Query         gi|254780895|ref|YP_003065308.1| hypothetical protein CLIBASIA_03960 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 91
No_of_seqs    84 out of 86
Neff          2.7 
Searched_HMMs 39220
Date          Mon May 30 00:12:26 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780895.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam06627 DUF1153 Protein of u 100.0       0       0  295.1   9.8   90    1-90      1-90  (90)
  2 PRK09413 insertion sequence 2   90.8     0.6 1.5E-05   27.5   5.1   59   25-83      5-63  (121)
  3 pfam01527 Transposase_8 Transp  88.8     1.2 3.1E-05   25.7   5.4   46   29-74      3-48  (75)
  4 TIGR01542 A118_put_portal phag  75.3     6.8 0.00017   21.4   4.8   41   37-77    442-483 (489)
  5 pfam04611 AalphaY_MDB Mating t  71.2       4  0.0001   22.7   2.9   74   17-91     36-113 (147)
  6 pfam01710 Transposase_14 Trans  70.5     7.2 0.00018   21.2   4.0   32   40-72     10-41  (120)
  7 TIGR03573 WbuX N-acetyl sugar   68.1     6.8 0.00017   21.4   3.5   24   35-58    288-311 (343)
  8 PRK10265 chaperone-modulator p  61.6     7.6 0.00019   21.1   2.7   23   49-71      7-29  (101)
  9 pfam05416 Peptidase_C37 Southa  54.2     5.3 0.00014   22.0   0.9   65   12-77    199-269 (535)
 10 COG0114 FumC Fumarase [Energy   49.2      19 0.00048   18.9   3.0   37   36-72    417-455 (462)
 11 COG2963 Transposase and inacti  46.6      31 0.00078   17.6   5.4   49   30-78      5-54  (116)
 12 TIGR00979 fumC_II fumarate hyd  45.8     7.5 0.00019   21.1   0.6   29   43-71    425-453 (459)
 13 pfam05126 consensus             45.6      32 0.00081   17.5   5.6   40   37-76    426-466 (473)
 14 pfam03683 UPF0175 Uncharacteri  42.3      36 0.00092   17.2   4.4   39   37-78     22-60  (76)
 15 pfam05181 XPA_C XPA protein C-  40.0       9 0.00023   20.7   0.2   23   46-68      2-24  (52)
 16 pfam04405 ScdA_N Domain of Unk  39.6      27 0.00068   18.0   2.6   25   46-70     28-52  (56)
 17 pfam08418 Pol_alpha_B_N DNA po  39.2      28 0.00072   17.8   2.7   30   51-80     13-43  (240)
 18 COG3645 Uncharacterized phage-  38.8      41   0.001   16.9   3.7   39   34-72     30-70  (135)
 19 PTZ00294 glycerol kinase; Prov  38.4      41  0.0011   16.9   5.8   43   34-76    449-505 (510)
 20 pfam05459 Herpes_UL69 Herpesvi  37.8      42  0.0011   16.8   3.4   43   27-79     28-70  (218)
 21 pfam11112 PyocinActivator Pyoc  36.7      29 0.00075   17.7   2.4   22   49-70     14-37  (76)
 22 pfam03333 PapB Adhesin biosynt  36.3      45  0.0011   16.7   3.7   25   49-73     53-77  (91)
 23 COG3415 Transposase and inacti  35.1      47  0.0012   16.5   3.4   47   36-84      9-55  (138)
 24 pfam11630 DUF3254 Protein of u  35.0      27 0.00068   18.0   2.0   20   38-57     75-94  (97)
 25 PRK08963 fadI 3-ketoacyl-CoA t  34.4      47  0.0012   16.6   3.2   26   50-77    186-211 (436)
 26 TIGR02335 hydr_PhnA phosphonoa  33.1      19 0.00049   18.8   1.0   46   16-64    285-330 (408)
 27 PRK09190 hypothetical protein;  32.4      30 0.00077   17.7   1.9   46    8-53     32-77  (221)
 28 KOG1317 consensus               32.2      45  0.0011   16.7   2.8   37   38-74    444-482 (487)
 29 TIGR03652 FeS_repair_RIC iron-  30.7      44  0.0011   16.7   2.5   28   47-74     25-52  (216)
 30 PRK10251 phosphopantetheinyltr  28.6      26 0.00066   18.0   1.1   42   16-61     24-69  (207)
 31 KOG1489 consensus               28.3      25 0.00065   18.1   1.0   24    4-27    230-253 (366)
 32 KOG3279 consensus               28.2      62  0.0016   15.9   5.4   55   36-91    186-245 (283)
 33 pfam00945 Rhabdo_ncap Rhabdovi  28.2      34 0.00088   17.3   1.6   25   47-71    218-242 (406)
 34 pfam05120 GvpG Gas vesicle pro  27.3      59  0.0015   16.0   2.7   47   26-72      7-60  (80)
 35 pfam05225 HTH_psq helix-turn-h  27.2      64  0.0016   15.8   3.1   29   39-67      6-34  (45)
 36 TIGR02984 Sig-70_plancto1 RNA   26.9      54  0.0014   16.2   2.4   22   58-79     56-77  (190)
 37 pfam11470 TUG GLUT4 regulating  26.6      37 0.00095   17.1   1.6   15   52-66     23-37  (65)
 38 TIGR02233 Myxo_sigma_rel Myxoc  26.1      67  0.0017   15.6   3.5   47   22-74     49-95  (106)
 39 COG2306 Predicted RNA-binding   24.7      65  0.0017   15.7   2.5   38   39-81    126-163 (183)
 40 COG3522 Predicted component of  24.3      45  0.0011   16.7   1.6   22    9-30     64-88  (446)
 41 pfam05321 HHA Haemolysin expre  23.5      70  0.0018   15.5   2.5   28   57-85     19-46  (57)
 42 PRK06366 acetyl-CoA acetyltran  23.4      76  0.0019   15.3   2.8   23   51-73    164-186 (388)
 43 PRK09052 acetyl-CoA acetyltran  22.6      79   0.002   15.2   3.3   32   50-84    156-187 (399)
 44 PRK09270 frcK putative fructos  22.0      36 0.00091   17.2   0.8   33   25-64    171-203 (230)
 45 COG2049 DUR1 Allophanate hydro  21.7      68  0.0017   15.6   2.1   24   45-68     90-116 (223)
 46 smart00719 Plus3 Short conserv  21.2      64  0.0016   15.8   1.9   18   56-73     91-108 (109)
 47 PRK10853 hypothetical protein;  20.9      76  0.0019   15.3   2.3   31   58-91     34-64  (118)

No 1  
>pfam06627 DUF1153 Protein of unknown function (DUF1153). This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=100.00  E-value=0  Score=295.11  Aligned_cols=90  Identities=60%  Similarity=0.950  Sum_probs=88.3

