain with separable domains
           homologous to the K and L subunits of the E. coli
           enzyme, and is found in yeasts and other eukaryotes and
           in some bacteria, including Citrobacter freundii. The
           member from tomato has been shown to phosphorylate
           dihydroxyacetone, 3,4-dihydroxy-2-butanone, and some
           other aldoses and ketoses (PubMed:11985845).
          Length = 574

 Score = 25.4 bits (56), Expect = 6.2
 Identities = 8/26 (30%), Positives = 12/26 (46%)

Query: 50  AAEKAAEAARKAAEQAAEAAKKAAEK 75
              +A EA +     A +AA+  AE 
Sbjct: 511 PFVEALEAGKSNLNAAVKAAEAGAEA 536


>gnl|CDD|178220 PLN02610, PLN02610, probable methionyl-tRNA synthetase.
          Length = 801

 Score = 25.5 bits (56), Expect = 6.6
 Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 5/68 (7%)

Query: 40  KALLDEATQKAAEKAA--EAARKAAEQAAEA---AKKAAEKIIHKDKKKPKENQEVNEVP 94
           K L DE  +   EK A  +A R A  +AAEA   AK+  +K +    KK +  +      
Sbjct: 570 KELKDEEVEAYREKFAGSQADRAARAEAAEAKKLAKQLKKKALSDGGKKKQGKKAGGGGK 629

Query: 95  VAANIEPE 102
             A  E E
Sbjct: 630 SKAAAERE 637


>gnl|CDD|150226 pfam09481, CRISPR_Cse1, CRISPR-associated protein Cse1
           (CRISPR_cse1).  Clusters of short DNA repeats with
           non-homologous spacers, which are found at regular
           intervals in the genomes of phylogenetically distinct
           prokaryotic species, comprise a family with recognisable
           features. This family is known as CRISPR (short for
           Clustered, Regularly Interspaced Short Palindromic
           Repeats). A number of protein families appear only in
           association with these repeats and are designated Cas
           (CRISPR-Associated) proteins. This entry, represented by
           CT1972 from Chlorobaculum tepidum, is found in the
           CRISPR/Cas subtype Ecoli regions of many bacteria (most
           of which are mesophiles), and not in Archaea. It is
           designated Cse1.
          Length = 475

 Score = 25.4 bits (56), Expect = 6.8
 Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 4/53 (7%)

Query: 25  DPVAPPPPQTLAERGKALLDEATQ--KAAEKAAEAARKAAEQAAEAAKKAAEK 75
             + P P   L++    L  +  +   AAE+AA A R A ++A  A  K A+ 
Sbjct: 368 MDLLPLPAALLSDED--LRAQIKEAVDAAEEAARALRSALKEAWFALGKDAKG 418


>gnl|CDD|179357 PRK01973, PRK01973, septum formation inhibitor; Reviewed.
          Length = 271

 Score = 25.5 bits (56), Expect = 7.4
 Identities = 25/70 (35%), Positives = 30/70 (42%), Gaps = 16/70 (22%)

Query: 44  DEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKENQEVNEVPVAANIEPES 103
           DEA   AAE AA AA  AAE AA A   AA                  E P A   E  +
Sbjct: 115 DEAAAAAAEAAAPAAAAAAEAAAAAPAAAA----------------APEPPPAPAPEAVA 158

Query: 104 QETQQQVINK 113
            ++Q  VI++
Sbjct: 159 AQSQTLVIDR 168


>gnl|CDD|183371 PRK11904, PRK11904, bifunctional proline
           dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
           Reviewed.
          Length = 1038

 Score = 25.2 bits (56), Expect = 8.1
 Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 9/56 (16%)

Query: 22  GQADPVAPPPPQTLAERGKAL--LDEATQKAAEKAAEAARKAAE--QAAEAAKKAA 73
           G+A PV  P     A+R + +  +  A  +  E+A  AAR A          ++AA
Sbjct: 561 GEARPVVSP-----ADRRRVVGEVAFADAEQVEQALAAARAAFPAWSRTPVEERAA 611


>gnl|CDD|151683 pfam11241, DUF3043, Protein of unknown function (DUF3043).  Some
          members in this family of proteins with unknown
          function are annotated as membrane proteins. This
          cannot be confirmed.
          Length = 168

 Score = 25.3 bits (56), Expect = 8.1
 Identities = 13/29 (44%), Positives = 17/29 (58%)

Query: 46 ATQKAAEKAAEAARKAAEQAAEAAKKAAE 74
            +KAA+KAA AAR+     A AA  A +
Sbjct: 23 EDRKAAKKAARAARRERRARARAAMMAGD 51


>gnl|CDD|184912 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 620

 Score = 25.3 bits (56), Expect = 8.2
 Identities = 13/87 (14%), Positives = 22/87 (25%)

Query: 3   RLKYQIILLSLLSTTMASCGQADPVAPPPPQTLAERGKALLDEATQKAAEKAAEAARKAA 62
           RL  ++ LL LL +   S          P             + +    ++AA       
Sbjct: 349 RLWLEVTLLGLLPSAFISEIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPP 408

Query: 63  EQAAEAAKKAAEKIIHKDKKKPKENQE 89
            +A+      AE               
Sbjct: 409 AKASPPIPVPAEPTEPSPTPPANAANA 435


