Query         gi|254780909|ref|YP_003065322.1| hypothetical protein CLIBASIA_04040 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 159
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 00:28:23 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780909.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam09487 HrpB2 Bacterial type  83.9     1.6 4.1E-05   22.7   3.9   58   20-77      3-64  (117)
  2 COG5567 Predicted small peripl  81.2     1.5 3.7E-05   22.9   2.8   32    1-33      1-32  (58)
  3 PRK10259 hypothetical protein;  80.2     1.6   4E-05   22.7   2.7   57    1-58      1-63  (86)
  4 PRK10866 outer membrane protei  79.7     4.6 0.00012   20.0   6.3   55    1-56      1-56  (243)
  5 cd03406 Band_7_3 A subgroup of  68.2       9 0.00023   18.3   5.7   45   29-73    155-207 (280)
  6 TIGR02558 HrpB2 type III secre  67.3     4.3 0.00011   20.1   2.3   70   16-86      6-83  (124)
  7 COG4314 NosL Predicted lipopro  60.5       6 0.00015   19.3   2.0   37    1-40      1-37  (176)
  8 PRK09859 multidrug efflux syst  60.3      11 0.00027   17.9   3.2   25    1-25      1-25  (385)
  9 KOG2962 consensus               53.3      17 0.00043   16.7   5.9   53   33-86    185-237 (322)
 10 TIGR02722 lp_ uncharacterized   45.3      20  0.0005   16.3   2.6   54    2-56      1-58  (215)
 11 PRK02998 prsA peptidylprolyl i  36.8      26 0.00067   15.6   2.2   31    1-31      1-32  (283)
 12 COG5510 Predicted small secret  34.2      27 0.00068   15.5   1.9   40    1-44      2-41  (44)
 13 PRK11397 dacD D-alanyl-D-alani  33.7      30 0.00075   15.2   2.1   27   11-37     13-39  (390)
 14 pfam02987 LEA_4 Late embryogen  30.6      39   0.001   14.5   3.6   33   44-76      9-41  (44)
 15 pfam11839 DUF3359 Protein of u  24.9      50  0.0013   13.9   5.3   23    3-25      4-27  (97)
 16 TIGR01059 gyrB DNA gyrase, B s  24.6      50  0.0013   13.9   2.7   16   64-79    394-409 (818)
 17 PRK09578 periplasmic multidrug  23.1      54  0.0014   13.7   2.9   21    8-28     10-30  (385)
 18 PRK03577 acid shock protein pr  21.6      58  0.0015   13.5   5.7   32   54-85     66-97  (102)
 19 pfam08085 Entericidin Enterici  20.1      62  0.0016   13.4   2.1   22    1-22      1-22  (42)
 20 pfam12602 FinO_N Fertility inh  20.1      63  0.0016   13.3   1.9   13   47-59     50-62  (72)

No 1  
>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.
Probab=83.87  E-value=1.6  Score=22.65  Aligned_cols=58  Identities=36%  Similarity=0.560  Sum_probs=37.9

Q ss_pred             HCCCCCCCCCCCHHHHHHHHHHHHHHHHHH---H-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             304668899987067888657888888789---8-899999999988999999999999987
Q gi|254780909|r   20 SCGQADPVAPPPPQTLAERGKALLDEATQK---A-AEKAAEAARKAAEQAAEAAKKAAEKII   77 (159)
Q Consensus        20 scgqadpvappppqtlaergkalldeatqk---a-aekaaeaarkaaeqaaeaakkaaekii   77 (159)
                      ..+-+.|++|.||+.|++|-.+|...+.+-   + +-....+..+..+--.++-++..+.+.
T Consensus         3 ~t~a~~p~~p~~~~~la~rFqALM~~a~~aPp~~~~~~~~s~vsklv~~qda~~r~~~~d~~   64 (117)
T pfam09487         3 GTGAAPPVAPAPPQELVERFQALMASAPPAPPAAQASEGPSAVSRLVETQDAAVRKVLDDVL   64 (117)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98889999997779999999999808999997556654357999999986899999888999