Q ss_pred             CCCCCCCCCCEEECCCCCCCCHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHCHHH
Q ss_conf             96420323226777999833532175998850367799999999860886999999770679999999999999839986
Q gi|254780895|r    1 MTEKIQSHMKYVIGPDGSPLTIANLPPPNTRRWVARRKAEVVAAVKGGLLSLEEACQIYTLTVEEFLSWQASIVQHGLAG   80 (91)
Q Consensus         1 m~e~~~~~~~~V~gPdGs~lt~aDLPp~~T~RWVasRKA~VV~aV~~GLis~~EA~~rY~LS~EEf~~W~~av~~hG~~g   80 (91)
                      |......+|++|+|||||+||++||||+||+||||||||+||+||+|||||++|||+||+||+|||.+|++++++||++|
T Consensus         1 M~l~kv~gpr~V~~PdGs~lt~aDLPp~~T~RWVasRKA~VV~aV~~GLis~~EA~~rY~LS~EEf~~W~~av~~hG~~g   80 (90)
T pfam06627         1 MYLKKVEGPRSVTLPDGSPLTRADLPPPDTRRWVASRKAAVVAAVRGGLLSRDEACERYGLSEEEFAAWQRAVDRHGEAG   80 (90)
T ss_pred             CCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf             97443689853778999833001188988740468888899999981777899999996788999999999999966888


Q ss_pred             HHHHHHHHHC
Q ss_conf             8875777633
Q gi|254780895|r   81 LRTTQIQKYR   90 (91)
Q Consensus        81 Lr~T~lQ~YR   90 (91)
                      ||+|+||+||
T Consensus        81 Lr~T~lq~yR   90 (90)
T pfam06627        81 LRATRLQQYR   90 (90)
T ss_pred             HHHHHHHHCC
T ss_conf             8898887519


No 2  
>PRK09413 insertion sequence 2 OrfA protein; Reviewed
Probab=90.78  E-value=0.6  Score=27.49  Aligned_cols=59  Identities=14%  Similarity=0.258  Sum_probs=51.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHCHHHHHH
Q ss_conf             75998850367799999999860886999999770679999999999999839986887
Q gi|254780895|r   25 LPPPNTRRWVARRKAEVVAAVKGGLLSLEEACQIYTLTVEEFLSWQASIVQHGLAGLRT   83 (91)
Q Consensus        25 LPp~~T~RWVasRKA~VV~aV~~GLis~~EA~~rY~LS~EEf~~W~~av~~hG~~gLr~   83 (91)
                      +-|.--|||..--|+++|..-...=.|..+.|++++++..-|..|.+.+..-|..+..+
T Consensus         5 ~G~erRRrws~~EK~~IV~es~ePG~sVs~VARrHGi~~~qlf~WRr~~~eG~~~AV~a   63 (121)
T PRK09413          5 LGPEKRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQEGSLTAVAA   63 (121)
T ss_pred             CCCCHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCC
T ss_conf             57204126888999999999956998499999994998999999999986212113467


No 3  
>pfam01527 Transposase_8 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family.
Probab=88.80  E-value=1.2  Score=25.70  Aligned_cols=46  Identities=17%  Similarity=0.195  Sum_probs=42.1

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             8850367799999999860886999999770679999999999999
Q gi|254780895|r   29 NTRRWVARRKAEVVAAVKGGLLSLEEACQIYTLTVEEFLSWQASIV   74 (91)
Q Consensus        29 ~T~RWVasRKA~VV~aV~~GLis~~EA~~rY~LS~EEf~~W~~av~   74 (91)
                      -.+||..-=|.++|+.+..+=.|..+.|+.|++|..-|.-|.+...
T Consensus         3 krrrys~efK~~~V~~~~~~g~sv~~var~~gi~~~~l~~W~k~~~   48 (75)
T pfam01527         3 RRRRYSEEFKARAVKESLEPGASVSELAREHGVSPATLYKWRKKYR   48 (75)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             8888999999999999980998499999998959999999999984


No 4  
>TIGR01542 A118_put_portal phage portal protein, putative, A118 family; InterPro: IPR006432    These sequences represent a family of phage minor structural proteins. The protein is suggested to be the head-tail connector, or portal protein, on the basis of its position in the phage gene order, its presence in mature phage, its size, and its conservation across a number of complete genomes of tailed phage that lack other candidate portal proteins. Several other known portal protein families lack clear homology to this family and to each other ..
Probab=75.25  E-value=6.8  Score=21.38  Aligned_cols=41  Identities=29%  Similarity=0.385  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHH-CCCCHHHHHHHHHHHHHHC
Q ss_conf             9999999986088699999977-0679999999999999839
Q gi|254780895|r   37 RKAEVVAAVKGGLLSLEEACQI-YTLTVEEFLSWQASIVQHG   77 (91)
Q Consensus        37 RKA~VV~aV~~GLis~~EA~~r-Y~LS~EEf~~W~~av~~hG   77 (91)
                      .-+.-+.||..|.++++-|+.| |++++||=.+|...|+.--
T Consensus       442 ~~~~~~~avnag~~p~k~al~r~~n~tEeeAdEwaa~i~~e~  483 (489)
T TIGR01542       442 KLDAYLKAVNAGVIPKKIALQRAYNVTEEEADEWAAEIDKEK  483 (489)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHCCH
T ss_conf             578898998606602899999861798879999999872110


No 5  
>pfam04611 AalphaY_MDB Mating type protein A alpha Y mating type dependent binding region. This region is important for the mating type dependent binding of Y protein to the A alpha Z protein of another mating type in Schizophyllum commune.
Probab=71.24  E-value=4  Score=22.70  Aligned_cols=74  Identities=26%  Similarity=0.382  Sum_probs=53.4

Q ss_pred             CCCCCHHHCCCCCCCCHHHHHHHHH---HHHHHCCCCCHHHHHHHCCCCHHH-HHHHHHHHHHHCHHHHHHHHHHHHCC
Q ss_conf             9833532175998850367799999---999860886999999770679999-99999999983998688757776339
Q gi|254780895|r   17 GSPLTIANLPPPNTRRWVARRKAEV---VAAVKGGLLSLEEACQIYTLTVEE-FLSWQASIVQHGLAGLRTTQIQKYRE   91 (91)
Q Consensus        17 Gs~lt~aDLPp~~T~RWVasRKA~V---V~aV~~GLis~~EA~~rY~LS~EE-f~~W~~av~~hG~~gLr~T~lQ~YRq   91 (91)
                      -+.++.+-||+||-.- +-+|--++   -+++.+.|-.-|+||.|+.-+.|| |..=..+|.-|...-|-.-|++-|-|
T Consensus        36 ~t~v~fdpLp~P~ld~-lr~rL~~a~LPpk~iksal~aYe~AC~RWr~~l~e~F~~tA~svsP~Nlhll~~LR~rlyt~  113 (147)
T pfam04611        36 TTTVHFDPLPTPDLDG-LRTRLQEAKLPPKAIKSALSAYEKACARWRSDLEEAFDITAKSVSPHNLHLLELLRFRLYTQ  113 (147)
T ss_pred             CCCCCCCCCCCCCHHH-HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             9887658899965689-99999874898688999999999999999988999999987635811589999999999999


No 6  
>pfam01710 Transposase_14 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterized as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily.
Probab=70.46  E-value=7.2  Score=21.24  Aligned_cols=32  Identities=19%  Similarity=0.472  Sum_probs=29.2