>gnl|CDD|130057 TIGR00984, 3a0801s03tim44, mitochondrial import inner membrane,
           translocase subunit.  translocase (Tom) import receptor,
           five proteins of the Tom channel complex, five proteins
           of the inner membrane translocase (Tim) and three
           "motor" proteins. This family is specific for the Tim
           proteins.
          Length = 378

 Score = 24.8 bits (54), Expect = 8.9
 Identities = 12/40 (30%), Positives = 21/40 (52%)

Query: 40  KALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHK 79
           KA   E  +K  +  AE A+ AAE   ++A+   +  ++K
Sbjct: 71  KAWESELGKKMKKAGAETAKTAAEHVDKSAEPVRDTAVYK 110


>gnl|CDD|179957 PRK05183, hscA, chaperone protein HscA; Provisional.
          Length = 616

 Score = 25.1 bits (56), Expect = 9.1
 Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 4/39 (10%)

Query: 41  ALLDEATQKAAEKAAEAARKAAE----QAAEAAKKAAEK 75
            LL  A + A + A  A R+ A+     A EAA KA +K
Sbjct: 552 DLLSAAERAAIDAAMAALREVAQGDDADAIEAAIKALDK 590


>gnl|CDD|147874 pfam05957, DUF883, Bacterial protein of unknown function
          (DUF883).  This family consists of several hypothetical
          bacterial proteins of unknown function.
          Length = 94

 Score = 24.8 bits (55), Expect = 9.1
 Identities = 14/37 (37%), Positives = 20/37 (54%)

Query: 36 AERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKA 72
          AE  +   + A   A E+  +AA  AAE+A +AA  A
Sbjct: 29 AEELRERAEAALDDARERLGDAADAAAERARDAADAA 65


>gnl|CDD|184531 PRK14135, recX, recombination regulator RecX; Provisional.
          Length = 263

 Score = 24.8 bits (55), Expect = 9.2
 Identities = 10/23 (43%), Positives = 14/23 (60%)

Query: 63  EQAAEAAKKAAEKIIHKDKKKPK 85
           E   E A+K AEK++ K +K P 
Sbjct: 152 EDQIEVAQKLAEKLLKKYQKLPF 174


>gnl|CDD|167031 PRK00708, PRK00708, sec-independent translocase; Provisional.
          Length = 209

 Score = 24.8 bits (54), Expect = 9.3
 Identities = 21/59 (35%), Positives = 23/59 (38%), Gaps = 1/59 (1%)

Query: 26  PVAPPPPQTLAERGKALLDEATQKAAEKAAEAAR-KAAEQAAEAAKKAAEKIIHKDKKK 83
           P  PP     A         A   AA KA    R K+   AA+AA K  E I  K  KK
Sbjct: 124 PETPPAVPVPAPAPAVAAAAAQAAAAPKAPAKPRAKSPRPAAKAAPKPTETITAKKAKK 182


>gnl|CDD|184510 PRK14105, PRK14105, selenophosphate synthetase; Provisional.
          Length = 345

 Score = 24.7 bits (54), Expect = 9.5
 Identities = 10/36 (27%), Positives = 15/36 (41%)

Query: 43  LDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIH 78
            +    KA E    + R A     EA ++  EKI +
Sbjct: 203 KEYIINKAIELMTTSNRYALLALREAEEEVGEKIAN 238


>gnl|CDD|183449 PRK12334, PRK12334, nucleoside triphosphate pyrophosphohydrolase;
           Reviewed.
          Length = 277

 Score = 25.0 bits (55), Expect = 9.9
 Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 2/57 (3%)

Query: 26  PVAPPPPQTLAERGKALLDE--ATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKD 80
           PV   P +   +   ALL    A   AA   AEAA +AA +      +AAE+    D
Sbjct: 214 PVPLAPAEDSEDELGALLLALVAVAVAAGVDAEAALRAAVRDFRDRIRAAERAAAAD 270


>gnl|CDD|161856 TIGR00395, leuS_arch, leucyl-tRNA synthetase, archaeal and
           cytosolic family.  The leucyl-tRNA synthetases belong to
           two families so broadly different that they are
           represented by separate models. This model includes both
           archaeal and cytosolic eukaryotic leucyl-tRNA
           synthetases; the eubacterial and mitochondrial forms
           differ so substantially that some other tRNA ligases
           score higher by this model than does any eubacterial
           LeuS.
          Length = 938

 Score = 24.8 bits (54), Expect = 9.9
 Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 2/34 (5%)

Query: 63  EQAAEAAKKA--AEKIIHKDKKKPKENQEVNEVP 94
           + AA   KK   A  II        EN++ N VP
Sbjct: 897 KAAARFIKKEVGALVIIEFSADSFPENKKRNAVP 930


  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
   0.299    0.115    0.295 

Gapped
Lambda     K      H
   0.267   0.0640    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,344,569
Number of extensions: 135482
Number of successful extensions: 1606
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1186
Number of HSP's successfully gapped: 480
Length of query: 159
Length of database: 5,994,473
Length adjustment: 86
Effective length of query: 73
Effective length of database: 4,136,185
Effective search space: 301941505
Effective search space used: 301941505
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 17 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.7 bits)
S2: 53 (24.4 bits)