No 2  
>COG5567 Predicted small periplasmic lipoprotein [Cell motility and secretion]
Probab=81.19  E-value=1.5  Score=22.88  Aligned_cols=32  Identities=31%  Similarity=0.593  Sum_probs=24.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCHH
Q ss_conf             963034488999888766530466889998706
Q gi|254780909|r    1 MKRLKYQIILLSLLSTTMASCGQADPVAPPPPQ   33 (159)
Q Consensus         1 mkrlkyqiillsllsttmascgqadpvappppq   33 (159)
                      ||++---..++.+|+ +.|.||+-.|.--||-.
T Consensus         1 mk~~~~s~~ala~l~-sLA~CG~KGPLy~Ppad   32 (58)
T COG5567           1 MKNVFKSLLALATLF-SLAGCGLKGPLYFPPAD   32 (58)
T ss_pred             CHHHHHHHHHHHHHH-HHHHCCCCCCCCCCHHH
T ss_conf             904899999999999-99852667876278243


No 3  
>PRK10259 hypothetical protein; Provisional
Probab=80.21  E-value=1.6  Score=22.67  Aligned_cols=57  Identities=30%  Similarity=0.392  Sum_probs=38.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHH------HHHHHHHHHHHHHHHHHHHH
Q ss_conf             96303448899988876653046688999870678886------57888888789889999999
Q gi|254780909|r    1 MKRLKYQIILLSLLSTTMASCGQADPVAPPPPQTLAER------GKALLDEATQKAAEKAAEAA   58 (159)
Q Consensus         1 mkrlkyqiillsllsttmascgqadpvappppqtlaer------gkalldeatqkaaekaaeaa   58 (159)
                      ||.+||-+..+.|-+... ..--|+||.+.++|.|-.-      |-.-||+-.-+-++||.++.
T Consensus         1 MK~ik~~~aa~aLs~~SF-gsfAA~~v~~~qa~~l~~iG~VSa~gA~tL~~Le~~LA~KA~~aG   63 (86)
T PRK10259          1 MKTINTVVAAMALSTLSF-GVFAAEPVTASQAQNMNKIGVVSADGASTLDALEAKLAEKAAAAG   63 (86)
T ss_pred             CCHHHHHHHHHHHHHHHH-HHHHCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHCC
T ss_conf             914899999999998226-765414146322125665279982488886899999999999748


No 4  
>PRK10866 outer membrane protein assembly complex subunit YfiO; Provisional
Probab=79.72  E-value=4.6  Score=19.96  Aligned_cols=55  Identities=27%  Similarity=0.447  Sum_probs=36.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCCC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             963034488999888766530466-88999870678886578888887898899999
Q gi|254780909|r    1 MKRLKYQIILLSLLSTTMASCGQA-DPVAPPPPQTLAERGKALLDEATQKAAEKAAE   56 (159)
Q Consensus         1 mkrlkyqiillsllsttmascgqa-dpvappppqtlaergkalldeatqkaaekaae   56 (159)
                      |+|+|+-+++ .+|+-.+++|+-. +.+.--+|+.+-+.|...++..--..|-+.-|
T Consensus         1 m~~~k~l~~~-~~l~l~l~gCs~~~~~~~~~~~~~~Y~~A~~~~~~~~y~~A~~~fe   56 (243)
T PRK10866          1 MTRMKYLVAA-ATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWKQAITQLE   56 (243)
T ss_pred             CCHHHHHHHH-HHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             9458999999-9999999876899888889999999999999998789999999999


No 5  
>cd03406 Band_7_3 A subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin.  Many of these band 7 domain-containing proteins are lipid raft-associated.  Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes.  Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions.  Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins.  Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins.  Prokaryotic H
Probab=68.24  E-value=9  Score=18.25  Aligned_cols=45  Identities=40%  Similarity=0.485  Sum_probs=33.6