Q ss_pred             HHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             999998608869999997706799999999999
Q gi|254780895|r   40 EVVAAVKGGLLSLEEACQIYTLTVEEFLSWQAS   72 (91)
Q Consensus        40 ~VV~aV~~GLis~~EA~~rY~LS~EEf~~W~~a   72 (91)
                      -|+++|..|. |..||+++|++|.--..-|..-
T Consensus        10 rVl~~ve~G~-S~~eaA~~F~Is~~Tv~rWlkr   41 (120)
T pfam01710        10 KVIDYIESGG-SITEASKVFQIGRATIYRWLKR   41 (120)
T ss_pred             HHHHHHHCCC-CHHHHHHHHCCCHHHHHHHHHC
T ss_conf             9999998699-9999999937029999999855


No 7  
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an 
Probab=68.08  E-value=6.8  Score=21.39  Aligned_cols=24  Identities=21%  Similarity=0.397  Sum_probs=19.3

Q ss_pred             HHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             779999999986088699999977
Q gi|254780895|r   35 ARRKAEVVAAVKGGLLSLEEACQI   58 (91)
Q Consensus        35 asRKA~VV~aV~~GLis~~EA~~r   58 (91)
                      -++....-.-||.|.||+|||++.
T Consensus       288 ~r~~~~~s~~IR~g~itReEAl~l  311 (343)
T TIGR03573       288 GRATDHASIDIRSGRITREEAIEL  311 (343)
T ss_pred             CCCCHHHHHHHHCCCCCHHHHHHH
T ss_conf             848468999998599899999999


No 8  
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=61.65  E-value=7.6  Score=21.11  Aligned_cols=23  Identities=17%  Similarity=0.232  Sum_probs=20.6

Q ss_pred             CCCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             86999999770679999999999
Q gi|254780895|r   49 LLSLEEACQIYTLTVEEFLSWQA   71 (91)
Q Consensus        49 Lis~~EA~~rY~LS~EEf~~W~~   71 (91)
                      -+|.+|-|.++++|.|++.+|+.
T Consensus         7 t~Tl~Elc~~~gi~~e~l~e~Ve   29 (101)
T PRK10265          7 TFTITEFCLHTGVSEEELNEIVG   29 (101)
T ss_pred             EEEHHHHHHHHCCCHHHHHHHHH
T ss_conf             97699999771989999999999


No 9  
>pfam05416 Peptidase_C37 Southampton virus-type processing peptidase. Corresponds to Merops family C37. Norwalk-like viruses (NLVs), including the Southampton virus, cause acute non-bacterial gastroenteritis in humans. The NLV genome encodes three open reading frames (ORFs). ORF1 encodes a polyprotein, which is processed by the viral protease into six proteins.
Probab=54.15  E-value=5.3  Score=22.03  Aligned_cols=65  Identities=17%  Similarity=0.171  Sum_probs=44.1

Q ss_pred             EECCCCCCCCHHHCCCCCCC--CHHHHHHHHHHHHHHCCCC----CHHHHHHHCCCCHHHHHHHHHHHHHHC
Q ss_conf             77799983353217599885--0367799999999860886----999999770679999999999999839
Q gi|254780895|r   12 VIGPDGSPLTIANLPPPNTR--RWVARRKAEVVAAVKGGLL----SLEEACQIYTLTVEEFLSWQASIVQHG   77 (91)
Q Consensus        12 V~gPdGs~lt~aDLPp~~T~--RWVasRKA~VV~aV~~GLi----s~~EA~~rY~LS~EEf~~W~~av~~hG   77 (91)
                      ++|-|+ ..+.-++|+....  .|.+..+++.+.+..+..-    .-.-|..+++||.||+.+.-+--+.-|
T Consensus       199 ~~~h~~-~~~~~~~~~~~~~~~~~~~~~~~~~~e~kKgKnk~GRg~k~~aFs~rGLSDEEYdEykkiREer~  269 (535)
T pfam05416       199 PFGHDX-EVTYYDGCESEEDDEGWYIEPQDATPEGKKGKNKKGRGKKHNAFSRRGLSDEEYDEYKKIREERG  269 (535)
T ss_pred             CCCCCC-HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             744210-01211477885322245557220350002465565777766520025898678899988888727


No 10 
>COG0114 FumC Fumarase [Energy production and conversion]
Probab=49.17  E-value=19  Score=18.86  Aligned_cols=37  Identities=27%  Similarity=0.175  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHH--CCCCCHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             79999999986--08869999997706799999999999
Q gi|254780895|r   36 RRKAEVVAAVK--GGLLSLEEACQIYTLTVEEFLSWQAS   72 (91)
Q Consensus        36 sRKA~VV~aV~--~GLis~~EA~~rY~LS~EEf~~W~~a   72 (91)
                      --||+-|+--.  -|.--.|.|++.=-||+|||..|..-
T Consensus       417 YdkAa~IAK~A~keg~tlreaa~~~G~lte~efd~~v~P  455 (462)
T COG0114         417 YDKAAKIAKKAHKEGTTLREAALELGLLSEEEFDKLVDP  455 (462)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHCCH
T ss_conf             389999999998779829999988388899999986399


No 11 
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=46.61  E-value=31  Score=17.61  Aligned_cols=49  Identities=16%  Similarity=0.324  Sum_probs=42.6

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCC-CHHHHHHHHHHHHHHCH
Q ss_conf             85036779999999986088699999977067-99999999999998399
Q gi|254780895|r   30 TRRWVARRKAEVVAAVKGGLLSLEEACQIYTL-TVEEFLSWQASIVQHGL   78 (91)
Q Consensus        30 T~RWVasRKA~VV~aV~~GLis~~EA~~rY~L-S~EEf~~W~~av~~hG~   78 (91)
                      .++|-.-=|.++|+.+.-+=-|..++|+.|++ +..-+..|.+.....+.
T Consensus         5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~   54 (116)
T COG2963           5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGG   54 (116)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHCCC
T ss_conf             36489999999999998178359999999487753789999999987257


No 12 
>TIGR00979 fumC_II fumarate hydratase, class II; InterPro: IPR005677    Fumarase C catalyzes the stereospecific interconversion of fumarate to L-malate as part of the metabolic citric acid or Kreb's cycle. The recent three-dimensional structure of fumarase C from Escherichia coli has identified a binding site for anions which is generated by side chains from three of the four subunits within the tetramer. These same side chains are found in the three most highly conserved regions within the class II fumarate hydratase family. Putative fumarases from several species (Mycobacterium tuberculosis, Streptomyces coelicolor, Pseudomonas aeruginosa) branch deeply, although within the same branch of a phylogenetic tree rooted by aspartate ammonia-lyase sequences.; GO: 0004333 fumarate hydratase activity, 0006106 fumarate metabolic process, 0045239 tricarboxylic acid cycle enzyme complex.
Probab=45.82  E-value=7.5  Score=21.14  Aligned_cols=29  Identities=34%  Similarity=0.423  Sum_probs=21.4

Q ss_pred             HHHHCCCCCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             99860886999999770679999999999
Q gi|254780895|r   43 AAVKGGLLSLEEACQIYTLTVEEFLSWQA   71 (91)
Q Consensus        43 ~aV~~GLis~~EA~~rY~LS~EEf~~W~~   71 (91)
                      .|-..|+==.|+|++.=-||+|||++|+.
T Consensus       425 ~Ahk~GitLKeaAl~Lg~Lse~eFD~~V~  453 (459)
T TIGR00979       425 KAHKEGITLKEAALELGLLSEEEFDKWVV  453 (459)
T ss_pred             HHHHCCCCHHHHHHHCCCCCHHHCCCCCC
T ss_conf             99743977789997448978688278279