Q ss_pred             CCCHHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9870678--------88657888888789889999999998899999999999
Q gi|254780909|r   29 PPPPQTL--------AERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAA   73 (159)
Q Consensus        29 ppppqtl--------aergkalldeatqkaaekaaeaarkaaeqaaeaakkaa   73 (159)
                      |-.|.++        +||-|.|.-+-+||..||-||..||-|.--||-....+
T Consensus       155 PkiPe~Ir~NyE~me~EKTkllia~q~QkvvEKeaETerk~AviEAEk~a~V~  207 (280)
T cd03406         155 PKIPEAIRRNYELMEAEKTKLLIAIQKQKVVEKEAETERKKAVIEAEKVAQVA  207 (280)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99819999999999867888999999999999887778889999898888888


No 6  
>TIGR02558 HrpB2 type III secretion protein HrpB2; InterPro: IPR013391    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..
Probab=67.33  E-value=4.3  Score=20.14  Aligned_cols=70  Identities=26%  Similarity=0.359  Sum_probs=38.4

Q ss_pred             HHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH--HHHHHH--H-HHHHHHHHHHHHHHHHHHHH---HHHHHCCCCH
Q ss_conf             7665304668899987067888657888888789--889999--9-99998899999999999998---7643217500
Q gi|254780909|r   16 TTMASCGQADPVAPPPPQTLAERGKALLDEATQK--AAEKAA--E-AARKAAEQAAEAAKKAAEKI---IHKDKKKPKE   86 (159)
Q Consensus        16 ttmascgqadpvappppqtlaergkalldeatqk--aaekaa--e-aarkaaeqaaeaakkaaeki---ihkdkkkpke   86 (159)
                      ++..+-+-..|++++|||.|++|=.||+..+.+.  +..+..  + -+|-.+.|-++- ++..+.|   -..+++++-+
T Consensus         6 ~~~~~~~a~~~~aa~~~~~l~~rF~ALm~~~~~~~~~~~r~~e~s~is~Lv~~~d~~v-r~~~~~v~~~~~~a~~~~l~   83 (124)
T TIGR02558         6 AAAVSTPAVAPTAAEPPAELVERFQALMRKAAVEPPALARSKEPSAISRLVAAQDAEV-RAVVDDVEALEERAPEMSLE   83 (124)
T ss_pred             HHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHCCCCCHH
T ss_conf             0112223567778872057878999986217899731212057318999998641898-89998899887417888888


No 7  
>COG4314 NosL Predicted lipoprotein involved in nitrous oxide reduction [Energy production and conversion]
Probab=60.47  E-value=6  Score=19.31  Aligned_cols=37  Identities=38%  Similarity=0.671  Sum_probs=27.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHH
Q ss_conf             9630344889998887665304668899987067888657
Q gi|254780909|r    1 MKRLKYQIILLSLLSTTMASCGQADPVAPPPPQTLAERGK   40 (159)
Q Consensus         1 mkrlkyqiillsllsttmascgqadpvappppqtlaergk   40 (159)
                      |||+-.-|.++++|   .|.|+++.--+||-|-.+.++.-
T Consensus         1 mkr~Lla~la~~~l---lAgC~~~ed~~~p~P~~i~~~s~   37 (176)
T COG4314           1 MKRTLLAILAVTAL---LAGCRQAEDGAPPLPRQITDRSM   37 (176)
T ss_pred             CCHHHHHHHHHHHH---HHHCCHHHCCCCCCCCCCCCCCC
T ss_conf             94037999999999---87534311389998702145542


No 8  
>PRK09859 multidrug efflux system protein MdtE; Provisional
Probab=60.33  E-value=11  Score=17.87  Aligned_cols=25  Identities=20%  Similarity=0.414  Sum_probs=18.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             9630344889998887665304668
Q gi|254780909|r    1 MKRLKYQIILLSLLSTTMASCGQAD   25 (159)
Q Consensus         1 mkrlkyqiillsllsttmascgqad   25 (159)
                      |+|-+|.+|.|-++..-+++|+...
T Consensus         1 m~~k~~~li~ll~~~~lL~gC~~~~   25 (385)
T PRK09859          1 MNRRRKLLIPLLFCGAMLTACDDKS   25 (385)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             9820678999999999995379997