No 13 
>pfam05126 consensus
Probab=45.61  E-value=32  Score=17.52  Aligned_cols=40  Identities=30%  Similarity=0.378  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHCCCCCHHHHHH-HCCCCHHHHHHHHHHHHHH
Q ss_conf             999999998608869999997-7067999999999999983
Q gi|254780895|r   37 RKAEVVAAVKGGLLSLEEACQ-IYTLTVEEFLSWQASIVQH   76 (91)
Q Consensus        37 RKA~VV~aV~~GLis~~EA~~-rY~LS~EEf~~W~~av~~h   76 (91)
                      .++.-...|..|+++..+++. .|++|+||-..|...|...
T Consensus       426 e~~~~~~~VaaG~~~~~~yl~k~yg~teeEA~k~l~ei~~e  466 (473)
T pfam05126       426 TLNRDTKAVNAGMIPKKIALQRNYNITEEEADEWAAMIAKE  466 (473)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             99989999875887599999998499999999999998750


No 14 
>pfam03683 UPF0175 Uncharacterized protein family (UPF0175). This family contains small proteins of unknown function.
Probab=42.27  E-value=36  Score=17.21  Aligned_cols=39  Identities=23%  Similarity=0.374  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHCH
Q ss_conf             999999998608869999997706799999999999998399
Q gi|254780895|r   37 RKAEVVAAVKGGLLSLEEACQIYTLTVEEFLSWQASIVQHGL   78 (91)
Q Consensus        37 RKA~VV~aV~~GLis~~EA~~rY~LS~EEf~~W~~av~~hG~   78 (91)
                      |.+..|.--..|.||+..|++.-++|..||..   ...++|.
T Consensus        22 r~~~Ai~lY~~g~iS~gkAaelag~s~~eF~~---~L~~~~I   60 (76)
T pfam03683        22 RLELAIKLYERGKISLGKAAELAGMSRWEFLE---LLARRGI   60 (76)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHH---HHHHCCC
T ss_conf             99999999984984899999997999999999---9998799


No 15 
>pfam05181 XPA_C XPA protein C-terminus.
Probab=39.97  E-value=9  Score=20.71  Aligned_cols=23  Identities=35%  Similarity=0.287  Sum_probs=20.2

Q ss_pred             HCCCCCHHHHHHHCCCCHHHHHH
Q ss_conf             60886999999770679999999
Q gi|254780895|r   46 KGGLLSLEEACQIYTLTVEEFLS   68 (91)
Q Consensus        46 ~~GLis~~EA~~rY~LS~EEf~~   68 (91)
                      .|-|||..||.+.|-|++.||..
T Consensus         2 k~sLiTKTeaKe~YLLtD~eL~~   24 (52)
T pfam05181         2 KYSLLTKTECKEDYLLTDPELKD   24 (52)
T ss_pred             CCCCEEHHHHHHHHCCCCCCCCC
T ss_conf             64212202365655245711053


No 16 
>pfam04405 ScdA_N Domain of Unknown function (DUF542). This domain is always found in conjunction with the HHE domain (pfam03794) at the N-terminus.
Probab=39.56  E-value=27  Score=17.98  Aligned_cols=25  Identities=44%  Similarity=0.509  Sum_probs=21.4

Q ss_pred             HCCCCCHHHHHHHCCCCHHHHHHHH
Q ss_conf             6088699999977067999999999
Q gi|254780895|r   46 KGGLLSLEEACQIYTLTVEEFLSWQ   70 (91)
Q Consensus        46 ~~GLis~~EA~~rY~LS~EEf~~W~   70 (91)
                      -||-.|++|||+.-+|..+++.+=.
T Consensus        28 CgG~~~L~eA~~~~~ld~~~vl~~L   52 (56)
T pfam04405        28 CGGKVSLAEACKEKGLDPEEVLAEL   52 (56)
T ss_pred             CCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf             8998069999988298999999999


No 17 
>pfam08418 Pol_alpha_B_N DNA polymerase alpha subunit B N-terminal. This is the eukaryotic DNA polymerase alpha subunit B N-terminal domain which is involved in complex formation. Also see pfam04058.
Probab=39.20  E-value=28  Score=17.83  Aligned_cols=30  Identities=30%  Similarity=0.715  Sum_probs=24.1

Q ss_pred             CHHHHHHHCCCCHHH-HHHHHHHHHHHCHHH
Q ss_conf             999999770679999-999999999839986
Q gi|254780895|r   51 SLEEACQIYTLTVEE-FLSWQASIVQHGLAG   80 (91)
Q Consensus        51 s~~EA~~rY~LS~EE-f~~W~~av~~hG~~g   80 (91)
                      .+.+-|..|+||.|| |..|+.-.-..|...
T Consensus        13 eL~sl~~l~~ls~edL~~kWesf~~~~~~~~   43 (240)
T pfam08418        13 KLESLCKLHRLSEEDLFIKWESFSTNRGLED   43 (240)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             9999999819999999999999985458986


No 18 
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=38.80  E-value=41  Score=16.89  Aligned_cols=39  Identities=23%  Similarity=0.480  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHH--HCCCCCHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             677999999998--608869999997706799999999999
Q gi|254780895|r   34 VARRKAEVVAAV--KGGLLSLEEACQIYTLTVEEFLSWQAS   72 (91)
Q Consensus        34 VasRKA~VV~aV--~~GLis~~EA~~rY~LS~EEf~~W~~a   72 (91)
                      ++.-|++-+.+|  ..|||+.-|.|.-+++.+-.|..|-+.
T Consensus        30 ~~~PKv~f~D~v~~~~gli~~re~AK~lkige~~l~~~L~e   70 (135)
T COG3645          30 IAAPKVEFADAVVEASGLILFRELAKLLKIGENRLFAWLRE   70 (135)
T ss_pred             HHCCCHHHHHHHHCCCCCEEHHHHHHHHCCCHHHHHHHHHH
T ss_conf             74711388998851766251999999976377899999998


No 19 
>PTZ00294 glycerol kinase; Provisional
Probab=38.45  E-value=41  Score=16.86  Aligned_cols=43  Identities=19%  Similarity=0.298  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHHCCCC-CHHHHHHHCCCC-------------HHHHHHHHHHHHHH
Q ss_conf             67799999999860886-999999770679-------------99999999999983
Q gi|254780895|r   34 VARRKAEVVAAVKGGLL-SLEEACQIYTLT-------------VEEFLSWQASIVQH   76 (91)
Q Consensus        34 VasRKA~VV~aV~~GLi-s~~EA~~rY~LS-------------~EEf~~W~~av~~h   76 (91)
                      ....-|++.+||-.|+. |++||.+.-.-.             .+.|.+|+++|+|.
T Consensus       449 ~~alGaAilAavg~G~~~s~~eA~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~~~~~  505 (510)
T PTZ00294        449 TTALGAALCAGLAAGVWTSLEEVKALSRRENSTVSPIMSDKQREARIAEWNLAVKRS  505 (510)
T ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCEECCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             089999999999819899999999747778948868999999999999999999875


No 20 
>pfam05459 Herpes_UL69 Herpesvirus transcriptional regulator family. This family includes UL69 and IE63 that are transcriptional regulator proteins.
Probab=37.83  E-value=42  Score=16.80  Aligned_cols=43  Identities=30%  Similarity=0.484  Sum_probs=32.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHCHH
Q ss_conf             99885036779999999986088699999977067999999999999983998
Q gi|254780895|r   27 PPNTRRWVARRKAEVVAAVKGGLLSLEEACQIYTLTVEEFLSWQASIVQHGLA   79 (91)
Q Consensus        27 p~~T~RWVasRKA~VV~aV~~GLis~~EA~~rY~LS~EEf~~W~~av~~hG~~   79 (91)
                      +.+..-|++-|+..+    ++.  ++.+++.    +.||-.+|......||..
T Consensus        28 ~~n~~~~~~lR~~~i----~n~--~L~~lla----~aDEtlsW~k~~~~h~l~   70 (218)
T pfam05459        28 SLNAELWRALREFAI----RNE--GLVELLA----SADETLSWLKLHLVHGLP   70 (218)
T ss_pred             CCCHHHHHHHHHHHH----HCC--CHHHHHH----HHHHHHHHHHHHHHCCCC
T ss_conf             544999999999999----668--8999999----999999999999986998


No 21 
>pfam11112 PyocinActivator Pyocin activator protein PrtN. PrtN is a transcriptional activator for pyocin synthesis genes. It activates the expression of various pyocin genes by interaction with the DNA sequences conserved in the 5' noncoding regions of the pyocin genes.
Probab=36.68  E-value=29  Score=17.71  Aligned_cols=22  Identities=32%  Similarity=0.582  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHC--CCCHHHHHHHH
Q ss_conf             86999999770--67999999999
Q gi|254780895|r   49 LLSLEEACQIY--TLTVEEFLSWQ   70 (91)
Q Consensus        49 Lis~~EA~~rY--~LS~EEf~~W~   70 (91)
                      .|++++.|+.|  +||.+.|..=.
T Consensus        14 ~IpL~~v~~~yF~~lt~~~~~rk~   37 (76)
T pfam11112        14 IIPLDEVCEDYFPHLTPKTFKRKI   37 (76)
T ss_pred             CCCHHHHHHHHHCCCCHHHHHHHH
T ss_conf             773999999992669999999999


No 22 
>pfam03333 PapB Adhesin biosynthesis transcription regulatory protein. This family includes PapB, DaaA, FanA, FanB, and AfaA.
Probab=36.27  E-value=45  Score=16.65  Aligned_cols=25  Identities=16%  Similarity=0.102  Sum_probs=19.6

Q ss_pred             CCCHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             8699999977067999999999999
Q gi|254780895|r   49 LLSLEEACQIYTLTVEEFLSWQASI   73 (91)
Q Consensus        49 Lis~~EA~~rY~LS~EEf~~W~~av   73 (91)
                      =.|+.|||++|+.+..-|..=.+.+
T Consensus        53 G~srkevCe~~~Vn~gyfS~~L~~L   77 (91)
T pfam03333        53 GYSRKEVCERHNVNNGYFSISLGRL   77 (91)
T ss_pred             CCCHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             8649999987297799999999999


No 23 
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=35.08  E-value=47  Score=16.54  Aligned_cols=47  Identities=28%  Similarity=0.374  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHCHHHHHHH
Q ss_conf             7999999998608869999997706799999999999998399868875
Q gi|254780895|r   36 RRKAEVVAAVKGGLLSLEEACQIYTLTVEEFLSWQASIVQHGLAGLRTT   84 (91)
Q Consensus        36 sRKA~VV~aV~~GLis~~EA~~rY~LS~EEf~~W~~av~~hG~~gLr~T   84 (91)
                      -|++.++ .+.++=+|..||-.+++.|.---.-|+....+-|.. |..+
T Consensus         9 ~R~~~~~-~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~-l~~~   55 (138)
T COG3415           9 LRERVVD-AVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLD-LPPK   55 (138)
T ss_pred             HHHHHHH-HHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCC-CCCC
T ss_conf             9999999-999768549999999692299999999873335331-5676


No 24 
>pfam11630 DUF3254 Protein of unknown function (DUF3254). This family of proteins is most likely a family of anti-lipopolysaccharide factor proteins however this cannot be confirmed.
Probab=35.04  E-value=27  Score=17.97  Aligned_cols=20  Identities=35%  Similarity=0.433  Sum_probs=16.0

Q ss_pred             HHHHHHHHHCCCCCHHHHHH
Q ss_conf             99999998608869999997
Q gi|254780895|r   38 KAEVVAAVKGGLLSLEEACQ   57 (91)
Q Consensus        38 KA~VV~aV~~GLis~~EA~~   57 (91)
                      +-=|-+|..+||||.+||-.
T Consensus        75 rDFV~KA~~~gLiTeedA~~   94 (97)
T pfam11630        75 RDFVQKALQAGLITEEEANA   94 (97)
T ss_pred             HHHHHHHHHCCCCCHHHHHH
T ss_conf             99999999848865989988


No 25 
>PRK08963 fadI 3-ketoacyl-CoA thiolase; Reviewed
Probab=34.35  E-value=47  Score=16.57  Aligned_cols=26  Identities=15%  Similarity=0.146  Sum_probs=20.1

Q ss_pred             CCHHHHHHHCCCCHHHHHHHHHHHHHHC
Q ss_conf             6999999770679999999999999839
Q gi|254780895|r   50 LSLEEACQIYTLTVEEFLSWQASIVQHG   77 (91)
Q Consensus        50 is~~EA~~rY~LS~EEf~~W~~av~~hG   77 (91)
                      .+-|+.+++|++|.||..+|-  +..|-
T Consensus       186 ~tAE~~A~~~gIsReeqD~~A--~~Sh~  211 (436)
T PRK08963        186 DTAEQMAKTYGISREQQDALA--HRSHQ  211 (436)
T ss_pred             HHHHHHHHHHCCCHHHHHHHH--HHHHH
T ss_conf             999999999599999999999--99999


No 26 
>TIGR02335 hydr_PhnA phosphonoacetate hydrolase; InterPro: IPR012710   This family consists of examples of phosphonoacetate hydrolase, an enzyme specific for the cleavage of the C-P bond in phosphonoacetate. Phosphonates are organic compounds with a direct C-P bond that is far less labile than the C-O-P bonds of phosphate attachment sites. Phosphonates may be degraded for phosphorus and energy by broad spectrum C-P lyase encoded by a large operon or by specific enzymes for some of the more common phosphonates in nature. This family represents an enzyme from the latter category. It may be found encoded near genes for phosphonate transport and for other specific phosphonatases ..
Probab=33.06  E-value=19  Score=18.79  Aligned_cols=46  Identities=26%  Similarity=0.306  Sum_probs=25.1

Q ss_pred             CCCCCCHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHH
Q ss_conf             9983353217599885036779999999986088699999977067999
Q gi|254780895|r   16 DGSPLTIANLPPPNTRRWVARRKAEVVAAVKGGLLSLEEACQIYTLTVE   64 (91)
Q Consensus        16 dGs~lt~aDLPp~~T~RWVasRKA~VV~aV~~GLis~~EA~~rY~LS~E   64 (91)
                      .||-.+.-=+-|.+.+-  +=--|+-+.||. -.|+++.||+||.|-++
T Consensus       285 LGsfvr~ylr~p~di~a--~~~faa~i~GVe-~VL~R~qacqR~~LP~D  330 (408)
T TIGR02335       285 LGSFVRAYLRDPVDIEA--MMDFAAAIAGVE-AVLDREQACQRFELPED  330 (408)
T ss_pred             HHHHHHHHHCCCCCHHH--HHHHHHCCCCHH-HHCCHHHHHHHCCCCCC
T ss_conf             03467776517667889--999985032056-65077899986078865