No 9  
>KOG2962 consensus
Probab=53.32  E-value=17  Score=16.67  Aligned_cols=53  Identities=40%  Similarity=0.396  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCH
Q ss_conf             678886578888887898899999999988999999999999987643217500
Q gi|254780909|r   33 QTLAERGKALLDEATQKAAEKAAEAARKAAEQAAEAAKKAAEKIIHKDKKKPKE   86 (159)
Q Consensus        33 qtlaergkalldeatqkaaekaaeaarkaaeqaaeaakkaaekiihkdkkkpke   86 (159)
                      +.-+|+.|-|..--+||.+||-||.-||-|---||-.-..+ +|..+.|---||
T Consensus       185 ~ME~EkTKlLiA~ekQkVvEKeAETerkkAviEAEK~AqVa-~I~~qqkl~EKe  237 (322)
T KOG2962         185 LMEAEKTKLLIAAEKQKVVEKEAETERKKAVIEAEKNAQVA-KILMQQKLMEKE  237 (322)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH
T ss_conf             88777656678888888999877788889998898776799-999998865567


No 10 
>TIGR02722 lp_ uncharacterized lipoprotein; InterPro: IPR014094   Members of this protein family are restricted to the Proteobacteria, and all are predicted lipoproteins. In genomes that contain the thiK gene for the salvage enzyme thiamin kinase, the member of this family is encoded nearby..
Probab=45.30  E-value=20  Score=16.29  Aligned_cols=54  Identities=20%  Similarity=0.318  Sum_probs=30.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHCCCC--CCCCCCCHHHHHHHHH--HHHHHHHHHHHHHHHH
Q ss_conf             63034488999888766530466--8899987067888657--8888887898899999
Q gi|254780909|r    2 KRLKYQIILLSLLSTTMASCGQA--DPVAPPPPQTLAERGK--ALLDEATQKAAEKAAE   56 (159)
Q Consensus         2 krlkyqiillsllsttmascgqa--dpvappppqtlaergk--alldeatqkaaekaae   56 (159)
                      ||++| ||++-++.-..++|.+-  .++-|-+|++.-----  .+-..-++..+++-.+
T Consensus         1 k~~~~-l~~~~~~Al~L~GC~~~~~~y~~~~~~~~~~~~~~tl~~~~~d~~~~a~~~~~   58 (215)
T TIGR02722         1 KKYKI-LIFVALLALLLSGCVSQRVAYTDATDPQPVEPVTPTLGLSSTDLEPIANKMIQ   58 (215)
T ss_pred             CHHHH-HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCHHHHHHHCC
T ss_conf             83787-89999999998546887266568875667776057766888672334765138


No 11 
>PRK02998 prsA peptidylprolyl isomerase; Reviewed
Probab=36.81  E-value=26  Score=15.55  Aligned_cols=31  Identities=26%  Similarity=0.383  Sum_probs=21.7

Q ss_pred             CCCHHHHHHHHHHHHH-HHHHCCCCCCCCCCC
Q ss_conf             9630344889998887-665304668899987
Q gi|254780909|r    1 MKRLKYQIILLSLLST-TMASCGQADPVAPPP   31 (159)
Q Consensus         1 mkrlkyqiillsllst-tmascgqadpvappp   31 (159)
                      ||+-|.-+..+++.|. +++.||..+.|+---
T Consensus         1 Mkkkk~~~~~~~~~~~l~LaaC~s~~~vat~k   32 (283)
T PRK02998          1 MKKKKLFIGTIISCVVLALSACGSSDNVVTSK   32 (283)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEC
T ss_conf             93589999999999999998668998179843