No 27 
>PRK09190 hypothetical protein; Provisional
Probab=32.42  E-value=30  Score=17.66  Aligned_cols=46  Identities=28%  Similarity=0.497  Sum_probs=31.9

Q ss_pred             CCCEEECCCCCCCCHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCHH
Q ss_conf             3226777999833532175998850367799999999860886999
Q gi|254780895|r    8 HMKYVIGPDGSPLTIANLPPPNTRRWVARRKAEVVAAVKGGLLSLE   53 (91)
Q Consensus         8 ~~~~V~gPdGs~lt~aDLPp~~T~RWVasRKA~VV~aV~~GLis~~   53 (91)
                      -++.|.+|||.+.---.---|.---||......+-.|+.-++++..
T Consensus        32 LiRfV~~Pdg~vvpD~~~klPGRG~wv~~~r~~l~~A~~k~~f~ra   77 (221)
T PRK09190         32 LIRFVVGPDGQVVPDLKRKLPGRGLWVSADRAAVEEAVAKKLFARA   77 (221)
T ss_pred             CEEEEECCCCEEEECCCCCCCCCCEEECCCHHHHHHHHHCCHHHHH
T ss_conf             6799988998187676778999833542899999999962849898


No 28 
>KOG1317 consensus
Probab=32.20  E-value=45  Score=16.68  Aligned_cols=37  Identities=35%  Similarity=0.372  Sum_probs=26.4

Q ss_pred             HHHHHH--HHHCCCCCHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             999999--9860886999999770679999999999999
Q gi|254780895|r   38 KAEVVA--AVKGGLLSLEEACQIYTLTVEEFLSWQASIV   74 (91)
Q Consensus        38 KA~VV~--aV~~GLis~~EA~~rY~LS~EEf~~W~~av~   74 (91)
                      ||+-++  |-..|---.+||++.--|++|+|.+|+.--.
T Consensus       444 ~aa~iAK~AHKng~TLk~~Al~lGvltee~F~ewV~Pe~  482 (487)
T KOG1317         444 NAAKIAKTAHKNGTTLKEEALKLGVLTEEQFDEWVVPEK  482 (487)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHCHHH
T ss_conf             688999976526876899898855475998876508774


No 29 
>TIGR03652 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers.
Probab=30.67  E-value=44  Score=16.69  Aligned_cols=28  Identities=36%  Similarity=0.502  Sum_probs=23.5

Q ss_pred             CCCCCHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             0886999999770679999999999999
Q gi|254780895|r   47 GGLLSLEEACQIYTLTVEEFLSWQASIV   74 (91)
Q Consensus        47 ~GLis~~EA~~rY~LS~EEf~~W~~av~   74 (91)
                      ||=.|+.|||+.-++..+++..=..+..
T Consensus        25 gG~~~L~eac~~~~ld~~~ll~~L~~l~   52 (216)
T TIGR03652        25 GGNVSLAEACKEKGLDPDEILAELNALQ   52 (216)
T ss_pred             CCCHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             9961699999884989999999999998


No 30 
>PRK10251 phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex; Provisional
Probab=28.58  E-value=26  Score=18.04  Aligned_cols=42  Identities=24%  Similarity=0.203  Sum_probs=26.6

Q ss_pred             CCCCCCHHH---CC-CCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCC
Q ss_conf             998335321---75-99885036779999999986088699999977067
Q gi|254780895|r   16 DGSPLTIAN---LP-PPNTRRWVARRKAEVVAAVKGGLLSLEEACQIYTL   61 (91)
Q Consensus        16 dGs~lt~aD---LP-p~~T~RWVasRKA~VV~aV~~GLis~~EA~~rY~L   61 (91)
                      |-..++-+|   || |+.-.|.|..||||-++|=.    --.+|+...+.
T Consensus        24 Dp~~f~~~d~~~lP~~asL~rAv~KRraEflAGR~----~Ar~AL~~lG~   69 (207)
T PRK10251         24 DPASFHEQDLLWLPHYAQLQHAGRKRKAEHLAGRI----AAVYALREYGY   69 (207)
T ss_pred             CHHHCCHHHCCCCCCHHHHHHHHHHHHHHHHHHHH----HHHHHHHHCCC
T ss_conf             84668974605699838988878899999999999----99999997199


No 31 
>KOG1489 consensus
Probab=28.32  E-value=25  Score=18.08  Aligned_cols=24  Identities=29%  Similarity=0.411  Sum_probs=20.1

Q ss_pred             CCCCCCCEEECCCCCCCCHHHCCC
Q ss_conf             203232267779998335321759
Q gi|254780895|r    4 KIQSHMKYVIGPDGSPLTIANLPP   27 (91)
Q Consensus         4 ~~~~~~~~V~gPdGs~lt~aDLPp   27 (91)
                      +++|++-.|---|.+.||+||+|-
T Consensus       230 TL~P~iG~v~yddf~q~tVADiPG  253 (366)
T KOG1489         230 TLRPHIGTVNYDDFSQITVADIPG  253 (366)
T ss_pred             EECCCCCEEECCCCCEEEECCCCC
T ss_conf             444641125135451468504765


No 32 
>KOG3279 consensus
Probab=28.23  E-value=62  Score=15.86  Aligned_cols=55  Identities=29%  Similarity=0.351  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHH-CHHHH----HHHHHHHHCC
Q ss_conf             79999999986088699999977067999999999999983-99868----8757776339
Q gi|254780895|r   36 RRKAEVVAAVKGGLLSLEEACQIYTLTVEEFLSWQASIVQH-GLAGL----RTTQIQKYRE   91 (91)
Q Consensus        36 sRKA~VV~aV~~GLis~~EA~~rY~LS~EEf~~W~~av~~h-G~~gL----r~T~lQ~YRq   91 (91)
                      -|+|++..--+.=+|..+|| +-|+|+.+|-..=|+..+.. -..-|    +..-||+.||
T Consensus       186 Er~A~I~~KY~~F~IPEeEA-EW~GLtL~EAirKQ~~lEe~~~PvPLk~~f~~~LieqLrq  245 (283)
T KOG3279         186 ERQAEILKKYRRFLIPEEEA-EWYGLTLLEAIRKQKQLEEAEKPVPLKLEFRGKLIEQLRQ  245 (283)
T ss_pred             HHHHHHHHHHHHHCCCHHHH-HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
T ss_conf             87899999988752866664-5751039999999887775258852799999999999986


No 33 
>pfam00945 Rhabdo_ncap Rhabdovirus nucleocapsid protein. The Nucleocapsid (N) Protein is said to have a "tight" structure. The carboxyl end of the N-terminal domain possesses an RNA binding domain. Sequence alignments show 2 regions of reasonable conservation, approx. 64-103 and 201-329. A whole functional protein is required for encapsidation to take place.
Probab=28.19  E-value=34  Score=17.33  Aligned_cols=25  Identities=32%  Similarity=0.760  Sum_probs=21.3

Q ss_pred             CCCCCHHHHHHHCCCCHHHHHHHHH
Q ss_conf             0886999999770679999999999
Q gi|254780895|r   47 GGLLSLEEACQIYTLTVEEFLSWQA   71 (91)
Q Consensus        47 ~GLis~~EA~~rY~LS~EEf~~W~~   71 (91)
                      .||.++...|+--++|.+||..|.-
T Consensus       218 aaL~sl~h~~~~~glt~~e~~~Wif  242 (406)
T pfam00945       218 SGLVSFTHLCKVTGLSIEEAITWIF  242 (406)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             9988899999993998999888851


No 34 
>pfam05120 GvpG Gas vesicle protein G. These proteins are involved in the formation of gas vesicles.
Probab=27.30  E-value=59  Score=15.98  Aligned_cols=47  Identities=19%  Similarity=0.300  Sum_probs=37.5

Q ss_pred             CCCCCCCHHHHHHHHHH-------HHHHCCCCCHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             59988503677999999-------998608869999997706799999999999
Q gi|254780895|r   26 PPPNTRRWVARRKAEVV-------AAVKGGLLSLEEACQIYTLTVEEFLSWQAS   72 (91)
Q Consensus        26 Pp~~T~RWVasRKA~VV-------~aV~~GLis~~EA~~rY~LS~EEf~~W~~a   72 (91)
                      -|....-||+.+-.+..       ++|+--|+.++.+++.=.+|+|||..=+.-
T Consensus         7 aPvrG~~Wiaeqi~e~Ae~e~yDp~~i~~~L~~L~~~le~GEI~Eeefd~~Ede   60 (80)
T pfam05120         7 APVRGVIWIAEQVQEEAERQYYDPENLRAELAELQRQLEAGEISEEEFDRQEEE   60 (80)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             650049999999999999986488999999999999988589998999878999


No 35 
>pfam05225 HTH_psq helix-turn-helix, Psq domain. This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence.
Probab=27.21  E-value=64  Score=15.75  Aligned_cols=29  Identities=31%  Similarity=0.497  Sum_probs=24.2

Q ss_pred             HHHHHHHHCCCCCHHHHHHHCCCCHHHHH
Q ss_conf             99999986088699999977067999999
Q gi|254780895|r   39 AEVVAAVKGGLLSLEEACQIYTLTVEEFL   67 (91)
Q Consensus        39 A~VV~aV~~GLis~~EA~~rY~LS~EEf~   67 (91)
                      .+-+.+|+.|-+|...|...|++..--+.
T Consensus         6 ~~Al~av~~g~~S~~kAa~~ygIP~sTL~   34 (45)
T pfam05225         6 AEALEAVRNGKMSLRKAARKYGIPRSTLW   34 (45)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCCCHHHHH
T ss_conf             99999999199679999999789858999


No 36 
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1; InterPro: IPR014326   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    This group of sigma factors are members of the sigma-70 family (IPR014284 from INTERPRO) and are apparently found only in the Planctomycetaceae family including the genus s Gemmata and Pirellula, in which seven sequences are found.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=26.91  E-value=54  Score=16.21  Aligned_cols=22  Identities=32%  Similarity=0.421  Sum_probs=17.4

Q ss_pred             HCCCCHHHHHHHHHHHHHHCHH
Q ss_conf             7067999999999999983998
Q gi|254780895|r   58 IYTLTVEEFLSWQASIVQHGLA   79 (91)
Q Consensus        58 rY~LS~EEf~~W~~av~~hG~~   79 (91)
                      .-+-|++||..|-|.|-.+-+.
T Consensus        56 fRG~t~~Ef~~WLR~IL~~~l~   77 (190)
T TIGR02984        56 FRGKTEGEFAGWLRQILANVLA   77 (190)
T ss_pred             HCCCCHHHHHHHHHHHHHHHHH
T ss_conf             3289857899999999999999


No 37 
>pfam11470 TUG GLUT4 regulating protein TUG. TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site.
Probab=26.57  E-value=37  Score=17.13  Aligned_cols=15  Identities=47%  Similarity=0.879  Sum_probs=12.9

Q ss_pred             HHHHHHHCCCCHHHH
Q ss_conf             999997706799999
Q gi|254780895|r   52 LEEACQIYTLTVEEF   66 (91)
Q Consensus        52 ~~EA~~rY~LS~EEf   66 (91)
                      ++|||+.+++..+++
T Consensus        23 L~~ac~k~~l~~~~~   37 (65)
T pfam11470        23 LEEACKKFGLDPSEY   37 (65)
T ss_pred             HHHHHHHHCCCHHHC
T ss_conf             999999809984463


No 38 
>TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein.
Probab=26.09  E-value=67  Score=15.63  Aligned_cols=47  Identities=19%  Similarity=0.273  Sum_probs=39.9

Q ss_pred             HHHCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             32175998850367799999999860886999999770679999999999999
Q gi|254780895|r   22 IANLPPPNTRRWVARRKAEVVAAVKGGLLSLEEACQIYTLTVEEFLSWQASIV   74 (91)
Q Consensus        22 ~aDLPp~~T~RWVasRKA~VV~aV~~GLis~~EA~~rY~LS~EEf~~W~~av~   74 (91)
                      .=+.|-.++-|||+.=|...-..++-+|      -+|-.|+..|..|--++|.
T Consensus        49 lY~~hrStvaR~v~~are~Ll~~Tr~~L------aeRL~L~~~el~Sllrlv~   95 (106)
T TIGR02233        49 LYGVHRSTVARWVAGARELLLERTRQEL------AERLRLTSSELDSLLRLVS   95 (106)
T ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHH------HHHHCCCHHHHHHHHHHHH
T ss_conf             8478861699999999999999989987------6740788677899988784


No 39 
>COG2306 Predicted RNA-binding protein, associated with RNAses E/G family [General function prediction only]
Probab=24.71  E-value=65  Score=15.72  Aligned_cols=38  Identities=21%  Similarity=0.232  Sum_probs=25.6

Q ss_pred             HHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHCHHHH
Q ss_conf             9999998608869999997706799999999999998399868
Q gi|254780895|r   39 AEVVAAVKGGLLSLEEACQIYTLTVEEFLSWQASIVQHGLAGL   81 (91)
Q Consensus        39 A~VV~aV~~GLis~~EA~~rY~LS~EEf~~W~~av~~hG~~gL   81 (91)
                      -+.-.|+++||||.+.+.+-|. +.+    =..+..++|-.+-
T Consensus       126 DEL~~Al~~GlIT~~qf~~Ay~-~a~----aVe~elr~g~~~~  163 (183)
T COG2306         126 DELEDALRYGLITPEQFEKAYR-TAN----AVEAELRNGKFPP  163 (183)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHH-HHH----HHHHHHHCCCCCH
T ss_conf             9999998727778899999999-999----9999986487641


No 40 
>COG3522 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and    vesicular transport]
Probab=24.30  E-value=45  Score=16.65  Aligned_cols=22  Identities=41%  Similarity=0.810  Sum_probs=12.1