No 12 
>COG5510 Predicted small secreted protein [Function unknown]
Probab=34.24  E-value=27  Score=15.50  Aligned_cols=40  Identities=35%  Similarity=0.473  Sum_probs=24.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             96303448899988876653046688999870678886578888
Q gi|254780909|r    1 MKRLKYQIILLSLLSTTMASCGQADPVAPPPPQTLAERGKALLD   44 (159)
Q Consensus         1 mkrlkyqiillsllsttmascgqadpvappppqtlaergkalld   44 (159)
                      |||...-|+++-|.|+..++|.-..-+.    +..-.-|+++-|
T Consensus         2 mk~t~l~i~~vll~s~llaaCNT~rG~G----~DIq~~G~al~~   41 (44)
T COG5510           2 MKKTILLIALVLLASTLLAACNTMRGAG----KDIQSGGKALSD   41 (44)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHCCC----HHHHHHHHHHHH
T ss_conf             0489999999999999998866300223----648888898775


No 13 
>PRK11397 dacD D-alanyl-D-alanine carboxypeptidase; Provisional
Probab=33.69  E-value=30  Score=15.24  Aligned_cols=27  Identities=26%  Similarity=0.385  Sum_probs=20.9

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHH
Q ss_conf             998887665304668899987067888
Q gi|254780909|r   11 LSLLSTTMASCGQADPVAPPPPQTLAE   37 (159)
Q Consensus        11 lsllsttmascgqadpvappppqtlae   37 (159)
                      |-+++-+.+.|+++-+..|.||.--|+
T Consensus        13 ~~~~~~~~~~~~~~~~~~p~~P~i~A~   39 (390)
T PRK11397         13 LFVFNLSSAFAAENIPFSPQPPAIDAG   39 (390)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCE
T ss_conf             999999998740457789999965533


No 14 
>pfam02987 LEA_4 Late embryogenesis abundant protein. Different types of LEA proteins are expressed at different stages of late embryogenesis in higher plant seed embryos and under conditions of dehydration stress. The function of these proteins is unknown.
Probab=30.59  E-value=39  Score=14.53  Aligned_cols=33  Identities=55%  Similarity=0.519  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             888789889999999998899999999999998
Q gi|254780909|r   44 DEATQKAAEKAAEAARKAAEQAAEAAKKAAEKI   76 (159)
Q Consensus        44 deatqkaaekaaeaarkaaeqaaeaakkaaeki   76 (159)
                      -|+...+.+|+.|..--+++.+.|+-..+++|+
T Consensus         9 ~eakD~t~~Kage~KD~aaeKa~e~KD~a~ek~   41 (44)
T pfam02987         9 KEAKDATAEKAGEYKDYAAEKAGEAKDKAAEKA   41 (44)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             876565888710377889986202357888870


No 15 
>pfam11839 DUF3359 Protein of unknown function (DUF3359). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.
Probab=24.87  E-value=50  Score=13.92  Aligned_cols=23  Identities=35%  Similarity=0.414  Sum_probs=12.6

Q ss_pred             CHHHHH-HHHHHHHHHHHHCCCCC
Q ss_conf             303448-89998887665304668
Q gi|254780909|r    3 RLKYQI-ILLSLLSTTMASCGQAD   25 (159)
Q Consensus         3 rlkyqi-illsllsttmascgqad   25 (159)
                      -||+.- .|-+||.+..+|...-|
T Consensus         4 llk~s~i~laallaggcaslseed   27 (97)
T pfam11839         4 LLKFSAIALAALLAGGCASLSEED   27 (97)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf             899999999999974312321888


No 16 
>TIGR01059 gyrB DNA gyrase, B subunit; InterPro: IPR011557   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .    Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively.   This entry represents the B subunit (gyrB) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrB has two functional domains: an N-terminal ATPase and a C-terminal responsible for subunit interactions, the latter differing between subunit B and single polypeptide topoisomerase II .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=24.64  E-value=50  Score=13.89  Aligned_cols=16  Identities=50%  Similarity=0.453  Sum_probs=10.6

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999999999998764
Q gi|254780909|r   64 QAAEAAKKAAEKIIHK   79 (159)
Q Consensus        64 qaaeaakkaaekiihk   79 (159)
                      ||.||||||-|-.-.|
T Consensus       394 ~AReAArkARELtRRK  409 (818)
T TIGR01059       394 RAREAARKARELTRRK  409 (818)
T ss_pred             HHHHHHHHHHHHCCCC
T ss_conf             9988756644300166


No 17 
>PRK09578 periplasmic multidrug efflux lipoprotein precursor; Reviewed
Probab=23.11  E-value=54  Score=13.72  Aligned_cols=21  Identities=24%  Similarity=0.444  Sum_probs=11.7

Q ss_pred             HHHHHHHHHHHHHCCCCCCCC
Q ss_conf             889998887665304668899
Q gi|254780909|r    8 IILLSLLSTTMASCGQADPVA   28 (159)
Q Consensus         8 iillsllsttmascgqadpva   28 (159)
                      ++++-++...+++||+..+-+
T Consensus        10 ~l~~l~~~~~L~gC~~~~~~~   30 (385)
T PRK09578         10 ALAALVAAFALAGCGKGDSDA   30 (385)
T ss_pred             HHHHHHHHHHHHCCCCCCCCC
T ss_conf             999999999981679998787


No 18 
>PRK03577 acid shock protein precursor; Provisional
Probab=21.58  E-value=58  Score=13.53  Aligned_cols=32  Identities=53%  Similarity=0.568  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99999998899999999999998764321750
Q gi|254780909|r   54 AAEAARKAAEQAAEAAKKAAEKIIHKDKKKPK   85 (159)
Q Consensus        54 aaeaarkaaeqaaeaakkaaekiihkdkkkpk   85 (159)
                      .+.+..++.+|-+.++||-..|--|+.-++|-
T Consensus        66 kak~~qkap~QKAQAAKKH~kkk~hk~~~kp~   97 (102)
T PRK03577         66 KAKAEQKAPEQKAQAAKKHAKKKHHKTPAKPA   97 (102)
T ss_pred             HHHHHHHCHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             54555408088999999999886046888844


No 19 
>pfam08085 Entericidin Entericidin EcnA/B family. This family consists of the entericidin antidote/toxin peptides. The entericidin locus is activated in stationary phase under high osmolarity conditions by rho-S and simultaneously repressed by the osmoregulatory EnvZ/OmpR signal transduction pathway. The entericidin locus encodes tandem paralogous genes (ecnAB) and directs the synthesis of two small cell-envelope lipoproteins which can maintain plasmids in bacterial population by means of post-segregational killing.
Probab=20.14  E-value=62  Score=13.35  Aligned_cols=22  Identities=36%  Similarity=0.605  Sum_probs=16.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             9630344889998887665304
Q gi|254780909|r    1 MKRLKYQIILLSLLSTTMASCG   22 (159)
Q Consensus         1 mkrlkyqiillsllsttmascg   22 (159)
                      |||+.--++++.+++...+.|.
T Consensus         1 Mk~~~~~~~~l~~~~~~lagCN   22 (42)
T pfam08085         1 MKKLIALLLALLLLALVLAGCN   22 (42)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCH
T ss_conf             9236999999999999986122


No 20 
>pfam12602 FinO_N Fertility inhibition protein N terminal. This domain family is found in bacteria, and is typically between 62 and 102 amino acids in length. The family is found in association with pfam04352. The FinOP (fertility inhibition) system of F-like plasmids consists of an antisense RNA (FinP) and a 22 kDa protein (FinO) which act in concert to prevent the translation of TraJ, the positive regulator of the transfer operon.
Probab=20.07  E-value=63  Score=13.34  Aligned_cols=13  Identities=62%  Similarity=0.557  Sum_probs=5.7

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             7898899999999
Q gi|254780909|r   47 TQKAAEKAAEAAR   59 (159)
Q Consensus        47 tqkaaekaaeaar   59 (159)
                      -|+.+||++.++.
T Consensus        50 Kqkl~ekaar~ae   62 (72)
T pfam12602        50 KQKLDEKAARAAE   62 (72)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             8888899988889


Done!