Q ss_pred             CCEEECCCCCCCCHH---HCCCCCC
Q ss_conf             226777999833532---1759988
Q gi|254780895|r    9 MKYVIGPDGSPLTIA---NLPPPNT   30 (91)
Q Consensus         9 ~~~V~gPdGs~lt~a---DLPp~~T   30 (91)
                      .-..+.|||+++.+.   |||||=+
T Consensus        64 ~a~gv~PDGtpf~ip~~~~lP~pL~   88 (446)
T COG3522          64 SASGVLPDGTPFSIPGDDDLPPPLD   88 (446)
T ss_pred             EEEEECCCCCEECCCCCCCCCCCCC
T ss_conf             5447769997553767788999968


No 41 
>pfam05321 HHA Haemolysin expression modulating protein. This family consists of haemolysin expression modulating protein (HHA) homologues. YmoA and Hha are highly similar bacterial proteins downregulating gene expression in Yersinia enterocolitica and Escherichia coli, respectively.
Probab=23.45  E-value=70  Score=15.53  Aligned_cols=28  Identities=25%  Similarity=0.375  Sum_probs=21.3

Q ss_pred             HHCCCCHHHHHHHHHHHHHHCHHHHHHHH
Q ss_conf             77067999999999999983998688757
Q gi|254780895|r   57 QIYTLTVEEFLSWQASIVQHGLAGLRTTQ   85 (91)
Q Consensus        57 ~rY~LS~EEf~~W~~av~~hG~~gLr~T~   85 (91)
                      -+|.||.+|+....+|.| |-.+-|..-+
T Consensus        19 ~~~~L~~~e~~~f~~AaD-HR~AEl~m~k   46 (57)
T pfam05321        19 KRYKLPGDELEAFNSAAD-HRLAELTMGK   46 (57)
T ss_pred             HHCCCCHHHHHHHHHHHH-HHHHHHHHCC
T ss_conf             425488899999999999-9999999730


No 42 
>PRK06366 acetyl-CoA acetyltransferase; Provisional
Probab=23.35  E-value=76  Score=15.33  Aligned_cols=23  Identities=22%  Similarity=0.202  Sum_probs=18.5

Q ss_pred             CHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             99999977067999999999999
Q gi|254780895|r   51 SLEEACQIYTLTVEEFLSWQASI   73 (91)
Q Consensus        51 s~~EA~~rY~LS~EEf~~W~~av   73 (91)
                      +-|.-+++|++|.||+..|--.-
T Consensus       164 tAE~~a~~~gisRe~~D~~A~~S  186 (388)
T PRK06366        164 SAERTARKYGITREMADEYSVQS  186 (388)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             99999999797999999999999


No 43 
>PRK09052 acetyl-CoA acetyltransferase; Provisional
Probab=22.59  E-value=79  Score=15.24  Aligned_cols=32  Identities=13%  Similarity=0.303  Sum_probs=21.8

Q ss_pred             CCHHHHHHHCCCCHHHHHHHHHHHHHHCHHHHHHH
Q ss_conf             69999997706799999999999998399868875
Q gi|254780895|r   50 LSLEEACQIYTLTVEEFLSWQASIVQHGLAGLRTT   84 (91)
Q Consensus        50 is~~EA~~rY~LS~EEf~~W~~av~~hG~~gLr~T   84 (91)
                      ++-|..+++|++|.||...|  ++..| ..+.++.
T Consensus       156 ~tAE~~A~~~~isRe~qD~~--A~~Sh-~rA~~A~  187 (399)
T PRK09052        156 LTAEKVAEQWKVSREDQDAF--ALESH-QKAIAAQ  187 (399)
T ss_pred             HHHHHHHHHHCCCHHHHHHH--HHHHH-HHHHHHH
T ss_conf             89999999969899999999--99999-9999987


No 44 
>PRK09270 frcK putative fructose transport system kinase; Reviewed
Probab=22.03  E-value=36  Score=17.24  Aligned_cols=33  Identities=33%  Similarity=0.401  Sum_probs=21.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHH
Q ss_conf             7599885036779999999986088699999977067999
Q gi|254780895|r   25 LPPPNTRRWVARRKAEVVAAVKGGLLSLEEACQIYTLTVE   64 (91)
Q Consensus        25 LPp~~T~RWVasRKA~VV~aV~~GLis~~EA~~rY~LS~E   64 (91)
                      -|+...++|++.|.      +.+| +|.++|.+||.=+..
T Consensus       171 ~~~~~~~~Rli~R~------~~~G-~s~e~a~~r~~~nD~  203 (230)
T PRK09270        171 APAEVLRERLVARK------LAGG-LSPEAARAFYLRNDG  203 (230)
T ss_pred             CCHHHHHHHHHHHH------HHCC-CCHHHHHHHHHHCCC
T ss_conf             89999999999999------8729-999999999971661


No 45 
>COG2049 DUR1 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]
Probab=21.71  E-value=68  Score=15.61  Aligned_cols=24  Identities=33%  Similarity=0.311  Sum_probs=20.3

Q ss_pred             HHCC---CCCHHHHHHHCCCCHHHHHH
Q ss_conf             8608---86999999770679999999
Q gi|254780895|r   45 VKGG---LLSLEEACQIYTLTVEEFLS   68 (91)
Q Consensus        45 V~~G---Lis~~EA~~rY~LS~EEf~~   68 (91)
                      |.||   --.+++.++..+||.||+-.
T Consensus        90 V~Y~~~~GpDL~~va~~~gls~~evI~  116 (223)
T COG2049          90 VVYGGEYGPDLAEVARHNGLSVEEVIE  116 (223)
T ss_pred             EEECCCCCCCHHHHHHHCCCCHHHHHH
T ss_conf             076898898899999881999999999


No 46 
>smart00719 Plus3 Short conserved domain in transcriptional regulators. Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.
Probab=21.17  E-value=64  Score=15.76  Aligned_cols=18  Identities=33%  Similarity=0.560  Sum_probs=13.5

Q ss_pred             HHHCCCCHHHHHHHHHHH
Q ss_conf             977067999999999999
Q gi|254780895|r   56 CQIYTLTVEEFLSWQASI   73 (91)
Q Consensus        56 ~~rY~LS~EEf~~W~~av   73 (91)
                      +.-=..|++||..|.+++
T Consensus        91 vSn~~fte~E~~~w~~~~  108 (109)
T smart00719       91 ISNQDFTEEEFQRWKQAI  108 (109)
T ss_pred             EECCCCCHHHHHHHHHHH
T ss_conf             638989999999999971


No 47 
>PRK10853 hypothetical protein; Provisional
Probab=20.90  E-value=76  Score=15.33  Aligned_cols=31  Identities=19%  Similarity=0.242  Sum_probs=24.2

Q ss_pred             HCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHCC
Q ss_conf             7067999999999999983998688757776339
Q gi|254780895|r   58 IYTLTVEEFLSWQASIVQHGLAGLRTTQIQKYRE   91 (91)
Q Consensus        58 rY~LS~EEf~~W~~av~~hG~~gLr~T~lQ~YRq   91 (91)
                      .=.+|.+++..|.   +.+|...|=-|+=+.||+
T Consensus        34 ~~~~~~~~l~~wl---~~~G~~~liN~rgtt~R~   64 (118)
T PRK10853         34 VDGLDSELLNGFI---AELGWEALLNTRGTTWRK   64 (118)
T ss_pred             CCCCCHHHHHHHH---HHCCHHHHHCCCCCHHHH
T ss_conf             4698999999999---962989875166635664


Done!